Hi Warren et al.,


I have been using Pymol for quite a while (years) and have not seen documentation on these two questions.  This is probably because I am still using rc0.99, but I promise to switch to the $$ release as soon as my grant comes in!


1st question:  Is there a way to selectively clip?  For example, I am showing a surface rendering of the inside of a binding pocket and the ligand inside.  I want to clip away the front half of the pocket, leaving the ligand intact.  I loaded my structure containing the ligand and deleted the ligand atoms. I then loaded a copy of my structure (renamed) and deleted everything in the second loaded structure but the ligand.  I tried masking the ligand, but that apparently only masks selections. Is there a way to “mask” the ligand from clipping.  I can do this in BallView, but it does not load the C-C bonds of the ligand correctly.  Besides, I prefer working in Pymol.


2nd question:  I recently gave a PowerPoint presentation to our department and showed the structure using the *.psw feature and an embedded hyperlink in the presentation.  I then was able to toggle through F1, F2, F3 etc…  using PgDn.  It worked great and got an enthusiastic response. I guess this is a PowerPoint question, but is there a way to keep PowerPoint from displaying the warning message before opening the file?  That is the only time I needed to go back to the podium during my talk.





Eric Peterson, PhD

Department of Pharmacology and Toxicology

Center for Alcohol and Drug Abuse Studies

College of Medicine

University of Arkansas for Medical Sciences


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