The reference for Coot has now been published:
You can use this BibTeX database entry (which can be imported into EndNote)... format as you please:
@Article{emsley04:coot,
author = {Paul Emsley and Kevin Cowtan},
title = {Coot: Model-Building Tools for Molecular Graphics},
journal = {Acta Crystallographica Section D - Biological Crystallography},
year = 2004,
volume = 60,
pages = 2126-2132
}
Coot was published in the proceedings of the 2003 CCP4 Study Weekend (you can download the paper from there - it's Open Access).
See Bill Scott's Coot Page.
Download the appropriate tar file for you system. Untar it. Add the bin directory (the one that contains coot and coot-real) to your path and you are ready to go... You should not need to edit or use the setup/coot* files.
Try first the a binary from binaries/nightlies, if that fails then try one from binaries. If there is not an exact match with your i*86 system, then the RedHat-8 binary is probably the best fallback. If that fails, get in touch with me and we'll work something out.
Nancy Vogelaar used the RedHat 8 binary distribution and needed to do some extra fiddling - documented here.
Raji Edayathumangalam used the RedHat 7.2 binary distribution on Mandrake Linux 8.2 and needed to do some extra fiddling - documented here.
Coot runs on Fedora Core 4, using the Fedora Core 3 binaries after making the following link
$ ln -s /usr/lib/libpt_linux_x86_r.so.1.8.4 $COOT_PREFIX/lib/libpt.so.1.6.5
Kay Diederichs reports that coot-0.0.18-binary-Linux-Fedora-Core-1.tar.gz works with RedHat Enterprise 3 if one makes the following link first:
$ ln -s /usr/lib/libpt.so.1.4.7 $COOT_PREFIX/lib/libpt.so.1.5.0
Dirk Kostrewa thought that it was not necessary to make this link using the current Red Hat 8 binary tar.
Michael Latchem reports that coot-0.0.20-binary-Linux-Fedora-Core-1.tar.gz works with SuSE 9.1 if one makes the following link first:
$ ln -s /usr/lib/libpt_linux_x86_r.so.1.6.5 $COOT_PREFIX/lib/libpt.so.1.5.0
Christophe Briand reports that Coot version 0.1 runs on Suse 9.3, using the Redhat 8 binary after making the following link
$ ln -s /usr/lib/libImlib2.so.1.1.1 /usr/lib/libImlib.so.11
[I presume that
$ ln -s /usr/lib/libImlib2.so.1.1.1 $COOT_PREFIX/lib/libImlib.so.11
would also work.]
You need to install the imlib-1.9.14-215 rpm.
ln -s /opt/gnome/lib64/libImlib.so.1.9.14 $COOT_PREFIX/lib/libImlib.so.11or
ln -s /opt/gnome/lib/libImlib.so.1.9.14 $COOT_PREFIX/lib/libImlib.so.11depending on your architecture.
Dirk Kostrewa has got coot working on his Debian system. Here are his notes.
First, see the Mac OS X notes above - if you ignore that and want to use the binary tar distribution anyway, here are some extra notes:
Coot depends on various other packages and I assume that fink is used to provide them. Among the extra packages is guile - however, the most recently released version of guile is not the default version of guile for fink (I don't know why). To get fink to install the correct version you need guile16, or more explicitly:
apt-get install guile16 guile16-libs guile16-shlibs guile16-dev
This will provide (strangely enough) /sw/lib/libguile12.dylib and /sw/lib/libguile-ltdl.1.dylib
In fact there may be other things that you don't have already. Here's the complete list:
apt-get install gtk+ glib glib-shlibs guile16 guile16-libs guile16-shlibs guile16-dev glut glut-shlibs gtkglarea imlib
or maybe I mean fink install ... those things.
If you have problems with libtiff of the form:
dyld: Library not loaded: /sw/lib/libtiff.3.dylib Referenced from: /usr/local/coot/bin/coot-real Reason: Incompatible library version: coot-real requires version 11.0.0 or later, but libtiff.3.dylib provides version 3.6.0 Trace/BPT trap
Then take this tar file and install it in your $COOT_PREFIX.
You will need (if you don't alread have them) fw_gcc fw_urt fw_libungif (i.e. libungif) and imlib from SGI Freeware.
The md5sum is a means to determine if the file was corrupted during transfer. Run md5sum on the downloaded tar file and compare the result to the md5sum file on the server. If the results are the same, then the tar file is uncorrupted.
$ coot coot: error while loading shared libraries: libpt.so.1.6.5: cannot open shared object file: No such file or directory
You need to install pwlib:
pwlib-1.6.5-1
dyld: coot version mismatch for library: /sw/lib/libtiff.3.dylib (compatibility version of user: 3.6.0 greater than library's version: 3.5.0)
This is because you have the default fink (stable). Coot is part of unstable fink so you need to enable the unstable branch (see Bill Scott's page (above)).
dyld: Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /Users/xxx/coot-0.1.2_bin/lib/libjpeg.62.dylib
Atsushi Nakagawa says that this can be fixed by replacing xxx/Darwin-chihiro.chem.york.ac.uk-pre-release/lib/libjpeg.dylib with /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
Or read the advice in $COOT_PREFIX/bin/coot about Intel Mac usage.
