On Thu, Aug 19, 2010 at 3:46 PM,
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.
If you didn't have explicit hydrogens, there's no way for phenix.refine (or any other refinement program) to tell that there's a clash. Minimization algorithms are "dumb", in the sense that they know nothing about chemistry, only restraints, and rotating around a bond often requires passing over large energy barriers (a major reason why simulated annealing is used). Recent versions of phenix.refine can optionally re-fit sidechain rotamers and flip N/Q/H residues to minimize bad contacts, and more features like this will be added over time, but it's tricky.
It's very suspicious that hydrogens are bumping into the C-alpha if there is space for them elsewhere; the tools in Phenix should almost never do this unless there is something else wrong with the model. But it's difficult to guess without seeing the structure.
-Nat
I think I may have over-reacted (this being my first structure and all) By "clash" I meant contacts closer then 2.2A (most 1-1.5A). There are only about 28 of these involving side chain Hydrogens out of over 1600 residues. Only one involves the CA. The rest are basically hydrogen bonds where the hydrogens should be rotated away from the heroatom. Most of the other 50 involved contacts with misplaced waters I still need to clean-up. I think this may be normal. However, I still can't acount for the four residues that had hydrogens off in space. Thanks for all your help. -Yarrow
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