<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Jason,<br>
<br>
<blockquote
cite="mid:OF13E9A7F8.6B958B9D-ON86257706.00141F5F-86257706.00141F65@unmc.edu"
type="cite"><font
face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<div>Just a thought, but running the default "phenix.refine" command
is going to refine individual atomic coordinates and ADPs, unless you
specify otherwise. </div>
</font></blockquote>
<br>
where ADPs can be refined as individual isotropic or individual
anisotropic. Plus, it will refined occupancies in some cases:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm#anch20">http://www.phenix-online.org/documentation/refinement.htm#anch20</a><br>
<br>
<blockquote
cite="mid:OF13E9A7F8.6B958B9D-ON86257706.00141F5F-86257706.00141F65@unmc.edu"
type="cite"><font
face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<div>At 3.3A are you sure you have enough data to model all of these
parameters? </div>
</font></blockquote>
<br>
Most of the time at 3.3A you can refine individual ADPs and
coordinates. Just use tighter restraints. Of course it's case dependent
and in each case you need to see what would work best.<br>
<br>
<blockquote
cite="mid:OF13E9A7F8.6B958B9D-ON86257706.00141F5F-86257706.00141F65@unmc.edu"
type="cite"><font
face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<div>Even with heavy restraints, i'm not sure individual coordinate
refinement is feasible. </div>
</font></blockquote>
<br>
Why? I've see such a case only once, when refining against 60% complete
neutron data at 3A resolution where the model contained all H/D
explicitly present (not riding) -:)<br>
<br>
<blockquote
cite="mid:OF13E9A7F8.6B958B9D-ON86257706.00141F5F-86257706.00141F65@unmc.edu"
type="cite"><font
face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size="2">
<div>Perhaps doing a rigid-body refinement of multiple groups with
grouped ADPs would yield better results. You could even model in TLS
groups. <br>
</div>
</font></blockquote>
<br>
It is always good to use TLS, at 1.7A or at 6A resolution (slides
30-36):<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf">http://www.phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf</a><br>
<br>
<font size="2"><font
face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif">Pavel.<br>
<br>
</font></font>
</body>
</html>