Please see the following URLs for reference. Basically you are duplicating an object and then setting one (say Model A) with some level of transparency and one (say Model B) without transparency. And then 'hiding' portions of Model B (using 'cartoon skip') would reveal the transparency in Model A. This allows you to set the transparency levels for a selected region (or regions) show in cartoon representation. For example, if you had a protein that you wanted to show the first half without transparency and the second half with 50% transparency, you would duplicate the object (mod1 and mod2), and then set cartoon transparency for mod2 to 50%. Then make a selection for the second half of mod1 and use cartoon skip to skip this selection. This should result in the first half having no transparency and the second half being 50% transparent.
http://www.pymolwiki.org/index.php/Cartoon#Breaking_Up_a_Visualization_with_Cartoon_Skip http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg09861.html Hope this helps! Cheers, Nick ________________________________________ From: Robert Hanson [hans...@stolaf.edu] Sent: Friday, June 07, 2013 2:38 PM To: Noinaj, Nicholas (NIH/NIDDK) [F] Cc: Gianluigi Caltabiano; James Starlight; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Cartoon transparency I must say, 'cartoon skip' does not do what I thought it would do. fetch 1RV1 cartoon skip, i. 55 # now a helix section is turned into a loop cartoon skip, i. 56 # now there is a break, but two non-helix ends cartoon skip, i. 57 # now there is a break, with two non-helix ends I guess I understand the idea that in PyMOL a cartoon is like a bond -- between two elements rather than being associated with one (perhaps?) -- but why change the helix to a loop before it ends? Is there a way around that? Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
