The Coot User Manual

Table of Contents

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Coot User Manual


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1 Introduction

This document is the Coot User Manual, giving an overview of the interactive features. Other documentation includes the Coot Reference Manual and the Coot Tutorial. These documents should be distributed with the source code.


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1.1 Citing Coot and Friends

If have found this software to be useful, you are requested (if appropriate) to cite:

"Features and Development of Coot" P Emsley, B Lohkamp, W Scott, and K Cowtan Acta Cryst. (2010). D66, 486-501 Acta Crystallographica Section D-Biological Crystallography 66: 486-501

The reference for the REFMAC5 Dictionary is:

REFMAC5 dictionary: "Organization of Prior Chemical Knowledge and Guidelines for its Use" Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S Long F, Murshudov GN Acta Crystallographica Section D-Biological Crystallography 60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004"

If using "SSM Superposition", please cite:

"Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions" Krissinel E, Henrick K Acta Crystallographica Section D-Biological Crystallography 60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004

The reference for the the Electron Density Server is:

GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A Wählby, TA Jones (2004), "The Uppsala Electron-Density Server", Acta Crystallographica Section D-Biological Crystallography 60, 2240-2249.

Please also cite the primary literature for the received structures.


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1.2 What is Coot?

Coot is a molecular graphics application. Its primary focus is crystallographic macromolecular model-building and manipulation rather than representation i.e. more like Frodo than Rasmol. Having said that, Coot can work with small molecule (SHELXL) and electron microscopy data, be used for homology modelling, make passably pretty pictures and display NMR structures.

Coot is Free Software. You can give it away. If you don’t like the way it behaves, you can fix it yourself.


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1.3 What Coot is Not

Coot is not:


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1.4 Hardware Requirements

The code is designed to be portable to any Unix-like operating system. Coot certainly runs on RedHat Linux of various sorts, Fedora, Ubuntu, Debian, SuSe Linux and MacOS X. There is also a Window port (called WinCoot).

If you want to port to some other operating system, you are welcome 4. Note that your task will be eased by using GNU GCC to compile the programs components.

1.4.1 Mouse

Coot works best with a 3-button mouse and works better if it has a scroll-wheel too (see Chapter 2 for more details) 5.


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1.5 Environment Variables

Coot responds to several environment variables that modify its behaviour.

And of course extension language environment variables are used too:

Normally, these environment variables will be set correctly in the coot shell script.


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1.6 Command Line Arguments

Rather that using the GUI to read in information, you can use the following command line arguments:

So, for example, one might use:


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1.7 Web Page

Coot has a web page:

There you can read more about the CCP4 molecular graphics project in general and other projects which are important for Coot 7.


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1.8 Crash

Coot might crash on you - it shouldn’t.

Whenever Coot manipulates the model, it saves a backup pdb file. There are backup files in the directory coot-backup 8. You can recover the session (until the last edit) by reading in the pdb file that you started with last time and then use File -> Recover Session….

I would like to know about coot crashing 9 so that I can fix it as soon as possible. If you want your problem fixed, this involves some work on your part sadly.

First please make sure that you are using the most recent version of coot. I will often need to know as much as possible about what you did to cause the bug. If you can reproduce the bug and send me the files that are needed to cause it, I can almost certainly fix it 10 - especially if you use the debugger (gdb) and send a backtrace too11. Note that you may have to source the contents of bin/coot so that the libraries are can be found when the executable dynamically links.


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2 Mousing and Keyboarding

How do we move around and select things?

Left-mouse Drag

Rotate view

Ctrl Left-Mouse Drag

Translates view

Shift Left-Mouse

Label Atom

Right-Mouse Drag

Zoom in and out

Ctrl Shift Right-Mouse Drag

Rotate View around Screen Z axis

Middle-mouse

Centre on atom

Scroll-wheel Forward

Increase map contour level

Scroll-wheel Backward

Decrease map contour level

See also Chapter Hints and Usage Tips for more help.


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2.1 Next Residue

``Space''

Next Residue

``Shift'' ``Space''

Previous Residue

See also “Recentring View” (Section Recentring View).


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2.2 Keyboard Contouring

Use + or - on the keyboard if you don’t have a scroll-wheel.


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2.3 Mouse Z Translation and Clipping

Here we can change the clipping and Translate in Screen Z

Ctrl Right-Mouse Drag Up/Down

changes the slab (clipping planes)

Ctrl Right-Mouse Drag Left/Right

translates the view in screen Z


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2.4 Keyboard Translation

Keypad 3

Push View (+Z translation)

Keypad .

Pull View (-Z translation)


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2.5 Keyboard Zoom and Clip

N

Zoom out

M

Zoom in

D

Slim clip

F

Fatten clip


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2.6 Scrollwheel

When there is no map, using the scroll-wheel has no effect. If there is exactly one map displayed, the scroll-wheel will change the contour level of that map. If there are two or more maps, the map for which the contour level is changed can be set using either HID -> Scrollwheel -> Attach scroll-wheel to which map? and selecting a map number or clicking the "Scroll" radio button for the map in the Display Manager.

You can turn off the map contour level changing by the scroll wheel using:

(set-scroll-by-wheel-mouse 0)

(the default is 1 [on]).


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2.7 Selecting Atoms

Several Coot functions require the selecting of atoms to specify a residue range (for example: Regularize, Refine (Section Regularization and Real Space Refinement) or Rigid Body Fit Zone (Section Rigid Body Refinement)). Select atoms with the Left-mouse. See also Picking (Section sec_picking).

Use the scripting function (quanta-buttons) to make the mouse functions more like other molecular graphics programs to which you may be more accustomed 12.


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2.8 Virtual Trackball

You may not completely like the way the molecule is moved by the mouse movement 13. To change this, try: HID -> Virtual Trackball -> Flat. To do this from the scripting interface: (vt-surface 1) 14.

If you do want screen-z rotation screen-z rotation, you can either use Shift Right-Mouse Drag or set the Virtual Trackball to Spherical Surface mode and move the mouse along the bottom edge of the screen.


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2.9 More on Zooming

The function (quanta-like-zoom) adds the ability to zoom the view using just Shift + Mouse movement 15.

There is also a Zoom slider (Draw -> Zoom) for those without a right-mouse button.


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3 General Features

The map-fitting and model-building tools can be accessed by using Calculate -> Model/Fit/Refine…. Many functions have tooltips 16 describing the particular features and are documented in Chapter Modelling and Building.

F5:

posts the Model/Fit/Refine dialog

F6:

posts the Go To Atom Window

F7:

posts the Display Control Window


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3.1 Version number

The version number of Coot can be found at the top of the “About” window (Help -> About).

This will return the version of coot:

$ coot --version

There is also a script function to return the version of coot:

(coot-version)


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3.2 Antialiasing

The built-in antialiasing (for what it’s worth) can be enabled using:

(set-do-anti-aliasing 1)

The default is 0 (off).

This can also be activated using Edit Preferences -> Others -> Antialiasing -> Yes.

If you have an nVidia graphics card, external antialiasing can be actived setting the environment variable __GL_FSAA_MODE. For me a setting of 5 works nicely and gives a better image than using Coot’s built-in antialiasing.

Also for nVidia graphics card users, there is the application nvidia-settings:

Antialiasing Setting -> Override Application Settings and slide the slider to the right. On restarting Coot, it should be in antialias mode 17.


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3.3 Molecule Number

Coot is based on the concept of molecules. Maps and coordinates are different representations of molecules. The access to the molecule is via the molecule number. It is often important therefore to know the molecule number of a particular molecule.

The Molecule Number of a molecule can be found by clicking on an atom of that molecule (if it has coordinates of course). The first number in brackets in the resulting text in the status bar and console is the Molecule Number. The Molecule Number can also be found in Display Control window (Section Display Manager). It is also displayed on the left-hand side of the molecule name in the option menus of the “Save Coordinates” and “Go To Atom” windows.


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3.4 Display Issues

The “graphics” window is drawn using OpenGL. It is considerably smoother (i.e. more frames/sec) when using a 3D accelerated X server.

The view is orthographic (i.e. the back is the same size as the front). The default clipping is about right for viewing coordinate data, but is often a little too “thick” for viewing electron density. It is easily changed (see Section Clipping Manipulation).

Depth-cueing is linear and fixed on.

The graphics window can be resized, but it has a minimum size of 400x400 pixels.

3.4.1 Stereo

Hardware Stereo is an option for Coot (Draw -> Stereo… -> Hardware Stereo -> OK), side-by-side stereo is not an option.

The angle between the stereo pairs (the stereo separation) can be changed to suit your personal tastes using:

(set-hardware-stereo-angle-factor angle-factor)

where angle-factor would typically be between 1.0 and 2.0

3.4.2 Pick Cursor

When asked to pick a residue or atom, the cursor changes from the normal arrow shape to a "pick" cursor. Sometimes it is difficult to see the default pick cursor, so you can change it using the function

(set-pick-cursor-index i)

where i is an integer less than 256. The cursors can be viewed using an external X program:

xfd -fn cursor

3.4.3 Origin Marker

A yellow box called the “origin marker” marks the origin. It can be removed using:

(set-show-origin-marker 0)

Its state can be queried like this:

(show-origin-marker-state)

which returns an number (0 if it is not displayed, 1 if it is).


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3.5 Screenshot

A simple screenshot (image dump) can be made using Draw -> Screenshot -> Simple…. Note that in side by side stereo mode you only get the left-hand image.


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3.6 Raster3D output

Output suitable for use by Raster3D’s “render” can be generated using the scripting function

(raster3d file-name)

where file-name is such as "test.r3d" 18.

There is a keyboard key to generate this file, run “render” and display the image: Function key F8.

You can also use the function

(render-image)

which will create a file coot.r3d, from which “render” produces coot.png. This png file is displayed using ImageMagick’s display program (by default). Use something like:

(set! coot-png-display-program "gqview")

to change that to different display program ("gqview" in this case).

(set! coot-png-display-program "open")

would use Preview (by default) on Macintosh.

To change the widths of the bonds and density “lines” use (for example):

(set-raster3d-bond-thickness 0.1)

and

(set-raster3d-density-thickness 0.01)

Similarly for bones:

(set-raster3d-bone-thickness 0.05)

To turn off the representations of the atoms (spheres):

(set-renderer-show-atoms 0)


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3.7 Display Manager

This is also known as “Map and molecule (coordinates) display control”. Here you can select which maps and molecules you can see and how they are drawn 19. The “Display” and “Active” are toggle buttons, either depressed (active) or undepressed (inactive). The “Display” buttons control whether a molecule (or map) is drawn and the “Active” button controls if the molecule is clickable 20 (i.e. if the molecule’s atoms can be labeled).

The "Scroll" radio buttons sets which map is has its contour level changed by scrolling the mouse scroll wheel.

By default, the path names of the files are not displayed in the Display Manager. To turn them on:

(set-show-paths-in-display-manager 1)

If you pull across the horizontal scrollbar in a Molecule view, you will see the “Render as” menu. You can use this to change between normal “Bonds (Colour by Atom)”,“Bonds (Colour by Chain)” and “C\alpha” representation There is also available “No Waters” and “C\alpha + ligands” representations.


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3.8 The Modelling Toolbar

You might not want to have the right-hand-side vertical toolbar that contains icons for some modelling operations 21 displayed:

(hide-modelling-toolbar)

to bring it back again:

(show-modelling-toolbar)


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3.9 The file selector

3.9.1 File-name Filtering

The “Filter” button in the fileselection filters the filenames according to extension. For coordinates files the extensions are “.pdb” “.brk” “.mmcif” and others. For data: “.mtz”, “.hkl”, “.phs”, “.cif” and for (CCP4) maps “.ext”, “.msk” and “.map”. If you want to add to the extensions, the following functions are available:

where extension is something like: ".mycif".

If you want the fileselection to be filtered without having to use the "Filter" button, use the scripting function

(set-filter-fileselection-filenames 1)

3.9.2 Filename Sorting

If you like your files initially sorted by date (rather than lexicographically, which is the default) use:

(set-sticky-sort-by-date)

3.9.3 Save Coordinates Directory

Some people prefer that the fileselection for saving coordinates starts in the original directory (rather than the directory from which they last imported coordinates). This option is for them:

(set-save-coordinates-in-original-directory 1)


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3.10 Scripting

There is an compile-time option of adding a script interpreter. Currently the options are python and guile. It seems possible that in future you will be able to use both in the same executable. The binary distribution of Coot are linked with guile, others with python.

Hundreds of commands are made available for use in scripting by using SWIG, some of which are documented here. Other functions documented less well, but descriptions for them can be found at the end of this manual.

Commands described throughout this manual (such as (vt-surface 1)) can be evaluated directly by Coot by using the “Scripting Window” (Calculate -> Scripting…). Note that you type the commands in the upper entry widget and the command gets echoed (in red) and the return value and any output is displayed in the text widget lower (green). The typed command should be terminated with a carriage return 22. Files 23 can be evaluated (executed) using Calculate -> Run Script….

Note that in scheme (the usual scripting language of Coot), the parentheses are important.

To execute a script file from the command line use the --script filename arguments (except when also using the command line argument --no-graphics, in which case you should use -s filename).

After you have used the scripting window, you may have noticed that you can no longer kill Coot by using Ctrl-C in the console. To recover this ability:

(exit)

in the scripting window.


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3.10.1 Python

Coot has an (optional) embedded python interpreter. Thus the full power of python is available to you. Coot will look for an initialization script ($HOME/.coot.py) and will execute it if found. This file should contain python commands that set your personal preferences.

3.10.1.1 Python Commands

The scripting functions described in this manual are formatted suitable for use with guile, i.e.:

(function arg1 arg2…)

If you are using Python instead: the format needs to be changed to:

function(arg1,arg2…)

Note that dashes in guile function names become underscores for python, so that (for example) (raster-screen-shot) becomes raster_screen_shot().


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3.10.2 Scheme

The scheme interpreter is made available by embedding guile. The initialization script used by this interpreter is $HOME/.coot. This file should contain scheme commands that set your personal preferences.


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3.10.3 Coot State

The “state” of Coot is saved on Exit and written to a file called 0-coot.state.scm (scheme) 0-coot.state.py (python). This state file contains information about the screen centre, the clipping, colour map rotation size, the symmetry radius, and other molecule related parameters such as filename, column labels, coordinate filename etc..

Use Calculate -> Run Script… to use this file to re-create the loaded maps and models that you had when you finished using Coot 24 last time. A state file can be saved at any time using (save-state) which saves to file 0-coot.state.scm or (save-state-filename "thing.scm") which saves to file thing.scm.

When Coot starts it can optionally run the commands in 0-coot.state.scm.

Use (set-run-state-file-status i) to change the behaviour: i is 0 to never run this state file at startup, i is 1 to get a dialog option (this is the default) and i is 2 to run the commands without question.


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3.10.4 Key Binding

“Power users” of Coot might like to write their own functions and bind that function to a keyboard key. How do they do that?

By using the add-key-binding function:

(add-key-binding function-name key function)

where key is a quoted string (note that upper case and lower case keys are distinguished - activate get upper case key binding you need to chord the shift key 25).

for example:

(add-key-binding "Refine Active Residue with Auto-accept" "x" refine-active-residue)

Have a look at the key bindings section on the Coot wiki for several more examples.


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3.10.5 User-Defined Functions

“Power users” of Coot might also like to write their own functions that occur after picking an atom (or a number of atoms)

(user-defined-click n_clicks udfunc)

define a function func which runs after the user has made n_clicked atom picks. func is called with a list of atom specifiers - the first member of which is the molecule number.


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3.11 Backups and Undo

By default, each time a modification is made to a model, the old coordinates are written out 26. The backups are kept in a backup directory and are tagged with the date and the history number (lower numbers are more ancient 27). The “Undo” function discards the current molecule and loads itself from the most recent backup coordinates. Thus you do not have to remember to “Save Changes” - coot will do it for you 28.

If you have made changes to more than one molecule, Coot will pop-up a dialog box in which you should set the “Undo Molecule” i.e. the molecule to which the Undo operations will apply. Further Undo operations will continue to apply to this molecule until there are none left. If another Undo is requested Coot checks to see if there are other molecules that can be undone, if there is exactly one, then that molecule becomes the “Undo Molecule”, if there are more than one, then another Undo selection dialog will be displayed.

You can set the undo molecule using the scripting function:

(set-undo-molecule imol)

If for reasons of strange system29 requirements you want to remove the path components of the backup file name you can do so using:

(set-unpathed-backup-file-names 1)

3.11.1 Redo

The “undone” modifications can be re-done using this button. This is not available immediately after a modification 30.

3.11.2 Restoring from Backup

There may be certain circumstances 31 in which you wish to restore from a backup but can’t get it by the “Undo” mechanism described above. In that case, start coot as normal and then open the (typically most recent) coordinates file in the directory coot-backup (or the directory pointed to the environment variable COOT_BACKUP_DIR if it was set) . This file should contain your most recent edits. In such a case, it is sensible for neatness purposes to immediately save the coordinates (probably to the current directory) so that you are not modifying a file in the backup directory.

See also Section Crash.


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3.12 View Matrix

It is sometimes useful to use this to orient the view and export this orientation to other programs. The orientation matrix of the view can be displayed (in the console) using:

(view-matrix)

Also, the internal representation of the view can be returned and set using:

(view-quaternion) to return a 4-element list

(set-view-quaternion i j k l) which sets the view quaternion.

So the usage of these functions would be something like:

(let ((v (view-quaternion)))
   ;; manipulate v here, maybe
   (apply set-view-quaternion v))

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3.13 Space Group and Symmetry

Occasionally you may want to know the space group of a particular molecule. Interactively (for maps) you can see it using the Map Properties button in the Molecule Display Control dialog.

There is a scripting interface function that returns the space group for a given molecule 32:

(show-spacegroup imol)

You can force a space group onto a molecule using the following:

(set-space-group imol space-group)

where space-group is one of the standard CCP4 space group names (e.g. "P 21 21 21").

To show the symmetry operators of a particular molecule use: (get-symmetry imol) which will return a list of strings.

Sometimes molecular replacement solutions (for example) create models with chains non-optimally placed relative to each other - a symmetry-related copy would be more apealling (but would be equivalent, crystalographically). For example, to move the B chain to a symmetry-related position:

Centre on an atom in the symmetry-related B chain (where you want the B chain to be)

Extensions -> Modelling -> Symm Shift Reference Chain Here.


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3.14 Recentring View

If you don’t want smooth recentring (sliding) Edit -> Preferences -> Smooth Recentring -> Off. You can also use this dialog to speed it up a bit (by decreasing the number of steps instead of turning it off).


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3.15 Views

Coot has a views interface (you might call them ”scenes“) that define a particular orientation, zoom and view centre. Coot and linearly interpolate between the views. The animation play back speed can be set with the ”Views Play Speed“ menu item - default is a speed of 10.

The views interface can be found under the Extensions menu item.


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3.16 Clipping Manipulation

The clipping planes (a.k.a. “slab” ) can be adjusted using Edit -> Clipping and adjusting the slider. There is only one parameter to change and it affects both the front and the back clipping planes 33. The clipping can also be changed using keyboard “D” and “F”.

It can also be changed with Ctrl + Right-mouse drag up and down. Likewise the screen-Z can be changed with Ctrl + Right-mouse left and right 34.

One can “push” and “pull” the view in the screen-Z direction using keypad 3 and keypad “.” (see Section Keyboard Z Translation).


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3.17 Background colour

The background colour can be set either using a GUI dialog (Edit$ -> Background Colour) or the function (set-background-colour 0.00 0.00 0.00), where the arguments are 3 numbers between 0.0 and 1.0, which respectively represent the red, green and blue components of the background colour. The default is (0.0, 0.0, 0.0) (black).


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3.18 Unit Cell

If coordinates have symmetry available then unit cells can be drawn for molecules (Draw -> Cell & Symmetry -> Show Unit Cell?).


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3.19 Rotation Centre Pointer

There is a pink pointer at the centre of the screen that marks the rotation centre. The size of the pointer can be changed using Edit -> Pink Pointer Size… or using scripting commands: (set-rotation-centre-size 0.3).


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3.20 Orientation Axes

The green axes showing the orientation of the molecule are displayed by default. To remove them use the scripting function;

(set-draw-axes 0)


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3.21 Pointer Distances

The Rotation Centre Pointer is sometimes called simply “Pointer”. One can find distances to the pointer from any active set of atoms using “Pointer Distances” (under Measures). If you move the Pointer (e.g. by centering on an atom) and want to update the distances to it, you have to toggle off and on the “Show Pointer Distances” on the Pointer Distances dialog.


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3.22 Crosshairs

Crosshairs can be drawn at the centre of the screen, using either the C key35 in graphics window or Draw -> Crosshairs…. The ticks are at 1.54Å, 2.7Å and 3.8Å.


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3.23 3D Annotations

Positions in 3D space can be annotated with 3D text. The mechanism to do this can be found under Extensions -> Representations -> 3D Annotations. 3D Annotations can be saved to and loaded from a file.


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3.24 Frame Rate

Sometimes, you might as yourself “how fast is the computer?” 36. Using Calculate -> Frames/Sec you can see how fast the molecule is rotating, giving an indication of graphics performance. It is often better to use a map that is more realistic and stop the picture whizzing round. The output is written to the status bar and the console, you need to give it a few seconds to “settle down”. It is best not to have other widgets overlaying the GL canvas as you do this.

The contouring elapsed time 37 gives an indication of CPU performance.


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3.25 Program Output

Due to its “in development” nature (at the moment), Coot produces a lot of “console” 38 output - much of it debugging or “informational”. This will go away in due course. You are advised to run Coot so that you can see the console and the graphics window at the same time, since feedback from atom clicking (for example) is often written there rather than displayed in the graphics window.


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4 Coordinate-Related Features


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4.1 Reading coordinates

The format of coordinates that can be read by coot is either PDB or mmCIF. To read coordinates, choose File -> Read Coordinates from the menu-bar. Immediately after the coordinates have been read, the view is (by default) recentred to the centre of this new molecule and the molecule is displayed. The recentring of the view after the coordinates have been read can be turned off by unclicking the "Recentre?" radio-button.

To disable the recentring of the view on reading a coordinates file via scripting, use: (set-recentre-on-read-pdb 0). However, when reading a coordinates file from a script it is just as good (if not better) to use (handle-read-draw-molecule-with-recentre filename 0) - the additional 0 means “don’t recentre”. And that affects just the reading of filename and not subsequent files.

By default coot does not allow reading coordinates with duplicated sequence numbers. To enable the reading of files with duplicated sequence numbers use the function:

(allow-duplicate-sequence-numbers)

Coot can read MDL mol files.

