Coot Scripting

Gettingstarted with coot

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Then run the script file (Calculate-Run script), which will give a new menu under validate to give you outliers in a button list form. NB if you put the file in your.coot-preference directory it will always be loaded. Bizarre connectivity of coordinate files I guess you see something like this. This should not happen any more (from Remove Coot Virus (STOP ransomware) and restore.Coot Virus files(full steps):.AUTOMATIC REMOVAL. Removal. Coot is a stand-alone portion of CCP4’s Molecular Graphics project. Its focus is crystallographic model-building and manipulation rather than representation (i.e. More like Frodo than Rasmol).

Loada molecule
'File,Open Coordinates'
Displaya map
'File,Open Map' if you have a map file (*.map)
'File, Open MTZ...' if you have an mtz file (*.mtz)
The latter option is preferable to 'File, Auto Open MTZ' since one cancheck that the correct amplitudes are used.
Managing molecules andmaps
To switch maps and molecules on and of use 'Draw, Display Manager'.Here you can also delete molecules and maps.
To edit the color of the map push 'Properties' in the Display Manager.
To edit the contour level of a map, activate the 'scroll'optionfor that map in the Display Manager. Now in the graphics window scrollthe mouse wheel up to increase the contour level and down to decreasethe contour level.
To set the size of the displayed maps, use 'Edit, Map Parameters'.
Display mode
In the Display manager also the Display mode is set. The most importantstyles are:
'Bonds (Colour by atom)': To analyze regions of a protein molecule bydisplaying all atoms.
'C-alphas/Backbone': To show the CA trace.
'CAs + Ligands': To show the Calpha trace and exogenous ligands.
Mouse control (Rotate,Zoom, Center)
To rotate the molecule, press the left mouse button and move the mouse.
To zoom in and out, press the right mouse button and move the mouse.
To center on a new atom, click on the atom with the middle mouse button.
To shift the molecule, press CTRL and the left mouse button and movethe mouse.
d: press letter 'd' to decrease the slab thickness
f: press letter 'f' in incease the slab thickness
Center on a residue
To center on a residue click with the middle mouse button onto theresidue.
To center on a residue, use 'Draw, Goto Atom'
Alternatively, use the sequence view: 'Draw, Sequence view'
Atom labels/Residueinformation
If you click with SHIFT-left_mouse_button or if you double click on anatom, it will be labeled. If you need further information on a residueor atom use the option 'Edit, Residue Info'
Showing symmetryequivalent atoms
Use option 'Draw, Cell & Symmetry':
To analyze a crystal contact, use a small radius of 13 Ang. and displaya sphere (Button 'symmetry by molecule')
To analyze a crystal packing, use a large radius and display as CAs(Button 'symmetry by molecule')
Saving an image (snapshot)
Draw, Screenshot, simple
Making backup files
During all modelbuilding, it is a good idea to save the results fromtime to time in order to avoid a loss of the model due to aprogramcrash or user errors.
Make a backup with 'File, Save State...'. From time to time also choosea new filename instead of overwriting the previous backup file,,, etc. You can later read these backup fileswith 'Calculate, Run Script...'
You can also save the molecule that you are building to a file with thecommand 'File, Save Coordinates...'. Make sure to choose the rightmolecule.
Comparing structures /Superpositions
Read this for moreinformation on making superpositions.
Topology based alignment:Calculate, SSM superimpose.Specify the two pdb files to be superimposed and the chain names ifnecessary. If you need to superimpose only a domain or region of aprotein chain, first prepare pdb files which only contain the domainsto be superimposed. The superimposed coordinates can also be saved to afile.

Residue based alignment:Calculate, LSQsuperimpose. Specify the two pdb files to be superimposedand theregions if necessary (as usually). Unfortunately, you can only specifyone region for each chain. Coot seems to be able to figure out missingregions. However for one example it was crucial to specify at least thecorrect equivalent residues at the N-terminus and a deletion andmissing residues at the C-terminus were detected correctly. Alwayscheck the text output! In the text window the aligned regions, the rmsdeviations and the superposition matrix is given.

Model building
There are two main menus with model building commands.

