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 PyMOL will try to run in internally if you pass no arguments to contact_map_visualizer. Your setup looks like this will work. PyMOL> load structure.pdb PyMOL> contact_map_visualizer Hope that helps. Cheers, Thomas On 03/22/2012 12:19 PM, Suhaila Haji Mohd Hussin wrote: > 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: bell_beaut...@hotmail.com > To: spel...@users.sourceforge.net > CC: pymol-users@lists.sourceforge.net > 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: 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 ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
