Alan, 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.
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?). 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. Andreas On 15/02/2010 10:42, Alan wrote: > Dear Michael, > > I am using Pymol 1.2r3pre and APBS 1.2, all installed via FINK in my Mac > (10.6.2). > > I start pymol, build a TRP, call apbs plugin, set grid, run apbs and I > can see surface and all, but when trying your commands > below, pymol-generated doesn't exist for me. > > Either I am doing something wrong or I don't have the right version of > Pymol and/or Apbs. > > May you clarify me here? This addition to the plugin would be very welcome. > > Thanks in advance, > > Alan > > On Sat, Feb 13, 2010 at 04:55, > <pymol-users-requ...@lists.sourceforge.net > <mailto:pymol-users-requ...@lists.sourceforge.net>> wrote: > > Message: 3 > Date: Wed, 10 Feb 2010 20:26:47 -0500 > From: Michael Lerner <mgler...@gmail.com <mailto:mgler...@gmail.com>> > Subject: [PyMOL] Showing electric field lines > To: pymol mailinglist <pymol-users@lists.sourceforge.net > <mailto:pymol-users@lists.sourceforge.net>> > Message-ID: > <e4c539ed1002101726k30ae7cbcm2482f11fe09dc...@mail.gmail.com > <mailto:e4c539ed1002101726k30ae7cbcm2482f11fe09dc...@mail.gmail.com>> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > Someone recently asked me if there was a way to display field lines with > PyMOL or with an external plugin. Here's what I wrote: > > It turns out that PyMOL recently grew the ability to display field > lines. > After you've run APBS, you'll have a map object called > pymol-generated. Try > this series of commands from the PyMOL prompt: > > gradient my_grad, pymol-generated > ramp_new my_grad_ramp, pymol-generated > color my_grad_ramp, my_grad > > > > > -- > 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 -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk ------------------------------------------------------------------------------ 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