4.1.1 A Note on Space Groups Names

Coot uses the space group on the “CRYST1” line of the pdb file. The space group should be one of the xHM symbols listed (for example) in the CCP4 dictionary file syminfo.lib. So, for example, "R 3 2 :H" should be used in preference to "H32".

4.1.2 Read multiple coordinate files

The reading multiple files using the GUI is not available (at the moment). However the following scripting functions are available:

(read-pdb-all)

which reads all the “*.pdb” files in the current directory

(multi-read-pdb glob-pattern dir)

which reads all the files matching glob-pattern in directory dir. Typical usage of this might be:

(multi-read-pdb "a*.pdb" ".")

Alternatively you can specify the files to be opened on the command line when you start coot (see Section Command Line Arguments).

4.1.3 SHELX .ins/.res files

SHELX ".res" (and ".ins" of course) files can be read into Coot, either using the GUI File -> Open Coordinates… or by the scripting function:

(read-shelx-ins-file file-name)

where file-name is quoted, such as "thox.ins".

Although Coot should be able to read any SHELX ".res" file, it may currently have trouble displaying the bonds for centro-symmetric structures.

ShelxL atoms with negative PART numbers are given alternative configuration identifiers in lower case.

To write a SHELX ".ins" file:

(write-shelx-ins-file imol file-name)

where imol is the number of the molecule you wish to export.

This will be a rudimentary file if the coordinates were initially from a "PDB" file, but will contain substantial SHELX commands if the coordinates were initially generated from a SHELX ins file.


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4.2 Atom Info

Information about about a particular atom is displayed in the text console when you click using middle-mouse. Information for all the atoms in a residue is available using Info -> Residue Info….

The temperature factors and occupancy of the atoms in a residue can be set by using Edit -> Residue Info….


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4.3 Atom Labeling

Use Shift + left-mouse to label atom. Do the same to toggle off the label. The font size is changeable using Edit -> Font Size…. The newly centred atom is labelled by default. To turn this off use:

(set-label-on-recentre-flag 0)

Some people prefer to have atom labels that are shorter, without the slashes and residue name:

(set-brief-atom-labels 1)

To change the atom label colour, use:

(set-font-colour 0.9 0.9 0.9)


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4.4 Atom Colouring

The atom colouring system in coot is unsophisticated. Typically, atoms are coloured by element: carbons are yellow, oxygens red, nitrogens blue, hydrogens white and everything else green (see Section Display Manager for colour by chain). However, it is useful to be able to distinguish different molecules by colour, so by default coot rotates the colour map of the atoms (i.e. changes the H value in the HSV 39 colour system). The amount of the rotation depends on the molecule number and a user-settable parameter:

The default value is 31^\circ.

Also one is able to select only the Carbon atoms to change colour in this manner: (set-colour-map-rotation-on-read-pdb-c-only-flag 1).

The colour map rotation can be set individually for each molecule by using the GUI: Edit -> Bond Colours....


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4.5 Bond Parameters

The various bond parameters can be set using the GUI dialog Draw -> Bond Parameters or via scripting functions.

The represention style of the molecule that has the active residue (if any) can be changed using the scroll wheel with Ctrl and Shift.

4.5.1 Bond Thickness

The thickness (width) of bonds of individual molecules can be changed. This can be done via the Bond Parameters dialog or the scripting interface:

(set-bond-thickness thickness imol)

where imol is the molecule number.

The default thickness is 3 pixels. The bond thickness also applies to the symmetry atoms of the molecule. The default bond thickness for new molecules can be set using:

(set-default-bond-thickness thick)

where thick is an integer.

There is no means to change the bond thickness of a residue selection within a molecule.

4.5.2 Display Hydrogens

Initially, hydrogens are displayed. They can be undisplayed using

(set-draw-hydrogens mol-no 0) 40

where mol-no is the molecule number.

There is a GUI to control this too, under “Edit -> Bond Parameters”.

4.5.3 NCS Ghosts Coordinates

It is occasionally useful when analysing non-crystallographically related molecules to have “images” of the other related molecules appear matched onto the current coordinates. It is important to understand that these ghosts are for displaying differences of NCS-related molecules by structure superposition, not displaying neighbouring NCS related molecules. As you read in coordinates in Coot, they are checked for NCS relationships and clicking on “Edit -> Bond Parameters -> Show NCS Ghosts” -> “Yes” -> “Apply” will create “ghost” copies of them over the reference chain 41.

Sometimes SSM does not provide a good (or even useful) matrix. In that case, we can specify the residue range ourselves and let the LSQ algorithm provide the matrix. A gui dialog for this operation can be found under Extensions -> NCS -> NCS Ghosts by Residue Range….

The scripting function is used like this:

(manual-ncs-ghosts imol resno-start resno-end ncs-chain-ids)

Typical usage: (manual-ncs-ghosts 0 1 10 (list "A" "B" "C"))

note that in ncs-chain-ids, the NCS master/reference chain-id goes first.

4.5.4 NCS Maps

Coot can use the relative transformations of the NCS-related molecules in a coordinates molecule to transform maps. Use Calculate -> NCS Maps… to do this (note the NCS maps only make sense in the region of the reference chain (see above).

Note also that the internal representation of the map is not transformed. If you try to export a NCS overlay map you will get an untransformed map. A transformed map only makes sense around a given point (and when using transformed maps in Coot, this reference point is changed on the fly, thus allowing map transformations on the fly). [This applies to NCS overlap maps, NCS averaged maps are transformed].

This will also create an NCS averaged map 42.

4.5.5 Using Strict NCS

Coot can use a set of strict NCS matrices to specify NCS which means that NCS-related molecules can appear like convention symmetry-related molecules.

(add-strict-ncs-matrix imol ncs-chain-id ncs-target-chain-id m11 m12 m13 m21 m22 m23 m31 m32 m33 t1 t2 t3)

where ncs-chain-id might be "B", "C" "D" (etc.) and ncs-target-chain-id is "A", i.e. the B, C, D molecules are NCS copies of the A chain.

for icosahedral symmetry the translation components t1, t2, t3 will be 0.

You need to turn on symmetry for molecule imol and set the displayed symmetry object type to "Display Near Chains".


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4.6 Download coordinates

Coot provides the possibility to download coordinates from an OCA 43. (e.g. EBI) server 44 (File -> Get PDB Using Code…). A pop-up entry box is displayed into which you can type a PDB accession code. Coot will then connect to the web server and transfer the file. Coot blocks as it does this (which is not ideal) but on a semi-decent internet connection, it’s not too bad. The downloaded coordinates are saved into a directory called coot-download.

It is also possible to download mmCIF data and generate a map. This currently requires a properly formatted database structure factors mmCIF file 45.


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4.7 Get Coordinates and Map from EDS

Using this function we have the ability to download coordinates and view the map from structures in the Electron Density Server (EDS) at Uppsala University. This is a much more robust and faster way to see maps from deposited structures. This function can be found under the File menu item.

This feature was added with the assistance of Gerard Kleywegt. If you use the EDS, please cite GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A Wählby & TA Jones (2004), "The Uppsala Electron-Density Server", Acta Cryst. D60, 2240-2249.


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4.8 Save Coordinates

On selecting from the menus File -> Save Coordinates… you are first presented with a list of molecules which have coordinates. As well as the molecule number, there is the molecule name - very frequently the name of the file that was read in to generate the coordinates in coot initially. However, this is only a molecule name and should not be confused with the filename to which the coordinates are saved. The coordinates filename can be selected using the Select Filename… button.

If your filename ends in .cif, .mmcif or .mmCIF then an mmCIF file will be written (not a “PDB” file).


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4.9 Setting the Space Group

If for some reason, the pdb file that you read does not have a space group, or has the wrong space group, then you can set it using the following function:

(set-space-group imol symbol)

e.g.:

(set-space-group 0 "P 41 21 2")


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4.10 Anisotropic Atoms

By default anisotropic atom information is not represented 46. To turn them on, use Draw -> Anisotropic Atoms -> Show Anisotropic Atoms? -> Yes, or the command: (set-show-aniso 1).

You cannot currently display thermal ellipsoids 47 for isotropic atoms.


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4.11 Symmetry

Coordinates symmetry is “dynamic”. Symmetry atoms can be labeled 48.

Every time you recentre, the symmetry coordinates are updated. The information shown contains the atom information and the symmetry operation number and translations needed to generate the atom in that position. To show the symmetry operator as a string (rather than a (1-based) index into the list of symmetry operators (as is the default)) Use Draw -> Show Symmetry> -> Expanded Symmetry Atom Labels. Coot generates symmetry related atoms by moving the current set close to the origin by a translation, performing the symmetry expansion around the origin and moving the the symmetry coordinates back by applying the inverse of the origin translation. The origin translation is also displayed in curly braces, e.g. “{1 -1 0}”.

By default symmetry atoms are not displayed.

If you want coot to display symmetry coordinates without having to use the gui, add to your ~/.coot the following:

(set-show-symmetry-master 1)

The symmetry can be represented as C\alphas. This along with representation of the molecule as C\alphas (Section Display Manager) allow the production of a packing diagram.

4.11.1 Missing symmetry

Sometimes (rarely) coot misses symmetry-related molecules that should be displayed. In that case you need to expand the shift search (the default is 1):

(set-symmetry-shift-search-size 2)

This is a hack, until the symmetry search algorithm is improved.


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4.12 Sequence View

The protein is represented by one letter codes and coloured according to secondary structure. These one letter codes are active - if you click on them, they will change the centre of the graphics window - in much the same way as clicking on a residue in the Ramachandran plot.


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4.13 Print Sequence

The single letter code (of the imolth molecule) is written out to the console in FASTA format. Use can use this to cut and paste into other applications:

(print-sequence imol)


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4.14 Environment Distances

Environment distances are turned on using Info -> Environment Distances…. Contacts to other residues are shown and to symmetry-related atoms if symmetry is being displayed. The contacts are coloured by atom type 49.


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4.15 Distances and Angles

The distance between atoms can be found using Info -> Distance 50. The result is displayed graphically, and written to the console.


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4.16 Zero Occupancy Marker

Atoms of zero occupancy are marked with a grey spot. To turn off these markers, use:

(set-draw-zero-occ-markers 0)

Use an argument of 1 to turn them on.


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4.17 Atomic Dots

You can draw dots round arbitrary atom selections

(dots imol atom-selection dot-density radius) The function returns a handle.

e.g. put a sphere of dots around all atoms of the 0th molecule (it might be a set of heavy atom coordinates) at the default dot density and radius:

(dots 0 "/1" "heavy-atom-sites" 1 1)

You can’t change the colour of the dots.

There is no internal mechanism to change the radius according to atom type. With some cleverness you might be able to call this function several times and change the radius according to the atom selection.

There is a function to clear up the dots for a particular molecule imol and dots set identifier dots-handle

(clear-dots imol dots-handle)

There is a function to return how many dots sets there are for a particular molecule imol:

(n-dots-set imol)


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4.18 Ball and Stick Representation

Fragments of the molecule can be rendered as a “ball and stick” molecule:

(make-ball-and-stick imol atom-selection bond-thickness sphere-size draw-spheres-flag)

e.g. (make-ball-and-stick 0 "/1/A/10-20" 0.3 0.4 1)

The ball-and-stick representation can be cleared using:

(clear-ball-and-stick imol)


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4.19 Mean, Median Temperature Factors

Coot can be used to calculate the mean (average) and median temperatures factors:

(average-temperature-factor imol)

(median-temperature-factor imol)

-1 is returned if there was a problem 51.


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4.20 Secondary Structure Matching (SSM)

The excellent SSM alogrithm52 of Eugene Krissinel is available in Coot. The GUI interface is straight-forward and can be found under Calculate -> SSM Superpose. You can specify the specific chains that you wish to match using the "Use Specific Chain" check-button.

There is a scripting level function which gives even finer control:

(superpose-with-atom-selection imol1 imol2 mmdb-atom-selection-string-1 mmdb-atom-selection-string-2 move-copy-flag )

the move-copy-flag should be 1 if you want to apply the transformation to a copy of imol2 (rather than imol2 itself). Otherwise, move-copy-flag should be 0.

mmdb atom selection strings (Coordinate-IDs) are explained in detail in the mmdb manual.

Briefly, the string should be formed in this manner:

/mdl/chn/seq(res).ic/atm[elm]:aloc

e.g. "/1/A/12-130/CA"

<p><a href="http://www.ebi.ac.uk/~keb/cldoc/object/cl_obj_surf.html#CoordinateID">The mmdb manual CoordinateID description</a>.</p>


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4.21 Least-Squares Fitting

There is a simple GUI for this Calculate -> LSQ Superpose…

The scripting interface to LSQ fitting is as follows:

(simple-lsq-match ref-start-resno ref-end-resno ref-chain-id imol-ref mov-start-resno mov-end-resno mov-chain-id imol-mov match-type)

where:

e.g.: (simple-lsq-match 940 950 "A" 0 940 950 "A" 1 'main)

More sophisticated (match molecule number 1 chain “B” on to molecule number 0 chain “A”):

(define match1 (list 840 850 "A" 440 450 "B" 'all))

(define match2 (list 940 950 "A" 540 550 "B" 'main))

(clear-lsq-matches)

(set-match-element match1)

(set-match-element match2)

(apply-lsq-matches 0 1) ; match molecule number 1 onto molecule number 0.


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4.22 Ligand Overlaying

The scripting function

(overlap-ligands imol-ligand imol-ref chain-id-ref resno-ref)

returns a rotation+translation operator which can be applied to other molecules (and maps). Here, imol-ligand is the molecule number of the ligand (which is presumed to be a a molecule on its own - Coot simply takes the first residue that it finds). imol-ref chain-id-ref resno-ref collectively describe the target position for the moving imol-ligand molecule.

The convenience function

(overlay-my-ligands imol-mov chain-id-mov resno-mov imol-ref chain-id-ref resno-ref)

wraps overlap-ligands.

The GUI for the function can be found under

Extensions -> Modelling -> Supperpose Ligands…


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4.23 Writing PDB files

As well as the GUI option File -> Save Coordinates… there is a scripting options available:

(write-pdb-file imol pdb-file-name)

which writes the imolth coordinates molecule to filename.

To write a specific residue range:

(write-residue-range-to-pdb-file imol chain-id start-resno endresno pdb-file-name)


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5 Modelling and Building

The functions described in this chapter manipulate, extend or build molecules and can be found under Calculate -> Model/Fit/Refine…. When activated, the dialog "stays on top" of the main graphics window 53. Some people think that this is not always desirable, so this behaviour can be undone using:

(set-model-fit-refine-dialog-stays-on-top 0)


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5.1 Regularization and Real Space Refinement

Coot will read the geometry restraints for refmac and use them in fragment (zone) idealization - this is called “Regularization”. The geometrical restraints are, by default, bonds, angles, planes and non-bonded contacts. You can additionally use torsion restraints by Calculate -> Model/Fit/Refine… -> Refine/Regularize Control -> Use Torsion Restraints. Truth to tell, this has not been successful in my hands (sadly).

“RS (Real Space) Refinement” (after Diamond, 1971 54) in Coot is the use of the map in addition to geometry terms to improve the positions of the atoms. Select “Regularize” from the “Model/Fit/Refine” dialog and click on 2 atoms to define the zone (you can of course click on the same atom twice if you only want to regularize one residue). Coot then regularizes the residue range. At the end Coot, displays the intermediate atoms in white and also displays a dialog, in which you can accept or reject this regularization. In the console are displayed the \chi^2 values of the various geometrical restraints for the zone before and after the regularization. Usually the \chi^2 values are considerably decreased - structure idealization such as this should drive the \chi^2 values toward zero.

The use of “Refinement” is similar - with the addition of using a map. The map used to refine the structure is set by using the “Refine/Regularize Control” dialog. If you have read/created only one map into Coot, then that map will be used (there is no need to set it explicitly).

Use, for example, (set-matrix 20.0)

to change the weight of the map gradients to geometric gradients. The higher the number the more weight that is given to the map terms 55. The default is 60.0. This will be needed for maps generated from data not on (or close to) the absolute scale or maps that have been scaled (for example so that the sigma level has been scaled to 1.0).

For both “Regularize Zone” and “Refine Zone” one is able to use a single click to refine a residue range. Pressing A on the keyboard while selecting an atom in a residue will automatically create a residue range with that residue in the middle. By default the zone is extended one residue either size of the central residue. This can be changed to 2 either side using (set-refine-auto-range-step 2).

Intermediate (white) atoms can be moved around with the mouse (click and drag with left-mouse, by default). Refinement will proceed from the new atom positions when the mouse button is released. It is possible to create incorrect atom nomenclature and/or chiral volumes in this manner - so some care must be taken. Press the A key as you left-mouse click to move atoms more “locally” (rather than a linear shear) and Ctrl key as you left-mouse click to move just one atom.

In more up to date versions, Coot will display colour patches (something like a traffic light system) representing the chi squared values of each of types of geometric feature refined. Typically “5 greens” is the thing to aim for, the colour changes occurring at chi squared values 2, 5 and 8 (8 being the most red).

To prevent the unintentional refinement of a large number of residues, there is a “heuristic fencepost” of 20 residues. A selection of than 20 residues will not be regularized or refined. The limit can be changed using the scripting function: e.g. (set-refine-max-residues 30).


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5.1.1 Dictionary

The geometry description for residues, monomers and links used by Coot are in the standard mmCIF format. Because this format alows multiple comp_ids (residue types) to be described within a cif loop, it is hard to tell when a dictionary entry needs to be overwritten when reading a new file. Therefore Coot makes this extra constraint: that the “chem_comp” loop should appear first in the comp list data item - if this is the case, then Coot can overwrite an old restraint table for a particular comp_id/residue-type when a new one is read.

By default, the geometry dictionary entries for only the standard residues are read in at the start 56. It may be that your particular ligand is not amongst these. To interactively add a dictionary entry use File -> Import CIF Dictionary.

There is a selector in the cif dictionary file chooser that allow you to select the molecule to which molecule refers. Each of the indididual molecules can be specifically selected. “All“ means that the dictionary refers to all loaded molecules and “Auto“ means that the dictionary will be applied to all model molecules if the comp_id/residue name is not on the non-auto-load list and will choose the latest model molecule if the comp_id/residue name is on the non-auto-load list. By default the non-auto-load list consists of INH, LIG, DRG, XXX, and the series LG0-9.

Alternatively, you can use the function:

(read-cif-dictionary filename)

and add this to your .coot file (this may be the preferred method if you want to read the file on more than one occasion).

Note: the dictionary also provides the description of the ligand’s torsions.


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5.1.2 Sphere Refinement

Sphere refinement selects residues within a certain distance of the residue at the centre of the screen and includes them for real space refinement. In this way, one can select residues that are not in a linear range. This technique is useful for refining disulfide bonds and glycosidic linkages.

To enable sphere refinement, Right-mouse click in the right hand side of the horizontal toolbutton menu, Manage buttons -> [Tick] Sphere Refine -> Apply. You will need a python-enabled Coot to do this.

The following adds a key binding (Shift-R) that refines resides that are within 3.5Å of the residue at the centre of the screen:

        
(define *sphere-refine-radius* 3.5)

(add-key-binding "Refine residues in a sphere" "R"
    (lambda ()
     (using-active-atom
      
      (let* ((rc-spec (list aa-chain-id aa-res-no aa-ins-code))
	     (ls (residues-near-residue aa-imol rc-spec *sphere-refine-radius*)))
	(refine-residues aa-imol (cons rc-spec ls))))))



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5.1.3 Refining Specific Residues

You can specify the residues that you want to refine without using a linear or sphere selection usine refine-residues. For example:

(refine-residues 0 '(("L" 501 "") ("L" 503 "")))

will refine residues A501 and A503 (and residue A502 (if it exists) will be an anchoring residue - used in optimizing the link geometry of the atoms in A501 and A503).


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5.1.4 Refining Carbohydrates

Refining carbohydrates monomers should be as straightforward as refining a protein residue. Coot will look in the dictionary for the 3-letter code for the particular residue type, if it does not find it, Coot will try to search for dictionary files using “-b-D” or “-a-L” extensions.

When refining a group of carbohydrates, the situation needs a bit more explanation. For each residue pair with tandem residue numbers specified in the refinement range selection, Coot checks if these residue types are are furanose or pyranose in the dictionary, and if the are both one or the other, then it tries to see if there are any of the 11 link types (BETA1-4, BETA2-3, ALPHA1-2 and so on) specified in the dictionary. It does this by a distance check of the potentially bonding atoms. If the distance is less than 3.0Å, then a glycosidic bond is made and used in the refinement.

Bonds between protein and carbohydrate and branched carbohydrates can be refined using “Sphere Refinement”.

Instead of using a sphere to make a residue selection, you can specify the residues directly using refine-residues, for example:

(refine-residues 0 '(("L" 501 "") ("L" 503 "")))

LINK and LINKR cards are not yet used to determine the geometry of the restraints.


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5.1.5 Planar Peptide Restraints

By default, Coot uses a 5 atom (CA-1, C-1, O-1, N-2, CA-2) planar peptide restraints. These restraints should help in low resolution fitting (the main-chains becomes less distorted), reduce accidental cis-peptides and may help “clean up” Ramachandran plots.

(add-planar-peptide-restraints)

And similarly they can be removed:

(remove-planar-peptide-restraints)

There is also a GUI to add and remove these restraints in Extensions -> Refine… -> Peptide Restraints…


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5.1.6 The UNK residue type

The UNK residue type is a special residue type to Coot. It has been added for use with Buccaneer. Don’t give you ligand (or anything else) the 3-letter-code UNK or confusion will result 57.


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5.1.7 Moving Zero Occupancy Atoms

By default, atoms with zero occupancy are moved when refining and regularizing. This can sometimes be inconvenient. To turn of the movement of atoms with zero occupancy when refining and regularizing:

(set-refinement-move-atoms-with-zero-occupancy 0)


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5.2 Changing the Map for Building/Refinement

You can change the map that is used for the fitting and refinement tools using the Select Map... button on the Model/Fit/Refine dialog.


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5.3 Rotate/Translate Zone

“Rotate/Translate Zone” from the “Model/Fit/Refine” menu allows manual movement of a zone. After pressing the “Rotate/Translate Zone” button, select two atoms in the graphics canvas to define a residue range 58, the second atom that you click will be the local rotation centre for the zone. The atoms selected in the moving fragment have the same alternate conformation code as the first atom you click. To actuate a transformation, click and drag horizontally across the relevant button in the newly-created “Rotation & Translation” dialog. The axis system of the rotations and translations are the screen coordinates. Alternatively 59, you can click using left-mouse on an atom in the fragment and drag the fragment around. Use Control Left-mouse to move just one atom, rather than the whole fragment. If you click Control Left-mouse whilst not over an atom then you can rotate the fragment using mouse drag. Click “OK” (or press Return) when the transformation is complete.

