<div>Hi Pavel,</div>
<div>thanks a lot for your fast response!</div>
<div>Here some clarification:</div>
<div>- somehow, the adjustments of the B weights were not taken into account at all. Ie. a "diff" on the pdb-files from jobs run with wxu_scale=0.5 and wxu_scale=2.0 shows that they are identical. While the log file acknowledges the "Command line parameter definitions" for wxu_scale=1 and wxc_scale=2, during the refinement section it states that wxc_scale =
1.0 and wxu_scale=2.16.</div>
<div>- yes, I included a TLS refinement. Are TLS refinement ans wxu_scale mutually exclusive? How would one proceed in this situation?</div>
<div> </div>
<div>Cheers</div>
<div>Jan<br><br> </div>
<div><span class="gmail_quote">On 9/18/07, <b class="gmail_sendername">Pavel Afonine</b> <<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Jan,<br><br>> in the final stages of refining a structure, I would like to optimize<br>> the restraint weights for geometry and B factors.
<br><br>Good idea! Although phenix.refine computes "optimal" weight<br>automatically, the values vary from structure to structure.<br><br>> It seems to work fine for geometry by defining<br>> "refinement.target_weights.wxc_scale=1.0
".<br><br>Yes, I would try an array of values 0.25, 0.5, 1.0, 1.5, 2.0, 2.5.<br><br>> However, when the respective definition for B-factors does not seem to<br>> have an impact at all.<br><br>This is very weird. We exercise this in out tests regularly, so it
<br>changing wxu_scale should have an impact. It may be that values range<br>for you structure is somehow different... Can you try the extreme<br>values: very big (wxu_scale=10) and very small (wxu_scale=0.1) and see<br>if this makes a difference? Are you using TLS (if yes, then this
<br>behavior is explainable)?<br><br>> The main reason why I try to fiddle around with the B-weights is that<br>> coot gives me a whole bunch of red bars in the Temperature factor<br>> variance analysis...<br><br>
The variability of ADP depends on many factors: resolution, model used<br>for global motion (TLS), how internal degrees of freedom modeled ... I<br>do not know if Coot analysis takes this all into account. Otherwise I<br>
would use the "red bars" analysis with some care.<br><br>Pavel.<br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org
</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></div><br>