[PyMOL] FW: FW: Query of running script of Contact Map Visualizer Plugin

[Suhaila H. M. H. <bel...@ho...>]

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: bel...@ho...
To: sp...@us...
CC: pym...@li...
Subject: RE: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin
Date: Thu, 22 Mar 2012 23:12:54 +1200







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: Thu, 22 Mar 2012 09:46:05 +0100
> From: sp...@us...
> To: bel...@ho...
> CC: pym...@li...
> Subject: Re: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin
> 
> 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 ]]
> 
> The plugin now can convert XPM automatically to PNG (again requires the 
> "Image" module from PIL).
> 
> Furthermore, if gromacs is installed properly (more precisely: g_mdmat 
> is found in PATH from a running PyMOL session), the plugin now can also 
> generate contact maps on the fly if you do not provide the image_file 
> argument.
> 
> Hope this all works and will make your task easier.
> 
> Cheers,
>    Thomas
> 
> On 03/22/2012 02:14 AM, Suhaila Haji Mohd Hussin wrote:
> > Nobody has replied this yet. I still need to know.
> >
> > Cheers,
> > Suhaila.
> >
> > ------------------------------------------------------------------------
> > From: bel...@ho...
> > To: pym...@li...
> > Subject: Query of running script of Contact Map Visualizer Plugin
> > Date: Wed, 21 Mar 2012 00:41:20 +1200
> >
> > Hello
> >
> > I know the plugin mentioned above (in the Subject) will work if I go to
> > Plugin > Manage Plugins > Install > contact_map_visualizer
> >
> > I get that.
> >
> > But nothing happens if I run the plugin if I go to File > Run >
> > contact_map_visualizer.py I do this because I need it for my project,
> > preferably running the script via this method.
> >
> > Can anyone please tell me why it is not working on the second method? I
> > know it's a plugin and it's just a python script anyway, no?
> >
> > Regards,
> > *Suhaila*
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen