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:
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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
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,
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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
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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