Hi Tsjerk,
Thanks a lot for reply.. All I wanted to try was to use povray instead of
pymol's internal ray tracer. Now if you type "help povray", it will come
with a suggestion to use an age old patch and use smooth_color.
----------------------------------------------------
PyMOL>help povray
DESCRIPTION
PovRay: Persistance of Vision Support Information (EXPERIMENTAL)
The built-in ray-tracer (technically a ray-caster) is as fast or
faster than PovRay for most figures (provided that hash_max is
tuned for your system). However, PovRay blows PyMOL away when it
comes to rendering images without using lots of RAM, and with
PovRay you get the ability use perspective, textures, reflections,
infinite objects, and a superior lighting model.
PovRay does not include interpolated colors within triangles (!!),
so you must patch the source code in order to obtain this basic
functionality required for rendering molecular surfaces. Details
can be found on the DINO website.
http://www.biozentrum.unibas.ch/~xray/dino
To use PovRay, you must be running under Unix and have x-povray in
your path. Unfortunately, the developers of PovRay do not share
PyMOL's open-source philosophy, so you will need to download,
configure, patch (for smooth_color_triangles), and install it
yourself. Despite being free and open-source, PovRay's license
prevents it from being modified or conveniently combined with
PyMOL, and thus it serves as a textbook example for why open-source
licenses should be wholly non-restrictive.
Assuming that PovRay is built and in your path...
ray renderer=1 # will use PovRay instead of the built-in engine
set ray_default_renderer=1 # changes the default renderer to PovRay
ray # will now use PovRay by default
cmd.get_povray() # will give you a tuple of PovRay input strings
# which you can manipulate from Python
set smooth_color_triangles = 1 # is required in order to get decent
surfaces in PovRay. You must patch PovRay first.
--------------------------------------------------------------------------------------------
so I tired that link (the patch was moved since then to another address)
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg00868.html
but all that is useless since smooth_color_triangle itself doesnt exist. I
tried to change it to smooth_triangle and still povray didnt do anything. So
Now I tried your suggestions of manually editing the file and changing some
settings .. but I am not getting the result yet..
I am linking 3 pictures.
1. internal ray tracer (
http://picasaweb.google.com/lh/photo/c9LUJwzPEYjpVVC0ThkQhQ?feat=directlink)
2. using ray renderer=1 for povray (
http://picasaweb.google.com/lh/photo/0736f1oK9dRaB8fV7Zmm6g?feat=directlink)
3. applying ur settings (
http://picasaweb.google.com/lh/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink)
Pymol should probably update the "help povray" description so that it does
not mislead anymore.
Thanks !!
Abhi
On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote:
> Hi Abhi,
>
> I had a look and found that POV-Ray does not have a keyword
> 'smooth_color_triangle' (anymore), but this should be changed to
> 'smooth_triangle'. Also, the mesh2 object Pymol writes already for
> ages is far superior to a set of smooth_triangles. This leaves me a
> bit puzzled as what it is you mean. Could you link/post an example of
> the image as you get now and indicate what you want to have different?
> Maybe also try the change in lighting and finish I posted a few days
> ago on the list. It may well be that the default POV-Ray settings
> pymol uses for light and appearance are causing the problem.
>
> Cheers,
>
> Tsjerk
>
> On Mon, May 11, 2009 at 5:41 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
> > Hi Abhi,
> >
> > I got and read the e-mail through the list, but would have to test
> > with pymol >1.0 before being able to give a sensible reply. As I'm now
> > underway that's a bit too much for me :) I'll come back on this one
> > later.
> > By the way, you only sent this mail this afternoon. Don't expect
> > instant replies or assume something didn't come through just because
> > you didn't get an answer within a few hours :)
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, May 11, 2009 at 5:05 PM, Abhinav Verma <abhinav1...@gmail.com>
> wrote:
> >> Hi Tsjerk,
> >>
> >> I am sending this email personally to you (sorry for that). I am
> sorry,
> >> but I posted it to pymol mailing list but it seems to have been stuck
> >> somewhere.
> >> Any idea would be helpful,
> >>
> >> thanks,
> >> Abhi
> >>
> >> ---------- Forwarded message ----------
> >> From: Abhinav Verma <abhinav1...@gmail.com>
> >> Date: Mon, May 11, 2009 at 3:06 PM
> >> Subject: Using povray with pymol
> >> To: pymol-users <pymol-users@lists.sourceforge.net>
> >>
> >>
> >> I am trying to use povray tracer with pymol. I got povray and installed
> it
> >> and tried to follow the instructions for the patch.. The patch seems too
> old
> >> written in 1999 and the current povray code is cpp and not c. so I
> skipped
> >> that part.. and now when I set smooth_color_triangle = 1, I get the
> >> following parse error..
> >>
> >> pigment{color rgb<1.00001,0.0904,0.0000>}}
> >> mesh {
> >> smooth_color_triangle
> >> Parse Error: No triangles in triangle mesh.
> >>
> >> If I donot swich it on, I get really ugly colored picture from the
> >> tmp_povray.pov file generated by pymol.
> >> Any Ideas to get similars colors that comes with pymol inbuild ray
> tracer
> >> and use povray ( I want to use povray as pymol is crashing because of
> size )
> >>
> >> Thanks in advance,
> >> Abhi
> >>
> >>
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
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