[phenixbb] Geometry Restraints
mariosan at gmail.com
Thu Apr 19 05:46:02 PDT 2012
I am using a nightly build from around two weeks ago (dev-1021). I am
sending you some files.
On Thu, Apr 19, 2012 at 8:42 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Mario,
> are you using the latest Phenix? If not, please update your version of
> Phenix and try again:
> If this doesn't help, please send me the data and model (offlist) and I
> will have a look to see what's going on.
> On 4/19/12 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
> Is there a known procedure to deal with this? I feel that my geometry
> weighing term is too loose but I don't know exactly how to tighten it other
> than decreasing the wxc_scale parameter. I have gone and manually corrected
> bad positions before but given the low resolution nature of the structure
> the clashes tend to be reestablished during refinement.
> Thank you in advance for your help,
> Mario Sanches
> Postdoctoral Researcher
> Samuel Lunenfeld Research Institute
> Mount Sinai Hospital
> 600 University Ave
> Toronto - Ontario
> M5G 1X5
> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb
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> phenixbb at phenix-online.org
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
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