<!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 Carsten,<br>
<br>
in phenix.refine H atoms are treated as a very special case (if you are
not refining a structure at 0.37A resolution or so).<br>
<br>
Here is what refined for hydrogens by default:<br>
<br>
hydrogens<br>
{<br>
refine_sites = individual *riding<br>
refine_adp = one_b_per_residue *one_b_per_molecule individual<br>
refine_occupancies = one_q_per_residue *one_q_per_molecule
individual<br>
contribute_to_f_calc = True<br>
}<br>
<br>
You can stop refining occupancies for H by using
"hydrogens.refine_occupancies=none", same for their B-factors, but I
would never do it.<br>
<br>
Pavel.<br>
<br>
<br>
On 3/4/2008 11:26 AM, Schubert, Carsten [PRDUS] wrote:
<blockquote
cite="mid:889E20E3723D0C45A493DA5DA87D854E01E8761A@JNJUSRAGMS02.na.jnj.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; ">
<meta name="Generator"
content="MS Exchange Server version 6.5.7653.12">
<title>Question about occupancy refinement of riding hydrogens</title>
<!-- Converted from text/rtf format -->
<p><font face="Arial">I just noticed that occupancies of riding
hydrogens are being refined by default, in fact I am unable to turn
this feature off (CCI-APPs from Jan-8). I was just (very naively)
wondering what is the rationale behind this? The B-factor refinement
for riding hydrogens is already enabled and should take care of this or
not? It looks a bit odd to have hydrogens with occupancy 0.9 sitting
on a carbon with occupancy 1.0 at 2.0 A resolution.</font></p>
<p><font face="Arial">Cheers</font>
</p>
<p> <font face="Arial">Carsten</font>
</p>
<br>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
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://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>