<!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 Hena,<br>
<br>
1) refining group B-factor (one refinable B per group of atoms),
phenix.refine does not change the mutual distribution of B-factors
within the group. For example, if the original B-factors in the
group were<br>
<br>
10,20,30,40<br>
<br>
after the group B-factor refinement they can be<br>
<br>
10+b,20+b,30+b,40+b<br>
<br>
where b is refinable parameter that can be any number that
phenix.refine comes up with.<br>
<br>
2) If you really want the B-factor to be all the same, then you need
to reset them first to some meaningful number, say Wilson B or
average B:<br>
<br>
phenix.pdbtools model.pdb set_b_iso=50<br>
<br>
then do refinement.<br>
<br>
3) Note, that the default is<br>
<br>
group_adp_refinement_mode = *one_adp_group_per_residue \<br>
two_adp_groups_per_residue
group_selection<br>
<br>
and if you change it to<br>
<br>
group_adp_refinement_mode = one_adp_group_per_residue \<br>
*two_adp_groups_per_residue
group_selection<br>
<br>
phenix.refine will refine two B-factors per residue: one for side-
and one for main-chain atoms of the residue.<br>
<br>
4) For more details, see "On atomic displacement parameters..."
article here:<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/newsletter/CCN_2010_07.pdf">http://www.phenix-online.org/newsletter/CCN_2010_07.pdf</a><br>
<br>
5) In my experience highly restrained refinement of individual ADPs
works almost always better than any of the group B refinement
options mentioned above. phenix.refine uses unique type of
restraints for individual isotropic B refinement that we introduced
back in 2005: see above article for details.<br>
<br>
Pavel.<br>
<br>
On 7/15/11 12:17 PM, Hena Dutta wrote:
<blockquote
cite="mid:CAH9JkpRg_jE035Z_EGUy43B3rXKW2M_sHPheq=md7VvG8TbLdA@mail.gmail.com"
type="cite">Hi,<br>
I was trying to get one ADP per residue using the command as
suggested in the PHENIX document:<br>
<br>
<p class="first"><strong>Refining group isotropic B-factors</strong>
</p>
<p class="first">One B-factor per residue:
</p>
<pre class="literal-block">% phenix.refine data.hkl model.pdb strategy=group_adp
See a part of my out pdb file (column 11):
ATOM 6971 C2 ADE F 15 -29.960 -20.547 -31.167 1.00 23.82 F C
ATOM 6972 N1 ADE F 15 -30.382 -20.054 -32.336 1.00 24.20 F N
ATOM 6973 C6 ADE F 15 -30.077 -20.702 -33.471 1.00 21.52 F C
ATOM 6974 N6 ADE F 15 -30.496 -20.192 -34.629 1.00 20.08 F N
ATOM 6975 C5 ADE F 15 -29.321 -21.893 -33.361 1.00 21.08 F C
ATOM 6976 N7 ADE F 15 -28.823 -22.777 -34.307 1.00 22.85 F N
ATOM 6977 C8 ADE F 15 -28.193 -23.670 -33.593 1.00 21.80 F C
ATOM 6978 C2' ADE F 15 -27.648 -25.781 -31.357 1.00 22.11 F C
But, I got different temperature factors for different atoms in the same residue. Is that what I should get? How can I create one
temperature factor for each residue?
Regards...
Hena
</pre>
<br>
<br>
<div class="gmail_quote">On Thu, May 26, 2011 at 11:05 AM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000"> Hi Christian,<br>
<br>
the problem is that you did not ask phenix.refine to refine
the rest of the atoms isotropically (with your command below
you only refine anisotropic ADPs of atoms in chain Q, and
the B-factors of all the other atoms are not refined):<br>
<br>
<blockquote type="cite">
<div style="font-family: -moz-fixed; font-size: 12px;"
lang="x-unicode">
<pre> adp {
individual {
anisotropic = "chain Q"
}</pre>
</div>
</blockquote>
<br>
I would do it like this:<br>
<br>
adp {<br>
individual {<br>
anisotropic = chain Q and element CL<br>
isotropic = not (chain Q and element CL)<br>
}<br>
}<br>
<br>
Pavel.<br>
<br>
</div>
<br>
_______________________________________________<br>
phenixbb mailing list<br>
<a moz-do-not-send="true"
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a moz-do-not-send="true"
href="http://phenix-online.org/mailman/listinfo/phenixbb"
target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br>
</blockquote>
</div>
<br>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
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>
</pre>
</blockquote>
<br>
</body>
</html>