[phenixbb] Geometry Restraints

[Pavel Afonine]

Ok, in this case I need to look at the files ...

Pavel

On 4/19/12 5:46 AM, Mario Sanches wrote:
> I am using a nightly build from around two weeks ago (dev-1021).  I am 
> sending you some files.
> Thank you,
>
> Mario Sanches
>
> On Thu, Apr 19, 2012 at 8:42 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     Hi Mario,
>
>     are you using the latest Phenix? If not, please update your
>     version of Phenix and try again:
>
>     http://www.phenix-online.org/download/nightly_builds.cgi
>
>     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.
>
>     Pavel
>
>
>
>     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 ~190.
>>
>>     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
>>     Canada
>>     M5G 1X5
>>     http://ca.linkedin.com/in/mariosanches
>>
>>
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>
>
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>
>
>
> -- 
> Mario Sanches
> Postdoctoral Researcher
> Samuel Lunenfeld Research Institute
> Mount Sinai Hospital
> 600 University Ave
> Toronto - Ontario
> Canada
> M5G 1X5
> http://ca.linkedin.com/in/mariosanches
>
>
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