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The first menu is activated via 'Edit, Model/Fit/Refine'. Small buttonswith the graphical symbols are also accessible at the right side of thegraphics window. This menu contains mainly commands neededwhen agreat part of the main chain has already been built.
Many of the following command act on a region of residues which afteractivating the option is specified by clicking on the first and lastresidue of the region. By pressing the CTRL button, one can rotate themolecule to find the first and last residue. The region can also be asingle amino acid or a ligand.

Automaticallyfits and refines a region based on an electron density map.
Optimizesthe stereochemistry of a region (bond length and bondangles). Before acceptingyou may manually change the zone*.
Asubmenu opens to fix or unfix atoms, which should not be moved whenapplying automatic building commands.
Shiftsand rotates a region as a rigid body (no conformational changes) foroptimal fit to the electron density map.
Afterspecifiying the region a menu with dial buttons opens to move androtate the region manually.
Basedon alibrary of allowed side chain conformations ('rotamers') the one whichbest fits to the electron density is chosen. Will only work if the mainchain is built correctly. Otherwise choose 'real space refine zone'.
Afterclicking on a residue a list of allowed side chain conformations willshow up. Click through all rotamers until one is found which best fitsthe electron density. The main chain conformation should be correct.
Modifytheside chain conformation by manually changing all torsion angles (namedchi angles). With this option also high energy rotamers may be chosen,if necessary.
Byclickingon four atoms a torsion angle is defined which can be manually changed.This option is usually only used for ligand, for which no rotamerlibrary is available.
Flipsboth the carbonyl group and the NH group of the peptide bond by180°.
Flipsthe side chain conformation of His, Asn or Gln.
Thephi and psi angles of the peptide bond can be changed manually.
Mutatethe residue and automatically determine the best side chainconformation based on the electron density map.
Mutatethe residue.
Add an alanine residue to the N-terminus or C-terminusof thecurrent chain. After activating the option you click on a terminalresidue. Before accepting the new residue you may manually change theresidue*.
If the electron density indicates that the residue ispresentin two or more conformations, you can add the alternate conformationshere.
Place an atom at the current center of the view. Beforeactivating the option you should move the density feature, usually awater molecule or ion, to the center by moving the structurewithCTRL-left_mouse_button. Rotate with the left mouse button only andagain center the density until the density is completely centered.After activating the option you can choose the type of atom to add.
If you want to cancel an option like 'Regularize Zone'when picking atoms, choose this option.
With this option you can delete atoms, side chains orregions.
Undoan operation. Does not always work.
Redoan operation that was undone.
*Manualchanges:You can drag the whole residue or region with the left mouse button ormove an atom with CTRL-left_mouse_button.
The second menu is activated via 'Calculate, Other Modelling Tools...'.It mainly contains commands to start manual model building from scratch.
FindWaters...AddWater molecules to the model. This should only be done when the proteinmodel is mostly complete, otherwise too many water molecules are placedinto unmodeled protein density.
Cis<-> Trans
C-alphaBaton Mode ...Tobuild a Calpha trace by adding CA atoms to the end of the chain. Centeron a position where a CA atom is located and activate the option. Ifthere is no atom to center on, use CTRL-Left_Mouse_Button to center theposition. A number of putative next CA positions is shown, one isconnected with a white line to the current center. If this appears tobe correct hit'Accept' otherwise 'Try another' until the best choice is found. Besure to go in the right N->C direction, otherwise you need touse'Reverse Drirection' later. When you hit 'Accept' the position isaccepted and centered an new CA positions at a distance of 3.8 Ang. aresuggested. When the chain ends hit 'Dismiss'
CaZone -> MainchainWhena CA trace has been built, the next step is to convert this tocoordinates for all main chain atoms with the help of this option. Infact, a polyalanine model is built.
AddOXT to ResidueAddthe second oxygen to the terminal carboxylate group. This should bedone if this is really present in the crystallized construct, i.e. donot add this oxygen if further residues are present which can not bemodeled due to disorder.
ReverseDirectionIfthe main chain has been build in the wrong direction (C->N), usethis command to reverse the direction. A CA trace will be built withthe numbering reversed.
PlaceHelix Here
Choose'Undo' Molecule
Developer(s)Paul Emsley
Kevin D. Cowtan
Initial release2002
Stable release[1] / 1 April 2018; 2 years ago
Operating systemWindows, Linux, OS X, Unix
TypeMolecular modelling
LicenseGNU General Public License

Coot Scripting Tools

The program Coot (Crystallographic Object-Oriented Toolkit)[2][3] is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of atomic models into three-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy.


Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that tools for common tasks are 'discoverable' through familiar user interface elements (menus and toolbars), or by intuitive behaviour (mouse controls). Recent developments have enhanced the usability of the software for expert users, with customisable key bindings, extensions, and an extensive scripting interface.

Coot is free software, distributed under the GNU GPL. It is available from the Coot web site[4] originally at the University of York, and now at the MRC Laboratory of Molecular Biology. Pre-compiled binaries are also available for Linux and Windows from the web page and CCP4, and for Mac OS X through Fink and CCP4. Additional support is available through the Coot wiki and an active COOT mailing list.[5][6]

The primary author is Paul Emsley (MRC-LMB at Cambridge). Other contributors include Kevin Cowtan, Bernhard Lohkamp and Stuart McNicholas (University of York), William Scott (University of California at Santa Cruz), and Eugene Krissinel (Daresbury Laboratory).


Coot can be used to read files containing 3D atomic coordinate models of macromolecular structures in a number of formats, including pdb, mmcif, and Shelx files. The model may then be rotated in 3D and viewed from any viewpoint. The atomic model is represented by default using a stick-model, with vectors representing chemical bonds. The two halves of each bond are coloured according to the element of the atom at that end of the bond, allowing chemical structure and identity to be visualised in a manner familiar to most chemists.

Coot can also display electron density, which is the result of structure determination experiments such as X-ray crystallography and EM reconstruction. The density is contoured using a 3D-mesh. The contour level controlled using the mouse wheel for easy manipulation - this provides a simple way for the user to get an idea of the 3D electron density profile without the visual clutter of multiple contour levels. Electron density may be read into the program from ccp4 or cns map formats, though it is more common to calculate an electron density map directly from the X-ray diffraction data, read from an mtz, hkl, fcf or mmcif file.

Coot provides extensive features for model building and refinement (i.e. adjusting the model to better fit the electron density), and for validation (i.e. checking that the atomic model agrees with the experimentally derived electron density and makes chemical sense). The most important of these tools is the real space refinement engine, which will optimize the fit of a section of atomic model to the electron density in real time, with graphical feedback. The user may also intervene in this process, dragging the atoms into the right places if the initial model is too far away from the corresponding electron density.

Model building tools[edit]

Coot Real Space Refinement
Coot Add Terminal Residue

Tools for general model building:

  • C-alpha baton mode - trace the main chain of a protein by placing correctly spaced alpha-carbon atoms.
  • Ca Zone -> Mainchain - convert an initial trace of the alpha-carbon atoms to a full main-chain trace.
  • Place helix here - fit a sequence of amino acids in alpha helix conformation into density.
  • Place strand here - fit a sequence of amino acids in beta strand conformation into density.
  • Ideal DNA/RNA - build an ideal DNA or RNA fragment.
  • Find ligands - find and fit a model to any small molecule which may be bound to the macromolecule.

Tools for moving existing atoms:

  • Real space refine zone - optimize the fit of the model to the electron density, while preserving stereochemistry.
  • Regularize zone - optimize stereochemistry.
  • Rigid body fit zone - optimize the fit of a rigid body to the electron density.
  • Rotate/translate zone - manually position a rigid body.
  • Rotamer tools (auto fit rotamer, manual rotamer, mutate and autofit, simple mutate)
  • Torsion editing (edit chi angles, edit main chain torsions, general torsions)
  • Other protein tools (flip peptide, flip sidechain, cis <-> trans)

Tools for adding atoms to the model:

  • Find waters - add ordered solvent molecules to the model
  • Add terminal residue - extend a protein or nucleotide chain
  • Add alternate conformation
  • Place atom at pointer

Validation tools[edit]

Coot Script

Coot Ramachandran plot validation tool
Coot density fit validation tool

In macromolecular crystallography, the observed data is often weak and the observation-to-parameter ratio near 1. As a result, it is possible to build an incorrect atomic model into the electron density in some cases. To avoid this, careful validation is required. Coot provides a range of validation tools, listed below. Having built an initial model, it is usual to check all of these and reconsider any parts of the model which are highlighted as problematic before deposition of the atomic coordinates with a public database.

