Hi Suhaila,
I uploaded a modified version (2.1) of the contact map visualizer
plugin. It now provides a command so it can be called from command line.
This will also work if you run the script instead of installing it as
a plugin.
USAGE
contact_map_visualizer [ image_file [, selection
But I get the following errors. Could anyone please help me in
overcoming this error?
Traceback (most recent call last):
File C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py,
line 338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File C:\Program
Hello Thomas.
Where exactly did you upload the modified script? I can't see any attachment
here.
Cheers,Suhaila.
Date: Thu, 22 Mar 2012 09:46:05 +0100
From: spel...@users.sourceforge.net
To: bell_beaut...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] FW: Query of
Oh I see what you mean now. It's on the website. I'll have a try with it right
away.
Many thanks Thomas!Suhaila
Date: Thu, 22 Mar 2012 09:46:05 +0100
From: spel...@users.sourceforge.net
To: bell_beaut...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] FW: Query of
Hi,
Is there a way to select a CGO object by clicking on it in the display?
Is it possible to add python handler for a mouse-click event?
The scenario is this: I draw some CGO objects to the display. When the
user clicks on one, I want to hide that object and display another one.
-Peter
Hello Thomas.
I tried running the following:
contact_map_visualizer [ contact-map.xpm [, contact-map.jpg]] on Linux terminal
command line
or is it supposed to be
contact_map_visualizer [ contact-map.xpm [, jpg]]
Or is it supposed to be running on PyMOL command line?
Cheers,
Suhaila
Date:
And also I checked via PyMOL command line that it doesn't contain g_mdmat but
my Linux terminal does have it.
How should I connect so that g_mdmat is found in PATH from a running PyMOL
session? Just move the Gromacs file directory under PyMOL?
Many thanks,
Suhaila.
From:
Hi Suhaila,
contact_map_visualizer is a PyMOL command, so you need to type it in
the PyMOL command line. You must not type the square brackets, these
denote optional arguments. Example:
PyMOL load structure.pdb
PyMOL contact_map_visualizer contact-map.xpm
g_mdmat is not a PyMOL command, but
Hello All,
I managed to solve the problem where many objects were not getting
included into a script created session all meta object with help
from Jason .
Once I got rid of duplicate object names either using python or the
setting auto_rename_duplicates..I could load around 250 objects
without
The imminent replacement of Mobile-Me by iCloud provides an impetus for me to
upgrade to Lion; but I'm currently happily using old-school stereo (i.e., a CRT
monitor + Crystal-Eyes LCD glasses) under Snow Leopard. Can anyone attest to
being able to use such equipment with Coot/PyMol under LIon?
Hi Peter,
Is there a way to select a CGO object by clicking on it in the display?
Is it possible to add python handler for a mouse-click event?
The scenario is this: I draw some CGO objects to the display. When the
user clicks on one, I want to hide that object and display another one.
You
Hello,
I was wondering if anyone could help me with some state mapping for movies. I
have 1000 states or so that are output from a dynamics simulation automatically
to pymol. I was wondering two things:
1. Can I hide the lines for state 500-1000 and show the lines for 1-500? I have
all the
OK. It does sound pretty weird prolly because the way I asked isn't precise.
We plot predicted contacts that can be viewed in various ways. So it'd be
better to create a GUI select menu or something like that for user's ease of
interacting with our project.
Suhaila.
From: tlin...@gmail.com
Jordan,
The 'hide' and 'show' commands to not take a state parameter. You
could use the multiplex option when loading the trajectories and
then use 'mdo' in the movie to control which states are shown/hidden.
This will slow down moviemaking and be a pain, but will get you where
you need to be.
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