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Hi Patrick,<br>
<br>
I think I have an answer for you (at least partial)...<br>
<br>
In your refinement run you do refinement of only group B-factors:
strategy=group_adp<br>
so the parameter wxc_scale=0.??? (which is used in restrained
individual coordinate refinement) is not used.<br>
<br>
Did you try to run it with the default strategy and using
"optimize_wxc=true optimize_wxu=true". It may take sometime (depending
on the size of your structure) but it is likely to give you the best
result. Alternatively, you can specify your own numbers for wxc_scale
and/or wxu_scale but make sure that you actually asked phenix.refine to
do refinement of individual coordinates and/or individual ADPs (by
making sure that individual_sites and/or individual_adp are in the
"strategy"). <br>
<br>
Please let me know if you have any other questions or problems!<br>
Pavel.<br>
<br>
PS> By default, phenix.refine refines individual coordinates and
B-factors, and occupancies of atoms in alternative conformations or
those having partial occupancies in input PDB file.<br>
<br>
<br>
<br>
<br>
On 7/10/09 1:43 PM, Patrick Loll wrote:
<blockquote cite="mid:B45D642B-C5F2-4F5F-A4F1-05318CFD8FC2@drexel.edu"
type="cite">Hi,
<div><br>
</div>
<div>I'm a little baffled. We have a 3 Å structure, and while the R
values seem OK, I'd like to tighten up the rmsd values for the
geometry. However, altering wxc_scale seems to have no effect.</div>
<div><br>
</div>
<div>Specifics: In a clean directory, I run the following command</div>
<div><br>
</div>
<div>phenix.refine X.mtz Y.pdb Z1.cif Z2.cif Z3.cif wxc_scale=0.???
strategy=group_adp (the cif files are libraries for different
ligands)</div>
<div><br>
</div>
<div>When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't
change at all, which makes no sense to me:</div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="Courier">For wxc_scale=0.5
r_work = 0.2672 r_free = 0.2900 bonds = 0.028 angles = 3.151</font></div>
<div>
<div><font class="Apple-style-span" face="Courier">For
wxc_scale=0.05 r_work = 0.2672 r_free = 0.2900 bonds = 0.028
angles = 3.151</font></div>
<div>
<div><font class="Apple-style-span" face="Courier">For
wxc_scale=0.005 r_work = 0.2672 r_free = 0.2900 bonds = 0.028
angles = 3.151</font></div>
<div><br>
</div>
</div>
<div>...you get the idea. </div>
</div>
<div><br>
</div>
<div>These were run with phenix-1.4-3. With phenix-1.4-56, we get
subtly different r values, but the bonds and angles numbers are the
same as shown above (to 3 decimal places!), and the numbers don't
change upon changing wxc_scale.</div>
<div><br>
</div>
<div>Am I missing something here? Is there a better way to tighten up
the geometry?</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Pat</div>
</div>
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<br>
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