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 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: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: 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-Struct... COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________________ From: [email protected] [[email protected]] on behalf of Martin Malý [[email protected]] Sent: Tuesday, June 01, 2021 5:18 AM To: [email protected] 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 ----- 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 [email protected] https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=DwIFBA&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=1QGZYVikGjURCJB_X5MzJDwJSQscFjQgZGWdrXuUDIk&s=wsfyjeYLYxStJAcVxhI9dyM3kzslY5zJWu34udF9y9E&e= Unsubscribe: [email protected]