Hi Blaine,
How can I extract them? do you know ?
Thanks
Mo
On Sun, Aug 15, 2021 at 5:42 PM Mooers, Blaine H.M. (HSC) <
blaine-moo...@ouhsc.edu> wrote:
> 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
> <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-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 [mohammad.goda...@gmail.com]
> Sent: Sunday, August 15, 2021 3:24 PM
> To: pymol-users@lists.sourceforge.net
> 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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