<!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 Daqi,<br>
<br>
<blockquote cite="mid:A920027B10F94065935FEF805363412A@daqiHP"
type="cite">
<div><font face="Calibri">I refined my structure (of which the data
is very anisotropic) using phenix.refine and with individual_sites,
individual_adp, and tls options turned on. From the refined
coordinates, the highest B-factor in the ANISO record (ie B_tls +
B_individual) is 305. This number looks rather high. Is it something
I should worry about? and is there an easy way to compute the
individual B-factor component?</font></div>
</blockquote>
<br>
- what is "high", what is "low", what is "acceptably high",... ? This
was discussed many times on both phenixbb and ccp4bb.<br>
<br>
- you can use phenix.tls <br>
For usage information just type phenix.tls and hit Enter, then read
message output to the screen.<br>
Using this command you can go back and forth between total and local
B-factors, as defined here:<br>
<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>
see slides #30-36.<br>
<br>
Note 1) going from individual components Utls, Uatom to Utotal is the
exact operation (numbers are computed exactly by the formula), while
going back: splitting Utotal into Utls and Uatom is an approximate
operation, since Utls is obtained as a least-squares fit of Utls to
Utotal (Utls_fit), and the Uatom then is Utotal - Utls_fit.<br>
<br>
Note 2) Uatom may be positive as well as negative or zero.<br>
<br>
Please let me know if you have any questions or need help with this.<br>
<br>
Pavel.<br>
<br>
</body>
</html>