Actually, one of the first of these images I made was of conotoxin floating above a see. Will that do? I'd still have to add the sunset though ;) O, and the checkered beach...

In regards the problem of Seth, it's good you've solved it. It is possible though to remove all statements about textures from a mesh2 object. You have to remove both the texture_list as well as the references to the textures. If you don't know what I'm talking about, you can check out the povray manual on mesh2. Besides, you may be better off using statements like

union { #include "moleculedef.inc" pigment {image_map{ " mypicturehere.gif" }} }

rather than changing the #default for that. Especially handy if you can find a snowboarder object you want to merge with your kinase piste...

By the way, I may try to write a script to process the mesh2 file from Pymol to strip out texture statements (and add them as #declares) if I can find some time. Also, it would be so nice to have a tidied up mesh2 file, rather than an endless set of triangles. mesh2 can be so much better (smaller, more efficient, easier to handle).



On 4/19/06, Thomas Stout <tstout@exelixis.com> wrote:

I'm glad you solved your problem, but more importantly when are we going to get to see this picture of an easter bunny on some wood-textured rendition of a half-submerged albumin glowing softly in the warm lights of a double sunset over an infinite lake lapping at the shores of a checkered beach???



-----Original Message-----
From: pymol-users-admin@lists.sourceforge.net on behalf of Seth Harris
Sent: Tue 4/18/2006 2:45 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RE: povray image mapping and default pigments

To answer my own question...instead of entirely taking out the pigment{blah
blah blah} statements from the texture_lists in the povray input as used to
work, I found that in this case replacing them with "pigment {}" statements
was still a permissible syntax and also allowed a #default pigment
declaration in the header file to override the molecular scene descriptions.

If you have no idea what I'm talking about, it's probably for the best.

Funny how often just describing your problem to someone else allows you to
lay it out logically enough to lead you to a solution...thanks for


---------- Forwarded message ----------
From: Seth Harris <seth00@gmail.com>
Date: Apr 18, 2006 2:18 PM
Subject: povray image mapping and default pigments
To: pymol-users@lists.sourceforge.net

 This is for the povray gurus out there...

Occasionally I muck around with the time-consuming practice of trying to map
pictures onto molecular surfaces with povray.

I had this working to some extent, but something has changed (I think with
the povray file format produced by pymol & make_pov where now there are
fancy texture_list texture and pigment statements, rather than simple
"pigment" ones.)

In the past, I set it up so that the povray file has a header (cameras,
lights, etc.) separate from the molecular scene description. Then I would
usually edit the header to apply some #default texture or pigment to use the
povray parlance. So the approach I used to use was to strip out all the
pigment {} statements from the molecular scene descriptor povray input with
a perl script, and then use the #default pigment {image_map{ "
mypicturehere.gif" }} syntax in the header to map the image on to the
surface...the practical uses of having a picture of someone, say,
snowboarding down a mountain mapped onto the surface of some kinase are just
endless. But that aside, the problem now is that these newer texture_list
statements aren't so amenable to this global pigment removal thing, and I
haven't quite figured out how best to get around this. (Couldn't remove them
entirely and putting in the image_map pigment thing didn't seem to work,
although maybe I just didn't get the right combination of open and closed
brackets {?}}})

Anyone have any experiences along these lines? As near as I can tell, there
was some switch in smooth triangle definitions with Povray 3.5 which was
capitalized on by some pymol 0.98 edition. Perhaps I have to go back to an
old archived version of pymol? Or, more sensibly, perhaps I should recognize
that pictures of easter bunnies or whatever don't belong on some
wood-textured rendition of a half-submerged albumin, glowing softly in the
warm light(s) of a double sunset over an infinite lake lapping at the shores
of a checkered beach. But for some reason journal editors seem to enjoy


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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
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+31 50 363 4336