Thanks, Thomas!
Your script works fine. I've tested in one pdb structure and it finds all
polar and salt-bridges perfectly.
As I've understood this script also is usefull for examination of the
ensemble of pdb structures in NMR-like format ( each pdb structure as the
individual state in pymol) is
Hello all,
I'm using Pymol v1.5 (from fink, so open source version) to trace large
scene that I have. To that end, I'm avoiding having PyMOL open and I wrote
a small python script to do the rendering for me. All goes well, except
this last part (don't mind the obvious variable names):
cmd.ray(wid
Hi João,
What about
cmd.png(default_name+'.png', dpi=300, ray=0)
Cheers,
-- Jason
On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues wrote:
> Hello all,
>
> I'm using Pymol v1.5 (from fink, so open source version) to trace large
> scene that I have. To that end, I'm avoiding having PyMOL open
Same result Jason, i also tried =false...
No dia 17 de Abr de 2012 20:45, "Jason Vertrees" <
jason.vertr...@schrodinger.com> escreveu:
> Hi João,
>
> What about
>
> cmd.png(default_name+'.png', dpi=300, ray=0)
>
> Cheers,
>
> -- Jason
>
>
> On Tue, Apr 17, 2012 at 11:18 AM, João Rodrigues
> wrote
João,
I'm not sure why this is giving you problems. Why do you have
renderer=2? Why not the default? Are you counting primitives? If so, I
suggest:
cmd.set("ray_default_renderer", 2)
# snapshot
cmd.png(myFile, width=w, height=h, dpi=d, ray=0)
# this will ray trace
cmd.png(myFile, width=w, hei
Hi Jason,
I've tried a lot of stuff, thus the renderer=2.. (i installed povray and
tried to use it). With the default option the result is the same.
cmd.png(default_name+'.png', width, height, dpi, ray=0)
Doing what you wrote still causes the renderer to kick in.. I'm a bit out
of ideas..
Cheer
It may be worth trying pymol 1.4 (instead of 1.5) - although this
shouldn't make a difference, it might provide some more information (you
also mentioned that you've got a large scene - depending on composition
1.4 may use less memory than 1.5).
You may also want to try using a pml script vs py
