Hi Mohammad,
I can confirm that the interfaceResidues.py script works in PyMOL version 1.5.2
running with Python3.8 on Mac OS 10.15.7.
You did not find interface residues in 1ak4 because chains A and B are more
than 15 Angstroms apart.
They have no direct interactions and hence have no interface. The first rule in
troubleshooting
PyMOL is to display and inspect the structure in the viewport to check your
assumptions about the structure.
However, chains C and D are close enough to interact. The following command
uses the
interfaceResidue() function to create an interface object called "interface"
that includes
all of the interacting residues between chains C and D.
interfaceResidues("1ak4", cA="c. C", cB="c. D", cutoff=1.0, selName="interface")
You do not need to use 'foundResidues =' to create another object.
In addition, cA in your command should be set equal to "c. A".
The c. is an abbreviation for "chain".
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-Structure-and-Function
COBRE in Structural Biology: https://www.ou.edu/structuralbiology
________________________________________
From: Mohammad Goodarzi [[email protected]]
Sent: Sunday, August 15, 2021 3:24 PM
To: [email protected]
Subject: [EXTERNAL] [PyMOL] extract interference residue
Hello Guys,
I am trying to extract the interference residue from a given protein PDB. I
have a protein named 1ak4 which has two chain A and B.
I open pymol, then go to file, the run the script from here
https://pymolwiki.org/index.php/InterfaceResidues#Simple_Example<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_InterfaceResidues-23Simple-5FExample&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=g8YHyNiGloFOsn1txDr06UZPT4xLrbEx0oH4IhUeltQ&s=_yZQI3Y7rTf4JHXGuW5ZmZIG4qSLy9d5L6PLbJ20VcM&e=>
Then I run the following command which gives me error
foundResidues = interfaceResidues("1ak4", cA="B", cB="B", cutoff=0.75,
selName="foundIn1QOX")
Could someone tell me how to identify the interference residue and extract it
from pymol?
Thanks
Mo
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