[phenixbb] tools to obtain ADP?

Pavel Afonine pafonine at lbl.gov
Wed Apr 6 11:15:23 PDT 2011

Hi Jason,

> Is there a convenient tool to obtain ADP for each chain or ligand or a 
> selective group?
> phenix.model_vs_data only gives an averaged ADP for everything and it 
> takes really long. Thanks.

phenix.pdbtools model.pdb --show-adp-statistics

will show you more detailed (in some sense) ADP statistics. However, it 
will not distinguish chains, etc.

If you want this statistics available per selected atoms (like chains), 
then it will take two steps:

1) Make a PDB file with atoms in question:

phenix.pdbtools model.pdb keep="chain A and resseq 1:100"

2) Compute B-factor statistics for the new file obtained at step "1":

phenix.pdbtools model_new.pdb --show-adp-statistics

I will add more functionality to phenix.pdbtools so in future it will do 
it all in one go.


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