Re: [phenixbb] Geometry Restraints

Sorry, I meant "optimeze x-ray/stereochemistry weight" (I ran both stereochemistry and ADP at one point to see what the effect would be). I always run real-space refinement on coot. I try to include a region around the residue(s) I am playing with to allow the structure to relax and to prevent local strain. I tend to select the "Ramachandran Restrains" and also select the appropriate secondary structure restraint when it is possible. I see regions with bad clashes solely because during refinement a side chain is being fit into a density peak that is to close to another residue atoms. I wonder if there is a way to tell the program to avoid clashes even if it is at the expense of real-space fitting? Mario Sanches On Thu, Apr 19, 2012 at 8:48 AM, Nathaniel Echols wrote:

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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

On Thu, Apr 19, 2012 at 7:37 AM, Mario Sanches wrote: the

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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.

Did you mean to type "Optimize X-ray/Stereochemistry weight" instead? That is the option you want to use in these situations; it usually results in much better geometry, with two caveats:

1) If the input geometry is already poor, this may result in a poor initial guess for the weight, and the optimization will not sample the right range.

2) Severe clashes are hard to fix automatically - the structure needs to be repacked to fix them, which is beyond the power of our minimizer.

One tip: always run real-space refinement in Coot when rebuilding your model. Getting the input geometry as good as possible seems to help phenix.refine (or any other refinement program) converge on acceptable values.

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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