Hi Patrick, I think I have an answer for you (at least partial)... In your refinement run you do refinement of only group B-factors: strategy=group_adp so the parameter wxc_scale=0.??? (which is used in restrained individual coordinate refinement) is not used. Did you try to run it with the default strategy and using "optimize_wxc=true optimize_wxu=true". It may take sometime (depending on the size of your structure) but it is likely to give you the best result. Alternatively, you can specify your own numbers for wxc_scale and/or wxu_scale but make sure that you actually asked phenix.refine to do refinement of individual coordinates and/or individual ADPs (by making sure that individual_sites and/or individual_adp are in the "strategy"). Please let me know if you have any other questions or problems! Pavel. PS> By default, phenix.refine refines individual coordinates and B-factors, and occupancies of atoms in alternative conformations or those having partial occupancies in input PDB file. 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

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