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

2015-01-09 Thread Tsjerk Wassenaar
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 wrote: Dear

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

2015-01-09 Thread Sampson, Jared
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

[PyMOL] exporting maps

2015-01-09 Thread Daniel Larsson
I have created a pseudo-low resolution electron density map from a PDB-file using the map_new command. Is it possible to export or save that map to a file? Any format should be fine. Daniel -- Dive into the World of

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

2015-01-09 Thread Floris van Eerden
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.