[phenixbb] Quick calculation of mean ADP

Dorothee Liebschner dcliebschner at lbl.gov
Tue Jun 1 11:11:24 PDT 2021

Hi Martin,

You could run the command line tool

phenix.b_factor_statistics model.pdb
to print information in standard output.

Or you can use a python script. I wrote a quick example (attached).
Run it like this:

python run_average_b.py model.pdb

Have a look at the cctbx documentation to see some cctbx example scripts:

Let us know if you have other questions.

Best wishes,


On Tue, Jun 1, 2021 at 3:21 AM Martin Malý <martin.maly at ibt.cas.cz> wrote:

> Dear mailing list members,
> I would like to calculate the mean ADP of a structure model (PDB) from a
> Python script using tools in CCTBX/PHENIX. I tried to find out how and
> dig it from Python source code but I have been unsuccessful yet. Please,
> how to do it (in Python)? Although It is quite easy to calculate it in
> on my own directly from PDB for isotropic ADPs, the situation can be a
> bit complicated for anisotropic ADPs...
> Thank you. Best regards,
> Martin Mal
> -----
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato
> e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato
> zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v.
> i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na
> uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani
> jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá
> předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i.
> Disclaimer: If not expressly stated otherwise, this e-mail message
> (including any attached files) is intended purely for informational
> purposes and does not represent a binding agreement on the part of
> Institute of Biotechnology of the Czech Academy of Sciences. The text of
> this message and its attachments cannot be considered as a proposal to
> conclude a contract, nor the acceptance of a proposal to conclude a
> contract, nor any other legal act leading to concluding any contract, nor
> does it create any pre-contractual liability on the part of Institute of
> Biotechnology of the Czech Academy of Sciences.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210601/ce8c5796/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: run_average_b.py
Type: text/x-python-script
Size: 977 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20210601/ce8c5796/attachment.bin>

More information about the phenixbb mailing list