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: spel...@users.sourceforge.net
> To: bell_beaut...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> 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: bell_beaut...@hotmail.com
> > To: pymol-users@lists.sourceforge.net
> > 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
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