Hi Thomas,
Thanls for the tip. I forget to mention that I only have this problem when
running PyMOL from a script.
I have not setted CHEMPY_DATA, PYMOL_DATA or PYMOL_PATH in my environment,
they are setted by the pymol script /user/bin/pymol.
I try setting those variables in my .bashrc file, but nothing happens.
After trying another options I finally create a symbolic link with the
command.
sudo ln -s /usr/share/chempy/ /usr/share/pymol/data/
Cheers,
Osvaldo.
---------- Forwarded message ----------
From: Thomas Holder <thomas.hol...@schrodinger.com>
To: pymol-users@lists.sourceforge.net
Cc:
Date: Thu, 01 Aug 2013 22:04:09 +0200
Subject: Re: [PyMOL] unable to import fragment
Hi Osvaldo,
I guess you have CHEMPY_DATA, PYMOL_DATA or PYMOL_PATH set in your
environment. Try to unset it first or set it to the correct path and
then run your script.
Hint: there must be a directory
$CHEMPY_DATA/fragments
or $PYMOL_DATA/chempy/fragments
or $PYMOL_PATH/data/chempy/
fragments
Cheers,
Thomas
Osvaldo Martin wrote, On 08/01/13 20:39:
> Hi,
>
> When Running PyMOL from a python script I get the error message
> "unable to import fragment XXX", where XXX is 'ala', 'cys', 'acetylene'
etc.
>
> I get this message when I try to use the mutagenesis wizard or any other
> function that need access to the fragment library, like adding a alanine
> residue with "ALT+A"
>
> The header of my script is
>
> import pymol
> from pymol import cmd, stored
> pymol.finish_launching()
>
> I try importing everything from pymol using
>
> from pymol import *
>
> but I get the same error.
>
> Thanks in advance.
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
------------------------------------------------------------------------------
Get your SQL database under version control now!
Version control is standard for application code, but databases havent
caught up. So what steps can you take to put your SQL databases under
version control? Why should you start doing it? Read more to find out.
http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
