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.
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:
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
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
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
-
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
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
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
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
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
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
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
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
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