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

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