[phenixbb] Geometry Restraints

Mario Sanches mariosan at gmail.com
Thu Apr 19 06:00:12 PDT 2012

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

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 at lbl.gov> wrote:

> On Thu, Apr 19, 2012 at 7:37 AM, Mario Sanches <mariosan at 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
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Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
M5G 1X5
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