[phenixbb] [EXTERNAL] Quick calculation of mean ADP

Mooers, Blaine H.M. (HSC) Blaine-Mooers at ouhsc.edu
Tue Jun 1 07:06:14 PDT 2021

Hi Martin,

How would you calculate the mean anisotropic ADP? 
What would be its meaning physically?

As you may know, the Beq is already on the line above the Uijs in the PDB file. 
It is derived from the trace of the tensor of U^(ij)s.
The Beq = 8*pi^2Ueq  where Ueq = 1/3(U^(11) + U^(22) + U^(33))

To obtain the mean Beq, use the following Python code.

from iotbx import pdb
pdb_name = '~/Downloads/4RBQ.pdb'
pdb_inp = pdb.input(file_name=pdb_name)
atoms = pdb_inp.atoms()
bfactors = atoms.extract_b()
bfactors.format_mean("%5.2f Ang.^2")

The answer in this case is

'18.17 Ang.^2'

To extract the Uijs, use the following,

uijs = atoms.extract_uij()

Best regards,


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology, College of Medicine
Director of the Laboratory of Biomolecular Structure and Function
Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
Full Member, Cancer Biology Program, Stephenson Cancer Center
University of Oklahoma Health Sciences Center

Mailing Address:
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Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd
BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Martin Malý [martin.maly at ibt.cas.cz]
Sent: Tuesday, June 01, 2021 5:18 AM
To: phenixbb at phenix-online.org
Subject: [EXTERNAL] [phenixbb] Quick calculation of mean ADP

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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