[phenixbb] tools to obtain ADP?
phenix.upitt at gmail.com
Wed Apr 6 11:45:16 PDT 2011
It sounds doable. One minor point is that for ligand, phenix.pdbtools needs
restrain file. For ADP statistics, it seems asking a bit too much.
On Wed, Apr 6, 2011 at 2:15 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
Structural Biology Department
University of Pittsburgh
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