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.

RE: [PyMOL] Raytracing interior surfaces. Problems in both PyMoland PovRay

orge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Daniel Rigden > Sent: Wednesday, November 23, 2005 5:03 AM > To: Jacob Poehlsgaard > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Raytracing interior surfaces. Problems > in both PyMolan

Re: [PyMOL] Raytracing interior surfaces. Problems in both PyMol and PovRay

Hi Jacob In Pymol, have you tried adding in a direct light source? e.g. set direct, 0.5 It worked nicely in a similar situation for me Daniel On Wed, 2005-11-23 at 11:42 +0100, Jacob Poehlsgaard wrote: > Hi folks > > > > I’m trying to visualize a section of the inner workings of the > rib

[PyMOL] Raytracing interior surfaces. Problems in both PyMol and PovRay

Hi folks I'm trying to visualize a section of the inner workings of the ribosome. To this end I've generated a surface and clipped it to reveal the internal structure I want to look at. This looks really good in the normal openGL view. When I raytrace it however, the part that's clipped away s

Re: [PyMOL] Raytracing "lies" in v0.98

346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jacob Corn Sent: Wednesday, May 25, 2005 3:52 PM To: pymol-users Subject: [PyMOL] Raytracing "lies" in v0.98 Hi all, I have a

RE: [PyMOL] Raytracing "lies" in v0.98

Jacob Corn > Sent: Wednesday, May 25, 2005 3:52 PM > To: pymol-users > Subject: [PyMOL] Raytracing "lies" in v0.98 > > Hi all, > I have a session that I am completely unable to render. If I > just issue a "ray" command, the view window shows a progress &

[PyMOL] Raytracing "lies" in v0.98

Hi all, I have a session that I am completely unable to render. If I just issue a "ray" command, the view window shows a progress bar and the command window eventually reports that raytracing has finished normally, but the view window isn't updated with the raytraced image. If I try to png the

Re: [PyMOL] raytracing with depth cue

Dear pymol users, I got an answer from several helpful people: I had somehow disabled the depth cue in the raytracing rendering: - There are two settings that give you an impression of depth. depth_cue for the OpenGL display and ray_trace_fog for the ray tracer set ray_trace_fog, 1 to pres

[PyMOL] raytracing and depth cue

Dear Pymol users, When I raytrace (using the built-in raytracer) the depth cue disappears. Is there any way to get a high resolution (ray traced) image with depth cue? regards, Anders -- Anders Østergaard Madsen Centre for Crystallographic Studies

[PyMOL] raytracing with depth cue

Dear Pymol users, When I raytrace (using the built-in raytracer) the depth cue disappears. Is there any way to get a high resolution image with depth cue? regards, Anders -- Anders Østergaard Madsen Centre for Crystallographic Studies

[PyMOL] Raytracing

Hi, I'm using MacPymol 0.95, and have suddenly started having a MAJOR problem when raytracing. I.e. it crashes every time I try to do it. I have re-started the computer, re-installed MacPymol, and it still does it. It didn't used to do it, it sort of started doing it sporadically (once in ma

Re: [PyMOL] pymol raytracing crash

593-4020 > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > > ad...@lists.sourceforge.net] On Behalf Of Thomas Siegmund > > Sent: Wednesday, September 10, 2003 6:16 AM > > To: pymol-users@lists.sourceforge.net > >

RE: [PyMOL] pymol raytracing crash

> To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol raytracing crash > > Hi everybody, > > I am new to pymol. So maybe I'm doing something wrong, but pymol almost > everytime crashes when I try to raytrace a picture. I had some success > with > small prote

[PyMOL] pymol raytracing crash

Hi everybody, I am new to pymol. So maybe I'm doing something wrong, but pymol almost everytime crashes when I try to raytrace a picture. I had some success with small protein structures in cartoon representation. The same molecule in lines or sticks representation crashes the pymol raytracer.