Hi Floris -
Tsjerk is correct. You can set spec_reflect for a selection. Something like:
set spec_reflect, 0, all and not organic
This would turn of specular reflection on anything that’s not a “ligand” atom.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jan 9, 2015, at 10:42 AM, Tsjerk Wassenaar
<tsje...@gmail.com<mailto:tsje...@gmail.com>> wrote:
Hi Floris,
I'm not entirely sure whether these are object/selection or global properties.
But have you tried specifying the selection?
set spec_reflect, 0, protein
Haven't tried it myself, though.
Cheers,
Tsjerk
On Jan 9, 2015 4:07 PM, "Floris van Eerden"
<f.j.van.eer...@rug.nl<mailto:f.j.van.eer...@rug.nl>> wrote:
Dear all,
My question is if I can set for different molecules in my system, how much they
reflect light during ray-tracing
My current system is a protein which contains some cofactors.
The cofactors are coloured according to their B value and the protein is shown
as a transparant grey surface.
When I start Ray-tracing, I get a quite nice picture. The problem is however
that the transparant surface is reflecting the light, and becomes therefore at
some places not transparant, which makes it kinda difficult to see the
cofactors in the protein (which are the most important). I played around with
all the spec_reflect, spec_direct settings. When I set spec_reflect to 0, there
are no reflections anymore, but the image becomes rather dull.
I was wondering if it is possible to select somehow to make only the cofactors
inside the protein reflect the light, but not the protein surface. In VMD you
can do this for example by making molecules from different ‘materials’, e.g.
you can make your cofactors from a reflective material, and your protein
surface from a non reflective, transparant material. Is something similar
possible in Pymol???
Thanks for your suggestions,
Floris
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