Bartholomeus, You have run into limitations in PyMOL's handling of single objects.
The answer to both these questions is to split your molecule into multiple object and color/show independently. Use the "create" command to make copies, and then use alter to reassign secondary structure codes where needed. Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -----Original Message----- > From: Bartholomeus Kuettner [mailto:bkuett...@epost.de] > Sent: Tuesday, January 28, 2003 3:06 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] q: discrete colors and adjacent cartoon segments > > > Dear PyMol users, > > 1. > I'm puzzled with a coloring problem while coloring a protein molecule > accordingly to its secondary structure by using 'discrete > color' option: > If there are a helix and/or strand adjacent together (e.g. > helix from 1-10 > and sheet from 11-20) the small pseudo-loop region between > (arising from > atoms between last Calpha of the helix and first Calpha of > the strand) gets > colored like the latter partner (maybe because of its color > was defined at > last). What I'd like to do is to color this small pseudo loop > in a different > color. I've tried to color the atoms between last Calpha and > next Calpha > (C,N) individually but there was no effect. It seems to me, > that cartoon > coloring only corresponds to Calpha positions. So, is there a > way around to > color cartoon regions between secondary structure elements as > described > before? > > 2. > Is there a way to force PyMol to draw a cartoon which shows > two different > secondary strcuture elements (helix, strand) ending and > beginning at the > same residue? Maybe one can image a scenario where the N atom makes a > strand-like conformation while the CO group of the same > residue starts with > a helix. In another program it is/was possible to assign > helix and strand > ending and beginning in the same residue but when I try to > perfom with PyMol > only the last partner is shown correctly while the first partner gets > overrided in its last residue, e.g. cartoon "strand 1-10" and > "helix 10-20" > looks the same like "strand 1-9" and "helix 10-20". How one > could circumvent > this dilemma? > > Many thanks in advance! > > Greetings, > Bartholomeus > > > > ------------------------------------------------------- > This SF.NET email is sponsored by: > SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! > http://www.vasoftware.com > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
