[phenixbb] How to get a statistics of sidechain&mainchain Bfactors?
pafonine at lbl.gov
Wed Jan 5 15:36:30 PST 2011
> I used TLS+ADP refinement to get the final structure model, after
> that I used phenix.model_vs_data to get the statistics for table1.
> However there is no B factor statistics in the output.
- most of the necessary statistics is in phenix.refine .log file and in
PDB file header.
- phenix.model_vs_data reports pretty extended ADP statistics (for
macromolecule, solvent, ligands, etc..). For example, it has something
all (136 atoms): 4.4 44.1 10.9
side chains (48 atoms): 4.8 23.0 9.5
main chains (64 atoms): 4.4 9.8 6.4
macromolecule (112 atoms): 4.4 23.0 7.7
ligands (1 atom): 6.6 6.6 6.6
solvent (23 atoms): 8.8 44.1 26.8
and if you don't see this then please make sure you are using a recent
PHENIX version (I added this at least 6 months ago).
What are the numbers you are looking for ?
> Can I get the overall B factor by just simply averaging the B factors
> of each residue in the output text?
> Then how can I get the B factor value of the sidechains and that of
> the mainchain?
You don't need to do all this since the existing tools do it all for you.
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