[phenixbb] hydrogens in riding model create steric clashes after refinement

Jeff Headd jjheadd at lbl.gov
Thu Aug 19 16:38:55 PDT 2010

>No, I didn't previously have hydgrogens.  This is the first time I looked
> at close contacts with hydrogens present.  I submitted my pdb to the the
> PDB auto Deposition input tool which defines "close contacts" as less
> then 2.2 A
> After looking at these I could see that many were between hydroens of one
> side chain and usually an amid or sometimes CA of the mainchain.
> Sometimes they appeard hydrogen bonded but the hydrogens had to be rotated
> away.  All I had to do was rotate the hydrogens.  I was just suprised that
> this would not have been done in automatically in the refinement.

Hi Yarrow,

Have you run your model through the MolProbity server, or are you
basing your clash analysis only on the PDB tools?  MolProbity will
give you a more thorough analysis of your structure, and will allow
you to target areas of your model that are showing steric clashes due
to misfit residues rather than just slightly out of place hydrogens.
Most of the MolProbity validation tools for proteins are also
available in the PHENIX validation GUI if you happen to be working in
the GUI environment.

If you have any MolProbity specific questions, please let me know.


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