Re: [PyMOL] Renumber

[Oganesyan, V. <vah...@as...>]

Hi Annemarie,

Thank you for the offer. I was specifically interested in doing it PyMOL. It was my longtime firmly held belief and  I still do think that most of the PyMOL users are the biochemists that do not solve x-ray or EM structures. Hence the need to manipulate molecules, domains, numbering etc.

Regards,

Vaheh Oganesyan, Ph.D.
[cid:image001.png@01D643CA.48E859D0]
R&D | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-5851
Vah...@as...<mailto:Oga...@me...>



From: hon...@bi... <hon...@bi...>
Sent: Tuesday, June 16, 2020 1:42 AM
To: pym...@li...
Subject: Re: [PyMOL] Renumber



Hello Vaheh

Antibody structures are a mess to renumber, both due to the many different numbering schemes used in different structures, and to some older files not even adhering to pub standards, using the alternative localisation columns for the insertion letters specified by Kabat or Chothia nomenclature. That's why I titled my own contribution to the mess "Yet another numbering scheme ..."

https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats<https://www.researchgate.net/publication/2530255_Yet_Another_Numbering_Scheme_for_Immunoglobulin_Variable_Domains_An_Automatic_Modeling_and_Analysis_Tool/stats>

For mass renumbering of antibody variable domains, I actually use some homemade EXCEL Visual Basic macros that extract the sequences from the coordinates into a sequence alignment, and then renumber the pub files from the alignment.

If I had to do it in PyMOL, I would do it in multiple steps process: I would first change the numbering to sequential numbering, allowing me to then clear the insertion letters (resv or alt), then change the numbering to my own (AHo) scheme by shifting the numbering of each segment by adding the appropriate constant, starting with the most C-terminal segment to avoid problems due to duplicate residue numbers.

I would offer to send you my macro collection, but right now I am in the middle of fixing a number of things that broke due to the update to EXCEL 2019, so I have to ask you for patience.

best regards

Annemarie Honegger



Hi Vaheh,

I susoect that your issue is an edge case for PyMOL.
The resi variable is limited to integers (see https://pymolwiki.org/index.php/Property_Selectors<https://pymolwiki.org/index.php/Property_Selectors>).
Atoms with letters in the resi field are invisible to PyMOL.

You could write a python script to preprocess the coordinates, run the script from within PyMOL, and  then reload the modified coordinates into PyMOL.
It might be more expedient to use pdb_set from ccp4, antibody_numbering_converter.macosclangrelease in rosetta, or biopython.

Best regards,

Blaine


PS Half of our students work in OMRF labs. Our interactions with OMRF are as close as ever.


Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419