Editing Talk:APBS (section)

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] 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

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load 
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and 
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)