  • Ramachandran plot - validate the torsion angles of a protein chain.
  • Kleywegt plot - examine differences between the torsions of NCS-related chains.
  • Incorrect chiral volumes - check for chiral centres with the wrong handedness.
  • Unmodelled blobs - check for electron density not accounted for by existing atoms.
  • Difference map peaks - check for large differences between observed and calculated density.
  • Check/Delete waters - check for water molecules which do not fit the density.
  • Check waters by difference map variance
  • Geometry analysis - check for improbable bond lengths, angles, etc.
  • Peptide omega analysis - check for non-planar peptide bonds.
  • Temperature factor variance analysis -
  • GLN and ASN B-factor outliers -
  • Rotamer analysis - check for unusual protein side-chain conformations.
  • Density fit analysis - identify parts of the model which don't fit the density.
  • Probe clashes - check for Hydrogen atoms with inappropriate environments (using Molprobity).
  • NCS differences - check for general differences between NCS related chains.
  • Pukka puckers - check for unusual DNA/RNA conformations.

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Program architecture[edit]

Coot structure

Coot is built upon a number of libraries. Crystallographic tools include the Clipper library[7] for manipulating electron density and providing crystallographic algorithms, and the MMDB[8] for the manipulation of atomic models. Other dependencies include FFTW, and the GNU Scientific Library.

Much of the program's functionality is available through a scripting interface, which provides access from both the Python and Guile scripting languages.

Relation to CCP4mg[edit]

The CCP4mg molecular graphics software[9][10] from Collaborative Computational Project Number 4 is a related project with which Coot shares some code. The projects are focused on slightly different problems, with CCP4mg dealing with presentation graphics and movies, whereas Coot deals with model building and validation.

Impact in the crystallographic computing community[edit]

Coot ScriptingCoot scripting tutorial

The software has gained considerable popularity over the past 5 years, overtaking widely used packages such as 'O',[11] XtalView,[12] and Turbo Frodo.[13] The primary publication has been cited in over 21,000 independent scientific papers since 2004.[14]


  1. ^'Release'. 1 April 2018. Retrieved 22 October 2019.
  2. ^P. Emsley; B. Lohkamp; W.G. Scott; Cowtan (2010). 'Features and Development of Coot'. Acta Crystallographica. D66: 486–501. doi:10.1107/s0907444910007493. PMC2852313. PMID20383002.
  3. ^P. Emsley; K. Cowtan (2004). 'Coot: model-building tools for molecular graphics'. Acta Crystallographica. D60: 2126–2132. doi:10.1107/s0907444904019158. PMID15572765.
  4. ^'Coot'. Retrieved 2017-02-27.
  5. ^'Coot - CCP4 wiki'. Retrieved 2017-02-27.
  6. ^'Coot List At Www.Jiscmail.Ac.Uk'. JISCMail. Retrieved 2017-02-27.
  7. ^'Dr Kevin Cowtan - About staff, The University of York'. 2014-10-23. Retrieved 2017-02-27.
  8. ^[1]
  9. ^L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, P. Emsley, G. N. Murshudov, S. Cohen, A. Perrakis and M. Noble (2004). 'Developments in the CCP4 molecular-graphics project'. Acta Crystallogr. D60: 2288–2294.CS1 maint: multiple names: authors list (link)
  10. ^[2]
  11. ^'Home Page of Alwyn Jones'. Retrieved 2017-02-27.
  12. ^'CCMS Software - XtalView'. 2006-08-09. Retrieved 2017-02-27.
  13. ^'Turbo Frodo Description'. 1999-03-26. Retrieved 2017-02-27.
  14. ^'Coot model building tools for molecular graphics - Google Scholar'. Retrieved 2017-02-27.

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External links[edit]

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