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

Pavel Afonine pafonine at lbl.gov
Fri Aug 20 10:57:27 PDT 2010

  Hi Yarrow,

I could comment on this more specifically if you send me (to my email 
address, not to the whole phenixbb) the data and model files, and the 
exact phenix.refine command that you used to obtain your final model 
that has clashes you are mentioning.
Also, it will save me some time if you outline the residues in question.


On 8/20/10 10:20 AM, amadrona at uci.edu wrote:
>   On Thu, Aug 19, 2010 at 3:46 PM,<amadrona at uci.edu>  wrote:
>>> 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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