<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Tofayel,<br>
<br>
<blockquote
cite="mid:PS1PR01MB076418386ED86551DAAD304DE38D0@PS1PR01MB0764.apcprd01.prod.exchangelabs.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;"
dir="ltr">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. </div>
</blockquote>
<br>
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">
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;"
dir="ltr">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. <br>
</div>
</blockquote>
<br>
I can see how this may be useful and I will add this functionality
to phenix.real_space_refine.<br>
<br>
Just out of curiosity: why you want to keep some parts of the model
fixed?<br>
<br>
Pavel<br>
<br>
</body>
</html>