COOT FAQ

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Available topics:
• Coot crashed, can I get my work back?
  
• Coot crashes on my PC after saving a file.
  
• How do I get a map from shelx into coot?
  
• Real-space refinement messes up the protein geometry. My resolution is 3 A.

Coot crashed, can I get my work back?

Probably. Don't panic yet.

Restart coot. When it asks if you want to run the auto-save state, say yes. If it doesn't read in the files properly, read them in yourself. Then choose recover session, choose molecule, and your changes should be restored. This is generally pretty good at recovering your changes, but I get a feeling of deja vu sometimes, especially when deleting/adding waters..




Coot crashes on my PC after saving a file?

Don't save a file until you're done rebuilding. See answer (1) above for how to recover from a crash.




How do I get a map from shelx into coot?

Coot will read the shelx .fcf file containing calculated Fs and phases.

 

Real-space refinement messes up the protein geometry. My resolution is 3 A.

The default refinement parameters need to be changed at low resolution. Copy the following to a file called lores.scm (or something like that) (You can find it on django in /usr/local/setup-scripts/lores.scm. Either start coot with the switch --script=lores.scm or read it in using run script from the Calculate pulldown.

(add-planar-peptide-restraints)
(set-matrix 20.0)
(set-terminal-residue-do-rigid-body-refine 0)
(set-add-terminal-residue-do-post-refine 1)
(set-mutate-auto-fit-do-post-refine 1)

In the set-matrix command, lowering the weight tightens the geometry. If you are refining residues with a-helical or b-sheet structure, you can specify additional secondary structure restraints. Just be sure to remove them before rebuilding a loop region or you'll see your structure magically take on (for instance) helical characteristics regardless of what the electron density looks like.