[phenixbb] tightening geometry

Patrick Loll pat.loll at drexel.edu
Fri Jul 10 13:43:01 PDT 2009


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  

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  


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

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