Re: [PyMOL] Error running Contact Map Visualizer Plugin

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

I tried that just now, the error is still the same :(

Perhaps you're right about Gromacs XMP files aren't properly processed by ImageMagick.

While I'm looking, do you have other way?

Regards,
Suhaila

> Date: Tue, 13 Mar 2012 14:11:11 +0100
> Subject: Re: [PyMOL] Error running Contact Map Visualizer Plugin
> From: ts...@gm...
> To: bel...@ho...
> CC: pym...@li...
> 
> 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
> <bel...@ho...> 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: ts...@gm...
> >> To: bel...@ho...
> >> CC: pym...@li...
> >
> >>
> >> 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
> >> <bel...@ho...> 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
> >> >
> >> >
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> >>
> >>
> >> --
> >> 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