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<p>Hi Pavel,</p>
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<p>Thanks so much for your reply. Following your suggestion, I could apply "<span style="font-size: 12pt;">reference_coordinate_restraints" section from <a href="http://www.phenix-online.org/documentation/reference/real_space_refine.html" class="OWAAutoLink" id="LPlnk480349" previewremoved="true">http://www.phenix-online.org/documentation/reference/real_space_refine.html</a> and
it seems to be working perfect for me. </span> </p>
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<p>Regarding why do I like to keep some part fixed: In my cryo-EM density some parts are not resolved due to flexibility and I had to manually build models after low pass filtering the density. Because I still don't have suitable restraints in those parts,
a real space refinement is making the models go haywire. So, for the time being, I wanted to keep those difficult regions fixed. </p>
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<p style="color:rgb(0,0,0)">Best regards,</p>
<p style="color:rgb(0,0,0)">Tofayel</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Pavel Afonine <pafonine@lbl.gov><br>
<b>Sent:</b> Tuesday, November 29, 2016 10:46:11 PM<br>
<b>To:</b> #AHMED TOFAYEL#; PHENIX user mailing list<br>
<b>Cc:</b> Pavel Afonine<br>
<b>Subject:</b> Re: [phenixbb] Refine only selective chains in a complex using phenix.real_space_refine</font>
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<div>Hi Tofayel,<br>
<br>
<blockquote cite="mid:PS1PR01MB076418386ED86551DAAD304DE38D0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com" type="cite">
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Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex.
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no, sorry. Options:<br>
<br>
1) Create PDB file that contains only parts of the model that you want to refine and supply that to phenix.real_space_refine. This may work just fine but dangers are that refined part of the model may clash with the one that is not refined<br>
<br>
2) Refine entire model restraining positions of selected atoms to their initial coordinates.
<br>
<br>
<blockquote cite="mid:PS1PR01MB076418386ED86551DAAD304DE38D0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com" type="cite">
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During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line.
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I can see how this may be useful and I will add this functionality to phenix.real_space_refine.<br>
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Just out of curiosity: why you want to keep some parts of the model fixed?<br>
<br>
Pavel<br>
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