Re: [PyMOL] unable to import fragment

[Osvaldo M. <alo...@gm...>]

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 <tho...@sc...>
To: pym...@li...
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