Actually, the setting is set transparency_mode = 1
It's a long story, but if you start using transparency a lot, you'll find that there are times when you prefer not to see multiple layers of transparent objects, such as convoluted surfaces, for the sake of clarity. PyMOL defaults to that behavior. To change it so that all transparent layers are visible, use the setting above. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . 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 > Michael George Lerner > Sent: Saturday, November 20, 2004 12:23 PM > To: Seth Harris > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] RE: wire mesh spheres? > > > I think you're talking about the same thing I noticed .. if > so, I asked Warren about it and he said that it's on purpose; > PyMOL only shows the first transparent surface in order to > make transparent protein surfaces look less > confusing/cluttered/distracting. If that's what you're seeing, try > > set ray_transparency, 1 > > and raytracing again. > > -michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mler...@umich > > On Sat, 20 Nov 2004, Seth Harris wrote: > > > Continuing on the transparency aspects of the original question... > > When I ray trace Warren's recent example of transparent CGO's, it > > seems that of the objects behind a given transparent one, > only those > > that are fully opaque show through the front one. That is, the > > spheres in the back get blocked from showing through if they > > themselves have any transparency setting. This gives a somewhat > > inconsistent appearance as the front sphere, in this case, > will look > > selectively transparent or opaque in different regions. In > case the > > words aren't clear, I took the example and put the blue sphere in > > front so that the other three spheres, white, red, and > green are all partially hidden behind it, then do "ray". For > me, only the white sphere > > (which is opaque) shows through the blue one. I think I > had noticed this > > before, with non-CGO's too, so I was curious if it's a > known problem > > or has a fix? > > > > I was going to test povray, but this reminded me that sphere > > transparencies currently aren't passed on via make_pov to > the povray > > input script, but I know transparencies are honored by > make_pov for other types of objects. > > Perhaps a simple fix to have sphere transparency respected > as well? > > Once I manually edit the povray file to include the > "transmit" keyword > > in the pigment line the spheres do render as expected, with > all three > > showing through the front one regardless of each one's transparency. > > > > -Seth > > > > Warren's sample cgo code: > > > > from pymol.cgo import * > > from pymol import cmd > > > > obj = [ > > > > ALPHA, 1, > > COLOR, 1.0, 1.0, 1.0, > > SPHERE, 0.0, 0.0, 0.0, 0.5, > > > > ALPHA, 0.66, > > COLOR, 1.0, 0.0, 0.0, > > SPHERE, 1.0, 0.0, 0.0, 0.5, > > > > ALPHA, 0.33, > > COLOR, 0.0, 1.0, 0.0, > > SPHERE, 0.0, 1.0, 0.0, 0.5, > > > > ALPHA, 0.11, > > COLOR, 0.0, 0.0, 1.0, > > SPHERE, 0.0, 0.0, 1.0, 0.5, > > ] > > > > cmd.load_cgo(obj,'cgo01') > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS > > DOWNLOAD - A multidimensional database that combines robust > object and > > relational technologies, making it a perfect match for > Java, C++,COM, > > XML, ODBC and JDBC. www.intersystems.com/match8 > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: InterSystems CACHE FREE > OODBMS DOWNLOAD - A multidimensional database that combines > robust object and relational technologies, making it a > perfect match for Java, C++,COM, XML, ODBC and JDBC. > www.intersystems.com/match8 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
