p { margin-bottom: 0.08in; }
Dear Pymol users
I have to do TWO jobs simultaneously in
PYMOL.
JOB 1: Load multiple *sdf files
I have set of ligand files in *.sdf
format as follows:
/home/user/Model_1/cluster_1.sdf
/home/user/Model_1/cluster_2.sdf
Hi Renuka,
Check out the loadDir PyMOL script (
http://www.pymolwiki.org/index.php/LoadDir). You can do stuff like,
# load all PDBs in the directory ../
loadDir ../, *.pdb
# load all SDFs in ../../mySDFs
loadDir ../../mySDFs/state*.sdf
Cheers,
-- Jason
On Wed, Sep 22, 2010 at 9:12 AM,
The output of the get_view command does not save the size of the viewport.
Thus if you want to recreate an image for ray tracing so it will have the same
size and scale, one also needs to save the viewport dimensions. Is there some
way to access this information? The viewport command only
Still no ideas? Guys, how then you do movie without gui mode???
-- Forwarded message --
From: Sergey Ivanov icegood1...@gmail.com
Date: 2010/9/21
Subject: emovie scripting
To: pymol-users@lists.sourceforge.net
Hello, help me please create script that loads frames (say, 30) from
Sergey,
After looking over your data (in another email), PyMOL was not zooming
correctly because none of your atoms were connected. (PyMOL got the
extents right, but was still confused.) To get around this, you can
just create a simple connected object, like a methane (8 atoms) and
position
Hi Sergey,
I either use the GUI or when not in the UI I utilize the moviemaking commands:
mdo
mview
mset
Also, import movie and check out what it has to offer:
import movie
print dir(movie)
Here are some moviemaking references:
In preparing my test for the odd request that I just sent, I came
across what seems to be a bug in super. It has to do with this weird
nucleic acid thing I was talking about.
Here's the script this time:
from pymol import cmd
cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
I realize this is an edge case, where behavior is not always well
defined in programs, but I have a request for a behavior (and the
behavior actually seemed to change between 1.2 and 1.3)
My example script:
from pymol import cmd
cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
Hi Mark,
We used to be able to call this to get the viewport size. But,
somewhere along the line Warren removed this. I'll see if I can add
it back in, or find out why he removed it.
Cheers,
-- Jason
On Wed, Sep 22, 2010 at 2:06 PM, Mark A Saper sa...@umich.edu wrote:
The output of the