To change the rotation point to the centre of the intermediate atoms (rather than the second clicked atom), use the setting:

(set-rotate-translate-zone-rotates-about-zone-centre 1)


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5.4 Rigid Body Refinement

“Rigid Body Fit Zone” from the “Model/Fit/Refine” dialog provides rigid body refinement. The selection is zone-based 60. So to refine just one residue, click on one atom twice.

Sometimes no results are displayed after Rigid Body Fit Zone. This is because the final model positions had too many final atom positions in negative density. If you want to over-rule the default fraction of atoms in the zone that have an acceptable fit (0.75), to be (say) 0.25:

(set-rigid-body-fit-acceptable-fit-fraction 0.25)


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5.5 Simplex Refinement

Rigid body refinement via Nelder-Mead Simplex minimization is available in Coot. Simplex refinement has a larger radius of convergence and thus is useful in a position where simple rigid body refinement finds the wrong minimum. However the Simplex algorithm is much slower. Simplex refinement for a residue range start-resno to end-resno (inclusive) in chain chain-id can be accessed as follows:

(fit-residue-range-to-map-by-simplex start-resno end-resno alt-loc chain-id imol imol-for-map)

There is currently no GUI interface to Simplex refinement.


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5.6 Post-manipulation-hook

If you wanted automatically run a function after a model has been manipulated then you can do so using by creating a function that takes 2 arguments, such as:

(post-manipulation-hook imol manipulation-mode)

manipulation-mode is one of (DELETED), (MUTATED) or (MOVINGATOMS).

And of course imol is the model number of the maniplated molecule.

(It would of course be far more useful if this function was also passed a list of residues - that is something for the future).


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5.7 Baton Building

Baton build is most useful if a skeleton is already calculated and displayed (see Section Skeletonization). When three or more atoms have been built in a chain, Coot will use a prior probability distribution for the next position based on the position of the previous three. The analysis is similar to that of Oldfield & Hubbard (1994) 61, however it is based on a more recent and considerably larger database.

Little crosses are drawn representing directions in which is is possible that the chain goes, and a baton is drawn from the current point to one of these new positions. If you don’t like this particular direction 62, use Try Another. The list of directions is scored according to the above criterion and sorted so that the most likely is at the top of the list and displayed first as the baton direction.

When starting baton building, be sure to be about 3.8Å from the position of the first-placed C\alpha, this is because the next C\alpha is placed at the end of the baton, the baton root being at the centre of the screen. So, when trying to baton-build a chain starting at residue 1, centre the screen at about the position of residue 2.

It seems like a good idea to increase the map sampling to 2 or even 2.5 (before reading in your mtz file) [a grid sampling of about 0.5Å seems reasonable] when trying to baton-build a low resolution map. You can set the map sampling using Edit -> Map Parameters -> Map Sampling.

Occasionally, every point is not where you want to position the next atom. In that case you can either shorten or lengthen the baton, or position it yourself using the mouse. Use “b” on the keyboard to swap to baton mode for the mouse 63.

Baton-built atoms are placed into a molecule called “Baton Atom” and it is often sensible to save the coordinates of this molecule before quitting coot.

If you try to trace a high resolution map (1.5Å or better) you will need to increase the skeleton search depth from the default (10), for example:

(set-max-skeleton-search-depth 20)

Alternatively, you could generate a new map using data to a more moderate resolution (2Å), the map may be easier to interpret at that resolution anyhow 64.

The guide positions are updated every time the “Accept” button is clicked. The molecule name for these atoms is “Baton Build Guide Points” and is is not usually necessary to keep them.

5.7.1 Undo

There is also an “Undo” button for baton-building. Pressing this will delete the most recently placed C\alpha and the guide points will be recalculated for the previous position. The number of “Undo”s is unlimited. Note that you should use the “Undo” button in the Baton Build dialog, not the one in the “Model/Fit/Refine” dialog (Section Backups and Undo).

5.7.2 Missing Skeleton

Sometimes (especially at loops) you can see the direction in which the chain should go, but there is no skeleton (see Section Skeletonization) is displayed (and consequently no guide points) in that direction. In that case, “Undo” the previous atom and decrease the skeletonization level (Edit -> Skeleton Parameters -> Skeletonization Level). Accept the atom (in the same place as last time) and now when the new guide points are displayed, there should be an option to build in a new direction.

5.7.3 Building Backwards

The following scenario is not uncommon: you find a nice stretch of density and start baton building in it. After a while you come to a point where you stop (dismissing the baton build dialog). You want to go back to where you started and build the other way. How do you do that?


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5.8 Reversing Direction of Fragment

After you’ve build a fragment, sometimes you might want to change the direction of that fragment (this function changes an already existing fragment, as opposed to Backwards Building which sets up Baton Building to place new points in reverse order).

The fragment is defined as a contiguous set of residues numbers. So that you should be sure that other partial fragments which have the same chain id and that are not connected to this fragment have residue numbers that are not contiguous with the fragment you are trying to reverse.


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5.9 C\alpha -> Mainchain

Mainchain can be generated using a set of C\alphas as guide-points (such as those from Baton-building) along the line of Esnouf 66 or Jones and coworkers 67. Briefly, 6-residue fragments of are generated from a list of high-quality 68 structures. The C\alpha atoms of these fragments are matched against overlapping sets of the guide-point C\alphas. The resulting matches are merged to provide positions for the mainchain (and C\beta) atoms. This procedure works well for helices and strands, but less well 69 for less common structural features.

This function is also available from the scripting interface:

(db-mainchain imol chain-id resno-start resno-end direction)

where direction is either "backwards" or "forwards".

Recall that the chain-id needs to be quoted, i.e. use "A" not A. Note that chain-id is "" when the C\alphas have been built with Baton Mode in Coot.


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5.10 Backbone Torsion Angles

It is possible to edit the backbone \phi and \psi angles indirectly using an option in the Model/Fit/Refine’s dialog: “Edit Backbone Torsions..”. When clicked and an atom of a peptide is selected, this produces a new dialog that offers “Rotate Peptide” which changes this residues \psi and “Rotate Carbonyl” which changes \phi. Click and drag across the button 70 to rotate the moving atoms in the graphics window. You should know, of course, that making these modifications alter the \phi/\psi angles of more than one residue.


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5.11 Docking Sidechains

Docking sidechains means adding sidechains to a model or fragment that has currently only poly-Ala, where the sequence assignment is unknown. The algorithm is basically the same as in Cowtan’s Buccaneer, but with some corners cut to make things (more or less) interactive. The algorithm uses the shape of the density around the C-beta position to estimate the probability of each sidechain type at that position.

The function is accessed via the Extensions -> Dock Sequence menu item. First, a sequence should be assigned from a PIR file to a particular chain-id and model number. Secondly Extensions -> Dock Sequence -> Dock Sequence on this fragment…. Choose the model to build on and then Dock Sequence! If all goes well, the model will be updated with mutated residues and undergo rotamer seach for each of the new residues. If the sequence alignment is not sufficiently clear, then you will get a dialog suggesting that you extend or improve the fragment.


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5.12 Rotamers

The rotamers are generated 71 from the backbone independent sidechain library of the Richardsons group 72.

The m, t and p stand for “minus (-60)”, “trans (180)” and “plus (+60)”. There is one letter per \chi angle.

Use keyboard . and , to cycle round the rotamers.

5.12.1 Auto Fit Rotamer

“Auto Fit Rotamer” will try to fit the rotamer to the electron density. Each rotamer is generated, rigid body refined and scored according to the fit to the map. Fitting the second conformation of a dual conformation in this way will often fail - the algorithm will pick the best fit to the density - ignoring the position of the other atoms.

The algorithm doesn’t know if the other atoms in the structure are in sensible positions. If they are, then it is sensible not to put this residue too close to them, if they are not then there should be no restriction from the other atoms as to the position of this residue - the default is “are sensible”, which means that the algorithm is prevented from finding solutions that are too close to the atoms of other residues. (set-rotamer-check-clashes 0) will stop this.

There is a scripting interface to auto-fitting rotamers:

(auto-fit-best-rotamer resno alt-loc ins-code chain-id imol-coords imol-map clash-flag lowest-rotamer-probability)

where:

resno is the residue number

alt-loc is the alternate/alternative location symbol (e.g. "A" or "B", but most often "")

ins-code is the insertion code (usually "")

imol-coords is the molecule number of the coordinates molecule

imol-map is the molecule number of the map to which you wish to fit the side chains

clash-flag should the positions of other residues be included in the scoring of the rotamers (i.e. clashing with other other atoms gets marked as bad/unlikely)

lowest-rotamer-probability: some rotamers of some side chains are so unlikely that they shouldn’t be considered - typically 0.01 (1%).

You can change the auto-fit rotamer fitting algorithms using

(set-rotamer-search-mode mode)

where mode is one of (ROTAMERSEARCHAUTOMATIC), (ROTAMERSEARCHLOWRES) (i.e. "Backrub Rotamers" (vide infra)) or (ROTAMERSEARCHHIGHRES) (the conventional/high-resolution method using rigid-body fitting).

By default, the auto-fit rotamer method is (ROTAMERSEARCHAUTOMATIC).

5.12.1.1 Backrub Rotamers

By default, Auto Fit Rotamer will switch to “Backrub Rotamer” 73 mode when fitting against a map of worse than 2.7Å. This search mode moves the some atoms of the mainchain of the neighbouring residues. After rotation of the central residue and neighbouring atoms around the “backrub vector”, the individual peptides are back-rotated (along the peptide axis) so that the carbonyl oxygen are placed as near as possible to their original position. The Ramachandran plot is not used in this fitting algorithm.

5.12.2 De-clashing residues

Sometimes you don’t have a map 74 but nevertheless there are clashing residues 75 (for example after mutation of a residue range) and you need to rotate side-chains to a non-clashing rotamer. There is a scripting interface:

(de-clash imol chain-id start-resno end-resno)

start-resno is the residue number of the first residue you wish to de-clash

end-resno is the residue number of the last residue you wish to de-clash

imol is the molecule number of the coordinates molecule

This interface will not change residues with insertion codes or alternate conformation. The lowest-rotamer-probability is set to 0.01.


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5.13 Editing chi Angles

Instead of using Rotamers, one can instead change the \chi angles (often called “torsions”) “by hand” (using “Edit Chi Angles” from the “Model/Fit/Refine” dialog). To edit a residue’s \chi_1 press “1”: to edit \chi_2, “2”: \chi_3 “3” and \chi_4 “4”. Use left-mouse click and drag to change the \chi value. Use keyboard “0” 76 to go back to ordinary view mode at any time during the editing. Alternatively, one can use the “View Rotation Mode” or use the Ctrl key when moving the mouse in the graphics window. Use the Accept/Reject dialog when you have finished editing the \chi angles.

For non-standard residues, the clicked atom defines the base of the atom tree, which defines the “head” of the molecule (it’s the “tail” (twigs/leaves) that wags). To emphasise, then: it matters on which atom you click!

By default torsions for hydrogen atoms are turned off. To turn them on:

(set-find-hydrogen-torsions 1)

To edit the rotatable bonds of a ligand using this tool, you will need to have read in the mmCIF dictionary beforehand.


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5.14 Torsion General

You need to click on the torsion-general button, then click 4 atoms that describe the torsion - the first atom will be the base (non moving) part of the atom tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button. Move this dialog out of the way and then left mouse click and drag in the main window will rotate the "top" part of the residue round the clicked atoms 2 and 3. When you are happy, click "Accept".

If you are torsion generaling a residue that has an alt conf, then the atoms of residue that are moved are those that have the same alt conf as the 4th clicked atom (or have an blank alt conf).

5.14.1 Ligand Torsion angles

For ligands, you will need to read the mmCIF file that contains a description of the ligand’s geometry (see Section Regularization and Real Space Refinement). By default, torsions that move hydrogens are not included. Only 9 torsion angles are available from the keyboard torsion angle selection.


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5.15 Pep-flip

Coot uses the same pepflip scheme as is used in O (i.e. the C, N and O atoms are rotated 180^o round a line joining the C\alpha atoms of the residues involved in the peptide). Flip the peptide again to return the atoms to their previous position.


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5.16 Add Alternate Conformation

The allows the addition alternate (dual, triple etc.) conformations to the picked residue. By default, this provides a choice of rotamer (Section Rotamers). If there are not the correct main chain atoms a rotamer choice cannot be provided, and Coot falls back to providing intermediate atoms.

The default occupancy for new atoms is 0.5. This can be changed by using use slider on the rotamer selection window or by using the scripting function:

(set-add-alt-conf-new-atoms-occupancy 0.4)

The remaining occupancy of the atoms (after the new occupancy has been added) is split amongst the atoms that existed in the residue before the split. It is important therefore that the residues atoms have sane occupancies before adding an alternative conformation.

The default Split Type is to split the whole residue. If you want the default to be to split a residue after (and including) the CA, then add to your .coot file:

(set-add-alt-conf-split-type-number 0)


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5.17 Mutation

Mutations are available on a 1-by-1 basis using the graphics. After selecting “Mutate…” from the “Model/Fit/Refine” dialog, click on an atom in the graphics. A “Residue Type” window will now appear. Select the new residue type you wish and the residue in the graphics is updated to the new residue type 77. The initial position of the new rotamer is the a priori most likely rotamer. Note that in interactive mode, such as this, a residue type match 78 will not stop the mutation action occurring.

5.17.1 Mutating DNA/RNA

Mutation of DNA or RNA can be performed using “Simple Mutate” from the Model/Fit/Refine dialog. Residues need to be named "Ad", "Gr", "Ur" etc.

5.17.2 Multiple mutations

This dialog can be found under Calculate -> Mutate Residue Range. A residue range can be assigned a sequence and optionally fitted to the map. This is useful converting a poly-ALA model to the correct sequence 79.

Multiple mutations are also supported via the scripting interface. Unlike the single residue mutation function, a residue type match will prevent a modification of the residue 80. Two functions are provided: To mutate a whole chain, use (mutate-chain imol chain-id sequence) where:

chain-id is the chain identifier of the chain that you wish to mutate (e.g. "A") and

imol is molecule number.

sequence is a list of single-letter residue codes, such as "GYRESDF" (this should be a straight string with no additional spaces or carriage returns).

Note that the number of residues in the sequence chain and those in the chain of the protein must match exactly (i.e. the whole of the chain is mutated (except residues that have a matching residue type).)

To mutate a residue range, use

where

start-res-no is the starting residue for mutation

stop-res-no is the last residue for mutation, i.e. using values of 2 and 3 for start-res-no and stop-res-no respectively will mutate 2 residues.

Again, the length of the sequence must correspond to the residue range length. Note also that this is a protein sequence - not nucleic acid.

For mutation of nucleic acids, use:

(mutate-nucleotide-range imol chain-id resno-start resno-end sequence)

5.17.3 Mutating to a Non-Standard Residue

Sometimes one might like to model post-translational or other such modifications. How is that done, if the new residue type is not one of the standard residue types?

There is a scripting function:

(mutate-by-overlap imol chain-id resno new-three-letter-code)

This imports a model residue for the new residue type and overlays it on to the given residue by using graph-matching to determine the equivalent atoms.

The GUI for this can be found under Extensions -> Modelling -> Replace Residue... (for this to work, you need to be centred on the residue you wish to replace).

Note that if you are replacing are conventional protein residue with a modified form (e.g. replacing a TYR with a phoso-tyrosine or a LYS with an acetyl-lysine) you will need to make sure that the group of the resulting restraints is an L-peptide (use Edit -> Restraints to check and modify the restraints group. Likewise for modified RNA/DNA nucleotides, you need to specify the group as RNA or DNA as appropriate.

5.17.4 Mutate and Autofit

The function combines Mutation and Auto Fit Rotamer and is the easiest way to make a mutation and then fit to the map. You can currently only “Mutate and Autofit” protein residues (i.e. things with a rotamer dictionary.

5.17.5 Renumbering

Renumbering is straightforward using the renumber dialog available under Calculate -> Renumber Residue Range…. There is also a scripting interface:

(renumber-residue-range imol chain-id start-res-no last-resno offset)


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5.18 Importing Lignds/Monomers

You can import monomers (often ligands) using File -> Get Monomer…81 by providing the 3-letter code of your monomer/ligand. The resulting molecule will be moved so that it placed at the current screen centre.

Typically, when you are happy about the placement of the ligand, you’d then use Merge Molecules to add the ligand/monomer to the main set of coordinates.

This procedure creates a pdb file monomer-XXX.pdb and a dictionary file libcheck_XXX.cif in the directory in which Coot was started.

A future invocation of Get Monomer uses these file so that the monomer appears quickly 82.


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5.19 Ligand from SMILES strings

Similarly, you can generate ligands using File -> SMILES... and providing a SMILES string and a code for the residue name (this is your name for the residue type and a dictionary will be generated for the monomer of this type). This function is also a wrapper to LIBCHECK.


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5.20 Find Ligands

You are offered a selection of maps to search (you can only choose one at a time) and a selection of molecules that act as a mask to this map. Finally you must choose which ligand types you are going to search for in this map 83. Only molecules with less than 400 atoms are suggested as potential ligands.

If you do not have any molecules with less that 400 atoms loaded in Coot, you will get the message:

"Error: you must have at least one ligand to search for!"

New ligands are placed where the map density is and protein (mask) atoms are not). The masked map is searched for clusters using a default cut-off of 1.0\sigma. In weak density this cut-off may be too high and in such a case the cut-off value can be changed using something such as:

(set-ligand-cluster-sigma-level 0.8)

However, if the map to be searched for ligands is a difference map, a cluster level of 2.0 or 3.0 would probably be more appropriate (less likely to generate spurious sites).

Each ligand is fitted with rigid body refinement to each potential ligand site in the map and the best one for each site selected and written out as a pdb file. The clusters are sorted by size, the biggest one first (with an index of 0). The output placed ligands files have a prefix “best-overall” and are tagged by the cluster index and residue type of the best fit ligand in that site.

By default, the top 10 sites are tested for ligands - to increase this use:

(set-ligand-n-top-ligands 20)

5.20.1 Flexible Ligands

If the “Flexible?” checkbutton is activated, coot will generate a number of variable conformations (default 100) by rotating around the rotatable bonds (torsions). Each of these conformations will be fitted to each of the potential ligand sites in the map and the best one will be selected (again, if it passes the fitting criteria above).

Before you search for flexible ligands you must have read the mmCIF dictionary for that particular ligand residue type (File -> Import CIF dictionary).

Use:

(set-ligand-flexible-ligand-n-samples n-samples)

where n-samples is the number of samples of flexibility made for each ligand. Generally speaking, The more the number of rotatable bonds, the bigger this number should be.

By default the options to change these values are not in the GUI. To enable these GUI options, use the scripting function:

(ligand-expert)

5.20.2 Adding Ligands to Model

After successful ligand searching, one may well want to add that displayed ligand to the current model (the coordinates set that provided the map mask). To do so, use Merge Molecules (Section Merge Molecules).


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5.21 Flip Ligand

Sometimes a ligand is placed more or less in the correct position, but the orientation is wrong - or at least you might want to explore other possible orientation. To do that easily a function has been provided:

(flip-ligand imol chain-id residue-number)

This will flip the orientation of the residue around the Eigen vector corresponding to the largest Eigen value, exploring 4 possible orientations.

This function has been further wrapped to provide flipping for the active residue:

(flip-active-ligand)

This function can easily be bound to a key.


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5.22 Find Waters

As with finding ligands, you are given a choice of maps, protein (masking) atoms. A final selection has to be made for the cut-off level, note that this value is the number of standard deviation of the density of the map before the map has been masked. The default sigma level (water positions must have density above this level) is set for a “2Fo-Fc”-style map. If you want to use a difference map, you must change the sigma level (typically to 3 sigma) otherwise you run the risk of fitting waters to difference map noise peaks.

Then the map is masked by the masking atoms and a search is made of features in the map about the electron density cut-off value. Waters are added if the feature is approximately water-sized and can make sensible hydrogen bonds to the protein atoms. The new waters are optionally created in a new molecule called “Waters”.

You have control over several parameters used in the water finding:

(set-write-peaksearched-waters)

which writes ligand-waters-peaksearch-results.pdb, which contains the water peaks (from the clusters) without any filtering and ligand-waters.pdb which are a disk copy filtered waters that have been either added to the molecule or from which a new molecule has been created.

(set-ligand-water-to-protein-distance-limits min-d max-d) sets the minimum and maximum allowable distances between new waters and the masking molecule (usually the protein). Defaults are 2.4 and 3.2Å.

(set-ligand-water-spherical-variance-limit varlim) sets the upper limit for the density variance around water atoms. The default is 0.12.

The map that is marked by the protein and is searched to find the waters is written out in CCP4 format as "masked-for-waters.map".

5.22.1 Refinement Failure

Sometimes as a result of water fitting, you may see something like:

 WARNING:: refinement failure
           start pos: xyz = (      17.1,     34.76,     60.42)
           final pos: xyz = (     17.19,     34.61,     60.59)

When Coot finds a blob, it does a crude positioning of an atom at the centre of the grid points. It then proceeds to move to the peak of the blob by a series of translations. There are a certain number of cycles, and if it doesn’t reach convergence by the end of those cycles then you get the error message.

Often when you go to the position indicated, you can see why Coot had a problem in the refinement.

5.22.2 Blobs

After a water search, Coot will create a blobs dialog (see Section sec_blobs).


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5.23 Add Terminal Residue

This creates a new residue at the C or N terminal extension of the residue clicked by fitting to the map. \phi,\psi angle pairs are selected at random based on the Ramachandran plot probability (for a generic residue) and fitted to the density. By default there are 100 trials. It is possible that a wrong position will be selected for the terminal residue and if so, you can reject this fit and try again with Fit Terminal Residue 84. Each of the trial positions are scored according to their fit to the map 85 and the best one selected. It is probably a good idea to run “Refine Zone” on these new residues.

If you use the Extensions (Dock Sequence... -> Associate Sequence with Model) to apply a PIR sequence file to a model then Add Terminal Residue will use the sequence alignment to determine the residue type of the added residue.

Sometimes, particularly with low resolution maps, the added terminal residue will wander off to somewhere inappropriate. This can be addressed in a number of ways:

  1. (set-terminal-residue-do-rigid-body-refine 0) will disable rigid body fitting of the terminal residue fragment for each trial residue position (the default is 1 (on)) - this may help if the search does not provide good results.
  2. to anneal the newly added residue back to the clicked residue (no matter where it ended up being positioned): (set-add-terminal-residue-do-post-refine 1)
  3. (set-add-terminal-residue-n-phi-psi-trials 200) will change the number of trials (default is 100). This is useful if you think that Coot needs to search harder to find a good solution to the positioning of the next residue.

