[phenixbb] problem with alternate conformations

George Phillips georgep at rice.edu
Thu Jul 11 08:40:07 PDT 2013

That would be a great short term fix.  If the clash score sucks too badly in subsequent analyses of individual structures, I presume I can manually tweak the weights.


On Jul 11, 2013, at 10:17 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>>> 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 weights.
> Proper fix though is to make Probe or Reduce faster.
> Pavel
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George N. Phillips, Jr.
Ralph and Dorothy Looney Professor
Department of Biochemistry and Cell Biology
Rice University, MS140
6100 Main Street
Houston, Texas  77005-1892
Office: +1 713.348.6951

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