Hi Mo, I apologize. I did not fully address your question the first time.
In the internal gui on the right, click on the 'A' menu of the (interface) selection. Select "extract to object" or "copy to object". The new object called "obj1" can be saved to a cif file by selecting it while using "Export molecule" under the File pulldown. Alternatively, enter on the command line: save obj1.cif, obj1 You can save it to a PDBd file by simply changing the file extension to pdb. Best regards, Blaine ________________________________________ From: Mohammad Goodarzi [mohammad.goda...@gmail.com] Sent: Monday, August 16, 2021 9:19 AM To: Mooers, Blaine H.M. (HSC) Cc: pymol-users@lists.sourceforge.net Subject: Re: [EXTERNAL] [PyMOL] extract interference residue 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<mailto:blaine-moo...@ouhsc.edu>> wrote: Hi Mohammad, I can confirm that the interfaceResidues.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__interfaceResidues.py&d=DwQFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=Ii_pYmlADVqhxAchp82tnBCym3X5l89ANiXnV24jhOI&e=> 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ou.edu_structuralbiology&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=B15Mz_0x7gGI17o6LD8bBPswQ-uyRIMbCfUc-trD5No&e=> ________________________________________ From: Mohammad Goodarzi [mohammad.goda...@gmail.com<mailto:mohammad.goda...@gmail.com>] Sent: Sunday, August 15, 2021 3:24 PM To: pymol-users@lists.sourceforge.net<mailto: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=Q5cq0vYNIh7OQ34lxJLMnsiit0p4PTVIv14ivaZ0cCE&s=d_61y5nDwbx4-WMZXUiaHEcOTRtCXvyV0MuqW4WJGgU&e=><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 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
