I am using a nightly build from around two weeks ago (dev-1021). I am sending you some files. <div>Thank you,</div><div><br></div><div>Mario Sanches<br><br><div class="gmail_quote">On Thu, Apr 19, 2012 at 8:42 AM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span> wrote:<br>
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Hi Mario,<br>
<br>
are you using the latest Phenix? If not, please update your version
of Phenix and try again:<br>
<br>
<a href="http://www.phenix-online.org/download/nightly_builds.cgi" target="_blank">http://www.phenix-online.org/download/nightly_builds.cgi</a><br>
<br>
If this doesn't help, please send me the data and model (offlist)
and I will have a look to see what's going on.<br>
<br>
Pavel<div><div class="h5"><br>
<br>
<br>
On 4/19/12 5:37 AM, Mario Sanches wrote:
</div></div><blockquote type="cite"><div><div class="h5">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,<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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<br>
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<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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