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: firstname.lastname@example.org To: email@example.com CC: firstname.lastname@example.org Subject: RE: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin Date: Thu, 22 Mar 2012 23:12:54 +1200
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?
> Date: Thu, 22 Mar 2012 09:46:05 +0100 > From: email@example.com > To: firstname.lastname@example.org > CC: email@example.com > 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: firstname.lastname@example.org > > To: email@example.com > > 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