Every once in a while, I try to show a metal ion as a tranparent sphere and
inevetiably get stuck trying to make the tiny cartesian coordinate system that
appears at the center of the sphere disappear so it doesn't "show through".
Suggestions?
Tom Leyh BEGIN:VCARD
VERSION:2.1
N:Leyh;Thoma
Tom,
you need to hide the 'nonbonded' representation of your ion, which shows up as
a little coordinate system i.e.
hide nonbonded, chain I#if your ion is in chain I
show spheres, chain I
set sphere_transparency=0.5, chain I
Cheers,
Carsten
-Original Message-
From: Thomas
On Wed, Oct 29, 2008 at 11:39 AM, Thomas S. Leyh, Ph. D.
wrote:
> Every once in a while, I try to show a metal ion as a tranparent
> sphere and inevetiably get stuck trying to make the tiny cartesian
> coordinate system that appears at the center of the sphere disappear so it
> doesn't "show
Hi!
I would like to run pymol scripts on the command line only without
invoking the x-window because there is no need to display the structures
involved (and also no way because I will run this on a Linux computer
cluster). I am only interested in the pymol text output that can be
piped into
Hi Tanja,
Try:
pymol -qcd 'cmd.help("launching")' > pymol_launching.txt
and examine the resulting file :)
Cheers,
Tsjerk
On Wed, Oct 29, 2008 at 7:48 PM, Tanja Mittag wrote:
> Hi!
>
> I would like to run pymol scripts on the command line only without
> invoking the x-window because there is
Hmmm.
I'm probably over-complicating matters, but:
def before_load():
cmd.delete("all")
def after_load():
cmd.as("cartoon")
cmd.hide("nonbonded")
def wrapped_load(filename):
before_load()
cmd.load(filename)
after_load()
cmd.extend("wrapped_load", wrapped_load)
gilleain
Thanks Tsjerk, this was very helpful!
Cheers,
Tanja
Tsjerk Wassenaar wrote:
Hi Tanja,
Try:
pymol -qcd 'cmd.help("launching")' > pymol_launching.txt
and examine the resulting file :)
Cheers,
Tsjerk
On Wed, Oct 29, 2008 at 7:48 PM, Tanja Mittag wrote:
Hi!
I would like to r
