Hi Suhaila, mogrify modifies in-place, causing a mismatch between the extension and the format. I guess that the script decides based on the extension, and thus fails. Better is to use convert:
convert contactmap.xpm contactmap.png Do make sure that the conversion goes well. I'm not exactly sure whether Gromacs XPM files are properly processed by Imagemagick. Cheers, Tsjerk On Tue, Mar 13, 2012 at 2:05 PM, Suhaila Haji Mohd Hussin <bell_beaut...@hotmail.com> wrote: > Hello Tsjerk, > > When we run the plugin the dialog box is asking contact map to be in either > png or jpg format only. So I used ImageMagick to convert it and run the > following commands: > > mogrify -format jpg *.xpm > > or > > mogrify -format png *.xpm > > Cheers, > Suhaila > >> Date: Tue, 13 Mar 2012 14:01:21 +0100 >> Subject: Re: [PyMOL] Error running Contact Map Visualizer Plugin >> From: tsje...@gmail.com >> To: bell_beaut...@hotmail.com >> CC: pymol-users@lists.sourceforge.net > >> >> Hi Suhaila, >> >> It looks like it's trying to load the XPM file, in stead of the >> jpg/png. How did you invoke Pymol and what commands did you give? >> >> Cheers, >> >> Tsjerk >> >> On Tue, Mar 13, 2012 at 1:49 PM, Suhaila Haji Mohd Hussin >> <bell_beaut...@hotmail.com> wrote: >> > Hello everyone especially to people who have used Contact Map Visualizer >> > plugin before. >> > >> > Please refer the link below for more details of the issue: >> > http://www.pymolwiki.org/index.php/Contact_map_visualizer >> > >> > In that link I managed to generate the contact map successfully and >> > converted the format from xpm to either jpg or png. >> > >> > When I loaded the contact map it was alright but after then as I >> > loaded a >> > pdb file that generates the contact map it gives me the following error >> > instead of displaying the contact map which is shown in the link. >> > >> > Please help me what's this error all about? >> > >> > Error: 1 >> > <type 'exceptions.ValueError'> Exception in Tk callback >> > Function: <function <lambda> at 0xa180cdc> (type: <type 'function'>) >> > Args: () >> > Traceback (innermost last): >> > File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line >> > 1747, in __call__ >> > return apply(self.func, args) >> > File >> > "/usr/lib/pymodules/python2.7/pmg_tk/startup/contact_map_visualizer.py", >> > line 54, in <lambda> >> > self.menuBar.addmenuitem('Plugin', 'command','Contact Map >> > Visualizer',label >> > = 'Contact Map Visualizer',command = lambda s=self : >> > getImageLocation(s)) >> > File >> > "/usr/lib/pymodules/python2.7/pmg_tk/startup/contact_map_visualizer.py", >> > line 68, in getImageLocation >> > getPDBLocation(self) >> > File >> > "/usr/lib/pymodules/python2.7/pmg_tk/startup/contact_map_visualizer.py", >> > line 83, in getPDBLocation >> > loadImageOnScreen(self.file.name, self.pdbFile.name) >> > File >> > "/usr/lib/pymodules/python2.7/pmg_tk/startup/contact_map_visualizer.py", >> > line 118, in loadImageOnScreen >> > im = Image.open(image_file) >> > File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 1976, in open >> > return factory(fp, filename) >> > File "/usr/lib/python2.7/dist-packages/PIL/ImageFile.py", line 91, in >> > __init__ >> > self._open() >> > File "/usr/lib/python2.7/dist-packages/PIL/XpmImagePlugin.py", line 93, >> > in >> > _open >> > raise ValueError, "cannot read this XPM file" >> > <type 'exceptions.ValueError'>: cannot read this XPM file >> > Many thanks, >> > Suhaila >> > >> > >> > ------------------------------------------------------------------------------ >> > Keep Your Developer Skills Current with LearnDevNow! >> > The most comprehensive online learning library for Microsoft developers >> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> > Metro Style Apps, more. Free future releases when you subscribe now! >> > http://p.sf.net/sfu/learndevnow-d2d >> > _______________________________________________ >> > 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 >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ 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
