[phenixbb] How to get a statistics of sidechain&mainchain Bfactors?

Pavel Afonine pafonine at lbl.gov
Wed Jan 5 15:36:30 PST 2011

  Hi Yuan,

>    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 
like this:

       ADP (min,max,mean):
         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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