Reece, PyMOL already has full alpha support for transparency and backgrounds.
To get that floating effect in PowerPoint, Photoshop, or Keynote: set ray_opaque_background, off ray png my_alpha_image.png That's one of the reasons I like PNG format, but beware of using transparent images in web pages: Most current Windows versions of IE don't have alpha channel support with PNG files (or any 32-bit image format AFAIK). Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Reece Hart > Sent: Tuesday, April 27, 2004 8:54 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] True Black? > > On Tue, 2004-04-27 at 17:27, pdouc...@chem.ucla.edu wrote: > > Thanks for the suggestion. Unfortunately this still > gives me a very light > grey--nowhere near what you are seeing on your machine. > The molecule is > *clearly* visible against the black background. I am > using pymol on win XP. I > think I will put pymol on my linux machine and see if > that makes a difference. > > > Pete- > > I assume that what you're seeing is the result of minute > scattering during ray tracing (Warren- is this correct?). > That's just a guess. > > Whatever the cause, you might consider using an image editor > like the gimp <http://www.gimp.org/> (see * below; or > Photoshop on Windows, I guess) to select all pixels within > some distance of black and recoloring those as exactly black. > For a neater effect, you could add an alpha channel and make > the pixels transparent, in which case your ray traced image > would appear to "float" on whatever background you used. > > Come to think of it, perhaps this would make a useful setting > in PyMOL itself (unless it already exists and I just haven't > come across it): a flatten_background setting (a rgb > distance) which would cause any pixel within the that > distance of the background color to be set exactly to the > background color. If background color were extended to > include an alpha channel, then this idea would also provide > for transparent backgrounds. > > -Reece > > * If you're using gimp, do this: load the png, add an alpha > channel (Image > Alpha > Add Alpha Channel), then select by > color (Select > By Color..., then click black somewhere), > then either 1) fill with the bucket to set the color or 2) > cut the selection to make it transparent. > > > > > -- > Reece Hart, Ph.D. r...@gene.com, > http://www.gene.com/ > Genentech, Inc. 650-225-6133 (voice), > -5389 (fax) > Bioinformatics and Protein Engineering > 1 DNA Way, MS-93 > http://www.in-machina.com/~reece/ > South San Francisco, CA 94080-4990 re...@in-machina.com, > GPG: 0x25EC91A0 > <http://www.gimp.org/> >