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5.24 Add OXT Atom to Residue

At the C-terminus of a chain of amino-acid residues, there is a “modification” so that the C-O becomes a carbonyl, i.e. an extra (terminal) oxygen (OXT) needs to be added. This atom is added so that it is in the plane of the C\alpha, C and O atoms of the residue.

Scripting usage:

(add-OXT-to-residue imol residue-number insertion-code chain-id) 86,

where insertion-code is typically "".

Note, in order to place OXT, the N, CA, C and O atoms must be present in the residue - if (for example) the existing carbonyl oxygen atom is called “OE1” then this function will not work.


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5.25 Add Atom at Pointer

By default, “Add Atom At Pointer” will pop-up a dialog from which you can choose the atom type you wish to insert 87. Using (set-pointer-atom-is-dummy 1) you can by-pass this dialog and immediately create a dummy atom at the pointer position. Use an argument of 0 to revert to using the atom type selection pop-up on a button press.

The atoms are added to a new molecule called “Pointer Atoms”. They should be saved and merged with your coordinates outside of Coot.


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5.26 Place Helix

The idea is to place a helix more or less “here” (the screen centre) by fitting to the electron density map. The algorithm is straightforward. First we move to the local centre of density, then examine the density for characteristic directions and fit ideal helices (of length 20 residues) to these directions. The helix is then extended if possible (by checking the fit to the map of residues added in ideal helix conformation) and chopped back if not. If the fit is successful, the helix is created in a new molecule called “Helix”. If the fit is not successful, there is instead a message added to the status bar. You can build the majority of a helical protein in a few minutes using this method (you will of course have to assemble the helices and assign residue numbers and sequence later).

This is available as a scripting function (place-helix-here) and in the GUI (in the “Other Modelling Tools” dialog).


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5.27 Building Ideal DNA and RNA

The interface to building ideal polynucleotides can be found by pressing the “Ideal RNA/DNA…” button on the “Other Modelling Tools” dialog.

For a given sequence, a choice of DNA or RNA, A or B form, single or double stranded is presented.

The interface may not gracefully handle uracils in DNA, thymines in RNA or B form RNA.

The ideal B-form DNA is somewhat under-wound, needing 11 base-pairs to repeat (instead of the expected 10.5). There is no easy fix for this currently.


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5.28 Merge Molecules

The dialog for this opperation can be found under “Calculate” in the main menubar. This is typically used to add molecule fragments or residues that are in one molecule to the “working” coordinates 88.

The scripting interface is used like this

(merge-molecules molecule-list target-molecule)

e.g.

(merge-molecules (list 1 2 ) 0)

merges molecules 1 and 2 into molecule 0.


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5.29 Temperature Factor for New Atoms

The default temperature factor for new atoms is 30.0. This can be changed by the following

(set-default-temperature-factor-for-new-atoms 50.0)


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5.30 Applying NCS Edits

Let’s imagine that you have 3-fold NCS. You have molecule “A” as your master molecule and you make edits to that molecule. Now you want to apply the edits that you made to “A” (the NCS master chain ID) to the “B” and “C” molecules (i.e. you want the “B” and “C” molecules to be rotated/translated versions of the “A” molecule). How is that done?

There are now guis to NCS command to help you out (under Extensions). However, for completeness here are the scripting versions:

(copy-from-ncs-master-to-others imol master-chain-id)

If you have only a range of residues, rather than a whole chain to replace:

(copy-residue-range-from-ncs-master-to-others imol master-chain-id start-resno end-resno)

e.g.

(copy-residue-range-from-ncs-master-to-others 0 "A" 1 5)

If you want to copy a residue range to a specific chain, or specific list of chains (rather than all NCS peer chains) then make a list of the chain-ids that you wish replaced:

(copy-residue-range-from-ncs-master-to-chains 0 "A" 1 5 (list "C"))

in this case, just the residues in the "C" chain is replaced.


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5.31 Running Refmac

Use the “Run Refmac...” button to select the dataset and the coordinates on which you would like to run Refmac. Note that here Coot only allows the use of datasets which has Refmac parameters set as the MTZ file was read. By default, Coot displays the new coordinates and the new map generated from refmac’s output MTZ file. Optionally, you can also display the difference map.

You can add extra parameters (data lines) to refmac’s input by storing them in a file called refmac-extra-params in the directory in which you started coot.

You can also provide extra/replacement parameters for refmac by setting the variable refmac-extra-params to a list of strings, for example:

(set! refmac-extra-params (list "REFINE MATRIX 0.1" "MAKE HYDROGENS NO"))

Coot “blocks” 89 until Refmac has terminated 90.

The default refmac executable is refmac5 it is presumed to be in the path. If you don’t want this, it can be overridden using a re-definition either at the scripting interface or in one’s ~/.coot file e.g.:

After running refmac several times, you may find that you prefer if the new map that refmac creates (after refmac refinement) is the same colour as the previous one (from before this refmac refinement). If so, use:

(set-keep-map-colour-after-refmac 1)

which will swap the colours of then new and old refmac map so that the post-refmac map has the same colour as the pre-refmac map and the pre-refmac map is coloured with a different colour.


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5.32 Running SHELXL

Coot can read shelx .res files and write .ins files, and thus one can refine using SHELXL in a convenient manner using the function

(shelxl-refine imol . hkl-file-name)

(the hkl-file-name is an optional argument)

e.g.

(shelxl-refine 0)

or

(shelxl-refine 0 "insulin.hkl")

In the former case, coot will presume that there is a SHELX hkl file corresponding to the res file that you read in; if there is not coot will print a warning and not try to run shelxl. In the latter case, you can specify the location of the hkl file.

After shelxl has finished, coot will automatically read in the resulting res coordinates, the fcf file, convert the data to mmCIF format and read that, which generates a \sigma_A map and a difference map.

Coot creates a time stamped ins file and a time-stamped sym-link to the hkl file in the coot-shelxl directory.

Please note that the output ins file will not be particularly useful (and thus shelxl will fail) if the input file was not in SHELX ins format.

There is a GUI for this operation under the “Extensions” menu item.


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5.33 Clear Pending Picks

Sometimes one can click on a button 91 unintentionally. This button is there for such a case. It clears the expectation of an atom pick. This works not only for modelling functions, but also geometry functions (such as Distance and Angle).


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5.34 Delete

Single atoms or residues can be deleted from the molecule using “Delete…” from the “Model/Fit/Refine”dialog. Pressing this button results in a new dialog, with the options of “Residue” (the default), “Atom” and “Hydrogen Atoms”. Now click on an atom in the graphics - the deleted object will be the whole residue of the atom if “Residue” was selected and just that atom if “Atom” was selected. Note that if a residue has an alternative conformation, then “Delete Residue” will delete only the conformation that matches that alternative conformation specifier of the clicked atom.

Only waters are deletable if the "Water" check button is active and waters are not deletable if the "Residue/Monomer" check button is active. This is to reduce mis-clicking.

To rotate the view when in “Delete Mode”, use Ctrl left-mouse.

If you want to delete multiple items you can use check the “Keep Delete Active” check-button on this dialog This will will keep the dialog open, ready for deletion of next item.

An atom can be delete using the scripting

(delete-atom imol chain-id residue-no ins-code atom-name alt-conf)

Residues can be deleted using the scripting

(delete-residue imol chain-id residue-no ins-code)

Residue ranges can be deleted using the scripting

(delete-residue-range imol chain-id residue-no-start residue-no-end)

Chains can be deleted using the scripting

(delete-chain imol chain-id)

Sidechains can be deleted from a region:

(delete-side-chain-range imol chain-id residue-no-start residue-no-end)

or for a chain

(delete-sidechains-for-chain imol chain-id)


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5.35 Sequence Assignment

You can assign a (FASTA format) sequence to a molecule using:

(assign-fasta-sequence imol chain-id fasta-seq)

This function has been provided as a precursor to functions that will (as automatically as possible) mutate your current coordinates to one that has the desired sequence. It will be used in automatic side-chain assignment (at some stage in the future).


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5.36 Building Links and Loops

Coot can build missing linking regions or loops 92. The function can be found under Calculate -> Fit Loop -> Fit Loop by Rama Search or the scripting function:

(fit-gap imol chain-id start-resno stop-resno)

and

(fit-gap imol chain-id start-resno stop-resno sequence)

the second form will also mutate and try to rotamer fit the provided sequence.

Example usage: let’s say for molecule number 0 in chain "A" we have residues up to 56 and then a gap after which we have residues 62 and beyond:

(fit-gap 0 "A" 57 61 "TYPWS")


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5.37 Fill Partial Residues

After molecular replacement, the residues of your protein could well have the correct sequence but be chopped back to CG or CB atoms. There is a function to fill such partially-filled residues:

(fill-partial-residues imol)

This identifies residues with missing atoms, then fills them and does a rotamer fit and real-space refinement.

If you want to fill the side chain of just one residue

(fill-partial-residue imol chain-id res-no ins-code)

this does a auto-fit-best-rotamer and a refinement on the resulting side-chain position.


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5.38 Changing Chain IDs

You can change the chain ids of chains using Calculate -> Change Chain IDs…. Coot will block an attempt to change the whole of a chain and the target chain id already exists in the molecule.

If you use the "Residue Range" option then you can insert residues with non-conflicting residue number into pre-existing chains.


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5.39 Setting Occupancies

As well as the editing “Residue Info” to change occupancies of individual atoms, one can use a scripting function to change occupancies of a whole residue range:

example usage:

(zero-occupancy-residue-range 0 "A" 23 28)

This is often useful to zero out a questionable loop before submitting for refinement. After refinement (with refmac) there should be relatively unbiased density in the resulting 2Fo-Fc-style and difference maps.

Similarly there is a function to reverse this operation:


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5.40 Fix Nomenclature Errors

Currently this is available only in scripting form:

(fix-nomenclature-errors imol)

This will fix atoms nomenclature problems in molecule number imol according to the same criteria as WATCHECK 93 e.g. Chi-2 for Phe, Tyr, Asp, and Glu should be between -90 and 90 degrees. Note that Val and Leu nomenclature errors are also corrected.


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5.41 Rotamer Fix Whole Protein

There is an experimental scripting function

(fit-protein imol)

which does a auto-fit rotamer and Real Space Refinement for each residue. The graphics follow the refinement.


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5.42 Refine All Waters

All the waters in a model can be refined (that is, moved to the local density peak) using

(fit-waters imol)

This is a non-interactive function (the waters are moved without user intervention).


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5.43 Moving Molecules/Ligands

Often you want to move a ligand (or some such) from wherever it was read in to the position of interest in your molecule (i.e. the current view centre). There is a GUI to do this: Calculate -> Move Molecule Here.

There are scripting functions available for this sort of thing:

(molecule-centre imol)

will tell you the molecule centre of the imolth molecule.

(translate-molecule-by imol x-shift y-shift z-shift)

will translate all the atoms in molecule imol by the given amount (in Ångströms).

(move-molecule-to-screen-centre imol)

will move the imolth molecule to the current centre of the screen (sometimes useful for imported ligands). Note that this moves the atoms of the molecule - not just the view of the molecule.


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5.44 Modifying the Labels on the Model/Fit/Refine dialog

If you don’t like the labels "Rotate/Translate Zone" or "Place Atom at Pointer" and rather they said something else, you can change the button names using:

(set-model-fit-refine-rotate-translate-zone-label "Move Zone")

and

(set-model-fit-refine-place-atom-at-pointer "Add Atom")


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6 Map-Related Features


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6.1 Maps in General

Maps are “infinite,” not limited to pre-calculated volume (the “Everywhere You Click - There Is Electron Density” (EYC-TIED) paradigm) symmetry-related electron density is generated automatically. Maps are easily re-contoured. Simply use the scroll wheel on you mouse to alter the contour level (or -/+ on the keyboard).

Maps follow the molecule. As you recentre or move about the crystal, the map quickly follows. If your computer is not up to re-contouring all the maps for every frame, then use Draw -> Dragged Map… to turn off this feature.

6.1.1 Map Reading Bug

Unfortunately, there is a bug in map-reading. If the map is not a bona-fide CCP4 map 94, then coot will crash. Sorry. A fix is in the works but “it’s complicated”. That’s why maps are limited to the extension ".ext" and ".map", to make it less likely a non-CCP4 map is read.


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6.2 Create a Map

From MTZ, mmCIF and .phs data use File -> Open MTZ, CIF or phs…. You can then choose the MTZ columns for the Fourier synthesis. The button “Expert mode” also adds to the options any anomalous columns you may have in the MTZ file (a -90 degree phase shift will be applied). It also provides the option to apply resolution limits.

From a CCP4 map use File -> Read Map. After being generated/read, the map is immediately contoured and centred on the current rotation centre.

6.2.1 Auto-read MTZ file

This function allows Coot to read an MTZ file and make a map directly (without going through the column selection procedure). The default column labels for auto-reading are "FWT" and "PHWT" for the 2Fo-Fc-style map, "DELFWT" and "PHDELWT" for the difference map. You can change the column labels that Coot uses for auto-reading - here is an example of how to do that:

(set-auto-read-column-labels "2FOFCWT" "PHIWT" 0) (set-auto-read-column-labels "FOFCWT" "DELPHIWT" 1)

By default the difference map is created in auto-reading the MTZ file. If you don’t want a difference map, you can use the function:

(set-auto-read-do-difference-map-too 0)

6.2.2 Reading CIF data

There are several maps that can be generated from CIF files that contain observed Fs, calculated Fs and calculated phases:

6.2.3 Reading PHS data

There are 2 ways to read data by scripting:

(read-phs-and-make-map-using-cell-symm phs-file-name space-group-name a b c alpha beta gamma)

(read-pdb-and-make-map-with-reso-limits imol-previous phs-file-name reso-limit-low reso-limit-high)

The first specifies the cell explicitly, and alpha, beta and gamma are specified in degrees.

The second form allows the specification of resolution limits and takes the cell and symmetry from a previous molecule (typically a pdb file).


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6.3 Map Contouring

Maps can be re-contoured using the middle-mouse scroll-wheel (buttons 4 and 5 in X Window System(TM) terminology). Scrolling the mouse wheel will change the map contour level and the map it redrawn. If you have several maps displayed then the map that has its contour level changed can be set using HID -> Scrollwheel -> Attach scroll-wheel to which map?. If there is only one map displayed, then that is the map that has its contour level changed (no matter what the scroll-wheel is attached to in the menu). The level of the electron density is displayed in the top right hand corner of the OpenGL canvas.

Use keyboard + or - to change the contour level if you don’t have a scroll-wheel 95.

If you are creating your map from an MTZ file, you can choose to click on the “is difference map” button on the Column Label selection widget (after a data set filename has been selected) then this map will be displayed in 2 colours corresponding to + and - the map contour level.

If you read in a map and it is a difference map then there is a checkbutton to tell Coot that.

If you want to tell Coot that a map is a difference map after it has been read, use:

(set-map-is-difference-map imol)

where imol is the molecule number.

By default the change of the contour level is determined from the sigma of the map. You can change this in the map properties dialog or by using the scripting function:

(set-contour-by-sigma-step-by-mol step on/off? imol)

where

step is the difference in sigma from one level to the next (typically 0.2)

on/off? is either 0 (sigma stepping off) or 1 (sigma stepping on)

By default the map radius 96 is 10Å. The default increment to the electron density depends on whether or not this is a difference map (0.05 e^-/\AA^3 for a “2Fo-Fc” style map and 0.005 e^-/\AA^3 for a difference map). You can change these using Edit -> Map Parameters or by using the “Properties” button of a particular map in the Display Control (Display Manager) window.


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6.4 Map Extent

The extent of the map can be set using the GUI (Edit -> Map Parameters -> Map Radius) or by using the scripting function, e.g.:

(set-map-radius 13.2)


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6.5 Map Contour “Scrolling” Limits

Usually one doesn’t want to look at negative contour levels of a map97, so Coot has by default a limit that stops the contour level going beyond (less than) 0. To remove the limit:

(set-stop-scroll-iso-map 0) for a 2Fo-Fc style map

(set-stop-scroll-diff-map 0) for a difference map

To set the limits to negative (e.g. -0.6) levels:

(set-stop-scroll-iso-map-level -0.6)

and similarly:

(set-stop-scroll-diff-map-level -0.6)

where the level is specified in e^-/\AA^3.


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6.6 Map Line Width

The width of the lines that describe the density can be changed like this:

(set-map-line-width 2)

The default line width is 1.


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6.7 “Dynamic” Map colouring

By default, maps get coloured according to their molecule number. The starting colour (i.e. for molecule 0) is blue. The colour of a map can be changed by Edit -> Map Colour... The map colour gets updated as you change the value in the colour selector 98. Use “OK” to fix that colour.

As subsequent maps are read, they are coloured by rotation round a colour wheel. The default colour map step is 31 degrees. You can change this using:

(set-colour-map-rotation-for-map step)


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6.8 Difference Map Colouring

For some strange reason, some crystallographers 99 like to have their difference maps coloured with red as positive and green as negative, this option is for them:

(set-swap-difference-map-colours 1)

This option will allow the “blue is positive, red is negative” colour scheme on “Edit -> Map Colour”.


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6.9 Make a Difference Map

Using the “Make a Difference Map” function in the Extensions menu, one can make a difference from two arbitrary maps. The maps need not be on the same griding, or in the same space group even. The resulting map will be on the same griding and space group as the “Reference” map.


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6.10 Make an Averaged Map

There is a scripting interface to the generation of map averages. As above, the maps need not be on the same grid or in the same space group. The resulting map will have the same gridding and space group as the first map in the list. Typical usage:

(average-map '((1 1.0) (2 1.0))))

The argument to (average-map is a list of lists, each list element is a list of the map number and a weighting factor (1.0 in this case).


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6.11 Map Sampling

By default, the Shannon sampling factor is the conventional 1.5. Use larger values (Edit -> Map Parameters -> Sampling Rate) for smoother maps 100.

This value can be set by the scripting command

(set-map-sampling-rate 2.5)


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6.12 Dragged Map

By default, the map is re-contoured at every frame during a drag (Ctrl Left-mouse). Sometimes this can be annoyingly slow and jerky so it is possible to turn it off: Draw -> Dragged Map -> No.

To change this by scripting:

(set-active-map-drag-flag 0)


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6.13 Dynamic Map Sampling and Display Size

If activated (Edit -> Map Parameters -> Dynamic Map Sampling) the map will be re-sampled on a more coarse grid when the view is zoomed out. If “Display Size” is also activated, the box of electron density will be increased in size also. In this way, you can see electron density for big maps (many unit cells) and the graphics still remain rotatable.

If you want to have these functions active for all maps, add the following to your initialization file Scheme:

(set-dynamic-map-sampling-on) (set-dynamic-map-size-display-on)


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6.14 Skeletonization

The skeleton (also known as “Bones” 101) can be displayed for any map. A map can be skeletonized using Calculate -> Map Skeleton…. Use the option menu to choose the map and click “On” then “OK” to the generate the map (the skeleton is off by default).

The level of the skeleton can be changed by using Edit -> Skeleton Parameters… -> Skeletonization Level… and corresponds to the electron density level in the map. By default this value is 1.2 map standard deviations. The amount of map can be changed using Edit -> Skeleton Parameters… -> Skeleton Box Radius…102. The units are in Ångströms, with 40 as the default value.

The skeleton is often recalculated as the screen centre changes - but not always since it can be an irritatingly slow calculation. If you want to force a regeneration of the displayed skeleton, simply centre on an atom (using the middle mouse button) or press the S key.


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6.15 Map Sharpening

It can be educational (even useful at lower resolutions) to sharpen or blur a map. This can be achieved with the sharpening tool Calculate -> Map Sharpening…. By default, the maximum and minimum sharpness is +/- 200Å^2, this can be changed (in this case to 300) using:

(set-map-sharpening-scale-limit 300)

This currently only works on maps created by reading an MTZ (or other) reflection data file.


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6.16 Pattersons

Pattersons can be generated using the make-and-draw-patterson function. Example usage:

(make-and-draw-patterson mtz-file-name f-col sig-f-col)

where use-weights-flag is either 0 or 1.

e.g.

(make-and-draw-patterson "native.mtz" "FP_nat" "SIGFP_nat")


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6.17 Map Re-Interpolation

Maps can be re-interpolated to match a reference map.

(reinterp-map map-no reference-map-no)

will create a copy of map-no in the same cell, spacegroup and grid spacing as the reference-map-no map.


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6.18 Masks

A map can be masked by a set of coordinates. Use the scripting function:

(mask-map-by-molecule imol-map imol-model invert-mask?)

If invert-mask? is 0, this will create a new map that has density only where there are no (close) coordinates. If invert-mask? is 1 then the map density values will be set to zero everywhere except close to the atoms of molecule number imol-model.

The radius of the mask around each atom is 2.0Å by default. You can change this using:

(set-map-mask-atom-radius radius)

There is a GUI interface to Map Masking under the Extensions menu.

6.18.1 Example

If one wanted to show just the density around a ligand:

  1. Make a pdb file the contains just the ligand and read it in to Coot - let’s say it is molecule 1 and the ligand is residue 3 of chain “L”.
  2. Get a map that covers the ligand (e.g. from refmac). Let’s say this map is molecule number 2.
  3. Mask the map:

    (mask-map-by-molecule 2 1 1)

    This creates a new map. Turn the other maps off, leaving only the masked map.

To get a nice rendered image, press F8 (see Section Raster3D).


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6.19 Trimming

If you want to remove all the atoms 103 that lie “outside the map” (i.e. in low density) you can use

(trim-molecule-by-map imol-coords imol-map density-level delete/zero-occ?)

where delete/zero-occ? is 0 to remove the atoms and 1 to set their occupancy to zero.

There is a GUI interface for this feature under the “Extensions” menu item.


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6.20 Map Transformation

If you want to transform a map, you can do it thusly:

(transform-map imol rotation-matrix trans point radius)

where:

rotation-matrix is a 9-membered list of numbers for an orthogonal rotation matrix.

trans is a 3-membered list of numbers (distances in Ångstöms).

point is a 3-membered list of numbers (centre point in Ångstöms).

radius is a single number (also in Ångstöms).

This applies the rotation rotation-matrix and a translation trans to a map fragment, so that when the transformation is applied the centre of the new map is at point.

Example usage:

(transform-map 2 '(1 0 0 0 1 0 0 0 1) '(0 0 1) (rotation-centre) 10)

which transforms map number 2 by a translation of 1Å along the Z axis, centred at the screen centre for 10Å around that centre.

