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.