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Ok, in this case I need to look at the files ...<br>
<br>
Pavel<br>
<br>
On 4/19/12 5:46 AM, Mario Sanches wrote:
<blockquote
cite="mid:CAHBaby7=Z=0WGdc+5Uy5HSp_DLiJZPgtiFMOFp7R1pSu23gM+g@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Mario,<br>
<br>
are you using the latest Phenix? If not, please update
your version of Phenix and try again:<br>
<br>
<a moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://ca.linkedin.com/in/mariosanches"
target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
</div>
<br>
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<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 moz-do-not-send="true"
href="http://ca.linkedin.com/in/mariosanches" target="_blank">http://ca.linkedin.com/in/mariosanches</a><br>
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