Hi Chris, Here is a one compound setting command (copy and paste at the PyMOL command prompt above the viewport) that turns on valence for the ligand bonds in ligand RZS of the covid-19 protease structure PDB 5R82 while turning off the valence for the protein bonds.
set valence, on, resn RZS; set valence, off, not resn RZs For your second question, set the the stick radius for a single bond by specifying the two atoms hide sticks; set_bond stick_radius, 0.05, /5r82/B/A/RZS`1001/C07, /5r82/B/A/RZS`1001/C08; show sticks https://pymolwiki.org/index.php/Stick_radius Recent versions of PyMOL show the ligand as sticks rather than lines when first loaded into PyMOL. You may have to turn off sticks, reset the set radius of interest, and then turn the sticks back on. 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: Chris Fage [fage...@gmail.com] Sent: Friday, April 10, 2020 2:00 PM To: pymol-users@lists.sourceforge.net Subject: [EXTERNAL] [PyMOL] Apply valence settings to an object Dear Pymol Fanatics, I would like to show the valence of ligand bonds only and not those of the surrounding amino acid residues. Is there any easy way to do this, aside from manually editing every bond? I’m also curious how one would set the stick_ball setting for a single object and not the rest of the protein. Many thanks in advance! Best, Chris _______________________________________________ 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
