Ah ha! Yes, of course
Many thanks to you & Rob for catching that!
Note to self: *triple* shots of espresso next time :)
-Tom
-Original Message-
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Saturday, May 16, 2009 1:30 AM
To: Thomas Stout
Cc: pymol-users
Subject: Re
Denis,
Sorry, PyMOL only has protein charges coded at present. Perhaps the
APBS project's pdb2pqr utility might be able to assign charges to
canonoical ligands (such as ATP)?
http://apbs.sourceforge.net
Cheers,
Warren
> -Original Message-
> From: Chaix Denis [mailto:denis.ch...@cbs.cnr
Dear users
I'm trying to compare the electrostatic charge surface of my protein
with and without ligand, by using the command "generate vacuum
electrostatics".
that's works fine for the protein without ATP but that doesn't work with
the ligand.The surface obtaine doesn't take account the ligand
Hi Tsjerk!!,
Yes,, it is really an oldie.. ( I tried to patch, but the new code is cpp
and not c anymore for povray, so I left the oldie goldie ). All I need is to
get close to pymol trace.. i.e. the shine which is missing in my links to
the pictures in my previous mail (this is just a very simpl
Hi Abhi,
Oooh, that's an oldie alright. I only vaguely recollect that coming in
:) But you need to patch POV-Ray for it... Anyway, the mesh2 object
also allows for smoothly colored triangles, so in that sense there's
no need to really do it. The big question is really what do you want
to see and w
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
DESC
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
