Hi Andreas,

Thanks for your reply. See my comments please. Essentially, I need to install new apbs plubgin.

2010/2/15 Andreas Förster <docandreas@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:


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 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)