pymol-users

[PyMOL] Error running Contact Map Visualizer Plugin

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

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
 		 	   		  

Re: [PyMOL] Error running Contact Map Visualizer Plugin

[Tsjerk W. <ts...@gm...>]

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
>
> ------------------------------------------------------------------------------
> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...



-- 
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

Re: [PyMOL] Error running Contact Map Visualizer Plugin

[Tsjerk W. <ts...@gm...>]

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
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > 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 (PyM...@li...)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>> --
>> 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

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
> >> >
> >> >
> >> > ------------------------------------------------------------------------------
> >> > 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 (PyM...@li...)
> >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> > Archives: http://www.mail-archive.com/pym...@li...
> >>
> >>
> >>
> >> --
> >> 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

 		 	   		  

Re: [PyMOL] Error running Contact Map Visualizer Plugin

[Thomas H. <sp...@us...>]

On 03/13/2012 02:43 PM, Suhaila Haji Mohd Hussin wrote:
> 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.

it worked for me with:

convert contact-map.xpm contact-map.png

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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

You mean it worked after loading the contact map in png and pdb file on contact map visualizer plugin?
Suhaila.

> Date: Tue, 13 Mar 2012 14:50:08 +0100
> From: sp...@us...
> To: bel...@ho...
> CC: ts...@gm...; pym...@li...
> Subject: Re: [PyMOL] Error running Contact Map Visualizer Plugin
> 
> On 03/13/2012 02:43 PM, Suhaila Haji Mohd Hussin wrote:
> > 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.
> 
> it worked for me with:
> 
> convert contact-map.xpm contact-map.png
> 
> Cheers,
>    Thomas
> 
> -- 
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
 		 	   		  

Re: [PyMOL] Error running Contact Map Visualizer Plugin

[Thomas H. <sp...@us...>]

Suhaila Haji Mohd Hussin wrote, On 03/14/12 00:52:
> You mean it worked after loading the contact map in png and pdb file on 
> contact map visualizer plugin?

Yes.

>  > Date: Tue, 13 Mar 2012 14:50:08 +0100
>  > From: sp...@us...
>  > To: bel...@ho...
>  > CC: ts...@gm...; pym...@li...
>  > Subject: Re: [PyMOL] Error running Contact Map Visualizer Plugin
>  >
>  > On 03/13/2012 02:43 PM, Suhaila Haji Mohd Hussin wrote:
>  > > 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.
>  >
>  > it worked for me with:
>  >
>  > convert contact-map.xpm contact-map.png
>  >
>  > Cheers,
>  > Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

[PyMOL] Error running Contact Map Visualizer Plugin

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

I already got few replies regarding this issue but I still haven't solved and I don't even have the slightest idea what's causing it.
I tried mogrify, convert using ImageMagick, none of them works still giving me the following errors when after loading contact map & pdb file onContact Map Visualizer Plugin.
Any idea at all please let me know. 
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
 		 	   		   		 	   		  

Re: [PyMOL] Error running Contact Map Visualizer Plugin

[Tsjerk W. <ts...@gm...>]

Hi Suheila,

What were the exact commands you used, and what error did it come up with?
Just saying you tried mogrify and convert and the error was still there
isn't very informative to us.

Cheers,

Tsjerk

On Mar 18, 2012 2:39 PM, "Suhaila Haji Mohd Hussin" <
bel...@ho...> wrote:

 I already got few replies regarding this issue but I still haven't solved
and I don't even have the slightest idea what's causing it.

I tried mogrify, convert using ImageMagick, none of them works still giving
me the following errors when after loading contact map & pdb file on
Contact Map Visualizer Plugin.

Any idea at all please let me know.

Error: 1 <type 'exceptions.ValueError'> Exception in Tk callback Function:
<function <lambda> at 0...

------------------------------------------------------------------------------
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 (PyM...@li...)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pym...@li...

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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

Oh, please nevermind. I've already got it sorted. Thank you.
Suhaila

Date: Wed, 21 Mar 2012 06:31:40 +0100
Subject: Re: [PyMOL] Error running Contact Map Visualizer Plugin
From: ts...@gm...
To: bel...@ho...
CC: pym...@li...

Hi Suheila,
What were the exact commands you used, and what error did it come up with? Just saying you tried mogrify and convert and the error was still there isn't very informative to us.
Cheers,
Tsjerk
On Mar 18, 2012 2:39 PM, "Suhaila Haji Mohd Hussin" <bel...@ho...> wrote:





I already got few replies regarding this issue but I still haven't solved and I don't even have the slightest idea what's causing it.

I tried mogrify, convert using ImageMagick, none of them works still giving me the following errors when after loading contact map & pdb file onContact Map Visualizer Plugin.

Any idea at all please let me know. 

Error: 1
<type 'exceptions.ValueError'> Exception in Tk callback
Function: <function <lambda> at 0... 		 	   		  

------------------------------------------------------------------------------

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 (PyM...@li...)

Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Archives: http://www.mail-archive.com/pym...@li...