B-iso vs. B-aniso
Dear community, The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set. However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors? Any thoughts/opinions/call-outs from the community are welcome. Cheers, -- Yuri Pompeu
Dear community,
The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to
skuld.bmsc.washington.edu/~tlsmd/ActaD_68_468.pdf may be of interest properly refine it
anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set.
However, I have had a couple of cases where anisotropic B-factor
reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling
refinement significantly improved R-work and R-free, while maintaining a the B-factors?
Any thoughts/opinions/call-outs from the community are welcome. Cheers, -- Yuri Pompeu _______________________________________________
phenixbb mailing list
http://phenix-online.org/mailman/listinfo/phenixbb
-- Edwin Pozharski, PhD University of Maryland, Baltimore
On Mon, Sep 17, 2012 at 11:12 AM, Yuri
However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors?
I have also seen the anisotropic refinement work very well at this resolution, but there are certainly exceptions. Pavel has recommended that you leave the waters isotropic until about 1.2A, however (there are shortcuts for setting the selections for this and other common scenarios in the GUI). At any rate, if you really want to be certain, don't think there's any substitute for running the refinement both ways, isotropic and anisotropic, and seeing which works best. There are probably different opinions on how to judge whether anisotropic refinement is justified, but R-free should drop by at least 0.5%, and 1% is probably a more rigorous cutoff. One of the recent PDB-REDO papers had a description of their decision-making process for this, which I thought seemed sensible (they're using REFMAC, not Phenix, but the principle is the same in either case). -Nat
Hi Yuri,
The protein model I am refining has 400 amino acids (3320 atoms). Some real quick calculations tell me that to properly refine it anisotropically, I would need 119,520 observations. Given my unit-cell dimension and space-group it is equivalent to about a 1.24 A complete data set.
interesting how you managed to do this... In any case this number is likely to be useless as refinement target uses both, X-ray term and restraints accounted with some weight. There are various rules of thumb that are typically specific to refinement programs you use.. Depending on data and model quality you can refine all non-solvent atoms with anisotropic ADPs starting from about 1.7-1.5A and higher. At about 1.2A and higher you can refine solvent with anisotropic ADPs as well. Again, data quality and where you currently are with refinement is important.
However, I have had a couple of cases where anisotropic B-factor refinement significantly improved R-work and R-free, while maintaining a reasonable R-gap, for lower resolution models (1.4-1.5 A, around 70,000 reflections). What is the proper way of modelling the B-factors?
Try the above rules of thumb and see what pleases the R-factors (both, work, free and gap) and makes sensible ADPs. In gray areas, like "1.7A resolution great data" or "1.4A heavily incomplete data" try multiple plausible options. That's the most robust way to find the answer. Pavel
participants (4)
-
Edwin Pozharski -
Nathaniel Echols -
Pavel Afonine -
Yuri