Many thanks for your assistance, Blaine! For the second point, I wanted to use the stick_ball setting on the ligand only. I was able to modify your command as follows: hide sticks; set stick_ball, on, ligand; show sticks
Best wishes, Chris On Fri, Apr 10, 2020 at 9:37 PM Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > 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 >
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