[phenixbb] tightening geometry

Engin Ozkan eozkan at stanford.edu
Fri Jul 10 14:10:24 PDT 2009


Dear Pat,

Your strategy says group_adp only.  So you are not refining coordinates, 
only grouped B factors.  That would explain your bond and angles are not 
changing.

Engin


On 7/10/09 1:43 PM, Patrick Loll wrote:
> Hi,
>
> 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.
>
> Specifics:  In a clean directory, I run the following command
>
> 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)
>
> When I vary wxc_scale from 0.5 to 0.005, the geometry doesn't change 
> at all, which makes no sense to me:
>
> For  wxc_scale=0.5       r_work = 0.2672 r_free = 0.2900 bonds = 0.028 
> angles = 3.151
> For  wxc_scale=0.05      r_work = 0.2672 r_free = 0.2900 bonds = 0.028 
> angles = 3.151
> For  wxc_scale=0.005     r_work = 0.2672 r_free = 0.2900 bonds = 0.028 
> angles = 3.151
>
> ...you get the idea.
>
> 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.
>
> Am I missing something here? Is there a better way to tighten up the 
> geometry?
>
> Thanks,
>
> Pat
>
> ---------------------------------------------------------------------------------------
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA 19102-1192 USA
>
>
> (215) 762-7706
>
> pat.loll at drexelmed.edu <mailto:pat.loll at drexelmed.edu>
>
>
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>
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-- 
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111




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