I am trying to show the surface and ribbon representations together.
I want to give a nice glassy look of the surface but it does not work
too well. Does anyone have ideas on how to achieve that?
I know I can do it in PovRay but I'd love to achieve that effect in PyMol
with no extra program. Thank
Hugo Gutiérrez de Teran wrote:
> freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create
> direct context rendering for window 'PyMOL Viewer' This may hurt
> performance.
>
> But my system says I have freeglut installed:
>
> # yum search glut
> freeglut.i386
> You can, I believe, change this behavior so that Pymol will
> include HETATM records in surface calculations. I don't
> remember how, but Warren will probably chime in.
set surface_mode, 1
and be prepared to split your structure into separate objects before showing
surfaces.
Cheers,
DeLano
Hi Simon -
I think I know what the problem is. Is your ligand composed of 'HETATM's?
Pymol doesn't include HETATM records in calculating surfaces - this is
because most PDB files have waters etc. in them, and Warren wanted the user
to be able to load the PDB file and create a surface (for the pr
No. When I read in the pdb, containing the ligand and the protein
and simply calculate the surface, I get a surface for the protein,
but not the ligand.
Simon
On Nov 2, 2006, at 3:53 PM, Nicholas Noinaj wrote:
can you get a surface for the protein-ligand complex?
cheers,
nick
can you get a surface for the protein-ligand complex?
cheers,
nick
-Original Message-
From: Simon Holton
To: "Andrew Colasanti"
Date: Thu, 2 Nov 2006 15:36:55 +0100
Subject: Re: [PyMOL] Ligand Surface Representation
Maybe it wasn't clear from my original email, but I did try makin
Maybe it wasn't clear from my original email, but I did try making a
new object for the ligand and one for the 'empty' protein, but this
doesn't help :-(
Simon
On Nov 2, 2006, at 3:19 PM, Andrew Colasanti wrote:
Did you create a new object for the ligand? Try creating 2 objects,
one fo
In addition to the comments below, i don't think simply selecting the ligand
will do, you have to create it as a new object as noted below (not at Pymol WS
now or I would verify). Once you select the ligand, go to Actions button and
choose [create new object]. a new object will be created, pro
Did you create a new object for the ligand? Try creating 2 objects,
one for ligand and one for protein w/o ligand.
Andrew
On 11/2/06, Simon Holton wrote:
Hi Folks,
I'm trying to generate a surface for a ligand which is part of a
ligand-protein complex. I realise this is the other w
Hi Folks,
I'm trying to generate a surface for a ligand which is part of a
ligand-protein complex. I realise this is the other way around to
normal, but somehow when I select the ligand in pymol and then 'show
surface, ligand', absolutely nothing happens. No error, but no
surface. The
Hi Martin.
Ive also experimented with primitive shapes and cones. Its not possible to
get a rounded surface on the cone, as you cannot properly define the normals of
the surface without the quad based openGL primitives, which is not supported by
the inbuild raytracer. If you look in the Pymo
Hi Martin,
You may also be interested in this script which you can use to draw an
arrow from point A to point B:
cgo_arrow( start, end, radius, head_radius, head_length, name, state )
start = [ x1, y1, z1 ], end = [ x2, y2, z2 ]
For lots of arrows you can use:
cgo_arrows( X, radius, head_radi
Hi,
Pymol prebuild executable is running quite slow on my PC (linux FC5). It
gives the following error on start up:
freeglut (/home/hteran/tmp/programs/pymol/pymol.exe): Unable to create
direct context rendering for window 'PyMOL Viewer' This may hurt
performance.
But my system says I have fr
Hi James,
Maybe you can try another route. The ray_trace_mode, 3 gives very
eye-catching pictures. Make one image intended only to grab attention
and place it large in the centre of your poster. Make another image
you can use to fill your background (chose the x/y-ratio of your
poster for ray-tra
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