[phenixbb] Quick calculation of mean ADP

[Dorothee Liebschner]

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:
http://cci.lbl.gov/docs/cctbx/

Let us know if you have other questions.

Best wishes,

Dorothee


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
> -----
>
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-- 
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
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