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 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 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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://kong.med.nyu.edu/ On Jan 9, 2015, at 10:42 AM, Tsjerk Wassenaar tsje...@gmail.commailto: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.nlmailto: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 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.nethttp://goparallel.sourceforge.net/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto:PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] exporting maps
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 Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[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. 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 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
