Hi Thomas, If you display the SASA of the protein in PyMOL's viewport, you will see that it and that of the ligand have huge overlaps How do you define the interface in such a situation and how do you interpret it?
The interface of the molecular surfaces seems easier to interpret. Best regards, Blaine 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 ________________________________________ From: Thomas Evangelidis [teva...@gmail.com] Sent: Wednesday, May 20, 2020 9:14 AM To: pymol mailinglist Subject: [EXTERNAL] [PyMOL] How to compute the interface surface between ligand and protein? Greetings, I want to compute the interface surface between the ligand and the protein in batch mode for hundreds of thousands of PDBs, like the attached one (sample.pdb). I am interested in the interface surface of both of them. First I create two new molecules, the protein, and the ligand, and I work with them because the results I get when working with the original molecule (which contains both protein and ligand) are different. load sample.pdb create protein, polymer create ligand, resn LIG delete sample select prot_interface, protein within 3.5 of ligand; set dot_solvent, 0; get_area prot_interface; set dot_solvent, 1; get_area prot_interface; select lig_interface, ligand within 3.5 of protein; set dot_solvent, 0; get_area lig_interface; set dot_solvent, 1; get_area lig_interface; protein interface molecular surface = 1216.239 Angstroms^2 protein interface SASA = 763.095 Angstroms^2 ligand interface molecular surface = 748.867 Angstroms^2 ligand interface SASA = 977.608 Angstroms^2 I still don't understand why the interface molecular surface of the ligand is smaller than the interface SASA, while the opposite happens with the protein. Could someone please explain this to me and verify that I am computing the interface surfaces correctly? I thank you in advance. Thomas -- ====================================================================== Dr. Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.uochb.cz_web_structure_31.html-3Flang-3Den&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=_57VI-rsaa_XreiW4XyCB4JCeYxIgxYQMzE2-4tSVZY&e=>, Prague, Czech Republic & CEITEC - Central European Institute of Technology<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ceitec.eu_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=A2aVI7iISZXV0okVxr2DaiNghbfhZnUYoT3Yoev5S9U&e=>, Brno, Czech Republic email: teva...@gmail.com<mailto:teva...@gmail.com>, Twitter: tevangelidis<https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_tevangelidis&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=xm1YlcM5Yu2NrXsLFcftypRirhta1tskIsgqE4aGA0U&e=>, LinkedIn: Thomas Evangelidis<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_thomas-2Devangelidis-2D495b45125_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=attBDYWqEeZXqfolM-a1fEo5S7h671troeIdMmvv6Wo&e=> website: https://sites.google.com/site/thomasevangelidishomepage/<https://urldefense.proofpoint.com/v2/url?u=https-3A__sites.google.com_site_thomasevangelidishomepage_&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=kgJ3ggEDW_MHgArC60SMFo77wMerMvyyPjI3lu1Fj8U&s=B9x_aKai1Ed5wAeUbu0U8rN9y2bjXnsT6Cv8QC-UCqs&e=> _______________________________________________ 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
