Hi Andreas,
Thanks for your reply. See my comments please. Essentially, I need to
install new apbs plubgin.
2010/2/15 Andreas Förster <docandr...@gmail.com>
> my advice is to see if a dx file by another name has been created and, if
> so, use that to visualize the field lines.
>
> They are there:
pymol-generated.dx pymol-generated.in pymol-generated.pqr
Otherwise I wouldn't be able to see the elec surface.
> The full story is below, and might be more interesting to the developers of
> the apbs plugins. I'm using PyMOL 1.2r3pre and APBS 1.2 with openmpi
> installed via FINK on OSX 6.2.
>
> The old apbs plugin aborts with the following error:
>
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>
> The file that exists is pymol-generated-PE0.dx. When I change 'Temporary
> DX file' in the 'Temporary File Locations' tab to pymol-generated-PE0.dx, I
> get the same error, but now the file that exists is
> pymol-generated-PE0-PE0.dx (ad infinitum?).
>
> I see you are trying to use "apbs-mpi-openmpi" or similar. I am quite aware
of this as I contacted apbs Fink maintainer Bill Scott months ago. But since
then I didn't look at apbs plugin until now.
So I guess I have to follow:
http://pymolwiki.org/index.php/User:Mglerner
and maybe the rest of your email.
> Another problem with the original plugin is that the executables are not
> found. In my .bashrc I define
>
> export APBS_PSIZE='/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
> export APBS_BINARY='/sw/bin/apbs-mpi-openmpi'
>
> In the 'APBS Location', only 'APBS binary location' is set properly. 'APBS
> psize.py location' is incorrectly set to /sw/share/apbs/tools/manip/psize.py
>
>
> With the new apbs plugin (APBS Tools2), there's also a problem with the
> paths. Neither 'APBS binary location' nor 'APBS psize.py location' are set
> - but the 'pdb2pqr location' is. APBS Tools2 also creates
> pymol-generated-PE0.dx but is happy to work with it. (In fact, it says
> 'Could not find pymol-generated.dx so searching for
> pymol-generated-PE0.dx.') The field lines can be visualized as described by
> Michael.
>
Many thanks,
Alan
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
------------------------------------------------------------------------------
SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
http://p.sf.net/sfu/solaris-dev2dev
_______________________________________________
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
