[phenixbb] problem with alternate conformations

Pavel Afonine pafonine at lbl.gov
Thu Jul 11 08:17:08 PDT 2013

>> This
>> happens on the standard release and development version 1422.
>> Is there some way to turn off hydrogens as a work around?  Test files
>> available on request. : )
> Unfortunately the problem is that phenix.refine always (for the last
> couple of years) calculates the clashscore as part of coordinate
> refinement, instead of simply using the nonbonded restraints as a
> target, and the clashscore by definition takes hydrogens into account.
>   So there is no way to entirely avoid adding hydrogens if you are
> using the individual_sites strategy.

I can add a flag to disable reporting Molprobity statistics within 
phenix.refine: it's a trivial change. Currently it is always calculated, 
and in case of weight optimization it is actually used to select optimal 
Proper fix though is to make Probe or Reduce faster.


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