./coot: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory
You need to install these rpms:
freeglut-2.2.0-14 freeglut-devel-2.2.0-14
I don't know why it crashes. To work around, comment out (with a semicolon) "hello.scm" in the $COOT_PREFIX/share/coot/scheme/coot.scm file.
It's somewhat involved, but hopefully straightforward if you follow the autobuilder. Coot requires mmdb, clipper, glut, gtk, gtkglarea. gtkglarea requires gtk and OpenGL. gtk requires glib. clipper requires fftw, mccp4 and mmdb. Optionally you can enhance coot using gtk-canvas, libSSM, guile/guile-gtk/guile-gui/guile-www or python (the support for python is not so advanced).
These issues are sorted out in the autobuilder. Just download it, change a few parameters to fit your personal system at the top and execute it...
$ coot Acquiring application resources from /usr/programs/COOT/Linux-utonium.chem.york.ac.uk/share/coot/cootrc INFO:: splash_screen_pixmap_dir /usr/programs/COOT/Linux-utonium.chem.york.ac.uk/share/coot/pixmaps [snip] initializing molecules...done ERROR: In procedure primitive-load-path: ERROR: Unable to find file "ice-9/boot-9.scm" in load path
You need to install guile. We have the following guile packages:
umb-scheme-3.2-32 guile-devel-1.6.4-11 guile-1.6.4-11
Coot uses the REFMAC dictionary restraints to do regularization and refinement. These are not distributed with the coot source code. Unfortunately, the REFMAC dictionaries distributed in CCP4 4.2.2 are not in strict mmCIF format and coot fails to read them - this is fixed in the new version (CCP4 5.0). A message that says "dirty cif file?" means that the file was not read correctly. The 4.2.2 (and earlier) dictionaries need to be modified - this script will do that.
Any other mmCIF formatted restraints (such as those from the EBI database or PRODRG2) should work.
More information on the setting up of restraints files can be found in Section 1.5 of the Coot User Manual.
You mean this one?
load "coot-gui.scm" (Error in proc: misc-error args: (#f ~A ~S (no code for module (gtk gdk)) #f))
You need to install guile-gtk. Here is the source, but your distribution may have rpms.
Martin Moncrieffe found a way.
You mean something like this?
You have a non-default language. setenv LANG C (or LANG=C if you prefer) before starting coot. This has recently been added to the setup files in the source code (it is not in version 0.0).
The problem may also be due to LC_ALL. So, if the above doesn't work try also:
setenv LC_ALL C
setenv LC_NUMERIC C
if using bash, one would unset LC_ALL and unset LC_NUMERIC
Like this.
Things to look out for: Error reading all scm files, error reading Refmac dictionary files, error reading colours.def, error reading syminfo.lib, error finding splash-screen image, error reading cootrc file, error finding reference structures (e.g. from COOT_REF_STUCTS). So, if you get error messages or warning when coot start, you can expect it to be other than fully functional.
e.g.
Gtk-WARNING **: Unable to locate loadable module in module_path: "libbluecurve.so"
No, don't worry - Gtk just can't find a theme. Things will look a bit different to how they otherwise might, but everything will still work.
Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message.
ObjectCache: Leaked 0002 refs to P 2ac 2ab ObjectCache: Leaked 0002 refs to P 2ac 2ab Nuvw = ( 108, 132, 64)
are nothing to worry about. I will clean them up one day.
The default window focusing (using Metacity I believe) is a PITA when using Coot. Try this:
Hat -> Preferences -> Windows -> Select windows when the mouse moves over them: check that box.
Hat -> Preferences -> Windows -> To move a window, press and hold this key then grab the window:
Change from
Control
to Alt or Super
The default window focusing with the Aqua window manager is a PITA when using Coot. Try typing in a terminal this to set "Focus Follows Mouse":
$ defaults write com.apple.x11 wm_ffm true
On a more modern version of Mac OS X (10.5?), that might be:
$ defaults write org.x.X11 wm_ffm true
(thanks to William Scott for pointing that out).
Keyboard + and -.
"Add Terminal Residue" is known not to work on sgi (it just hangs - seemingly indefinately). I don't know why.
"I can't see the contour level at the top of the screen or and the atom labels are faint or non-existant."
This seems like a graphics driver bug, or a hardware problem. If you turn the screenbackground white you might be able to see the text.
"I'm bored of moving the dialogs around every coot session. How do I make coot know where I want them? "
You can use the "Position Dialogs" function in the Extensions menu.
For a more manual way, try this.
It works in quad buffered stereo mode ("stereo-in-a-window"). You will need a recent version and either use the Draw -> Stereo dialog or pass the argument --stereo
Until recently, the stereo had been inverted.
