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Oh, I just saw, there is a Find NCS restraints automatically button
in the Refinement Settings tab. Make sure that it is checked off.<br>
<br>
Engin<br>
<br>
On 3/25/10 9:19 AM, Engin Ozkan wrote:
<blockquote cite="mid:4BAB8D13.10802@stanford.edu" type="cite">
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I remember this. At least from running phenix.refine on
command-line, there is a parameter called ncs.find_automatically.
It is "True" by default. I remember spending several days trying
to change the NCS selections, until I found about this parameter.
So, unless you change this parameter to "False", your input is
always written over. I am not sure where this might be in the GUI,
but it could be the culprit. To see if this is the case, in the
Refinement Settings tab, go to All Parameters -> View all
settings. There, check under parameters -> refinement ->
ncs. You can also find it in the refine_??.eff file, just search
for this parameter.<br>
<br>
Best,<br>
Engin<br>
<br>
<br>
On 3/25/10 3:58 AM, hari jayaram wrote:
<blockquote
cite="mid:aad3caa31003250358o2d9960e5w2f9d79c7414ab418@mail.gmail.com"
type="cite">Hi I am quite sure I am doing something wrong , but
the refinement seems to always re-determine the NCS definitions
despite it being set in the ncs.params file in the project
defaults directory.
<div><br>
</div>
<div>Here is what I did:</div>
<div><br>
</div>
<div>
<ol>
<li>I set the NCS groups definition in the GUI to go from
residues 35:445 , </li>
<li>I check that using the view pick . Everything looks
fine </li>
<li>I click the Green update and exit button</li>
<li> I look at the ncs.params file in the project defaults
directory and it indeed reflects the changes . </li>
<li>I start the refinement from the GUI and the ncs section
seems to have been reset to 26:450 . I even tried adding
the ncs.params file to the Input files section, but to no
avail. The ncs seems to always get re-determined and I end
up getting an excessive distance stoppage of refinement. I
even made sure I dont have the Find NCS restraints
automatically button checked.</li>
</ol>
<div><br>
</div>
<div>Any idea why I cannot get the gui run refinement to
remember my ncs definitions.</div>
<div><br>
</div>
<div>Thanks in advance</div>
<div>Hari</div>
<div><br>
</div>
</div>
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<br>
<pre class="moz-signature" cols="72">--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111</pre>
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<br>
<br>
<pre class="moz-signature" cols="72">--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111</pre>
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