<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Vikram,<br>
<br>
you asked this or very similar question the other day and I replied
on 1/7/17, 08:07. Repeating:<br>
<br>
"""<br>
set nqh_flips=False or disable real-space refinement. That will stop
flips from happening.
<br>
<br>
I'd like to address this issue in phenix.refine centrally, so these
unwanted flips do not happen. For this it would be helpful to have
an example. Could you please send me model files before and after
refinement and the data file, and also tell what His flips?<br>
"""<br>
<br>
Excluding atoms from refinement:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates">http://phenix-online.org/documentation/reference/refinement.html#refinement-of-coordinates</a><br>
which is really the last resort.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 1/19/17 02:36, Vikram Dalal wrote:<br>
</div>
<blockquote
cite="mid:CAJ1_RsybYjQ94sZD0GORGrT0rqcD6mmvUbkjt-npYKFneqKvtg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi all,
<div><br>
</div>
<div><span style="font-size:12.8px">�I have 4 Mn (2 Mn in each
chain) in my protein structure. One Mn has 1 cordination
with water, 1 cordination with His and 4 cordination with
Asp. I model build the His in coot. Even this His is in bond
range with Mn. But, when i refine this model in phenix. This
His again flip other side (N terminal which has to cordinate
with Mn goes to other direction). I am facing this problem
only with His of A chain only while N of His of B chain are
towards Mn only.�</span>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px">Is there any option in pehnix
refinment where we can exclude a specific residue or atom in
refinment??�</div>
<div style="font-size:12.8px"><br>
</div>
<div style="font-size:12.8px"><br>
</div>
<div>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><br>
<br>
<b
style="margin:0px;padding:0px;word-wrap:break-word"><br>
</b></div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<br>
<br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
Unsubscribe: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.org</a></pre>
</blockquote>
<br>
</body>
</html>