<!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 Jonathan,<br>
<br>
currently it's not possible (if I correctly understand what you are
trying to do), but it will be available (hopefully) in the next version.<br>
<br>
Pavel.<br>
<br>
On 11/11/2008 3:13 AM, Jonathan Elegheert wrote:
<blockquote cite="mid:491968E3.3050908@ugent.be" type="cite">Hi Pavel,
<br>
<br>
Actually, I have 2 practical problems (see attachment) which I haven't
been able to deal with so far using phenix.refine (latest version).
<br>
<br>
Ligand A shows 2 stacking modes (A1 and A2) above an FMN cofactor. The
A2 conformation also overlaps partially with another partially occupied
ligand B. How do I couple the occupancy refinements of these
interrelated ligands? Until now, I solved it by refining the occupancy
as if ligand A has 3 modes; A1, A2 and A3 (= B). Otherwise, ligand B is
always pushed out of its density due to the anti-bumping restraints.
This is high res data (~1.5 A), so pretty decisive about atomic
positions.
<br>
<br>
The same question goes for the coupling of conformation C1 of an Ile
residue and water D on one hand, and conformation C2 of that Ile on the
other hand.
<br>
<br>
Thus far I've only been able to define these relations in SHELXL, but
it's not entirely clear to me how to do this in phenix.refine (which I
prefer for this dataset).
<br>
<br>
Many thanks in advance,
<br>
<br>
Jonathan Elegheert
<br>
PhD Student
<br>
L-ProBE, Ghent University
<br>
Belgium
<br>
<br>
Pavel Afonine wrote:
<br>
<blockquote type="cite">Ralf,
<br>
<br>
it's not that uncommon. See for example:
<br>
<a class="moz-txt-link-freetext" href="http://www.rcsb.org/pdb/files/1ejg.pdb">http://www.rcsb.org/pdb/files/1ejg.pdb</a>
<br>
<br>
Also, you may want to couple partially occupied residue's side chain
with partially occupied water.
<br>
<br>
Pavel.
<br>
<br>
<br>
On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote:
<br>
<blockquote type="cite">Hi Tassos,
<br>
<br>
<blockquote type="cite">However, I want to refine my MET residues
in double conformations, one
<br>
as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
<br>
to start with.
<br>
</blockquote>
<br>
In addition to what Pavel wrote: I just tried out the AMET BMSE mix
<br>
without giving any manual atom selections, and it works fine for me.
<br>
(P.S.: I'm thrilled to see this use of the
<br>
multiple-conformers-with-mixed-residue-names feature,
<br>
since it was a lot of work.)
<br>
<br>
Ralf
<br>
_______________________________________________
<br>
phenixbb mailing list
<br>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
<br>
</blockquote>
------------------------------------------------------------------------
<br>
<br>
_______________________________________________
<br>
phenixbb mailing list
<br>
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
<br>
</blockquote>
<br>
<hr size="4" width="90%"><br>
<center><img src="cid:part1.07060607.00070701@lbl.gov"></center>
<p><br>
</p>
<hr size="4" width="90%"><br>
<center><img src="cid:part2.03020906.09060808@lbl.gov"></center>
<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>