COOT Quick Reference Guide

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Our intention is not to provide in-depth model building support here at SSRL, but to offer an easy-to-use graphics program so that users who have collected data here can quickly look at their maps. For example, if a MAD data set has been collected and roughly phased using our solve script, the user may wish to quickly check the quality of the resultant maps to determine whether additional data should be collected to improve the solution. To this end, we have found the program COOT to be very easy to run and inspect electron density maps with no prior knowledge of the program.

Coot is molecular graphics program developed in York and is used for model building, model completion and validation. It has some features that resemble those of Turbo-Frodo, O, Quanta and XtalView's XFit, such as pull-down menus (see the image below), however Coot does not do many aspects of structure representation. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran plots. It also has a very robust superposition algorithm.

Screen capture from COOT showing a molecule and electron density.

Files, References and Documentation

Coot reads coordinate files in pdb format, and can also read pdb files which have been compressed with gzip. Coot reads maps in CCP4 format (such as those generated with FFT). Coot is also able to reads mtz files and can either calculate maps from data columns in the mtz file specified by the user, or it can automatically generate maps from mtz files containing map coefficients with column labels FWT, DELFWT, PHWT and PHDELWT (such as those produced by REFMAC).


The reference for the coot is:

Emsley P, Cowtan K (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.

If using "SSM Superposition", please cite:

Krissinel E, Henrick K (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D60, 2256-2268.


If you have detailed questions about these programs, please refer to the COOT documentation, available on-line.

In order to get you quickly started with Coot so that you can look at your MAD maps, here are some of the main commands you might need to know. This is not meant to be a detailed description of how to build you model or fit your sequence to the electron density. If you wish to continue using Coot once you leave SSRL we suggest that you download your own copy, go through the manual and the tutorial and have fun!

Mouse functions

Left-mouse Drag

Ctrl Left-Mouse Drag

Shift Left-Mouse

Right-Mouse Drag

Ctrl Shift Right-Mouse Drag


Scroll-wheel Forward

Scroll-wheel Backward

Ctrl Right-Mouse Drag Up/Down

Ctrl Right-Mouse Drag Left/Right

Rotate view

Translates view

Label Atom

Zoom in and out

Rotate View around Screen Z axis

Centre on atom

Increase map contour level

Decrease map contour level

changes the slab (clipping planes)

translates the view in screen Z

If you don't have a wheel mouse (for example, on an SGI), you can use the keyboard to increase and decrease the contour level as described below.

Some Keyboard controls

You can find a great little cheat-sheet here that you can print out and keep handy .










Next Residue

Previous Residue

Zoom out

Zoom in

Slim clip (slab less)

Fatten clip (slab more)

Open the Model/Fit/Refine dialog

Open the GoTo Atom Window

Open the Display Control Window

To increase or decrease contour levels on maps, use + or - on the keyboard. You need to make sure you are controlling the correct map (in cases where you have more than one map loaded). See the section on the Display Manager below for details

Useful Menu Items


open coordinates You can then browse for the pdb file you wish to load.
Auto Open MTZ You need to then specify a file which contains map coefficients with column labels FWT, DEFWT, PHWT and PHDELWT (such as output by REFMAC). Coot will automatically generate the Fo-Fc and 2Fo-Fc maps from this.
Open MTZ, CIF, phs etc You need to specify the file you wish to generate a map from, and then select the correct column names for amplitudes and phases (and weights if necessary). If your phases have come from SOLVE/RESOLVE or Shelxe then you will have to use this option to calculate your first Fo map.
Close molecule/map Used to delete a molecule or map from the display manager.
Save coordinates As the name implies, used to save any changes to a file.


Model/Fit/Refine This opens a floating menu (shown below) which contains all the functions necessary for modeling and refinement.
SSM SuperposeStarts the SSM superposition calculation and prompts for two models to superimpose.
Map SkeletonStarts a dialog box in which you can specify which map to skeletonize, normally from a RESOLVE map there will be just one option, your initial Fo map. You activate the skeleton by clicking the on radio button and then OK.


Go To Atom Opens a dialog box (see below left) in which you can choose the molecule you wish to work with, a chain name, residue number and atom name. Alternatively, there is a listing of the chains present in the map and these can be opened by clicking the + button to the left of the chain name. The residue number can then be browsed from the tree. To center on a particular residue, click that residue number and then click the Apply button. You will, by default, be centered on the CA atom.
Sequence View Selecting this option then allows you to browse a list of all the molecules currently open. Selecting an open molecule will then open a Sequence View dialog (see below right) with the sequences of the chains listed in one-letter format. To center on a particular residue, click on the residue label and the view on the screen automatically updates.
Cell & Symmetry Opens a Show Symmetry dialog which allows you to select how you want to display the symmetry atoms.

Display Manager

Clicking this option brings up the Display Control dialog box which lists the currently loaded Maps and Molecules. You are then able to toggle these various objects on and off using the Display button, change some map features (eg color) using the Properties button, or alter how you which to show the molecules (eg all atoms, CA only etc) using the Bonds pull-down menu. In the Linux and SGI versions of Coot, there is also a Scroll radio button beside each map name (see below). This button allows you to switch between the different maps so that the sigma levels can be changed.


Distances & Angles> Distances and angles will be displayed on the screen and in the console after mouse clicking on the atoms of interest.
Environment Distances Select the Show Residue Environment radio button and click OK. Then use the middle mouse button to click on any atom in a residue to see the contacts to all neighboring residues.


Ramachandran Plot This will give you a list of currently loaded molecules. Select the molecule you wish to calculate the Ramachandran plot for.
Check/Delete Waters This dialog box (see below left) allows you to list or delete water molecules which fall outside certain criteria. The default action is to Generate a List but you can also Delete Waters immediately if you so wish. If you choose to list the waters (this is the default), a window will appear with the water molecule names (below right). You can then work your way through the list by clicking on the water molecule name and visually inspecting each suspect water molecule.


Scrollwheel Used to change which map is controlled by the scrollwheel or the +/- keys if you are using keyboard contouring (in cases where more than one map is loaded).