[PyMOL] Error running Contact Map Visualizer Plugin

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 fo

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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 wrote: > Hello everyone especially to people who have used Contact Map Visualiz

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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

[PyMOL] How do I force a cartoon strand throuch a given Calpha?

Hello everyone, I am showing the structure in cartoon and a few residues in sticks, I do not want the mainchain atoms only the sidechains, but when I hide the mainchain a few residues in beta sheets lose connectivity to their bet sheet cartoon - how do I force a cartoon strand throuch a given Cal

Re: [PyMOL] How do I force a cartoon strand throuch a given Calpha?

Hi Petro, set cartoon_side_chain_helper, 1 http://pymolwiki.org/index.php/Cartoon_side_chain_helper Cheers, Thomas On 03/13/2012 01:45 PM, Pietro Roversi wrote: > Hello everyone, > > I am showing the structure in cartoon and a few residues in sticks, > I do not want the mainchain atoms only

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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 V

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 -- Thoma

[PyMOL] AxPymol and Meshes error?

Hi, I am getting an error when trying to use AxPymol within PPT. While i can open my PSW file within PyMOL and it looks great, it just won't display when called within the AxPymol plugin within PPT. I think i have narrowed the problem down to the fact that i am using a mesh (SAXS envelope) t

[PyMOL] plugin install error

Hi all, I want to install average_b.py. I follow the instructions from pymolwiki. But When I Install via Plugin>Install plugin from within PyMOL. I got an error message: Unable to write to plugin directory (insufficient privileges?) How to solve this problem? Thank you ! yamei -

Re: [PyMOL] plugin install error

Hi Yamei, instead of installing it as a "plugin", you can just run the script and then use the command that it provides. PyMOL> run path/to/average_b.py PyMOL> average_b (all) See also these PyMOLWiki pages: http://pymolwiki.org/index.php/Run http://pymolwiki.org/index.php/Running_Scripts The

[PyMOL] creating selections from electron density map

I have a pdb file and the corresponding electron density map. I can copy a selection from the pdb to make an independent object. I'd like to be able to select the electron density map for individual residues and ligands in my pdb file so I can view them away from all the other protein

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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: spel...@users.sourceforge.net > To: bell_beaut...@hotmail.com > CC: tsje...@gmail.com; pymol-users@lists.sourceforge.net > Subject: Re:

Re: [PyMOL] Error running Contact Map Visualizer Plugin

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: spel...@users.sourceforge.net > > To: bell_beaut...@hotmail.com > > CC: tsje.