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 <nechols@lbl.gov> wrote:
On Thu, Apr 19, 2012 at 7:37 AM, Mario Sanches <mariosan@gmail.com> 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.

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.

-Nat
_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb



--
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