Re: [phenixbb] Geometry Restraints

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 mailto:[email protected]> 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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-- 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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