[phenixbb] Geometry Restraints

Pavel Afonine pafonine at lbl.gov
Thu Apr 19 23:26:37 PDT 2012


the methods described in the paper you mention below are shown to work 
for some selected structures taken from PDB ( that is overall good 
structures). This is not Mario's case, unfortunately. It is not 
demonstrated that this methodology would work for poor models.

All the best,

On 4/19/12 10:05 PM, Tim Fenn wrote:
> On Thu, Apr 19, 2012 at 5:37 AM, Mario Sanches<mariosan at gmail.com>  wrote:
>> I am refining a low resolution structure (2.9A) using phenix.refine. As I
>> continue the refinement  Rwork/Rfree are dropping but my  geometry
>> statistics in general are very bad. My clashscore is getting worst and the
>> RMS(angle) is really high. I have tried to play with the "wxc_scale"
>>   parameter and also ran phenix selecting the "Optimize X-ray/ADP weight"
>> option. All attempts end with a RMS(angle) of ~3.8 and a Clashscore of
>> ~190.
> I'm guessing Pavel has already sorted this out - but an expert
> shouldn't be required to yield appropriate geometry/chemistry!  This
> sort of problem has been discussed previously:
> http://phenix-online.org/pipermail/phenixbb/2011-November/017906.html
> http://dx.doi.org/10.1107/S0907444911039060
> although that high of a clashscore could arise from something else?
> Regards,
> Tim
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