Re: [phenixbb] Geometry Restraints

Tim, 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, Pavel On 4/19/12 10:05 PM, Tim Fenn wrote:

On Thu, Apr 19, 2012 at 5:37 AM, Mario Sanches 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb