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(a)drexelmed.edu
