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. Thanks, Jeff