For various legacy reasons, the "transparency" setting only covers surface transparency. Try
set sphere_transparency, 0.5 set stick_transparency, 0.5 etc. 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 > Mark Mayer > Sent: Monday, September 26, 2005 3:33 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] transparency question > > Hi. > > Can anyone tell me how to get transparency to work? I'm using > Open-Source PyMOL version 0.98 on Mac OS X 10.3. > The command set transparency = 0.9 > does not generate errors in the text output window > > Setting: transparency set to 0.90000 > but nothing changes in the graphics window. > > I've tried command before as well as after drawing all my objects. > > I was planning to try and make transparent spheres around > some selected side chains, with rest of molecule drawn as > sticks and cartoons, so any advice (or example script) also > appreciated. > > many thanks > -- > Mark Mayer Ph.D. > LCMN NICHD NIH DHHS > Bldg 35, Room 3B 1002 MSC 3712 > 35 Lincoln Drive > Bethesda MD 20892 3712 > Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX > 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov > > Send packages, Fedex and anything requiring a signature to: > > Bldg 35, Room 3B 1004 > 35 Lincoln Drive > Bethesda MD 20892 > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv > or your very own Sony(tm)PSP. Click here to play: > http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
