It is a very sad news.
I've been asked to perform a PyMOL training next year in France. I will
dedicate this session to his memory.
If I can help anyway, tell me.
Best regards,
Jerome Pansanel
Le jeudi 05 novembre 2009 21:27:38, Jason Vertrees a écrit :
> PyMOLers,
>
> I have
version of PyMOL and copy the plugins (you can find
them in a pmg_tk/startup directory) in the new pmg_tk/startup directory. You
don't need to copy:
apbs_tools.py
__init__.py
remote_pdb_load.py
as these modules are provided by PyMOL.
Cheers,
Jerome Pansanel
Le jeudi 8 novembre 2007 15:44, X
Try to copy MySQLdb into:
C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\site-packages\
Jerome Pansanel
Le vendredi 9 mars 2007 19:54, DeVill a écrit :
> Hi!
>
> I know that as well... what I don't know is how to install it under PyMOL.
> If I were using simply python, than
File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ?
> import MySQLdb
> ImportError: No module named MySQLdb
> Error: unable to initialize plugin 'dbsearch'.
>
> Bye
> DeVill
>
> 2007/3/9, Jerome Pan
Hi,
Take a look on this plugin:
http://pymol-plugins.sourceforge.net/dbsearch.html
Cheers,
Jerome Pansanel
Le vendredi 9 mars 2007 14:24, DeVill a écrit :
> Hi!
>
> I would like to use direct mysql connection to a database in a plugin. Can
> you please tell me if there is a way to
id=222732
Cheers,
Jerome Pansanel
Hi,
Frowns is another Python-based chemical informatics library, but is no more
maintained. A great idea would be to initiate such project. We could based
the design on the CDK library (http://cdk.sourceforge.net/).
Comments or suggestions ?
Cheers,
Jerome Pansanel
Le lundi 20 novembre
db.gz')
+ pdbStream = StringIO.StringIO( pdbFile.read() )
+ pdbData = gzip.GzipFile(fileobj=pdbStream)
+ cmd.read_pdbstr(pdbData.read(), self.pdbCode)
***
If you have problem to deal with such piece of code, I can send you the
complete plugin.
C
Dear Selvaraj,
You will find useful resources about hydrogen bonding with PyMOL on:
http://www.rubor.de/bioinf/tips_modeling.html#addhbond
Regards,
Jerome Pansanel
Le mercredi 23 août 2006 22:48, selva raj a écrit :
> Dear Pymol users,
>Would anyone tell me how to draw hydrogen
Hello,
You can find some documentation about sulfur bonds on this page:
http://www.pymolwiki.org/index.php/Process_All_Files_In_Directory
If you are not successfull by using this resource, don't hesitate to post
again.
Cheers,
Jerome Pansanel
Selon Nagesh Chakka :
> Hello everyone
e pymol wiki (there is Plugin
directory). You can add a new category for swissprot plugin and use the pdb
category for the first plugin.
Regards,
Jerome Pansanel
> All comments and bugs please send an e-mail.
>
> Cheers
> Noel
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
> While we're discussin
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
> While we're discussin
u want.
Don't hesitate to ask for more features,
Cheers,
Jerome Pansanel
> Thanks
>
> J
u want.
Don't hesitate to ask for more features,
Cheers,
Jerome Pansanel
> Thanks
>
> J
Hi,
I think this software could be used:
http://www.tb-software.com/products3.html
http://www.tb-software.com/download/3dto3dsrc.zip
It's free (as in beer ideology).
Jerome Pansanel
Le Mercredi 08 Février 2006 19:29, scott_lu...@med.unc.edu a écrit :
> Thank you Jerome.
>
> Do y
o OBJ file.
Cheers,
Jerome Pansanel
Le Mercredi 08 Février 2006 05:03, scott_lu...@med.unc.edu a écrit :
> Is there any way to output in any of the following file formats?
> .max, .drf
> .3ds, .prj
> .ai
> .dem, .xml, .ddf
> .dwg, .dxf
> .fbx
> .htr
> .ige, .igs, .i
sidues on the (outside) surface of a cavity, with their labels)?
I publish today a pre-release of a PyMOL tutorial in french :
http://www.pansanel.net/chemistry/resources/PymolIntroduction.pdf
You can take a look !
Jerome Pansanel
> Thanks!
>
> -Charlotte
>
>
>
>
>
(name)
pymol.cmd.refresh()
pymol.cmd.delete(name)
Works fine with a Centrino (1.6GHz) laptop and Linux Debian (sarge).
Thanks,
Jerome Pansanel
Selon Warren DeLano :
> Jerome,
>
> Try calling
>
>pymol.cmd.refresh()
>
> before
>
>pymol.cmd.png(name)
&
e)
It works fine only if I have the function time.sleep(1). If not, I have only
empty pictures. Is there another solution to delete the molecule only when
the png file has been written ?
Thanks,
Jerome Pansanel
ck on a result
line, the structure is open into the PyMOL visualization window.
You can find the plugin at this address:
http://www.pansanel.net/chemistry/resources/pymol_pdbsearch.tar.gz
I'm waiting for your comments !
Thanks
Jerome Pansanel
ted!!
Hi,
Here is a usefull resource :
http://www.pymolwiki.org/index.php/Category:Plugins_Tutorial
Jerome Pansanel
heers,
Jerome Pansanel
Hi,
I've planned to write a french training document for PyMOL. I would enjoy that
some people help me by reading my draft, before I release it. This document
will be released under a Creative Common License (cc).
Thanks,
Jerome Pansanel
Le Lundi 10 Octobre 2005 09:29, Kristian Rot
Hello,
You can find modules inside some software package, like:
PyQuante (http://pyquante.sourceforge.net/)
FROWNS (http://frowns.sourceforge.net/)
MMTK (http://starship.python.net/crew/hinsen/MMTK/)
All these software are free software.
Regards,
Jerome PANSANEL
--
Jerome PANSANEL
http
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