P212121

The program COOT by Paul Emsley and Kevin Cowtan is simply, awesome (pdf paper citation).  I usually read the ‘tips’ that appear when starting the program and wanted to compile a comprehensive list:

Note: if this is difficult to read try pressing ‘ctrl then +’ as needed

1. To centre on a particular atom, click it with middle mouse (if that doesn’t seem to work it may be because the molecule is not active).
2. + and – on the keyboard change the contour level
3. To move just one atom (in Regularize, RS Refine, or Rotate/Translate mode) use Ctrl Left-mouse to pick an atom (you have to be accurate).
4. There is a mailing list for Coot development and discussion at http://www.jiscmail.ac.uk/lists/coot.html
5. Use Ctrl Left-mouse to drag (for example) a blob of density to the the pointer
6. Slow recentering? Try Draw -> Smooth Recentering and reduce the number of steps
7. Want distance of the atoms to the pointer? Use Measures -> Pointer Distances…
8. To label an atom: Shift Left-mouse on it
9. To make atoms be insensitive to clicking, deactivate it by unclicking that molecule’s "Active" button in the Display Control window
10. Can’t label or centre on some symmetry atoms? It’s a known bug. (For now, drag that atom closer to the centre of the screen).
11. Use function key ‘F8′ to make a rendered snapshot.
12. Use the Ctrl to rotate the view when changing Chi angles.
13. Too many cis peptides when using dragged refinement? Use the
    Planar Peptide Restraints’ suggested in the Coot FAQ.
14. Use the Ctrl to rotate the view when using Delete.
15. When in skeleton mode, new skeleton can be displayed around the current point using the ‘S’ key.
16. When in baton mode, the baton can be rotated independently from the Guide Points by using the ‘B’ key (it’s a toggle).
17. When Editing Chi Angles, switch between the angles quickly using the ‘1′, ‘2′, ‘3′, ‘4′ keys.
18. Use "refmac-extra-params" to pass refmac your personal parameters.
19. Use "(poly-ala imol)" to turn molecule number imol into poly-ALA. Use "(poly-ala imol ‘SER)" to turn it into poly-SER."
20. Use "(fit-protein imol)" to rotamer search and real-space refine all residue of molecule number imol."
21. Shift Ctrl right-mouse rotates round screen Z.
22. Ctrl + right-mouse + horizontal (left to right) mouse movement moves the view in screen Z.
23. Ctrl right-mouse up-down drag changes the slab.
24. Use "(set-idle-function-rotate-angle 0.05)" to change the spin speed.
25. (ligand-expert)" enables the GUI editting of some ligand-fitting parameters.
26. Use keyboard + and – to zoom in Ramachandran and Kleywegt Plots
27. The ‘U’ key undoes last nagivation (e.g. re-centering on new pdb file).
28. The ‘D’ and ‘F’ keys change the clipping/slabbing.
29. (view-matrix)" prints the current view matrix, useful for molscript, perhaps.
30. Baton-building low resolution maps is better done with maps that have increased sampling rate (2.0 or 2.5).
31. Coot can read SHELXL .res files. (It can write them too.)
32. Clear All Atom Labels" can be found under Measures -> Distances & Angles. Obviously.
33. Esc and Return are keyboard accelerators for Reject/Accept for Refinement and Regularization.
34. Restraints for alpha helical and beta-strand structure can in the Refinement/Regularization Control Panel
35. To disable coot tips: add "(no-coot-tips)" to your ~/.coot file.
36. It is possible to accidently invert chiral centres. Use Validate -> Chiral Centre to check.

Related Posts:

• Coot: How to Superimpose two Structures
• Coot: How to Simultaneously Mutate Multiple Residues
• Open PDB File using Coot
• How to get started with Coot
• How to Add a Symmetry Related Molecule using Coot

5 Responses so far | Have Your Say!

1. 

   Paul Emsley
   April 28th, 2009 at 12:11 PM #

   Ha, seeing them all like that, I see that there are some small typos. I’ve clarified things a touch. Thanks.

2. 

   admin
   April 28th, 2009 at 4:02 PM #

   We will keep our eyes open for the update, thanks for all your work with Coot it is truly appreciated!

3. 

   DrL
   May 4th, 2009 at 2:28 PM #

   I still don’t understand why Coot uses the old Ramachandran plots. Just integrate it with Richardson’s validation tool. (or maybe I have an old version of coot)

4. 

   Sean
   May 6th, 2009 at 9:02 PM #

   I assuming you are referring to MolProbity. I have not used MolProbity, does it have the ability to be updated as you adjust the amino acids?

   My guess the reasons for keeping the Ramachandran plot around is due to users being familiar with that type of output and that it can be updated on the fly.

5. 

   DrL
   May 6th, 2009 at 10:28 PM #

   I know they are working with the Phenix project to incorporate their analysis. I was under the impression that they were trying to work with Paul Emsley and incorporate it into coot. The issue is that the good old Ramachandran plot is based on very old data. I always put my final structure through Molprobity which gives much more satisfying result and analysis.