Kevin, The trick here is to use "create" instead of "select". Create makes new objects that can have independent settings.
load mol_obj.pdb # transfer a piece of the molecule into a new object create new_obj, chain A remove mol_obj in new_obj # adjust trasparency for the new object set cartoon_transparency, 0.5, new_obj Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Kevin Gardner > Sent: Wednesday, June 08, 2005 7:57 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] cartoon_transparency: setting value for > subset of residues in object > > Hi all: > I'd like to set a value for a selection of residues > within an object --- which I think might be tough given the > docs on the set command, but I'm open to suggestions. The > particular case here is setting cartoon_transparency, which > I'd like to use to make a subset of residues in a protein > more transparent than the neighbors. This works like a charm > if I read the protein segments in as individual objects > initially, but any attempts to make a selection on a single > object and set characteristics from there results in the > whole object being modified. > > I know that this is explicitly listed in the > documentation for set, so I'm looking for a workaround, e.g. > splitting the first object into multiples, etc.? > > FWIW, running MacPyMOL v0.98 --- on one of the last > PowerPC- driven Macs :) > > Sincerely, > Kevin > > -- > ********************************************************************** > Kevin Gardner, Ph.D. kevin.gard...@utsouthwestern.edu > Associate Professor - Dept. of Biochemistry - UT Southwestern Med Ctr > 214-645-6365/FAX: -6353 http://freedom7.swmed.edu > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput a projector? How fast can you ride your desk > chair down the office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
