PyMOL Molecular Graphics System

My guess is that you may still be showing sticks in the original object, =
instead of just cartoons.  If you have the same overlapping =
representation in two objects, it isn't predictable which will show up =
in the ray-tracer, and you can get exactly this behavior, where you see =
one color in OpenGL and a different one in the raytracer.

Here is the general sequence of steps you'll want to follow to insure =
success:

load prot.pdb
create cpy,prot
hide
show cartoon,prot
show sticks,cpy
color red,prot
color green,cpy
ray

--
mailto:warren@...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501



> -----Original Message-----
> From: Peter Stogios [mailto:pstogios@...]
> Sent: Tuesday, May 28, 2002 9:08 AM
> To: pymol-users@...
> Subject: [PyMOL] Colors and ray-tracing
>=20
>=20
> This topic was touched on before but I'm still having=20
> problems with it.
>=20
> Somebody asked how to color sticks differently from cartoons=20
> and Warren
> explained that this can be done by creating duplicate=20
> objects.  I managed
> to accomplish that, but when I ray-trace the image the=20
> cartoon takes the
> same color as the stick does.  As soon as I move the=20
> ray-traced image, it
> restores back to the different colors, as I want them.
>=20
> For example, I colored the cartoons in one object green,=20
> while I showed
> only sticks in the duplicate object and colored a specific=20
> residue stick
> blue.  When I ray-trace the image, the cartoon at that residue turns
> green, instead of staying blue.
>=20
> Is this a bug or how can I get around this?  Thanks in advance.
>=20
> --=20
> Peter Stogios
> Dept. of Medical Biophysics, Univ. of Toronto
>=20
>=20
> _______________________________________________________________
>=20
> Don't miss the 2002 Sprint PCS Application Developer's Conference
> August 25-28 in Las Vegas -- http://devcon.sprintpcs.com/adp/index.cfm
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

This topic was touched on before but I'm still having problems with it.

Somebody asked how to color sticks differently from cartoons and Warren
explained that this can be done by creating duplicate objects.  I managed
to accomplish that, but when I ray-trace the image the cartoon takes the
same color as the stick does.  As soon as I move the ray-traced image, it
restores back to the different colors, as I want them.

For example, I colored the cartoons in one object green, while I showed
only sticks in the duplicate object and colored a specific residue stick
blue.  When I ray-trace the image, the cartoon at that residue turns
green, instead of staying blue.

Is this a bug or how can I get around this?  Thanks in advance.

-- 
Peter Stogios
Dept. of Medical Biophysics, Univ. of Toronto