anisotropic ADP factor refinement and optimize_wxc
Dear All, I have just recently started using phenix.refine and I hope I can get some advice. I am trying to refine my structure with anisotropic ADP factors while also optimizing the weighting parameters.When I give the following command, anisotropic refinement is carried out but optimization is not carried out as far as I can see (ie the rms bond and angles are not reduced, which is one of my concerns at the moment). phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true strategy=individual_adp adp.individual.anisotropic="not element H" optimize_wxc=true --overwrite pdb output values REMARK Start: r_work = 0.1952 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1413 r_free = 0.2448 bonds = 0.015 angles = 1.646 If I give the following command, optimization occurs and rms bond and angle values decrease. phenix.refine protein1.pdb 072109checks.mtz optimize_wxc=true --overwrite REMARK Start: r_work = 0.2048 r_free = 0.2388 bonds = 0.015 angles = 1.646 REMARK Final: r_work = 0.1917 r_free = 0.2352 bonds = 0.009 angles = 1.301 Is it possible to refine both anisotropic B factors and optimize ADP factors in the same run. Any advice would be great. Thanks, Gordon
Hi Gordon, the target for ADP (B-factor) refinement is : T = wxu * wxu_scale * Txray + wu * Tadp and the target for coordinate refinement is: T = wxc * wxc_scale * Txray + wc * Tstereochemistry . The weights wxc (wxu) are determined automatically (similarly to CNS) as described in: Adams, P.D., Pannu, N.S., Read, R.J. & Brünger, A.T. (1997). Proc. Natl. Acad. Sci. 94, 5018-5023; the weight scale wxc_scale (wxu_scale) is 0.5 or 1.0 and the user can adjust it, wc (wu) = 1 (and the only purpose of it is to be able to turn off the restraints), Txray is x-ray target function (maximum-likelihood, least-squares, mlhl, ...), and Tadp (Tstereochemistry) is restraints term. When you use "optimize_wxc=true" you optimize weights for coordinate refinement, and to do similar thing for ADP refinement you need to use "optimize_wxu=true".
phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true strategy=individual_adp adp.individual.anisotropic="not element H" optimize_wxc=true --overwrite
This command above refines only anisotropic B-factors of non-H atoms, while the coordinates are not refined at all, and therefore the statement "optimize_wxc=true" is not used. I guess what you really meant is: phenix.refine protein1.pdb 072109checks.mtz ordered_solvent=true adp.individual.anisotropic="not element H" adp.individual.isotropic="element H" optimize_wxc=true optimize_wxu=true --overwrite By the way, what is the resolution of the data? If the geometry is still not good (it's another page to write to describe why it is potentially possible), then instead of using "optimize_wxc=true" try manually set up the weight putting less weight on X-ray term: use wxc_scale=XXX for this, where XXX is a value less than the default one (0.5). Say, try 0.2, 0.1, etc.
Is it possible to refine both anisotropic B factors and optimize ADP factors in the same run.
Yes. You can refine any set of parameters for any selected part of your structure in any combination. If it is still not clear, please fell free to send me the model and data and I will get back to you with the optimal refinement strategy that you can use in future as the example. Cheers, Pavel.
I have just recently started using phenix.refine
In this case you may find it helpful to have a look at this: http://phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1... which may give some overview of how things are working under the hood. Pavel.
participants (2)
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Joyce, Gordon M. (NIH/NIAID) [F] -
Pavel Afonine