[PyMOL] Clipping only protein

[Peterson, E. C <EPe...@ua...>]

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.

Thanks.

__________________________________
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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