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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