Here’s a more real-world example:

Let’s say we want to tranform the density over the “B” molecule to a position over the “A” molecule. First we do a LSQ transformation to get the rotation and translation that moves the “B” coordinates over the “A” coordinates:

In the terminal output we get:

|    0.9707,    0.2351,   0.05033|
|  -0.04676,      0.39,   -0.9196|
|   -0.2358,    0.8903,    0.3896|
(    -33.34,     21.14,     18.82)

The centre of the “A” molecule is at (58.456, 5.65, 11.108). So we do:

(transform-map 3 (list 0.9707 0.2351 0.05033 -0.04676 0.39 -0.9196 -0.2358 0.8903 0.3896) (list -33.34 21.14 18.82) (list 58.456 5.65 11.108) 8)

Which creates a map over the middle of the “A” molecule. Note that using a too high radius can cause overlap problems, so try with a small radius (e.g. 5.0) if the resulting map looks problematic.

Alternatively, instead of typing the whole matrix, you can use a coordinates least-squares fit to generate the matrix for you. (transform-map-using-lsq-matrix) does just that.

Heres how to use it:

(transform-map-using-lsq-matrix imol-ref ref-chain ref-resno-start ref-resno-end imol-mov mov-chain mov-resno-start mov-resno-end imol-map about-pt radius)

Hopefully the arguments are self explanatory (ref refers to the reference molecule, of course and about-pt is a 3-number list such as is returned by (rotation-centre)).

We can now export that map, if we want.


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6.21 Export Map

You can write out a map from Coot (e.g. one from NCS averaging, or masking or general transformation) using the export map function:

(export-map imol filename)

e.g.

(export-map 4 "ncs-averaged.map")


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7 Validation

The validation functions are still being added to from time to time. In future there will be more functions, particularly those that will interface to other programs.


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7.1 Ramachandran Plots

Ramachandran plots are “dynamic”. When you edit the molecule (i.e. move the coordinates of some of atoms) the Ramachandran plot gets updated to reflect those changes. Also the underlying \phi/\psi probability density changes according to the selected residue type (i.e. the residue under the mouse in the plot). There are 3 different residue types: GLY, PRO, and not-GLY-or-PRO 104.

When you mouse over a representation of a residue (a little square or triangle 105) the residue label pops up. The residue is “active” i.e. it can be clicked. The “graphics” view changes so that the C\alpha of the selected residue is centred. In the Ramachandran plot window, the current residue is highlighted by a green square.

The underlying distributions are taken from the Richardson’s Top500 structures http://kinemage.biochem.duke.edu/databases/top500.php.

The probability levels for acceptable (yellow) and preferred (red) are 0.2% and 2% respectively.

You can change the contour levels:

(set-ramachandran-plot-contour-levels 0.025 0.003)

You can change the “blocksize” (the default is 10 degrees) of the contours using

(set-ramachandran-plot-background-block-size 5)

These comes into effect when a new plot is created (it doesn’t change plots currently displayed).


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7.2 Geometry Analysis

A restraints-based geometry analysis of the molecule. The distortion is weighted by atom occupancy. The distortion of the geometry due to links is shared between the contributing residues.

Note that only the first model of a multi-model molecule is analysed.


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7.3 Chiral Volumes

The dictionary is used to identify the chiral atoms of each of the model’s residues. A clickable list is created of atoms whose chiral volume in the model is of a different sign to that in the dictionary.

During refinement and regularization, Coot will pop-up dialogs warning about chiral volume errors - if you have them. This can be annoying 106. You can inhibit this dialog like this:

(set-show-chiral-volume-errors-dialog 0)

7.3.1 Fixing Chiral Volume Errors

There are two obvious ways:

1) mutate and auto-fit rotamer (mutate it to the residue type that it is)

2) RS Refine the residue and invert the chiral centre by pulling an atom. Usually you can pull the CA to the other side of the plane made by the chiral neighbouring atoms (using ctrl left-click). Sometimes giving the CB a good old tweak is the easier way.

Inverting the CB of THR is easier, just move the OG so that the plane of the neighbours is on the other side of the CB (again with ctrl left-click).


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7.4 Blobs: a.k.a. Unmodelled density

This is an interface to the Blobs dialog. A map and a set of coordinates that model the protein are required.

A blob is region of relatively high residual election density that cannot be explained by a simple water. So, for example, sulfates, ligands, mis-placed sidechains or unbuilt terminal residues might appear as blobs. The blobs are in order, the biggest 107 at the top.


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7.5 Difference Map Peaks

This is one of the fastest ways to validate a model and its data (presuming that the difference map comes from a post-refinement mFo-DFc map). It highlights regions where the model and the data do not agree.

Lesser peaks within a certain distance (by default, 2.0Å) of a large peak are not shown. This cuts down on the number of times one is navigated to a particular region because of ripple or other noise peaks around a central peak.

This value can be queried:

(difference-map-peaks-max-closeness)

and adjusted:

(set-difference-map-peaks-max-closeness 0.1)


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7.6 Check Waters by Difference Map

Sometimes waters can be misplaced - taking the place of sidechains or ligands or crystallization agents such as phosphate for example 108. In such cases the variance of the difference map can be used to identify these problems.

This function is also useful to check anomalous maps. Often waters are placed in density that is really a something else, perhaps a cation, anion, sulphate or a ligand. If such an atom diffracts anomalously this can be identified and corrected.

By default the waters with a map variance greater than 3.5\sigma are listed. One can be more rigorous by using a lower cut-off:

(set-check-waters-by-difference-map-sigma-level 3.0)

The scripting interface is:

(check-waters-by-difference-map imol-coords imol-diff-map)

where imol-coords is the molecule number of the coordinates that contain the waters to be checked

imol-diff-map is the molecule number of the difference map (it must be a difference map, not an “ordinary” map). This difference map must have been calculated using the waters. So there is no point in doing this check immediately after “Find Waters”. You will need to run Refmac or some other refinement first first 109.


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7.7 Molprobity Tools Interface

The molprobity tools probe and reduce have been interfaced into Coot (currently, the interface is not as slick as it might be). However, the tools are useful and can be used in the following way:

first we need to tell Coot where to find the relevant executables (typically you would add the following lines to you ~/.coot file):

(define *probe-command* "/path/to/probe/executable")

(define *reduce-command* "/path/to/reduce/executable")

now the probe hydrogens and probe dots can be generated using Validate -> Probe Clashes (or in the Scripting Window):

(probe imol)

where imol is the molecule number of coordinates to be probed. A new molecule with Hydrogens is created (by reduce) and read in.

By default Coot creates a new molecule for the molecule that now has hydrogens. To change this:

(set! reduce-molecule-updates-current #t)

and that, as you can guess, replaces, rather than adds to the “probed” molecule.

This gives a "static" view of the molecule’s interactions.

To get a dynamic view (which is currently only enabled on rotating chi angles) add these to your ~/.coot file:

(set-do-probe-dots-on-rotamers-and-chis 1)

To get a semi-static view (dots are regenerated in the region of zone after a "Real Space Refinement"):

(set-do-probe-dots-post-refine 1)


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7.8 GLN and ASN B-factor Outliers

It is often difficult to detect by eye the correct orientation of the amino-carbonylo group of GLN and ASNs. However, we can use (properly refined) temperature factors to detect outliers. We take the Z value as half the difference between the B-factor of the NE2 and OE1 divided by the standard deviation of the B-factors of the rest of the residue. An analysis of GLNs and ASNs of high resolutions structures indicates that a Z value of greater than 2.25 indicates a potential (if not probable) flip. A “Fix” button is provided in the resultant dialog make this easy to do.

This analysis was added after discussions with Atsushi Nakagawa and so is called “Nakagawa’s Bees”.

The analysis does not check residues with multiple conformations.


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7.9 Validation Graphs

Coot provides several graphs that are useful for model validation (on a residue by residue basis): residue density fit, geometry distortion, temperature factor variance, peptide distortion and rotamer analysis.

7.9.1 Residue Density Fit

The density fit graph shows the density fit for residues. The score is the average electron density level at the atom centres of the atoms in the residue. The height of the blocks is inversely proportional to the density average.

The residue density fit is by default scaled to a map that is calculated on the absolute scale. Sometimes you might be using a map with density levels considerably different to this, which makes the residue density fit graph less useful. To correct for this you can use the scripting function:

(set-residue-density-fit-scale-factor factor)

where factor would be 1/(4* rmd_{map}) (as a rule of thumb).

(residue-density-fit-scale-factor) returns the current scale factor (default 1.0).

There is also a GUI to this:

Extensions -> Refine… -> Set Density Fit Graph Weight…

7.9.2 Rotamer Analysis

Residue rotamers are scored according to the prior likelihood. Note that when CD1 and CD2 of a PHE residue are exchanged (simply a nomenclature error) this can lead to large red blocks in the graph (apparently due to very unlikely rotamers). There are several other residues that can have nomenclature errors like this. To fix these problems use

(fix-nomenclature-errors imol)

7.9.3 Temperature Factor Variance

This idea is from Eleanor Dodson, who liked to use the standard deviation of a residue’s temperature factors to highlight regions of questionable structure.

Note that Hydrogens are ignored in this analysis.

7.9.4 Peptide Omega Angle Distortion

Some variability of the \omega is to be expected in the peptide bond. But not too much. Anything more than 13 degrees is suspicicous. Unexpected peptide bonds show up red by default. If cis peptides are to be expected, and should not marked as bad, then you can tell this to Coot using:

Edit -> Preferences -> Geometry -> Cis-Peptides -> No


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8 Representation


Up: Representation   [Contents][Index]

8.1 Surfaces

Coot uses the surface code from Gruber and Noble (2004).

Coot uses the partial charges of the atoms (the partial_charge field in the _chem_comp_atom block) from the charge dictionary item in the refmac (or other) cif dictionary. However, partial charges are only used under certain conditions

1) the molecule consists of less than 100 atoms

or

2) the number of atoms in the molecule that are hydrogens is at least 15% of the total number of atoms in the molecule

If partial charges are not used, then the fall-back is to use charges from side-chains charged at physiological pH (Arg, Lys, Asp, Glu).


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9 Hints and Usage Tips


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9.1 Documentation

This manual is on the web where it can be searched:

In the Menu item “About”, under “Online Docs URL...” there is a entry bar that can be used to search the Coot documentation via Google. The results are returned as a web page in web browser. The browser type can be specified as in this example:

(set-browser-interface "firefox")

Example usage can be found in xxx/share/coot/scheme/group-settings.scm


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9.2 Low Resolution

Building structures using low resolution data is a pain. We hope to make it less of a pain in future, but there are some things that you can do now.


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9.3 Coot Droppings

This describes the files and directory that coot leaves behind after it has been fed (sorry, I mean “used”). Everything except the 0-coot.state.scm state file can comfortably be deleted if needed after coot has finished.

You can stop the state and history files being written if you start coot with the --no-guano option.


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9.4 Clearing Backups

Coot will occasionally ask you to clear up the coot-backup directory. You can adjust the behaviour in a number of ways:

So, if you wanted to clear out everything more than 1 day old, every time, without Coot asking you about it:

(define *clear-out-backup-run-n-days* 0)
(define *clear-out-backup-old-days* 1)
(define (clear-backups-maybe) 
  (delete-coot-backup-files 'delete)
  (coot-real-exit 0))

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9.5 Getting out of “Translate” Mode

If you get stuck in "translate" mode in the GL canvas (i.e. mouse does not rotate the view as you would expect) simply press and release the Ctrl key to return to "rotate" mode.


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9.6 Getting out of “Continuous Rotation” Mode

The keyboard I key toggles the “continuous rotation” mode. The menu item Draw -> Spin View On/Off does the same thing.


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9.7 Getting out of “Label Atom Only” Mode

Similarly, if you are stuck in a mode where the “Model/Fit/Refine” buttons don’t work (the atoms are not selected, only the atom gets labelled), press and release the Shift key.


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9.8 Button Labels

Button labels ending in “…” mean that a new dialog will pop-up when this button is pressed.


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9.9 Picking

Note that left-mouse in the graphics window is used for both atom picking and rotating the view, so try not to click over an atom when trying to rotate the view when in atom selection mode.


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9.10 Resizing View

Click and drag using right-mouse (up and down or left and right) to zoom in and out.


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9.11 Scroll-wheel

To change the map to which the scroll-wheel is attached, use the scroll check button in the Display Manager or use HID -> Scrollwheel -> Attach Scrollwheel to which map?


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9.12 Slow Computer Configuration

Several of the parameters of Coot are chosen because they are reasonable on my “middle-ground” development machine. However, these parameters can be tweaked so that slower computers perform better:


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10 Other Programs


Up: Other Programs   [Contents][Index]

10.1 findligand

findligand is a stand-alone command-line program that uses the libraries of Coot.

findligand provides a number of command line arguments for increased flexibility:

One uses findligand like this:

$ findligand various-args ligand-pdb-file-name(s)

i.e. the example ligand pdb files that you wish to search for are given at the end of the command line.


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11 Scripting Functions


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11.1 Startup Functions


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11.1.1 set-prefer-python

function: set-prefer-python

tell coot that you prefer to run python scripts if/when there is an option to do so.


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11.1.2 prefer-python

function: prefer-python

the python-prefered mode.

This is available so that the scripting functions know whether on not to put themselves onto in as menu items.

If you consider using this, consider in preference use_gui_qm == 2, which is used elsewhere to stop python functions adding to the gui, when guile-gtk functions have alread done so. We should clean up this (rather obscure) interface at some stage.

return 1 for python is prefered, 0 for not.


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11.2 File System Functions


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11.2.1 make-directory-maybe

function: make-directory-maybe dir

Where dir is a string

make a directory dir (if it doesn’t exist) and return error code

If it can be created, create the directory dir, return the success status like mkdir: mkdir

Returns: zero on success, or -1 if an error occurred. If dir already exists as a directory, return 0 of course.


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11.2.2 set-show-paths-in-display-manager

function: set-show-paths-in-display-manager i

Where i is an integer number

Show Paths in Display Manager?

Some people don’t like to see the full path names in the display manager here is the way to turn them off, with an argument of 1.


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11.2.3 show-paths-in-display-manager-state

function: show-paths-in-display-manager-state

return the internal state

What is the internal flag?

Returns: 1 for "yes, display paths" , 0 for not


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11.2.4 add-coordinates-glob-extension

function: add-coordinates-glob-extension ext

Where ext is a string

add an extension to be treated as coordinate files


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11.2.5 add-data-glob-extension

function: add-data-glob-extension ext

Where ext is a string

add an extension to be treated as data (reflection) files


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11.2.6 add-dictionary-glob-extension

function: add-dictionary-glob-extension ext

Where ext is a string

add an extension to be treated as geometry dictionary files


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11.2.7 add-map-glob-extension

function: add-map-glob-extension ext

Where ext is a string

add an extension to be treated as geometry map files


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11.2.8 remove-coordinates-glob-extension

function: remove-coordinates-glob-extension ext

Where ext is a string

remove an extension to be treated as coordinate files


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11.2.9 remove-data-glob-extension

function: remove-data-glob-extension ext

Where ext is a string

remove an extension to be treated as data (reflection) files


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11.2.10 remove-dictionary-glob-extension

function: remove-dictionary-glob-extension ext

Where ext is a string

remove an extension to be treated as geometry dictionary files


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11.2.11 remove-map-glob-extension

function: remove-map-glob-extension ext

Where ext is a string

remove an extension to be treated as geometry map files


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11.2.12 set-sticky-sort-by-date

function: set-sticky-sort-by-date

sort files in the file selection by date?

some people like to have their files sorted by date by default


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11.2.13 unset-sticky-sort-by-date

function: unset-sticky-sort-by-date

do not sort files in the file selection by date?

removes the sorting of files by date


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11.2.14 set-filter-fileselection-filenames

function: set-filter-fileselection-filenames istate

Where istate is an integer number

on opening a file selection dialog, pre-filter the files.

set to 1 to pre-filter, [0 (off, non-pre-filtering) is the default


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11.2.15 filter-fileselection-filenames-state

function: filter-fileselection-filenames-state

, return the state of the above variable


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11.2.16 file-type-coords

function: file-type-coords file_name

Where file_name is a string

is the given file name suitable to be read as coordinates?


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11.2.17 open-coords-dialog

function: open-coords-dialog

display the open coordinates dialog


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11.2.18 set-file-chooser-selector

function: set-file-chooser-selector istate

Where istate is an integer number

this flag set chooser as default for windows, otherwise use selector 0 is selector 1 is chooser


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11.3 Widget Utilities


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11.3.1 set-main-window-title

function: set-main-window-title s

Where s is a string

set the main window title.

function added for Lothar Esser


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11.4 MTZ and data handling utilities


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11.4.1 manage-column-selector

function: manage-column-selector filename

Where filename is a string

given a filename, try to read it as a data file

We try as .phs and .cif files first


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11.5 Molecule Info Functions


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11.5.1 chain-n-residues

function: chain-n-residues chain_id imol

Where:

the number of residues in chain chain_id and molecule number imol

Returns: the number of residues


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11.5.2 molecule-centre-internal

function: molecule-centre-internal imol iaxis

Where:

internal function for molecule centre

Returns: status, less than -9999 is for failure (eg. bad imol);


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11.5.3 seqnum-from-serial-number

function: seqnum-from-serial-number imol chain_id serial_num

Where:

a residue seqnum (normal residue number) from a residue serial number

Returns: < -9999 on failure


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11.5.4 insertion-code-from-serial-number

function: insertion-code-from-serial-number imol chain_id serial_num

Where:

the insertion code of the residue.

Returns: NULL (scheme False) on failure.


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11.5.5 chain-id-scm

function: chain-id-scm imol ichain

Where:

the chain_id (string) of the ichain-th chain molecule number imol

Returns: the chain-id


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11.5.6 n-models

function: n-models imol

Where imol is an integer number

return the number of models in molecule number imol

useful for NMR or other such multi-model molecules.

return the number of models or -1 if there was a problem with the given molecule.


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11.5.7 n-chains

function: n-chains imol

Where imol is an integer number

number of chains in molecule number imol

Returns: the number of chains


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11.5.8 is-solvent-chain-p

function: is-solvent-chain-p imol chain_id

Where:

is this a solvent chain? [Raw function]

This is a raw interface function, you should generally not use this, but instead use (is-solvent-chain? imol chain-id)

This wraps the mmdb function isSolventChain().

Returns: -1 on error, 0 for no, 1 for is "a solvent chain". We wouldn’t want to be doing rotamer searches and the like on such a chain.


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11.5.9 is-protein-chain-p

function: is-protein-chain-p imol chain_id

Where:

is this a protein chain? [Raw function]

This is a raw interface function, you should generally not use this, but instead use (is-protein-chain? imol chain-id)

This wraps the mmdb function isAminoacidChain().

Returns: -1 on error, 0 for no, 1 for is "a protein chain". We wouldn’t want to be doing rotamer searches and the like on such a chain.


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11.5.10 is-nucleotide-chain-p

function: is-nucleotide-chain-p imol chain_id

Where:

is this a nucleic acid chain? [Raw function]

This is a raw interface function, you should generally not use this, but instead use (is-nucleicacid-chain? imol chain-id)

This wraps the mmdb function isNucleotideChain(). For completeness.

Returns: -1 on error, 0 for no, 1 for is "a nucleicacid chain". We wouldn’t want to be doing rotamer searches and the like on such a chain.


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11.5.11 n-residues

function: n-residues imol

Where imol is an integer number

return the number of residues in the molecule,

return -1 if this is a map or closed.


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11.5.12 n-atoms

function: n-atoms imol

Where imol is an integer number

return the atoms of residues in the molecule,

return -1 if this is a map or closed.


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11.5.13 remarks-scm

function: remarks-scm imol

Where imol is an integer number

return a list of the remarks of hte molecule number imol


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11.5.14 sort-chains

function: sort-chains imol

Where imol is an integer number

sort the chain ids of the imol-th molecule in lexographical order


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11.5.15 sort-residues

function: sort-residues imol

Where imol is an integer number

sort the residues of the imol-th molecule


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11.5.16 remarks-dialog

function: remarks-dialog imol

Where imol is an integer number

a gui dialog showing remarks header info (for a model molecule).


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11.5.17 print-header-secondary-structure-info

function: print-header-secondary-structure-info imol

Where imol is an integer number

simply print secondary structure info to the terminal/console. In future, this could/should return the info.


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11.5.18 add-header-secondary-structure-info

function: add-header-secondary-structure-info imol

Where imol is an integer number

add secondary structure info to the internal representation of the model


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11.5.19 copy-molecule

function: copy-molecule imol

Where imol is an integer number

copy molecule imol

Returns: the new molecule number. Return -1 on failure to copy molecule (out of range, or molecule is closed)


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11.5.20 add-ligand-delete-residue-copy-molecule

function: add-ligand-delete-residue-copy-molecule imol_ligand_new chain_id_ligand_new resno_ligand_new imol_current chain_id_ligand_current resno_ligand_current

Where:

Copy a molecule with addition of a ligand and a deletion of current ligand.

This function is used when adding a new (modified) ligand to a structure. It creates a new molecule that is a copy of the current molecule except that the new ligand is added and the current ligand/residue is deleted.


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11.5.21 exchange-chain-ids-for-seg-ids

function: exchange-chain-ids-for-seg-ids imol

Where imol is an integer number

Experimental interface for Ribosome People.

Ribosome People have many chains in their pdb file, they prefer segids to chainids (chainids are only 1 character). But coot uses the concept of chain ids and not seg-ids. mmdb allow us to use more than one char in the chainid, so after we read in a pdb, let’s replace the chain ids with the segids. Will that help?


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11.5.22 show-remarks-browswer

function: show-remarks-browswer

show the remarks browser


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11.6 Library and Utility Functions


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11.6.1 git-revision-count

function: git-revision-count

return the git revision count for for this build.


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11.6.2 svn-revision

function: svn-revision

an alias to git_revision_count() for backwards compatibility


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11.6.3 molecule-name

function: molecule-name imol

Where imol is an integer number

return the name of molecule number imol

Returns: 0 if not a valid name ( -> False in scheme) e.g. "/a/b/c.pdb" for "d/e/f.mtz FWT PHWT"


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11.6.4 molecule-name-stub-scm

function: molecule-name-stub-scm imol include_path_flag

Where:

return the molecule name without file extension


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11.6.5 molecule-name-stub-py

function: molecule-name-stub-py imol include_path_flag

Where:

return the molecule name without file extension


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11.6.6 set-molecule-name

function: set-molecule-name imol new_name

Where:

set the molecule name of the imol-th molecule


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11.6.7 coot-real-exit

function: coot-real-exit retval

Where retval is an integer number

exit from coot, give return value retval back to invoking process.


