On Tue, 2004-04-27 at 17:27, firstname.lastname@example.org 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.
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 (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.
* 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. email@example.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 firstname.lastname@example.org, GPG: 0x25EC91A0