Talk:APBS

From PyMOLWiki
Revision as of 18:40, 20 July 2010 by Rendereason (talk | contribs) (Making the default paths to work?: new section)
Jump to: navigation, search

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

Well done!

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it. Tree 18:21, 21 February 2008 (CST)

Question/Crash

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works. Tree 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine. Desastre 27 April 2008

Making the default paths to work?

I saw a discussion in the Pymolbb dated April 15, 2010 [1] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to: APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi' APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py' APBS_PDB2PQR_LOCATION = None TEMPORARY_FILE_DIR = None

I hope a solution to this issue can be posted in the wiki. --Rendereason 22:40, 20 July 2010 (UTC)