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<DIV> 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!</DIV>
<DIV>best,</DIV>
<DIV>Celina</DIV>
<DIV> </DIV>
<DIV>> <BR>> Which version are you using? We made some changes over the summer<BR>> that improve the geometry, especially the clashscore - these are<BR>> present in version 1.7.2. If you're still using an earlier version,<BR>> this might largely fix the problem. However, if there is<BR>> conformational strain in the model, it is difficult to fix severe<BR>> clashes without further rebuilding. You should inspect the clashes in<BR>> Coot (the Phenix GUI has shortcuts for this, but Coot alone also has<BR>> this capability) and fix as many as possible yourself. It is<BR>> recommended that you use explicit hydrogen atoms when doing this,<BR>> since the reason for clashes is often not obvious if only heavy atoms<BR>> are used. (You don't necessarily need to refine with heavy atoms<BR>> though - they're just an aid to visualizing clashes.)<BR>> <BR>> The rotamer problem may be related; there isn't much you can do with<BR>> these excep!
t fix them manually, but relieving some of the clashes may<BR>> help. The dihedral angle restraints simply aren't that strong, so in<BR>> areas of weak density it can be difficult to completely prevent<BR>> outliers.<BR>> <BR>> -Nat<BR>> <BR>> <BR>> ------------------------------<BR>> <BR>> </DIV> </div></body>
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