[phenixbb] Geometry Restraints - UPDATE

Mario Sanches mariosan at gmail.com
Wed Apr 25 06:39:40 PDT 2012

On Wed, Apr 25, 2012 at 9:36 AM, Edward A. Berry <BerryE at upstate.edu> wrote:

> 1. If you take the final refined structure and refine against the
> original anisotropic data, does the geometry go bad again? It would
> be interesting to know if fixing the anisotropy fixed the problem, or
> fixing the anisotropy improved the maps so you could see the problem
> and fix it in coot.

I didn't do this test, but it is simple enough. I will run it latter.

> 2. When you deposit the structure in the PDB, will you supply the
> anisotropy-corrected data, or the original raw data?

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.

> eab
> Mario Sanches wrote:
>> 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 ~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,
>> ______________________________**____________
>> 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/<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
>> Canada
>> M5G 1X5
>> http://ca.linkedin.com/in/**mariosanches<http://ca.linkedin.com/in/mariosanches>
>> ______________________________**_________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/**mailman/listinfo/phenixbb<http://phenix-online.org/mailman/listinfo/phenixbb>

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