<div>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:</div>
<div><br></div><div><br></div><div>__________________________________________</div>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. <div>
<br></div><div>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. </div>
<div><br></div><div>Thank you in advance for your help,</div><div>__________________________________________</div><div><br></div><div>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. </div>
<div><br></div><div>Pavel finally corrected it by using this server: <a href="http://services.mbi.ucla.edu/anisoscale/" target="_blank">http://services.mbi.ucla.edu/anisoscale/</a> 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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>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. </div><div><br></div><div>Thank you all again for the tips. </div>
<div><br></div><div>Mario Sanches</div><div><br></div><div><br></div><div><br></div><div><br>
</div><div><br></div>-- <br>Mario Sanches<br>Postdoctoral Researcher<br>Samuel Lunenfeld Research Institute<br>Mount Sinai Hospital<br>600 University Ave<br>Toronto - Ontario<br>
Canada<br>M5G 1X5<br><a href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>