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 :
- File → Fetch PDB using Accession Code
- Enter 7P9B and click Get
Structure

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):
- Open the Display Manager on the toolbar
- in the Molecule window, select Bonds (Colour by
chain)

Colors
To change the colors of the bonds:
- Go to Draw → Molecule → Bond Colours.
- Use the color picker or slider to adjust the bond colors as
desired.

Width
To change the width of the bonds:
- Go to Draw → Molecule → Bond Parameters.
- Change the pixels in Molecule Bond Width to 8.0 to
make the bonds thicker.

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:
Click the Py button on the right-hand side of
the horizontal toolbar to open the Python console (at the
bottom).
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
- Note: Replace
0
with the molecule index as shown in the
Display Manager if needed.

1.3 Ribbons
To create a ribbon representation:
- Navigate to Draw → Molecule → Ribbons: By Chain. A
small window will appear.
- 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:
- Navigate to Draw → Molecule → Molecular
Surface.

To undisplay the molecular surface:
- Go to Draw → View → Generic Display Objects.
- Either uncheck the molecular surface or click Delete All
Generic Display Objects to remove all generic objects from the
view.
1.5 Gaussian Surface
To create a Gaussian surface representation:
- Navigate to Draw → Molecule → Gaussian
Surface.
- In the window that appears, adjust the parameters as needed to
customize the surface.
- Click Calculate to generate the Gaussian
surface.

To undisplay the Gaussian surface:
- Go to Draw → View → Generic Display Objects.
- Either uncheck the Gaussian surface or click Delete All
Generic Display Objects to remove all generic objects from the
view.
1.6 Electrostatic Surface
To create an electrostatic surface representation:
- Navigate to Draw → Molecule → Electrostatic
Surface.

To undisplay the electrostatic surface:
- Go to Draw → View → Generic Display Objects.
- Either uncheck the electrostatic surface or click Delete All
Generic Display Objects to remove all generic objects from the
view.
1.7 Goodsell Style
To enable Goodsell style:
- Go to File → Curlew and install the Goodsell
Menu

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:
- Navigate to Measures → Environment Distances. A
small window will appear.
- Check Show Residue Environment
- Purple dashed lines represent hydrogen bonds, while yellow lines
indicate bumps.

2. Map Representation
Let’s load the map for 7p9b:
- File → Open Map
- Upload emd_13261.map and click
Open.

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

Colors
To change the color of the map:
- Open the Display Manager.
- In the Map window, select
Properties. A new dialog will appear.
- Click on Map Colour.
- Click the + button to open the color picker and
select a new color.
- Choose the desired color and press Select.

Smoothen
To make a smooth map:
- Navigate to Calculate → Map Tools → Make a Very Smooth
Copy.
- 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:
- Open the Display Manager.
- Undisplay or delete the original map.

Publication Tip
- Set the background color to white:
- Navigate to Draw → View → Background Colour and
select white.
- Adjust the map color to grey:
- Open the Display Manager, go to
Properties, and change the Map Colour
to grey.
- Modify the map opacity:
- In the Properties dialog, adjust the
Opacity slider to your preference.
- 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:
- Open the Display Manager.
- In the Map window, click on
Properties.
- 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:
- 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.
- 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:
- Go to Cryo-EM → Solidify Maps.

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.
- Navigate to Calculate → Map Tools → Mask Map by Atom
Selection.
- In the dialog that appears:
- Select the map you want to mask.
- Select the model.
- 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 .
- 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:
- Navigate to Draw → View → Background Colour.
- Choose from various shades of grey, white, or black.
3.2 Clipping Planes
To adjust the clipping planes:
- Use 1 and 2 to modify the front
clipping plane.
- Use 3 and 4 to modify the back
clipping plane.
3.3 Lighting
To adjust the lighting settings:
- Navigate to Draw → Shader Settings to open the
Shader Settings window.
- 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.

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:
- macOS Screenshot Tool: Press Command +
Shift + 4(or 5) to capture a selected area or Command +
Shift + 3 for the entire screen.