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11.6.8 coot-no-state-real-exit

function: coot-no-state-real-exit retval

Where retval is an integer number

exit without writing a state file


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11.6.9 coot-clear-backup-or-real-exit

function: coot-clear-backup-or-real-exit retval

Where retval is an integer number

exit coot doing clear-backup maybe


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11.6.10 coot-save-state-and-exit

function: coot-save-state-and-exit retval save_state_flag

Where:

exit coot, write a state file


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11.6.11 run-clear-backups

function: run-clear-backups retval

Where retval is an integer number

run clear-backups


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11.6.12 first-coords-imol

function: first-coords-imol

What is the molecule number of first coordinates molecule?

return -1 when there is none.


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11.6.13 first-small-coords-imol

function: first-small-coords-imol

molecule number of first small (<400 atoms) molecule.

return -1 on no such molecule


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11.6.14 first-unsaved-coords-imol

function: first-unsaved-coords-imol

What is the molecule number of first unsaved coordinates molecule?

return -1 when there is none.


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11.6.15 mmcif-sfs-to-mtz

function: mmcif-sfs-to-mtz cif_file_name mtz_file_name

Where:

convert the structure factors in cif_file_name to an mtz file.

Return 1 on success. Return 0 on a file without Rfree, return -1 on complete failure to write a file.


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11.7 Graphics Utility Functions


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11.7.1 set-do-anti-aliasing

function: set-do-anti-aliasing state

Where state is an integer number

set the bond lines to be antialiased


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11.7.2 do-anti-aliasing-state

function: do-anti-aliasing-state

return the flag for antialiasing the bond lines


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11.7.3 set-do-GL-lighting

function: set-do-GL-lighting state

Where state is an integer number

turn the GL lighting on (state = 1) or off (state = 0)

slows down the display of simple lines


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11.7.4 do-GL-lighting-state

function: do-GL-lighting-state

return the flag for GL lighting


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11.7.5 use-graphics-interface-state

function: use-graphics-interface-state

shall we start up the Gtk and the graphics window?

if passed the command line argument

no-graphics, coot will not start up gtk itself.

An interface function for Ralf.


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11.7.6 python-at-prompt-at-startup-state

function: python-at-prompt-at-startup-state

is the python interpreter at the prompt?

Returns: 1 for yes, 0 for no.


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11.7.7 start-graphics-interface

function: start-graphics-interface

start Gtk (and graphics)

This function is useful if it was not started already (which can be achieved by using the command line argument

no-graphics).

An interface for Ralf


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11.7.8 reset-view

function: reset-view

"Reset" the view

return 1 if we moved, else return 0.

centre on last-read molecule with zoom 100. If we are there, then go to the previous molecule, if we are there, then go to the origin.


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11.7.9 graphics-n-molecules

function: graphics-n-molecules

return the number of molecules (coordinates molecules and map molecules combined) that are currently in coot

Returns: the number of molecules (closed molecules are not counted)


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11.7.10 toggle-idle-spin-function

function: toggle-idle-spin-function

Spin spin spin (or not)


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11.7.11 toggle-idle-rock-function

function: toggle-idle-rock-function

Rock (not roll) (self-timed)


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11.7.12 set-rocking-factors

function: set-rocking-factors width_scale frequency_scale

Where:

Settings for the inevitable discontents who dislike the default rocking rates (defaults 1 and 1)


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11.7.13 set-idle-function-rotate-angle

function: set-idle-function-rotate-angle f

Where f is a number

how far should we rotate when (auto) spinning? Fast computer? set this to 0.1


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11.7.14 idle-function-rotate-angle

function: idle-function-rotate-angle

what is the idle function rotation angle?


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11.7.15 handle-read-draw-molecule

function: handle-read-draw-molecule filename

Where filename is a string

a synonym for read-pdb. Read the coordinates from filename (can be pdb, cif or shelx format)


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11.7.16 make-updating-model-molecule

function: make-updating-model-molecule filename

Where filename is a string

make a model molecule from the give file name.

If the file updates, then the model will be updated.


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11.7.17 allow-duplicate-sequence-numbers

function: allow-duplicate-sequence-numbers

enable reading PDB/pdbx files with duplicate sequence numbers


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11.7.18 set-convert-to-v2-atom-names

function: set-convert-to-v2-atom-names state

Where state is an integer number

shall we convert nucleotides to match the old dictionary names?

Usually (after 2006 or so) we do not want to do this (given current Coot architecture). Coot should handle the residue synonyms transparently.

default off (0).


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11.7.19 handle-read-draw-molecule-with-recentre

function: handle-read-draw-molecule-with-recentre filename recentre_on_read_pdb_flag

Where:

read coordinates from filename with option to not recentre.

set recentre_on_read_pdb_flag to 0 if you don’t want the view to recentre on the new coordinates.


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11.7.20 handle-read-draw-molecule-and-move-molecule-here

function: handle-read-draw-molecule-and-move-molecule-here filename

Where filename is a string

read coordinates from filename and recentre the new molecule at the screen rotation centre.


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11.7.21 read-pdb

function: read-pdb filename

Where filename is a string

read coordinates from filename


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11.7.22 assign-hetatms

function: assign-hetatms imol

Where imol is an integer number

some programs produce PDB files with ATOMs where there should be HETATMs. This is a function to assign HETATMs as per the PDB definition.


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11.7.23 hetify-residue

function: hetify-residue imol chain_id resno ins_code

Where:

if this is not a standard group, then turn the atoms to HETATMs.

Return 1 on atoms changes, 0 on not. Return -1 if residue not found.


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11.7.24 residue-has-hetatms

function: residue-has-hetatms imol chain_id resno ins_code

Where:

residue has HETATMs?

return 1 if all atoms of the specified residue are HETATMs, else, return 0. If residue not found, return -1.


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11.7.25 het-group-residues-scm

function: het-group-residues-scm imol

Where imol is an integer number

get the specs for hetgroups - waters are not counted as het-groups.


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11.7.26 het-group-residues-py

function: het-group-residues-py imol

Where imol is an integer number

get the specs for hetgroups - waters are not counted as het-groups.


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11.7.27 het-group-n-atoms

function: het-group-n-atoms comp_id

Where comp_id is a string

return the number of non-hydrogen atoms in the given het-group (comp-id).

Return -1 on comp-id not found in dictionary.


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11.7.28 replace-fragment

function: replace-fragment imol_target imol_fragment atom_selection

Where:

replace the parts of molecule number imol that are duplicated in molecule number imol_frag


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11.7.29 copy-residue-range

function: copy-residue-range imol_target chain_id_target imol_reference chain_id_reference resno_range_start resno_range_end

Where:

copy the given residue range from the reference chain to the target chain

resno_range_start and resno_range_end are inclusive.


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11.7.30 replace-residues-from-mol-scm

function: replace-residues-from-mol-scm imol_target imol_ref residue_specs_list_ref_scm

Where:

replace the given residues from the reference molecule to the target molecule


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11.7.31 clear-and-update-model-molecule-from-file

function: clear-and-update-model-molecule-from-file molecule_number file_name

Where:

replace pdb. Fail if molecule_number is not a valid model molecule. Return -1 on failure. Else return molecule_number


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11.7.32 screendump-image

function: screendump-image filename

Where filename is a string

dump the current screen image to a file. Format ppm

You can use this, in conjunction with spinning and view moving functions to make movies


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11.7.33 check-for-dark-blue-density

function: check-for-dark-blue-density

give a warning dialog if density it too dark (blue)


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11.7.34 set-draw-solid-density-surface

function: set-draw-solid-density-surface imol state

Where:

sets the density map of the given molecule to be drawn as a (transparent) solid surface.


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11.7.35 set-draw-map-standard-lines

function: set-draw-map-standard-lines imol state

Where:

toggle for standard lines representation of map.

This turns off/on standard lines representation of map. transparent surface is another representation type.

If you want to just turn off a map, don’t use this, use

.


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11.7.36 set-solid-density-surface-opacity

function: set-solid-density-surface-opacity imol opacity

Where:

set the opacity of density surface representation of the given map.

0.0 is totally transparent, 1.0 is completely opaque and (because the objects are no longer depth sorted) considerably faster to render. 0.3 is a reasonable number.


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11.7.37 set-flat-shading-for-solid-density-surface

function: set-flat-shading-for-solid-density-surface state

Where state is an integer number

set the flag to do flat shading rather than smooth shading for solid density surface.

Default is 1 (on.


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11.8 Interface Preferences


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11.8.1 set-scroll-by-wheel-mouse

function: set-scroll-by-wheel-mouse istate

Where istate is an integer number

Some people (like Phil Evans) don’t want to scroll their map with the mouse-wheel.

To turn off mouse wheel recontouring call this with istate value of 0


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11.8.2 scroll-by-wheel-mouse-state

function: scroll-by-wheel-mouse-state

return the internal state of the scroll-wheel map contouring


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11.8.3 set-auto-recontour-map

function: set-auto-recontour-map state

Where state is an integer number

turn off (0) or on (1) auto recontouring (on screen centre change) (default it on)


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11.8.4 get-auto-recontour-map

function: get-auto-recontour-map

return the auto-recontour state


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11.8.5 set-default-initial-contour-level-for-map

function: set-default-initial-contour-level-for-map n_sigma

Where n_sigma is a number

set the default inital contour for 2FoFc-style map

in sigma


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11.8.6 set-default-initial-contour-level-for-difference-map

function: set-default-initial-contour-level-for-difference-map n_sigma

Where n_sigma is a number

set the default inital contour for FoFc-style map

in sigma


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11.8.7 print-view-matrix

function: print-view-matrix

print the view matrix to the console, useful for molscript, perhaps


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11.8.8 get-view-quaternion-internal

function: get-view-quaternion-internal element

Where element is an integer number

internal function to get an element of the view quaternion. The whole quaternion is returned by the scheme function view-quaternion


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11.8.9 set-view-quaternion

function: set-view-quaternion i j k l

Where:

Set the view quaternion.


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11.8.10 apply-ncs-to-view-orientation

function: apply-ncs-to-view-orientation imol current_chain next_ncs_chain

Where:

Given that we are in chain current_chain, apply the NCS operator that maps current_chain on to next_ncs_chain, so that the relative view is preserved. For NCS skipping.


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11.8.11 apply-ncs-to-view-orientation-and-screen-centre

function: apply-ncs-to-view-orientation-and-screen-centre imol current_chain next_ncs_chain forward_flag

Where:

as above, but shift the screen centre also.


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11.8.12 set-fps-flag

function: set-fps-flag t

Where t is an integer number

set show frame-per-second flag


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11.8.13 get-fps-flag

function: get-fps-flag

set the state of show frames-per-second flag


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11.8.14 set-show-origin-marker

function: set-show-origin-marker istate

Where istate is an integer number

set a flag: is the origin marker to be shown? 1 for yes, 0 for no.


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11.8.15 show-origin-marker-state

function: show-origin-marker-state

return the origin marker shown? state


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11.8.16 hide-modelling-toolbar

function: hide-modelling-toolbar

hide the vertical modelling toolbar in the GTK2 version


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11.8.17 show-modelling-toolbar

function: show-modelling-toolbar

show the vertical modelling toolbar in the GTK2 version (the toolbar is shown by default)


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11.8.18 hide-main-toolbar

function: hide-main-toolbar

hide the horizontal main toolbar in the GTK2 version


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11.8.19 show-main-toolbar

function: show-main-toolbar

show the horizontal main toolbar in the GTK2 version (the toolbar is shown by default)


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11.8.20 show-model-toolbar-all-icons

function: show-model-toolbar-all-icons

show all available icons in the modelling toolbar (same as MFR dialog)


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11.8.21 show-model-toolbar-main-icons

function: show-model-toolbar-main-icons

show only a selection of icons in the modelling toolbar


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11.8.22 reattach-modelling-toolbar

function: reattach-modelling-toolbar

reattach the modelling toolbar to the last attached position


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11.8.23 set-model-toolbar-docked-position

function: set-model-toolbar-docked-position state

Where state is an integer number

to swap sides of the Model/Fit/Refine toolbar 0 (default) is right, 1 is left, 2 is top, 3 is bottom


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11.8.24 suck-model-fit-dialog

function: suck-model-fit-dialog

reparent the Model/Fit/Refine dialog so that it becomes part of the main window, next to the GL graphics context


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11.8.25 add-status-bar-text

function: add-status-bar-text s

Where s is a string

Put text s into the status bar.

use this to put info for the user in the statusbar (less intrusive than popup).


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11.8.26 set-model-fit-refine-dialog-stays-on-top

function: set-model-fit-refine-dialog-stays-on-top istate

Where istate is an integer number

model-fit-refine dialog stays on top


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11.8.27 model-fit-refine-dialog-stays-on-top-state

function: model-fit-refine-dialog-stays-on-top-state

return the state model-fit-refine dialog stays on top


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11.8.28 accept-reject-dialog-docked-state

function: accept-reject-dialog-docked-state

the accept/reject dialog docked state


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11.8.29 set-accept-reject-dialog-docked-show

function: set-accept-reject-dialog-docked-show state

Where state is an integer number

set the accept/reject dialog docked show state


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11.8.30 accept-reject-dialog-docked-show-state

function: accept-reject-dialog-docked-show-state

what is the accept/reject dialog docked show state?


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11.9 Mouse Buttons


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11.9.1 quanta-buttons

function: quanta-buttons

quanta-like buttons

Note, when you have set these, there is no way to turn them of again (other than restarting).


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11.9.2 quanta-like-zoom

function: quanta-like-zoom

quanta-like zoom buttons

Note, when you have set these, there is no way to turn them of again (other than restarting).


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11.9.3 set-control-key-for-rotate

function: set-control-key-for-rotate state

Where state is an integer number

Alternate mode for rotation.

Prefered by some, including Dirk Kostrewa. I don’t think this mode works properly yet


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11.9.4 control-key-for-rotate-state

function: control-key-for-rotate-state

return the control key rotate state


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11.9.5 blob-under-pointer-to-screen-centre

function: blob-under-pointer-to-screen-centre

Put the blob under the cursor to the screen centre. Check only positive blobs. Useful function if bound to a key.

The refinement map must be set. (We can’t check all maps because they are not (or may not be) on the same scale).

Returns: 1 if successfully found a blob and moved there. return 0 if no move.


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11.9.6 select-atom-under-pointer-scm

function: select-atom-under-pointer-scm

return scheme false or a list of molecule number and an atom spec


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11.9.7 select-atom-under-pointer-py

function: select-atom-under-pointer-py

return Python false or a list of molecule number and an atom spec


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11.10 Cursor Function


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11.10.1 normal-cursor

function: normal-cursor

normal cursor


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11.10.2 fleur-cursor

function: fleur-cursor

fleur cursor


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11.10.3 pick-cursor-maybe

function: pick-cursor-maybe

pick cursor maybe


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11.10.4 rotate-cursor

function: rotate-cursor

rotate cursor


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11.10.5 set-pick-cursor-index

function: set-pick-cursor-index icursor_index

Where icursor_index is an integer number

let the user have a different pick cursor

sometimes (the default) GDK_CROSSHAIR is hard to see, let the user set their own


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11.11 Model/Fit/Refine Functions


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11.11.1 post-model-fit-refine-dialog

function: post-model-fit-refine-dialog

display the Model/Fit/Refine dialog


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11.11.2 unset-model-fit-refine-dialog

function: unset-model-fit-refine-dialog

unset model/fit/refine dialog


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11.11.3 unset-refine-params-dialog

function: unset-refine-params-dialog

unset refine params dialog


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11.11.4 show-select-map-dialog

function: show-select-map-dialog

display the Display Manager dialog


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11.11.5 set-model-fit-refine-rotate-translate-zone-label

function: set-model-fit-refine-rotate-translate-zone-label txt

Where txt is a string

Allow the changing of Model/Fit/Refine button label from "Rotate/Translate Zone".


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11.11.6 set-model-fit-refine-place-atom-at-pointer-label

function: set-model-fit-refine-place-atom-at-pointer-label txt

Where txt is a string

Allow the changing of Model/Fit/Refine button label from "Place Atom at Pointer".


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11.11.7 post-other-modelling-tools-dialog

function: post-other-modelling-tools-dialog

display the Other Modelling Tools dialog


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11.11.8 set-refinement-move-atoms-with-zero-occupancy

function: set-refinement-move-atoms-with-zero-occupancy state

Where state is an integer number

shall atoms with zero occupancy be moved when refining? (default 1, yes)


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11.11.9 refinement-move-atoms-with-zero-occupancy-state

function: refinement-move-atoms-with-zero-occupancy-state

return the state of "shall atoms with zero occupancy be moved when refining?"


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11.12 Backup Functions


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11.12.1 make-backup

function: make-backup imol

Where imol is an integer number

make backup for molecule number imol


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11.12.2 turn-off-backup

function: turn-off-backup imol

Where imol is an integer number

turn off backups for molecule number imol


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11.12.3 turn-on-backup

function: turn-on-backup imol

Where imol is an integer number

turn on backups for molecule number imol


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11.12.4 backup-state

function: backup-state imol

Where imol is an integer number

return the backup state for molecule number imol

return 0 for backups off, 1 for backups on, -1 for unknown


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11.12.5 apply-undo

function: apply-undo

apply undo - the "Undo" button callback


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11.12.6 apply-redo

function: apply-redo

apply redo - the "Redo" button callback


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11.12.7 set-have-unsaved-changes

function: set-have-unsaved-changes imol

Where imol is an integer number

set the molecule number imol to be marked as having unsaved changes


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11.12.8 have-unsaved-changes-p

function: have-unsaved-changes-p imol

Where imol is an integer number

does molecule number imol have unsaved changes?

Returns: -1 on bad imol, 0 on no unsaved changes, 1 on has unsaved changes


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11.12.9 set-undo-molecule

function: set-undo-molecule imol

Where imol is an integer number

set the molecule to which undo operations are done to molecule number imol


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11.12.10 show-set-undo-molecule-chooser

function: show-set-undo-molecule-chooser

show the Undo Molecule chooser - i.e. choose the molecule to which the "Undo" button applies.


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11.12.11 set-unpathed-backup-file-names

function: set-unpathed-backup-file-names state

Where state is an integer number

set the state for adding paths to backup file names

by default directories names are added into the filename for backup (with / to _ mapping). call this with state=1 to turn off directory names


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11.12.12 unpathed-backup-file-names-state

function: unpathed-backup-file-names-state

return the state for adding paths to backup file names


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11.12.13 set-decoloned-backup-file-names

function: set-decoloned-backup-file-names state

Where state is an integer number

set the state for adding paths to backup file names

by default directories names are added into the filename for backup (with / to _ mapping). call this with state=1 to turn off directory names


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11.12.14 decoloned-backup-file-names-state

function: decoloned-backup-file-names-state

return the state for adding paths to backup file names


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11.12.15 backup-compress-files-state

function: backup-compress-files-state

return the state for compression of backup files


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11.12.16 set-backup-compress-files

function: set-backup-compress-files state

Where state is an integer number

set if backup files will be compressed or not using gzip


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11.13 Recover Session Function


Up: Recover Session Function   [Contents][Index]

11.13.1 recover-session

function: recover-session

recover session

After a crash, we provide this convenient interface to restore the session. It runs through all the molecules with models and looks at the coot backup directory looking for related backup files that are more recent that the read file. (Not very good, because you need to remember which files you read in before the crash - should be improved.)


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11.14 Map Functions


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11.14.1 calc-phases-generic

function: calc-phases-generic mtz_file_name

Where mtz_file_name is a string

fire up a GUI, which asks us which model molecule we want to calc phases from. On "OK" button there, we call map_from_mtz_by_refmac_calc_phases()


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11.14.2 map-from-mtz-by-refmac-calc-phases

function: map-from-mtz-by-refmac-calc-phases mtz_file_name f_col sigf_col imol_coords

Where:

Calculate SFs (using refmac optionally) from an MTZ file and generate a map. Get F and SIGF automatically (first of their type) from the mtz file.

Returns: the new molecule number, -1 on a problem.


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11.14.3 map-from-mtz-by-calc-phases

function: map-from-mtz-by-calc-phases mtz_file_name f_col sigf_col imol_coords

Where:

Calculate SFs from an MTZ file and generate a map.

Returns: the new molecule number.


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11.14.4 sfcalc-genmap

function: sfcalc-genmap imol_model imol_map_with_data_attached imol_updating_difference_map

Where:

Calculate structure factors from the model and update the given difference map accordingly.


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11.14.5 set-auto-updating-sfcalc-genmap

function: set-auto-updating-sfcalc-genmap imol_model imol_map_with_data_attached imol_updating_difference_map

Where:

As above, calculate structure factors from the model and update the given difference map accordingly - but difference map gets updated automatically on modification of the imol_model molecule.


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11.14.6 set-scroll-wheel-map

function: set-scroll-wheel-map imap

Where imap is an integer number

set the map that is moved by changing the scroll wheel and change_contour_level().


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11.14.7 set-scrollable-map

function: set-scrollable-map imol

Where imol is an integer number

return the molecule number to which the mouse scroll wheel is attached

set the map that has its contour level changed by the scrolling the mouse wheel to molecule number imol (same as

).


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11.14.8 scroll-wheel-map

function: scroll-wheel-map

the contouring of which map is altered when the scroll wheel changes?


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11.14.9 save-previous-map-colour

function: save-previous-map-colour imol

Where imol is an integer number

save previous colour map for molecule number imol


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11.14.10 restore-previous-map-colour

function: restore-previous-map-colour imol

Where imol is an integer number

restore previous colour map for molecule number imol


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11.14.11 set-active-map-drag-flag

function: set-active-map-drag-flag t

Where t is an integer number

set the state of immediate map upate on map drag.

By default, it is on (t=1). On slower computers it might be better to set t=0.


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11.14.12 get-active-map-drag-flag

function: get-active-map-drag-flag

return the state of the dragged map flag


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11.14.13 set-last-map-colour

function: set-last-map-colour f1 f2 f3

Where:

set the colour of the last (highest molecule number) map


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11.14.14 set-map-colour

function: set-map-colour imol red green blue

Where:

set the colour of the imolth map


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11.14.15 set-contour-level-absolute

function: set-contour-level-absolute imol_map level

Where:

set the contour level, direct control


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11.14.16 set-contour-level-in-sigma

function: set-contour-level-in-sigma imol_map level

Where:

set the contour level, direct control in r.m.s.d. (if you like that sort of thing)


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11.14.17 get-contour-level-absolute

function: get-contour-level-absolute imol

Where imol is an integer number

get the contour level


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11.14.18 get-contour-level-in-sigma

function: get-contour-level-in-sigma imol

Where imol is an integer number

get the contour level in rmd above 0.


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11.14.19 set-last-map-sigma-step

function: set-last-map-sigma-step f

Where f is a number

set the sigma step of the last map to f sigma


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11.14.20 set-contour-by-sigma-step-by-mol

function: set-contour-by-sigma-step-by-mol f state imol

Where:

set the contour level step

set the contour level step of molecule number imol to f and variable state (setting state to 0 turns off contouring by sigma level)


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11.14.21 data-resolution

function: data-resolution imol

Where imol is an integer number

return the resolution of the data for molecule number imol. Return negative number on error, otherwise resolution in A (eg. 2.0)


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11.14.22 model-resolution

function: model-resolution imol

Where imol is an integer number

return the resolution set in the header of the model/coordinates file. If this number is not available, return a number less than 0.


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11.14.23 export-map

function: export-map imol filename

Where:

export (write to disk) the map of molecule number imol to filename.

Return 0 on failure, 1 on success.


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11.14.24 export-map-fragment

function: export-map-fragment imol x y z radius filename

Where:

export a fragment of the map about (x,y,z)


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11.14.25 export-map-fragment-with-origin-shift

function: export-map-fragment-with-origin-shift imol x y z radius filename

Where:

export a fragment of the map about (x,y,z)


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11.14.26 export-map-fragment-to-plain-file

function: export-map-fragment-to-plain-file imol x y z radius filename

Where:

tmp interface for Hamish


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11.14.27 difference-map

function: difference-map imol1 imol2 map_scale

Where:

make a difference map, taking map_scale * imap2 from imap1, on the grid of imap1. Return the new molecule number. Return -1 on failure.


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11.14.28 reinterp-map

function: reinterp-map map_no reference_map_no

Where:

make a new map (a copy of map_no) that is in the cell, spacegroup and gridding of the map in reference_map_no.

Return the new map molecule number - return -1 on failure


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11.14.29 smooth-map

function: smooth-map map_no sampling_multiplier

Where:

make a new map (a copy of map_no) that is in the cell, spacegroup and a multiple of the sampling of the input map (a sampling factor of more than 1 makes the output maps smoother)


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11.14.30 average-map-scm

function: average-map-scm map_number_and_scales

Where map_number_and_scales is a SCM

make an average map from the map_number_and_scales (which is a list of pairs (list map-number scale-factor)) (the scale factors are typically 1.0 of course). The output map is in the same grid as the first (valid) map. Return -1 on failure to make an averaged map, otherwise return the new map molecule number.


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11.14.31 average-map-py

function: average-map-py map_number_and_scales

Where map_number_and_scales is a PyObject

make an average map from the map_number_and_scales (which is a list of pairs map_number, scale_factor. The output map is in the same grid as the first (valid) map. Return -1 on failure to make an averaged map, otherwise return the new map molecule number.


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11.15 Density Increment


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11.15.1 set-iso-level-increment

function: set-iso-level-increment val

Where val is a number

set the contour scroll step (in absolute e/A3) for 2Fo-Fc-style maps to val

The is only activated when scrolling by sigma is turned off


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11.15.2 set-diff-map-iso-level-increment

function: set-diff-map-iso-level-increment val

Where val is a number

set the contour scroll step for difference map (in absolute e/A3) to val

The is only activated when scrolling by sigma is turned off


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11.15.3 get-diff-map-iso-level-increment

function: get-diff-map-iso-level-increment

return difference maps iso-map level increment


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11.15.4 set-diff-map-iso-level-increment-from-text

function: set-diff-map-iso-level-increment-from-text text imol

Where:

set the difference maps iso-map level increment


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11.15.5 set-map-sampling-rate-text

function: set-map-sampling-rate-text text

Where text is a string

sampling rate

find the molecule for which the single map dialog applies and set the contour level and redraw


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11.15.6 set-map-sampling-rate

function: set-map-sampling-rate r

Where r is a number

set the map sampling rate (default 1.5)

Set to something like 2.0 or 2.5 for more finely sampled maps. Useful for baton-building low resolution maps.


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11.15.7 get-map-sampling-rate

function: get-map-sampling-rate

return the map sampling rate


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11.15.8 change-contour-level

function: change-contour-level is_increment

Where is_increment is an integer number

change the contour level of the current map by a step

if is_increment=1 the contour level is increased. If is_increment=0 the map contour level is decreased.


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11.15.9 set-last-map-contour-level

function: set-last-map-contour-level level

Where level is a number

set the contour level of the map with the highest molecule number to level


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11.15.10 set-last-map-contour-level-by-sigma

function: set-last-map-contour-level-by-sigma n_sigma

Where n_sigma is a number

set the contour level of the map with the highest molecule number to n_sigma sigma


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11.15.11 set-stop-scroll-diff-map

function: set-stop-scroll-diff-map i

Where i is an integer number

create a lower limit to the "Fo-Fc-style" map contour level changing

(default 1 on)


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11.15.12 set-stop-scroll-iso-map

function: set-stop-scroll-iso-map i

Where i is an integer number

create a lower limit to the "2Fo-Fc-style" map contour level changing

(default 1 on)


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11.15.13 set-stop-scroll-iso-map-level

function: set-stop-scroll-iso-map-level f

Where f is a number

set the actual map level changing limit

(default 0.0)


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11.15.14 set-stop-scroll-diff-map-level

function: set-stop-scroll-diff-map-level f

Where f is a number

set the actual difference map level changing limit

(default 0.0)


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11.15.15 set-residue-density-fit-scale-factor

function: set-residue-density-fit-scale-factor f

Where f is a number

set the scale factor for the Residue Density fit analysis


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11.16 Density Functions


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11.16.1 set-map-line-width

function: set-map-line-width w

Where w is an integer number

draw the lines of the chickenwire density in width w


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11.16.2 map-line-width-state

function: map-line-width-state

return the width in which density contours are drawn


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11.16.3 make-and-draw-map

function: make-and-draw-map mtz_file_name f_col phi_col weight use_weights is_diff_map

Where:

make a map from an mtz file (simple interface)

given mtz file mtz_file_name and F column f_col and phases column phi_col and optional weight column weight_col (pass use_weights=0 if weights are not to be used). Also mark the map as a difference map (is_diff_map=1) or not (is_diff_map=0) because they are handled differently inside coot.

Returns: -1 on error, else return the new molecule number


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11.16.4 make-and-draw-map-with-refmac-params

function: make-and-draw-map-with-refmac-params mtz_file_name a b weight use_weights is_diff_map have_refmac_params fobs_col sigfobs_col r_free_col sensible_f_free_col

Where:

as the above function, execpt set refmac parameters too

pass along the refmac column labels for storage (not used in the creation of the map)

Returns: -1 on error, else return imol


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11.16.5 make-and-draw-map-with-reso-with-refmac-params

function: make-and-draw-map-with-reso-with-refmac-params mtz_file_name a b weight use_weights is_diff_map have_refmac_params fobs_col sigfobs_col r_free_col sensible_f_free_col is_anomalous use_reso_limits low_reso_limit high_reso_lim

Where:

as the above function, except set expert options too.


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11.16.6 make-updating-map

function: make-updating-map mtz_file_name f_col phi_col weight use_weights is_diff_map

Where:

make a map molecule from the give file name.

If the file updates, then the map will be updated.


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11.16.7 valid-labels

function: valid-labels mtz_file_name f_col phi_col weight_col use_weights

Where:

does the mtz file have the columms that we want it to have?


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11.16.8 mtz-file-has-phases-p

function: mtz-file-has-phases-p mtz_file_name

Where mtz_file_name is a string

does the mtz file have phases?


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11.16.9 is-mtz-file-p

function: is-mtz-file-p filename

Where filename is a string

is the given filename an mtz file?


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11.16.10 cns-file-has-phases-p

function: cns-file-has-phases-p cns_file_name

Where cns_file_name is a string

does the given file have cns phases?


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11.16.11 auto-read-do-difference-map-too-state

function: auto-read-do-difference-map-too-state

return the flag to do a difference map (too) on auto-read MTZ

Returns: 0 means no, 1 means yes.


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11.16.12 set-auto-read-column-labels

function: set-auto-read-column-labels fwt phwt is_for_diff_map_flag

Where:

set the expected MTZ columns for Auto-reading MTZ file.

Not every program uses the default refmac labels ("FWT"/"PHWT") for its MTZ file. Here we can tell coot to expect other labels so that coot can "Auto-open" such MTZ files.

e.g. (set-auto-read-column-labels "2FOFCWT" "PH2FOFCWT" 0)


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11.16.13 set-map-radius

function: set-map-radius f

Where f is a number

set the extent of the box/radius of electron density contours for x-ray maps


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11.16.14 set-map-radius-em

function: set-map-radius-em radius

Where radius is a number

set the extent of the box/radius of electron density contours for EM map


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11.16.15 set-density-size

function: set-density-size f

Where f is a number

another (old) way of setting the radius of the map


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11.16.16 set-display-intro-string

function: set-display-intro-string str

Where str is a string

Give me this nice message str when I start coot.


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11.16.17 get-map-radius

function: get-map-radius

return the extent of the box/radius of electron density contours


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11.16.18 set-esoteric-depth-cue

function: set-esoteric-depth-cue istate

Where istate is an integer number

not everone likes coot’s esoteric depth cueing system

Pass an argument istate=1 to turn it off

(this function is currently disabled).


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11.16.19 esoteric-depth-cue-state

function: esoteric-depth-cue-state

native depth cueing system

return the state of the esoteric depth cueing flag


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11.16.20 set-swap-difference-map-colours

function: set-swap-difference-map-colours i

Where i is an integer number

not everone likes coot’s default difference map colouring.

Pass an argument i=1 to swap the difference map colouring so that red is positive and green is negative.


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11.16.21 set-map-is-difference-map

function: set-map-is-difference-map imol bool_flag

Where:

post-hoc set the map of molecule number imol to be a difference map

Returns: success status, 0 -> failure (imol does not have a map)


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11.16.22 map-is-difference-map

function: map-is-difference-map imol

Where imol is an integer number

map is difference map?


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11.16.23 another-level

function: another-level

Add another contour level for the last added map.

Currently, the map must have been generated from an MTZ file.

Returns: the molecule number of the new molecule or -1 on failure


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11.16.24 another-level-from-map-molecule-number

function: another-level-from-map-molecule-number imap

Where imap is an integer number

Add another contour level for the given map.

Currently, the map must have been generated from an MTZ file.

Returns: the molecule number of the new molecule or -1 on failure


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11.16.25 residue-density-fit-scale-factor

function: residue-density-fit-scale-factor

return the scale factor for the Residue Density fit analysis


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11.16.26 density-at-point

function: density-at-point imol_map x y z

Where:

return the density at the given point for the given map. Return 0 for bad imol


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11.17 Parameters from map


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11.17.1 mtz-hklin-for-map

function: mtz-hklin-for-map imol_map

Where imol_map is an integer number

return the mtz file that was use to generate the map

return 0 when there is no mtz file associated with that map (it was generated from a CCP4 map file say).


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11.17.2 mtz-fp-for-map

function: mtz-fp-for-map imol_map

Where imol_map is an integer number

return the FP column in the file that was use to generate the map

return 0 when there is no mtz file associated with that map (it was generated from a CCP4 map file say).

Caller should dispose of returned pointer.


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11.17.3 mtz-phi-for-map

function: mtz-phi-for-map imol_map

Where imol_map is an integer number

return the phases column in mtz file that was use to generate the map

return 0 when there is no mtz file associated with that map (it was generated from a CCP4 map file say). Caller should dispose of returned pointer.


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11.17.4 mtz-weight-for-map

function: mtz-weight-for-map imol_map

Where imol_map is an integer number

return the weight column in the mtz file that was use to generate the map

return 0 when there is no mtz file associated with that map (it was generated from a CCP4 map file say) or no weights were used. Caller should dispose of returned pointer.


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11.17.5 mtz-use-weight-for-map

function: mtz-use-weight-for-map imol_map

Where imol_map is an integer number

return flag for whether weights were used that was use to generate the map

return 0 when no weights were used or there is no mtz file associated with that map.


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11.17.6 map-parameters-scm

function: map-parameters-scm imol

Where imol is an integer number

return the parameter that made the map,

Returns: false or a string like ("xxx.mtz" "FPH" "PHWT" "" False)


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11.17.7 cell-scm

function: cell-scm imol

Where imol is an integer number

return the parameter that made the map,

Returns: false or a list like (45 46 47 90 90 120), angles in degress


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11.17.8 map-parameters-py

function: map-parameters-py imol

Where imol is an integer number

return the parameter of the molecule, something like (45 46 47 90 90 120), angles in degress

return the parameter that made the map,

Returns: False or something like ["xxx.mtz", "FPH", "PHWT", "", False]


Previous: map-parameters-py, Up: Parameters from map   [Contents][Index]

11.17.9 cell-py

function: cell-py imol

Where imol is an integer number

return the parameter that made the map,

Returns: False or something like [45, 46, 47, 90, 90, 120], angles in degress


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11.18 PDB Functions


Next: , Up: PDB Functions   [Contents][Index]

11.18.1 write-pdb-file

function: write-pdb-file imol file_name

Where:

write molecule number imol as a PDB to file file_name


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11.18.2 write-cif-file

function: write-cif-file imol file_name

Where:

write molecule number imol as a mmCIF to file file_name


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11.18.3 write-residue-range-to-pdb-file

function: write-residue-range-to-pdb-file imol chainid resno_start resno_end filename

Where:

write molecule number imol’s residue range as a PDB to file file_name


Previous: write-residue-range-to-pdb-file, Up: PDB Functions   [Contents][Index]

11.18.4 quick-save

function: quick-save

save all modified coordinates molecules to the default names and save the state too.


Next: , Previous: PDB Functions, Up: Scripting Functions   [Contents][Index]

11.19 Info Dialog


Next: , Up: Info Dialog   [Contents][Index]

11.19.1 info-dialog

function: info-dialog txt

Where txt is a string

create a dialog with information

create a dialog with information string txt. User has to click to dismiss it, but it is not modal (nothing in coot is modal).


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11.19.2 info-dialog-and-text

function: info-dialog-and-text txt

Where txt is a string

create a dialog with information and print to console

as info_dialog but print to console as well.


Previous: info-dialog-and-text, Up: Info Dialog   [Contents][Index]

11.19.3 info-dialog-with-markup

function: info-dialog-with-markup txt

Where txt is a string

as above, create a dialog with information

This dialog is left-justified and can use markup such as angled bracketted tt or i


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11.20 Refmac Functions


Next: , Up: Refmac Functions   [Contents][Index]

11.20.1 set-refmac-counter

function: set-refmac-counter imol refmac_count

Where:

set counter for runs of refmac so that this can be used to construct a unique filename for new output


Next: , Previous: set-refmac-counter, Up: Refmac Functions   [Contents][Index]

11.20.2 swap-map-colours

function: swap-map-colours imol1 imol2

Where:

swap the colours of maps

swap the colour of maps imol1 and imol2. Useful to some after running refmac, so that the map to be build into is always the same colour


Next: , Previous: swap-map-colours, Up: Refmac Functions   [Contents][Index]

11.20.3 set-keep-map-colour-after-refmac

function: set-keep-map-colour-after-refmac istate

Where istate is an integer number

flag to enable above

call this with istate=1


Previous: set-keep-map-colour-after-refmac, Up: Refmac Functions   [Contents][Index]

11.20.4 keep-map-colour-after-refmac-state

function: keep-map-colour-after-refmac-state

the keep-map-colour-after-refmac internal state

Returns: 1 for "yes", 0 for "no"


Next: , Previous: Refmac Functions, Up: Scripting Functions   [Contents][Index]

11.21 Symmetry Functions


Next: , Up: Symmetry Functions   [Contents][Index]

11.21.1 set-symmetry-size

function: set-symmetry-size f

Where f is a number

set the size of the displayed symmetry


Next: , Previous: set-symmetry-size, Up: Symmetry Functions   [Contents][Index]

11.21.2 get-show-symmetry

function: get-show-symmetry

is symmetry master display control on?


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11.21.3 set-show-symmetry-master

function: set-show-symmetry-master state

Where state is an integer number

set display symmetry, master controller


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11.21.4 set-show-symmetry-molecule

function: set-show-symmetry-molecule mol_no state

Where:

set display symmetry for molecule number mol_no

pass with state=0 for off, state=1 for on


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11.21.5 symmetry-as-calphas

function: symmetry-as-calphas mol_no state

Where:

display symmetry as CAs?

pass with state=0 for off, state=1 for on


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11.21.6 get-symmetry-as-calphas-state

function: get-symmetry-as-calphas-state imol

Where imol is an integer number

what is state of display CAs for molecule number mol_no?

return state=0 for off, state=1 for on


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11.21.7 set-symmetry-molecule-rotate-colour-map

function: set-symmetry-molecule-rotate-colour-map imol state

Where:

set the colour map rotation (i.e. the hue) for the symmetry atoms of molecule number imol


Next: , Previous: set-symmetry-molecule-rotate-colour-map, Up: Symmetry Functions   [Contents][Index]

11.21.8 symmetry-molecule-rotate-colour-map-state

function: symmetry-molecule-rotate-colour-map-state imol

Where imol is an integer number

should there be colour map rotation (i.e. the hue) change for the symmetry atoms of molecule number imol?

return state=0 for off, state=1 for on


Next: , Previous: symmetry-molecule-rotate-colour-map-state, Up: Symmetry Functions   [Contents][Index]

11.21.9 set-symmetry-colour-by-symop

function: set-symmetry-colour-by-symop imol state

Where:

set symmetry colour by symop mode


Next: , Previous: set-symmetry-colour-by-symop, Up: Symmetry Functions   [Contents][Index]

11.21.10 set-symmetry-whole-chain

function: set-symmetry-whole-chain imol state

Where:

set symmetry colour for the chain


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11.21.11 set-symmetry-atom-labels-expanded

function: set-symmetry-atom-labels-expanded state

Where state is an integer number

set use expanded symmetry atom labels


Next: , Previous: set-symmetry-atom-labels-expanded, Up: Symmetry Functions   [Contents][Index]

11.21.12 has-unit-cell-state

function: has-unit-cell-state imol

Where imol is an integer number

molecule number imol has a unit cell?

Returns: 1 on "yes, it has a cell", 0 for "no"


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11.21.13 undo-symmetry-view

function: undo-symmetry-view

Undo symmetry view. Translate back to main molecule from this symmetry position.


Next: , Previous: undo-symmetry-view, Up: Symmetry Functions   [Contents][Index]

11.21.14 first-molecule-with-symmetry-displayed

function: first-molecule-with-symmetry-displayed

return the molecule number.

Returns: -1 if there is no molecule with symmetry displayed.


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11.21.15 save-symmetry-coords

function: save-symmetry-coords imol filename symop_no shift_a shift_b shift_c pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc

Where:

save the symmetry coordinates of molecule number imol to filename

Allow a shift of the coordinates to the origin before symmetry expansion is apllied (this is how symmetry works in Coot internals).


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11.21.16 new-molecule-by-symmetry

function: new-molecule-by-symmetry imol name m11 m12 m13 m21 m22 m23 m31 m32 m33 tx ty tz pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc

Where:

create a new molecule (molecule number is the return value) from imol.

The rotation/translation matrix components are given in

coordinates.

Allow a shift of the coordinates to the origin before symmetry expansion is aplied.

Pass "" as the name-in and a name will be constructed for you.

Return -1 on failure.


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11.21.17 new-molecule-by-symmetry-with-atom-selection

function: new-molecule-by-symmetry-with-atom-selection imol name mmdb_atom_selection_string m11 m12 m13 m21 m22 m23 m31 m32 m33 tx ty tz pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc

Where:

create a new molecule (molecule number is the return value) from imol, but only for atom that match the mmdb_atom_selection_string.

The rotation/translation matrix components are given in

coordinates.

Allow a shift of the coordinates to the origin before symmetry expansion is aplied.

Pass "" as the name-in and a name will be constructed for you.

Return -1 on failure.


Next: , Previous: new-molecule-by-symmetry-with-atom-selection, Up: Symmetry Functions   [Contents][Index]

11.21.18 new-molecule-by-symop

function: new-molecule-by-symop imol symop_string pre_shift_to_origin_na pre_shift_to_origin_nb pre_shift_to_origin_nc

Where:

create a new molecule (molecule number is the return value) from imol.


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11.21.19 n-symops

function: n-symops imol

Where imol is an integer number

return the number of symmetry operators for the given molecule

return -1 on no-symmetry for molecule or inappropriate imol number


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11.21.20 origin-pre-shift-scm

function: origin-pre-shift-scm imol

Where imol is an integer number

return the pre-shift (the shift that translates the centre of the molecule as close as possible to the origin) as a list of ints or scheme false on failure


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11.21.21 origin-pre-shift-py

function: origin-pre-shift-py imol

Where imol is an integer number

return the pre-shift (the shift that translates the centre of the molecule as close as possible to the origin) as a list of ints or Python false on failure


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11.21.22 set-space-group

function: set-space-group imol spg

Where:

set the space group for a coordinates molecule

for shelx FA pdb files, there is no space group. So allow the user to set it. This can be initted with a HM symbol or a symm list for clipper.

This will only work on model molecules.

Returns: the success status of the setting (1 good, 0 fail).


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11.21.23 set-unit-cell-and-space-group

function: set-unit-cell-and-space-group imol a b c alpha beta gamma space_group

Where:

set the unit cell for a given model molecule

Angles in degress, cell lengths in Angstroms.

Returns: the success status of the setting (1 good, 0 fail).


Next: , Previous: set-unit-cell-and-space-group, Up: Symmetry Functions   [Contents][Index]

11.21.24 set-unit-cell-and-space-group-using-molecule

function: set-unit-cell-and-space-group-using-molecule imol imol_from

Where:

set the unit cell for a given model molecule using the cell of moecule imol_from

This will only work on model molecules.

Returns: the success status of the setting (1 good, 0 fail).


Previous: set-unit-cell-and-space-group-using-molecule, Up: Symmetry Functions   [Contents][Index]

11.21.25 set-symmetry-shift-search-size

function: set-symmetry-shift-search-size shift

Where shift is an integer number

set the cell shift search size for symmetry searching.

When the coordinates for one (or some) symmetry operator are missing (which happens sometimes, but rarely), try changing setting this to 2 (default is 1). It slows symmetry searching, which is why it is not set to 2 by default.


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11.22 History Functions


Next: , Up: History Functions   [Contents][Index]

11.22.1 print-all-history-in-scheme

function: print-all-history-in-scheme

print the history in scheme format


Next: , Previous: print-all-history-in-scheme, Up: History Functions   [Contents][Index]

11.22.2 print-all-history-in-python

function: print-all-history-in-python

print the history in python format


Next: , Previous: print-all-history-in-python, Up: History Functions   [Contents][Index]

11.22.3 set-console-display-commands-state

function: set-console-display-commands-state istate

Where istate is an integer number

set a flag to show the text command equivalent of gui commands in the console as they happen.

1 for on, 0 for off.


