<!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 Christina,<br>
<br>
I usually observe similar R/Rfree behavior when I use LS target instead
of maximum-likelihood. In fact, twin refinement in phenix.refine is
based on LS target function. This is just to share my observations;
it's not necessarily happening in your case.<br>
<br>
- How many of test reflections you have and how they are distributed in
resolution bins?<br>
- Just out of curiosity: did you try to ignore twinning and run
refinement with default target?<br>
- What if you don't run SA?<br>
- Did you try to play with target weights (try different values for
wxc_scale and wxu_scale) to see how this affect the R-factors?<br>
- Are you using the latest (or one of) phenix.refine?<br>
- Did you try to fill in water?<br>
<br>
Could you send a log file: may be we could spot something outstanding...<br>
<br>
Pavel.<br>
<br>
<br>
On 5/19/2008 1:32 PM, Christina Bourne wrote:
<blockquote cite="mid:172216.2237.qm@web30508.mail.mud.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div
style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div>Hello BB,</div>
<div>I am working on a structure that is twinned (merohedral) in
P41. Initial estimates of twinning fraction (via xtriage and Yeates
server) are around 0.37; in refinement they start around 0.49 and drop
to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per
AU; this gives good packing with no room for another mol. I have data
from 48-2.8A.</div>
<div>I should mention that data processing wasn't easy- this crystal
form also has an apparent epitaxial twin in the b dimension causing a
doubling in that dimension. During indexing (with SAINT) I applied a
transformation of 100 00.50 001 to the reflections, which then gave me
the expected cell and from Xprep the data looks OK. (Yes, I am trying
to grow different forms)</div>
<div>Maps look nice, although I wish my ligand had more/better
density.</div>
<div> </div>
<div>I ran phenix.refine with defaults, and included
twin_law="h,-k,-l", xray_data.r_free_flags.generate=true,
detwin.map_types.aniso_correct=true and also simulated_annealing=true.
My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270.
Geometry is somewhat tighter after refinement but is better (bonds
0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand,
and I can see a few spots where the model needs adjusting, but nothing
majorly wrong.</div>
<div> </div>
<div>Why is my Rfree hanging so high? Is it becaues I have bad
karma? Is it to do with the twinning? I am pretty sure my space group
is right (based on the above info and the maps look fine; Phaser could
not find a solution in P43). There isn't room for anything else in the
cell.</div>
<div> </div>
<div>Any opinions or suggestions are most welcome as I wait for
better xtals to grow...</div>
<div>Thanks in advance,</div>
<div>Christina</div>
</div>
<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>