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
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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
[email protected] mailto:[email protected]
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