Previous: set-console-display-commands-state, Up: History Functions   [Contents][Index]

11.22.4 set-console-display-commands-hilights

function: set-console-display-commands-hilights bold_flag colour_flag colour_index

Where:

set a flag to show the text command equivalent of gui commands in the console as they happen in bold and colours.

colour_flag: pass 1 for on, 0 for off.

colour_index 0 to 7 inclusive for various different colourings.


Next: , Previous: History Functions, Up: Scripting Functions   [Contents][Index]

11.23 State Functions


Next: , Up: State Functions   [Contents][Index]

11.23.1 save-state

function: save-state

save the current state to the default filename


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11.23.2 save-state-file

function: save-state-file filename

Where filename is a string

save the current state to file filename


Next: , Previous: save-state-file, Up: State Functions   [Contents][Index]

11.23.3 save-state-file-py

function: save-state-file-py filename

Where filename is a string

save the current state to file filename


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11.23.4 set-save-state-file-name

function: set-save-state-file-name filename

Where filename is a string

set the default state file name (default 0-coot.state.scm)


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11.23.5 save-state-file-name-scm

function: save-state-file-name-scm

the save state file name

Returns: the save state file name


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11.23.6 save-state-file-name-py

function: save-state-file-name-py

the save state file name

Returns: the save state file name


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11.23.7 set-run-state-file-status

function: set-run-state-file-status istat

Where istat is an integer number

set run state file status

0: never run it 1: ask to run it 2: run it, no questions


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11.23.8 run-state-file

function: run-state-file

run the state file (reading from default filenname)


Previous: run-state-file, Up: State Functions   [Contents][Index]

11.23.9 run-state-file-maybe

function: run-state-file-maybe

run the state file depending on the state variables


Next: , Previous: State Functions, Up: Scripting Functions   [Contents][Index]

11.24 The Virtual Trackball


Next: , Up: The Virtual Trackball   [Contents][Index]

11.24.1 vt-surface

function: vt-surface mode

Where mode is an integer number

How should the mouse move the view?

mode=1 for "Flat", mode=2 for "Spherical Surface"


Previous: vt-surface, Up: The Virtual Trackball   [Contents][Index]

11.24.2 vt-surface-status

function: vt-surface-status

return the mouse view status mode

mode=1 for "Flat", mode=2 for "Spherical Surface"


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11.25 Clipping Functions


Next: , Up: Clipping Functions   [Contents][Index]

11.25.1 set-clipping-back

function: set-clipping-back v

Where v is a number

set clipping plane back


Previous: set-clipping-back, Up: Clipping Functions   [Contents][Index]

11.25.2 set-clipping-front

function: set-clipping-front v

Where v is a number

set clipping plane front


Next: , Previous: Clipping Functions, Up: Scripting Functions   [Contents][Index]

11.26 Unit Cell interface


Next: , Up: Unit Cell interface   [Contents][Index]

11.26.1 get-show-unit-cell

function: get-show-unit-cell imol

Where imol is an integer number

return the stage of show unit cell for molecule number imol


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11.26.2 set-show-unit-cells-all

function: set-show-unit-cells-all istate

Where istate is an integer number

set the state of show unit cell for all molecules

1 for displayed 0 for undisplayed


Previous: set-show-unit-cells-all, Up: Unit Cell interface   [Contents][Index]

11.26.3 set-show-unit-cell

function: set-show-unit-cell imol istate

Where:

set the state of show unit cell for the particular molecule number imol

1 for displayed 0 for undisplayed


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11.27 Colour


Next: , Up: Colour   [Contents][Index]

11.27.1 set-colour-map-rotation-on-read-pdb

function: set-colour-map-rotation-on-read-pdb f

Where f is a number

set the hue change step on reading a new molecule


Next: , Previous: set-colour-map-rotation-on-read-pdb, Up: Colour   [Contents][Index]

11.27.2 set-colour-map-rotation-on-read-pdb-flag

function: set-colour-map-rotation-on-read-pdb-flag i

Where i is an integer number

shall the hue change step be used?


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11.27.3 set-colour-map-rotation-on-read-pdb-c-only-flag

function: set-colour-map-rotation-on-read-pdb-c-only-flag i

Where i is an integer number

shall the colour map rotation apply only to C atoms?


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11.27.4 set-colour-by-chain

function: set-colour-by-chain imol

Where imol is an integer number

colour molecule number imol by chain type


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11.27.5 set-colour-by-chain-goodsell-mode

function: set-colour-by-chain-goodsell-mode imol

Where imol is an integer number

colour molecule number imol by chain type, goodsell-like colour scheme


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11.27.6 set-colour-by-molecule

function: set-colour-by-molecule imol

Where imol is an integer number

colour molecule number imol by molecule


Previous: set-colour-by-molecule, Up: Colour   [Contents][Index]

11.27.7 set-symmetry-colour

function: set-symmetry-colour r g b

Where:

set the symmetry colour base


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11.28 Map colour


Next: , Up: Map colour   [Contents][Index]

11.28.1 set-colour-map-rotation-for-map

function: set-colour-map-rotation-for-map f

Where f is a number

set the colour map rotation (hue change) for maps

default: for maps is 14 degrees.


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11.28.2 set-molecule-bonds-colour-map-rotation

function: set-molecule-bonds-colour-map-rotation imol theta

Where:

set the colour map rotation for molecule number imol

theta is in degrees


Previous: set-molecule-bonds-colour-map-rotation, Up: Map colour   [Contents][Index]

11.28.3 get-molecule-bonds-colour-map-rotation

function: get-molecule-bonds-colour-map-rotation imol

Where imol is an integer number

Get the colour map rotation for molecule number imol.


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11.29 Anisotropic Atoms Interface


Next: , Up: Anisotropic Atoms Interface   [Contents][Index]

11.29.1 get-limit-aniso

function: get-limit-aniso

get the aniso radius limit


Next: , Previous: get-limit-aniso, Up: Anisotropic Atoms Interface   [Contents][Index]

11.29.2 get-show-limit-aniso

function: get-show-limit-aniso

get show the aniso limit


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11.29.3 get-show-aniso

function: get-show-aniso

return show-aniso-atoms state


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11.29.4 set-limit-aniso

function: set-limit-aniso state

Where state is an integer number

set the aniso atom limit


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11.29.5 set-show-aniso

function: set-show-aniso state

Where state is an integer number

set show aniso atoms


Next: , Previous: set-show-aniso, Up: Anisotropic Atoms Interface   [Contents][Index]

11.29.6 set-aniso-probability

function: set-aniso-probability f

Where f is a number

set aniso probability


Previous: set-aniso-probability, Up: Anisotropic Atoms Interface   [Contents][Index]

11.29.7 get-aniso-probability

function: get-aniso-probability

get aniso probability


Next: , Previous: Anisotropic Atoms Interface, Up: Scripting Functions   [Contents][Index]

11.30 Display Functions


Next: , Up: Display Functions   [Contents][Index]

11.30.1 set-graphics-window-size

function: set-graphics-window-size x_size y_size

Where:

set the window size


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11.30.2 set-graphics-window-position

function: set-graphics-window-position x_pos y_pos

Where:

set the graphics window position


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11.30.3 store-graphics-window-position

function: store-graphics-window-position x_pos y_pos

Where:

store the graphics window position


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11.30.4 graphics-window-size-and-position-to-preferences

function: graphics-window-size-and-position-to-preferences

store the graphics window position and size to zenops-graphics-window-size-and-postion.scm in the preferences directory.


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11.30.5 graphics-draw

function: graphics-draw

draw a frame


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11.30.6 zalman-stereo-mode

function: zalman-stereo-mode

try to turn on Zalman stereo mode


Next: , Previous: zalman-stereo-mode, Up: Display Functions   [Contents][Index]

11.30.7 hardware-stereo-mode

function: hardware-stereo-mode

try to turn on stereo mode


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11.30.8 stereo-mode-state

function: stereo-mode-state

what is the stero state?

Returns: 1 for in hardware stereo, 2 for side by side stereo, else return 0.


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11.30.9 mono-mode

function: mono-mode

try to turn on mono mode


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11.30.10 side-by-side-stereo-mode

function: side-by-side-stereo-mode use_wall_eye_mode

Where use_wall_eye_mode is an integer number

turn on side bye side stereo mode


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11.30.11 set-hardware-stereo-angle-factor

function: set-hardware-stereo-angle-factor f

Where f is a number

how much should the eyes be separated in stereo mode?


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11.30.12 hardware-stereo-angle-factor-state

function: hardware-stereo-angle-factor-state

return the hardware stereo angle factor


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11.30.13 set-model-fit-refine-dialog-position

function: set-model-fit-refine-dialog-position x_pos y_pos

Where:

set position of Model/Fit/Refine dialog


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11.30.14 set-display-control-dialog-position

function: set-display-control-dialog-position x_pos y_pos

Where:

set position of Display Control dialog


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11.30.15 set-go-to-atom-window-position

function: set-go-to-atom-window-position x_pos y_pos

Where:

set position of Go To Atom dialog


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11.30.16 set-delete-dialog-position

function: set-delete-dialog-position x_pos y_pos

Where:

set position of Delete dialog


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11.30.17 set-rotate-translate-dialog-position

function: set-rotate-translate-dialog-position x_pos y_pos

Where:

set position of the Rotate/Translate Residue Range dialog


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11.30.18 set-accept-reject-dialog-position

function: set-accept-reject-dialog-position x_pos y_pos

Where:

set position of the Accept/Reject dialog


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11.30.19 set-ramachandran-plot-dialog-position

function: set-ramachandran-plot-dialog-position x_pos y_pos

Where:

set position of the Ramachadran Plot dialog


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11.30.20 set-edit-chi-angles-dialog-position

function: set-edit-chi-angles-dialog-position x_pos y_pos

Where:

set edit chi angles dialog position


Previous: set-edit-chi-angles-dialog-position, Up: Display Functions   [Contents][Index]

11.30.21 set-rotamer-selection-dialog-position

function: set-rotamer-selection-dialog-position x_pos y_pos

Where:

set rotamer selection dialog position


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11.31 Smooth Scrolling


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11.31.1 set-smooth-scroll-flag

function: set-smooth-scroll-flag v

Where v is an integer number

set smooth scrolling


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11.31.2 get-smooth-scroll

function: get-smooth-scroll

return the smooth scrolling state


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11.31.3 set-smooth-scroll-steps

function: set-smooth-scroll-steps i

Where i is an integer number

set the number of steps in the smooth scroll

Set more steps (e.g. 50) for more smoothness (default 10).


Previous: set-smooth-scroll-steps, Up: Smooth Scrolling   [Contents][Index]

11.31.4 set-smooth-scroll-limit

function: set-smooth-scroll-limit lim

Where lim is a number

do not scroll for distances greater this limit


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11.32 Font Parameters


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11.32.1 set-font-size

function: set-font-size i

Where i is an integer number

set the font size


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11.32.2 get-font-size

function: get-font-size

return the font size

Returns: 1 (small) 2 (medium, default) 3 (large)


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11.32.3 set-font-colour

function: set-font-colour red green blue

Where:

set the colour of the atom label font - the arguments are in the range 0->1


Previous: set-font-colour, Up: Font Parameters   [Contents][Index]

11.32.4 set-use-stroke-characters

function: set-use-stroke-characters state

Where state is an integer number

set use stroke characters


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11.33 Rotation Centre


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11.33.1 set-rotation-centre-size

function: set-rotation-centre-size f

Where f is a number

set rotoation centre marker size


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11.33.2 recentre-on-read-pdb

function: recentre-on-read-pdb

return the recentre-on-pdb state


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11.33.3 set-recentre-on-read-pdb

function: set-recentre-on-read-pdb int

Where int is a short

set the recentre-on-pdb state


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11.33.4 set-rotation-centre

function: set-rotation-centre x y z

Where:

set the rotation centre


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11.33.5 go-to-ligand

function: go-to-ligand

centre on the ligand of the "active molecule", if we are already there, centre on the next hetgroup (etc)


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11.33.6 set-go-to-ligand-n-atoms-limit

function: set-go-to-ligand-n-atoms-limit n_atom_min

Where n_atom_min is an integer number

go to the ligand that has more than n_atom_min atoms


Previous: set-go-to-ligand-n-atoms-limit, Up: Rotation Centre   [Contents][Index]

11.33.7 set-reorienting-next-residue-mode

function: set-reorienting-next-residue-mode state

Where state is an integer number

rotate the view so that the next main-chain atoms are oriented in the same direction as the previous - hence side-chain always seems to be "up" - set this mode to 1 for reorientation-mode - and 0 for off (standard translation)


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11.34 Atom Selection Utilities


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11.34.1 median-temperature-factor

function: median-temperature-factor imol

Where imol is an integer number

return the median temperature factor for imol


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11.34.2 average-temperature-factor

function: average-temperature-factor imol

Where imol is an integer number

return the average temperature factor for the atoms in imol


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11.34.3 standard-deviation-temperature-factor

function: standard-deviation-temperature-factor imol

Where imol is an integer number

return the standard deviation of the atom temperature factors for imol


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11.34.4 clear-pending-picks

function: clear-pending-picks

clear pending picks (stop coot thinking that the user is about to pick an atom).


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11.34.5 set-default-temperature-factor-for-new-atoms

function: set-default-temperature-factor-for-new-atoms new_b

Where new_b is a number

set the default temperature factor for newly created atoms (initial default 20)


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11.34.6 default-new-atoms-b-factor

function: default-new-atoms-b-factor

return the default temperature factor for newly created atoms


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11.34.7 set-reset-b-factor-moved-atoms

function: set-reset-b-factor-moved-atoms state

Where state is an integer number

reset temperature factor for all moved atoms to the default for new atoms (usually 30)


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11.34.8 get-reset-b-factor-moved-atoms-state

function: get-reset-b-factor-moved-atoms-state

return the state if temperature factors shoudl be reset for moved atoms


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11.34.9 set-atom-attribute

function: set-atom-attribute imol chain_id resno ins_code atom_name alt_conf attribute_name val

Where:

set a numberical attibute to the atom with the given specifier.

Attributes can be "x", "y","z", "B", "occ" and the attribute val is a floating point number


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11.34.10 set-atom-string-attribute

function: set-atom-string-attribute imol chain_id resno ins_code atom_name alt_conf attribute_name attribute_value

Where:

set a string attibute to the atom with the given specifier.

Attributes can be "atom-name", "alt-conf", "element" or "segid".


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11.34.11 set-atom-attributes

function: set-atom-attributes attribute_expression_list

Where attribute_expression_list is a SCM

set lots of atom attributes at once by-passing the rebonding and redrawing of the above 2 functions


Previous: set-atom-attributes, Up: Atom Selection Utilities   [Contents][Index]

11.34.12 set-residue-name

function: set-residue-name imol chain_id res_no ins_code new_residue_name

Where:

set the residue name of the specified residue


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11.35 Skeletonization Interface


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11.35.1 skeletonize-map

function: skeletonize-map imol prune_flag

Where:

skeletonize molecule number imol

the prune_flag should almost always be 0.

NOTE:: The arguments to have been reversed for coot 0.8.3 and later (now the molecule number comes first).


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11.35.2 unskeletonize-map

function: unskeletonize-map imol

Where imol is an integer number

undisplay the skeleton on molecule number imol


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11.35.3 set-max-skeleton-search-depth

function: set-max-skeleton-search-depth v

Where v is an integer number

set the skeleton search depth, used in baton building

For high resolution maps, you need to search deeper down the skeleton tree. This limit needs to be increased to 20 or so for high res maps (it is 10 by default)


Previous: set-max-skeleton-search-depth, Up: Skeletonization Interface   [Contents][Index]

11.35.4 set-skeleton-box-size

function: set-skeleton-box-size f

Where f is a number

the box size (in Angstroms) for which the skeleton is displayed


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11.36 Save Coordinates


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11.36.1 save-coordinates

function: save-coordinates imol filename

Where:

save coordinates of molecule number imol in filename

Returns: status 1 is good (success), 0 is fail.


Previous: save-coordinates, Up: Save Coordinates   [Contents][Index]

11.36.2 set-save-coordinates-in-original-directory

function: set-save-coordinates-in-original-directory i

Where i is an integer number

set save coordinates in the starting directory


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11.37 Read Phases File Functions


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11.37.1 read-phs-and-coords-and-make-map

function: read-phs-and-coords-and-make-map pdb_filename

Where pdb_filename is a string

read phs file use coords to get cell and symm to make map

uses pending data to make the map.


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11.37.2 read-phs-and-make-map-using-cell-symm-from-previous-mol

function: read-phs-and-make-map-using-cell-symm-from-previous-mol phs_filename

Where phs_filename is a string

read a phs file, the cell and symm information is from previously read (most recently read) coordinates file

For use with phs data filename provided on the command line


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11.37.3 read-phs-and-make-map-using-cell-symm-from-mol

function: read-phs-and-make-map-using-cell-symm-from-mol phs_filename imol

Where:

read phs file and use a previously read molecule to provide the cell and symmetry information

Returns: the new molecule number, return -1 if problem creating the map (e.g. not phs data, file not found etc).


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11.37.4 read-phs-and-make-map-using-cell-symm

function: read-phs-and-make-map-using-cell-symm phs_file_name hm_spacegroup a b c alpha beta gamma

Where:

read phs file use coords to use cell and symm to make map

in degrees


Previous: read-phs-and-make-map-using-cell-symm, Up: Read Phases File Functions   [Contents][Index]

11.37.5 read-phs-and-make-map-with-reso-limits

function: read-phs-and-make-map-with-reso-limits imol phs_file_name reso_lim_low reso_lim_high

Where:

read a phs file and use the cell and symm in molecule number imol and use the resolution limits reso_lim_high (in Angstroems).


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11.38 Graphics Move


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11.38.1 undo-last-move

function: undo-last-move

undo last move


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11.38.2 translate-molecule-by

function: translate-molecule-by imol x y z

Where:

translate molecule number imol by (x,y,z) in Angstroms


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11.38.3 transform-molecule-by

function: transform-molecule-by imol m11 m12 m13 m21 m22 m23 m31 m32 m33 x y z

Where:

transform molecule number imol by the given rotation matrix, then translate by (x,y,z) in Angstroms


Previous: transform-molecule-by, Up: Graphics Move   [Contents][Index]

11.38.4 transform-zone

function: transform-zone imol chain_id resno_start resno_end ins_code m11 m12 m13 m21 m22 m23 m31 m32 m33 x y z

Where:

transform fragment of molecule number imol by the given rotation matrix, then translate by (x,y,z) in Angstroms


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11.39 Go To Atom Widget Functions


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11.39.1 post-go-to-atom-window

function: post-go-to-atom-window

Post the Go To Atom Window.


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11.39.2 go-to-atom-molecule-number

function: go-to-atom-molecule-number

the go-to-atom molecule number


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11.39.3 go-to-atom-chain-id

function: go-to-atom-chain-id

the go-to-atom chain-id


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11.39.4 go-to-atom-atom-name

function: go-to-atom-atom-name

the go-to-atom atom name


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11.39.5 go-to-atom-residue-number

function: go-to-atom-residue-number

the go-to-atom residue number


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11.39.6 go-to-atom-ins-code

function: go-to-atom-ins-code

the go-to-atom insertion code


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11.39.7 go-to-atom-alt-conf

function: go-to-atom-alt-conf

the go-to-atom alt conf


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11.39.8 set-go-to-atom-chain-residue-atom-name

function: set-go-to-atom-chain-residue-atom-name t1_chain_id iresno t3_atom_name

Where:

set the go to atom specification

It seems important for swig that the char * arguments are const char *, not const gchar * (or else we get wrong type of argument error on (say) "A"

Returns: the success status of the go to. 0 for fail, 1 for success.


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11.39.9 set-go-to-atom-chain-residue-atom-name-full

function: set-go-to-atom-chain-residue-atom-name-full chain_id resno ins_code atom_name alt_conf

Where:

set the go to (full) atom specification

It seems important for swig that the char * arguments are const char *, not const gchar * (or else we get wrong type of argument error on (say) "A"

Returns: the success status of the go to. 0 for fail, 1 for success.


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11.39.10 set-go-to-atom-chain-residue-atom-name-no-redraw

function: set-go-to-atom-chain-residue-atom-name-no-redraw t1 iresno t3 make_the_move_flag

Where:

set go to atom but don’t redraw


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11.39.11 update-go-to-atom-from-current-position

function: update-go-to-atom-from-current-position

update the Go To Atom widget entries to atom closest to screen centre.


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11.39.12 atom-spec-to-atom-index

function: atom-spec-to-atom-index mol chain resno atom_name

Where:

what is the atom index of the given atom?


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11.39.13 full-atom-spec-to-atom-index

function: full-atom-spec-to-atom-index imol chain resno inscode atom_name altloc

Where:

what is the atom index of the given atom?


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11.39.14 update-go-to-atom-window-on-changed-mol

function: update-go-to-atom-window-on-changed-mol imol

Where imol is an integer number

update the Go To Atom window


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11.39.15 update-go-to-atom-window-on-new-mol

function: update-go-to-atom-window-on-new-mol

update the Go To Atom window. This updates the option menu for the molecules.


Previous: update-go-to-atom-window-on-new-mol, Up: Go To Atom Widget Functions   [Contents][Index]

11.39.16 set-go-to-atom-molecule

function: set-go-to-atom-molecule imol

Where imol is an integer number

set the molecule for the Go To Atom

For dynarama callback sake. The widget/class knows which molecule that it was generated from, so in order to go to the molecule from dynarama, we first need to the the molecule - because

does not mention the molecule (see "Next/Previous Residue" for reasons for that). This function simply calls the graphics_info_t function of the same name.

Also used in scripting, where go-to-atom-chain-residue-atom-name does not mention the molecule number.

20090914-PE set-go-to-atom-molecule can be used in a script and it should change the go-to-atom-molecule in the Go To Atom dialog (if it is being displayed). This does mean, of course that using the ramachandran plot to centre on atoms will change the Go To Atom dialog. Maybe that is surprising (maybe not).


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11.40 Map and Molecule Control


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11.40.1 post-display-control-window

function: post-display-control-window

display the Display Constrol window


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11.40.2 set-map-displayed

function: set-map-displayed imol state

Where:

make the map displayed/undisplayed, 0 for off, 1 for on


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11.40.3 set-mol-displayed

function: set-mol-displayed imol state

Where:

make the coordinates molecule displayed/undisplayed, 0 for off, 1 for on


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11.40.4 set-display-only-model-mol

function: set-display-only-model-mol imol

Where imol is an integer number

from all the model molecules, display only imol

This stops flashing/delayed animations with many molecules


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11.40.5 set-mol-active

function: set-mol-active imol state

Where:

make the coordinates molecule active/inactve (clickable), 0 for off, 1 for on


Next: