Thank you Nat! I will try to fix as many clashes as I can in coot, and hope that I can manage to reduce it to around 20. ;) Also thank other suggestions and discussions! best, Celina

Which version are you using? We made some changes over the summer that improve the geometry, especially the clashscore - these are present in version 1.7.2. If you're still using an earlier version, this might largely fix the problem. However, if there is conformational strain in the model, it is difficult to fix severe clashes without further rebuilding. You should inspect the clashes in Coot (the Phenix GUI has shortcuts for this, but Coot alone also has this capability) and fix as many as possible yourself. It is recommended that you use explicit hydrogen atoms when doing this, since the reason for clashes is often not obvious if only heavy atoms are used. (You don't necessarily need to refine with heavy atoms though - they're just an aid to visualizing clashes.)

The rotamer problem may be related; there isn't much you can do with these except fix them manually, but relieving some of the clashes may help. The dihedral angle restraints simply aren't that strong, so in areas of weak density it can be difficult to completely prevent outliers.

-Nat

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