Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hello thanks for all your help! I managed to fix the issue with the ray_transparency_contrast setting. @Tsjerk Thanks for your help. But this afternoon I have to teach. Maybe some other day? Floris On 14-01-15 20:38, Sampson, Jared wrote: Thanks for the correction, Thomas. I saw the followi

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Thanks for the correction, Thomas. I saw the following in the terminal window and thought it meant the setting was applied as I intended: PyMOL>set spec_reflect, 0, all and not org Setting: spec_reflect set for 2105 atoms in object "1shv". PyMOL>set spec_reflect, 1, org Setting: spec_reflect s

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Thomas, Thanks for chiming in. I guess this would be a step towards textures/finishes. I would really like to see more extended support for those in Pymol. Of course that would mostly serve artistic purposes, but I'd gladly raise the suggestion that it can do wonders for highlighting :) Floris

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hi Floris, Tsjerk, Jared, all lighting settings in PyMOL are only global, so setting them on objects or selections will have no effect. This is not a bug, bug of course can be considered a missing feature. We will check how difficult this would be to implement on the object or atom level. Chee

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hello Jared and Tsjerk, I tried your suggestion, but unfortunately it does not work on my computer. When I type the command set spec_reflect, 0, all Pymol gives the following output: -->Setting: spec_reflect set to 0.0 in 8 objects. So it seems okay. But however when I raytrace, I still get a

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

Hello Jared, thanks for the conformation!!! I am going to try it out today! Floris On 09-01-15 16:55, Sampson, Jared wrote: 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 reflect

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

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://

Re: [PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

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" wrote: > Dear all, > > My question i

[PyMOL] raytracing a transparant surface, with reflections only on the cofactors inside

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.