<div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 25, 2012 at 9:36 AM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">1. If you take the final refined structure and refine against the<br>
original anisotropic data, does the geometry go bad again? It would<br>
be interesting to know if fixing the anisotropy fixed the problem, or<br>
fixing the anisotropy improved the maps so you could see the problem<br>
and fix it in coot.<br></blockquote><div><br></div><div><br></div><div>I didn't do this test, but it is simple enough. I will run it latter.</div><div>�</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
2. When you deposit the structure in the PDB, will you supply the<br>
anisotropy-corrected data, or the original raw data?<br></blockquote><div><br></div><div>That is a really good question. Is there any�recommendation�from the PDB regarding that? I tend to think that both should be available, since one is the raw data, and the other is the data the structure was refined against.�</div>
<div>�</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
eab<br>
<br>
Mario Sanches wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Last week I asked a question about geometry restraints at low<br>
resolution. I would like to thank you all that took the time to answer,<br>
specially Pavel for looking at the data. First, here is the original<br>
question:<br>
<br>
<br>
______________________________<u></u>____________<br>
I am refining a low resolution structure (2.9A) using phenix.refine. As<br>
I continue the refinement �Rwork/Rfree are dropping but my �geometry<br>
statistics in general are very bad. My clashscore is getting worst and<br>
the RMS(angle) is really high. I have tried to play with the "wxc_scale"<br>
�parameter and also ran phenix selecting the "Optimize X-ray/ADP<br>
weight" option. All attempts end with a RMS(angle) of ~3.8 and a<br>
Clashscore of ~190.<br>
<br>
Is there a known procedure to deal with this? I feel that my geometry<br>
weighing term is too loose but I don't know exactly how to tighten it<br>
other than decreasing the wxc_scale parameter. I have gone and manually<br>
corrected bad positions before but given the low resolution nature of<br>
the structure the clashes tend to be reestablished during refinement.<br>
<br>
Thank you in advance for your help,<br>
______________________________<u></u>____________<br>
<br>
It turns out that the reason to my nightmares was a highly anisotropic<br>
dataset. When I tried to fix geometry related problems in coot,<br>
phenix.refine was twisting the geometry back again, probably because it<br>
was trying to fit a lot of noise due to the anisotropy. Everything was<br>
getting worst, geometry, clashscore, and Ramachandran.<br>
<br>
Pavel finally corrected it by using this server:<br>
<a href="http://services.mbi.ucla.edu/anisoscale/" target="_blank">http://services.mbi.ucla.edu/<u></u>anisoscale/</a> �I should have been more<br>
diligent regarding that, since I could clearly see that my data was<br>
anisotropic from the diffraction images. I just didn't know how<br>
important this parameter could be. Anyways, phenix.xtriage will tell you<br>
if your data is anisotropic. The lesson is to pay attention to it.<br>
<br>
In my case, the quality of the electron density improved considerably,<br>
the geometry improved massively (manual intervention in coot was<br>
absolutely necessary, but now it stays correct after I manually fix the<br>
problems), clashscore lowered, etc.<br>
<br>
As a side note, it worked better without hydrogens in my case than with.<br>
It is certainly a parameter to try if you are having problems.<br>
<br>
Thank you all again for the tips.<br>
<br>
Mario Sanches<br>
<br>
<br>
<br>
<br>
<br>
--<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/<u></u>mariosanches</a><br>
<br>
<br>
<br></div></div>
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</blockquote>
<br>
</blockquote></div><br><br clear="all"><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>
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