The scripting functions (hardware-stereo-mode) and (mono-mode) can also change between modes (these don't work before version 0.0.21).
Yes.
Yes. Draw -> Stereo -> Zalman
[You will need to set up your screen for quad-buffered stereo system (not the more usual "full-screen" stereo) to even begin thinking about it].
Sue Roberts has some very useful advice.
So does Dirk Kostrewa.
1. Don't do it. Read in CNS data instead and let Coot take care of the map generation.
2. [Quoting Kevin Cowtan]
Change the setting in CNS which controls the extent of the output map. Instead of outputting a map covering a single molecule, you need to output a map covering a whole asymmetric unit (or if you prefer a whole unit cell).
The X-PLOR maps output by CNS are output in O mode, not Coot mode, by default. This is due to a fundamental difference in understanding what a map is between programs which work crystal space (e.g. Coot, Quanta, XtalView) and those which don't.
Green is positive
Red is negative
To change the colour scheme (other than simply changing the map colour wheel):
(set-swap-difference-map-colours 1)
Double-click on it
Shift-click on it
Press "L" labels atom closest to the centre of the screen.
There are 2 ways. Either create a file called refmac-extra params in the directory in which you started coot, e.g. refmac-extra-params
or
define (for example in you $HOME/.coot file) the variable refmac-extra-params, e.g.
(define refmac-extra-params
(list "WEIGHT 0.1"
"SOLVENT NO"
"REFI BREF ISOT"
"NCYCLES 6"))
By default, the refmac link library used by Coot now does include a planar restraint incorporating both CA atoms linked by a peptide.
As of version 0.4 the default is to have peptide plane restraints ON.
Use the Validation peptide distortion graph. That will show large red bars where there are cis peptides.
Method 1: Quite straightforwardly drag the density onto the pointer (centre of the screen) using Ctrl Left-mouse drag.
Method 2: bind the function (blob-under-pointer-to-screen-centre) to a key. Press that key.
You can then use Measures -> Pointer Distances if you wish.
Cntl Left-mouse-click over an intermediate (white) atom. Drag and drop. Make sure that you have focus in the graphics window when you press Ctrl (which, in Windows, that the graphics window has a blue title bar rather than a grey one). (You need to means be precise with the clicking - if the view rotates instead of the atom moving then you know that you have been insufficiently precise.)
Like this:
;; Bind a function to the "v" key (Shift-V would be bound to "V").
(add-key-binding "Place atom at pointer" "v"
(lambda ()
(set-pointer-atom-is-dummy 1)
(place-atom-at-pointer)))
Firstly, have you tried "Auto Fit Rotamer" or "Rotamers" before you try "Edit Chi Angles"?
Secondly, in Real Space Refinement mode it is often it is more convenient to change chi angles (implicitly) by moving just one atom.
The "Edit Chi Angles" torsion selection brings up a set of button, each button represents a rotatable bond. Click on one of these atoms then move the rotation in the graphics window as if you were trying rotate the view. There is a "Normal Rotation" button available to revert this rotation change.
The torsion selection can be also done by using the keyboard: "1" selects chi1, "2" selects chi2 etc. The just click and drag as you would normally to rotation the view, except now the atoms of the residue are rotated round the selected chi torsion... To return to normal rotation use keyboard "0".
As of 0.6 there is a "Reverse Fragment" in the Chi Angles dialog.
Standard protein residues will be rotated with the end of the side chain moving and the backbone fixed, regardless of the atom you click.
Q: I have a residue that has one or more missing mainchain atoms. I want to mutate a "fresh" residue in - but I can't. What should I do?
A: If any of the CA, C or N atoms of a residue are missing then mutate can't work (it needs these atoms to do the least-squares fit). This is what I do in such a case: first delete the residue, then add a new one with "Add Terminal Residue..." then "Mutate & Auto Fit..." to the required type, then Refine Zone.
Yes, Extensions -> Settings -> Set Spin Speed
Change the 0.04 to suite your hardware, of course.
No.
As of version 0.6, yes
This is fixed now. However, if you are using an old version, you need to make sure when you make the edit the entries that you have the "I-bar" cursor in the entry (rather than the pointer cursor elsewhere).
The issue here is the backup directory coot-backup. By default, it is created with strict permissions. I would recommend creating a directory to which you both can write and setenv COOT_BACKUP_DIR to that directory.
Bernhard Lohkamp has a web page for WinCoot and a FAQ.
You can find links to WinCoot (and other) pre-release binaries here.
Coot uses clipper's Ramachadran data - which is the Richardson's Top500.
We use the Richardsons' Rotamer Library.
By using google.
For example, if you wanted to make a search for Coot's "virtual trackball", use the google search:
virtual trackball coot site:www.ysbl.york.ac.uk
HTH : Hope This Helps
FYI : For Your Information
FWIW: For What It's Worth
AFAIR: As Far As I Recall
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