Creating Figures with Coot 1.1

Lucrezia Catapano - April 2025




Introduction

The Coot 1.1 graphics has been improved to the point of being useful for publication.
This tutorial will explain how to make high-quality figures of molecular models and maps with Coot 1.1.

1. Model Representations

Open Coot 1.1 and load a PDB file :


1.1 Bonds (Sticks)

Bonds are the default representation in Coot. To zoom in, hold Shift and use the Left Mouse Button. To center on a specific residue, press Ctrl G, type A7, and click OK.

Let’s display bond orders for the molecule (coot uses a kekulised representation):


Colors

To change the colors of the bonds:


Width

To change the width of the bonds:

You can also change the smoothness of the bonds by selecting Bond Smoothness


1.2 Ball and Stick

To create a ball and stick representation:

  1. Click the Py button on the right-hand side of the horizontal toolbar to open the Python console (at the bottom).

  2. Type the following commands and press Enter after each:

    • import coot
    • coot.set_atom_radius_scale_factor(0, 2.0) # Adjusts the atom radius scale factor
    • coot.set_bond_smoothness_factor(3) # Increases the smoothness of the balls


1.3 Ribbons

To create a ribbon representation:

  1. Navigate to Draw → Molecule → Ribbons: By Chain. A small window will appear.
  2. In the Display Manager, undisplay the model to disable the bond representation.

You can also enable the Ribbons: Rainbow and Ribbons: Sec. Struct. representations.


1.4 Molecular Surface

To create a molecular surface representation:

To undisplay the molecular surface:


1.5 Gaussian Surface

To create a Gaussian surface representation:

  1. Navigate to Draw → Molecule → Gaussian Surface.
  2. In the window that appears, adjust the parameters as needed to customize the surface.
  3. Click Calculate to generate the Gaussian surface.

To undisplay the Gaussian surface:


1.6 Electrostatic Surface

To create an electrostatic surface representation:

To undisplay the electrostatic surface:


1.7 Goodsell Style

To enable Goodsell style:

Then a Goodsell menu will appear on the horizontal toolbar.

The Goodsell representation offers three color schemes and the background colour is white by default.


1.8 Environment Distances

To display environment distances:


2. Map Representation

Let’s load the map for 7p9b:


2.1 Chickenwire

The default representation of the map is a chickenwire.

To increase the contour level, use the mouse scroll wheel.

Let’s increase the radius:

  1. Navigate to Draw → Molecule → Map Parameters.
  2. In the window that appears, adjust the Map Radius EM to 99 and press Apply.
  3. Press OK to close the window.


Colors

To change the color of the map:

  1. Open the Display Manager.
  2. In the Map window, select Properties. A new dialog will appear.
  3. Click on Map Colour.
  4. Click the + button to open the color picker and select a new color.
  5. Choose the desired color and press Select.


Smoothen

To make a smooth map:

  1. Navigate to Calculate → Map Tools → Make a Very Smooth Copy.
  2. Select the map you want to smooth and press OK.

This process may take some time depending on the size of the map. Once the new map is generated, it is recommended to avoid displaying both maps simultaneously to prevent visual clutter:


Publication Tip

  1. Set the background color to white:
    • Navigate to Draw → View → Background Colour and select white.
  2. Adjust the map color to grey:
    • Open the Display Manager, go to Properties, and change the Map Colour to grey.
  3. Modify the map opacity:
    • In the Properties dialog, adjust the Opacity slider to your preference.
  4. Fine-tune the clipping planes:
    • Use the keyboard shortcuts 3 and 4 to adjust the back clipping plane, and 1 and 2 to adjust the front clipping plane, until the desired view is achieved.


2.2 Surface

To create a surface representation of the map:

  1. Open the Display Manager.
  2. In the Map window, click on Properties.
  3. In the dialog that appears, set the Displayed Map Style to Surface.

This will render the map as a surface representation.


2.3 Mask the map

Mask map by chain

To mask the map by chains, follow these steps:

  1. Load the Cryo-EM module:
    • On the right-hand side, click the button with a plus sign and an arrow.
    • From the dropdown menu, select Cryo-EM. A new button will appear on the horizontal toolbar.
  2. Use the Cryo-EM → Mask Map by Chain option:
    • Click the newly added Cryo-EM button on the toolbar.
    • Select Mask Map by Chain from the menu.

The program will generate 10 new maps, each corresponding to one of the chains in the model. By default, these maps are displayed as chickenwire. To convert all maps to surface representations:


Mask map by atom selection

To mask the map by atom selection, such as for a ligand, follow these steps:

For example, we want to mask the map around LLP of chain A.

  1. Navigate to Calculate → Map Tools → Mask Map by Atom Selection.
  2. In the dialog that appears:
    • Select the map you want to mask.
    • Select the model.
  3. In the Atom Selection dialog:
    • Specify the ligand details using the format //A/386, which represents residue 386 in chain A (LLP).
    • Set the desired radius around the atoms.
    • Check Invert Masking .
  4. Press Mask Map to generate the masked map.

This process will create a new map focused on the selected ligand.


3. Shader Settings

3.1 Background

To change the background color:

3.2 Clipping Planes

To adjust the clipping planes:

3.3 Lighting

To adjust the lighting settings:

  1. Navigate to Draw → Shader Settings to open the Shader Settings window.
  2. Choose from the following modes:
    • Basic: The default mode with standard lighting.
    • Plain: Similar to Basic but with minimal shading.
    • Fancy: Enables advanced shading and lighting options for enhanced visualization.

drawing

Fancy Mode:

Brightness

You can increase and decrease the brightness of the model by adjusting the Brightness slider.


Gamma

Adjusting the gamma setting can make the model appear more pastel and brighter when increased, or more vibrant and saturated when decreased.


Screen-Space Ambient Occlusion

It is used to enhance the perception of depth and highlight cavities by simulating the way the light interacts with surfaces in a 3D environment. You can change the SSAO parameters such as the radius of the occlusion and the intensity of the effect. For high quality images turn up the kernel samples to the maximum.


Shadows

Shadows can be enabled or disabled in the Shader Settings window. When enabled, shadows will be cast by the model, enhancing the 3D effect. This can be used in combination with SSAO.


Depth Blur

Depth blur is a feature that simulates the effect of a camera lens, where objects at different distances from the camera appear blurred. You can adjust the blur focus depth and strength to control the intensity and range of the depth blur effect.


Outline

You can draw an outline around the model by checking the Outline box in the Shader Settings window.


4. Screenshots

Currently, the screenshot function is unavailable on some systems (including macOS) due to limitations with OpenGL support. The OpenGL screenshot feature requires OpenGL 4.4.

To capture screenshots, users are advised to use a third-party tool such as: