[phenixbb] Geometry Restraints - UPDATE

Mario Sanches mariosan at gmail.com
Wed Apr 25 06:05:57 PDT 2012

Last week I asked a question about geometry restraints at low resolution. I
would like to thank you all that took the time to answer, specially Pavel
for looking at the data. First, here is the original question:

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

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,

It turns out that the reason to my nightmares was a highly anisotropic
dataset. When I tried to fix geometry related problems in coot,
phenix.refine was twisting the geometry back again, probably because it was
trying to fit a lot of noise due to the anisotropy. Everything was getting
worst, geometry, clashscore, and Ramachandran.

Pavel finally corrected it by using this server:
http://services.mbi.ucla.edu/anisoscale/  I should have been more diligent
regarding that, since I could clearly see that my data was anisotropic from
the diffraction images. I just didn't know how important this parameter
could be. Anyways, phenix.xtriage will tell you if your data is
anisotropic. The lesson is to pay attention to it.

In my case, the quality of the electron density improved considerably, the
geometry improved massively (manual intervention in coot was absolutely
necessary, but now it stays correct after I manually fix the problems),
clashscore lowered, etc.

As a side note, it worked better without hydrogens in my case than with. It
is certainly a parameter to try if you are having problems.

Thank you all again for the tips.

Mario Sanches

Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
M5G 1X5
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