[PyMOL] Fwd: Help setting apbs tools2 on Mac

[RaDaniel C. 성준 <ren...@gm...>]

I want to bring to your attention the wiki entry I posted in pymolwiki
regarding the default loading paths for apbs:
After installing with fink, none of the default paths work.

http://pymolwiki.org/index.php/Talk:APBS#Making_the_default_paths_to_work.3F

If someone knows what is going on, please drop a line!
Many thanks in advance,
Daniel Ra

---------- Forwarded message ----------
From: RaDaniel Christian 성준 <ren...@gm...>
Date: Mon, Jun 7, 2010 at 7:07 PM
Subject: Help setting apbs tools2 on Mac
To: su...@de...


Can I get help with setting configuration files on pymol (cvs fink
version1.2r3pre)?

I modified the apbsplugin.py to have the following default locations
(taken from http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Visualization-through-the-new-APBS-
 OR  http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py)
:

APBS_BINARY_LOCATION = '/sw64/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = '/sw64/bin/pdb2pqr'
TEMPORARY_FILE_DIR = '/apbstemp'
but after installing by running xpymol as root, I still get this error:

Search dirs ['/sw64/lib/pymol-py26/ext/bin',
'/sw64/lib/pymol-py26/freemol/bin',
'/sw64/lib/pymol-py26/freemol/share/apbs',
'/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
'/sw64/bin/apbs-mpi-openmpi',
'/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
'/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin',
'/sw64/lib/pymol-py26/freemol/share/apbs',
'/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
'/sw64/bin/apbs-mpi-openmpi',
'/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
'/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
trying /sw64/lib/pymol-py26/ext/bin/psize.py
trying /sw64/lib/pymol-py26/ext/bin/psize
trying /sw64/lib/pymol-py26/freemol/bin/psize.py
trying /sw64/lib/pymol-py26/freemol/bin/psize
trying /sw64/lib/pymol-py26/freemol/share/apbs/psize.py
trying /sw64/lib/pymol-py26/freemol/share/apbs/psize
trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize.py
trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/psize
trying /sw64/bin/apbs-mpi-openmpi/psize.py
trying /sw64/bin/apbs-mpi-openmpi/psize
trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize.py
trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/psize
trying /sw64/bin/pdb2pqr/psize.py
trying /sw64/bin/pdb2pqr/psize
trying /sw/share/pdb2pqr/psize.py
trying /sw/share/pdb2pqr/psize
trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize.py
trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/psize
trying /sw64/bin/psize.py
trying /sw64/bin/psize
trying /sw64/sbin/psize.py
trying /sw64/sbin/psize
trying /usr/bin/psize.py
trying /usr/bin/psize
trying /bin/psize.py
trying /bin/psize
trying /usr/sbin/psize.py
trying /usr/sbin/psize
trying /sbin/psize.py
trying /sbin/psize
trying /usr/local/bin/psize.py
trying /usr/local/bin/psize
trying /usr/X11/bin/psize.py
trying /usr/X11/bin/psize
trying /usr/libexec/psize.py
trying /usr/libexec/psize
trying /Developer/Tools/psize.py
trying /Developer/Tools/psize
trying /usr/X11R6/bin/psize.py
trying /usr/X11R6/bin/psize
trying /sw64/share/xtal/ccp4-6.1.3/etc/psize.py
trying /sw64/share/xtal/ccp4-6.1.3/etc/psize
trying /sw64/share/xtal/ccp4-6.1.3/bin/psize.py
trying /sw64/share/xtal/ccp4-6.1.3/bin/psize
trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize.py
trying /sw64/share/xtal/ccp4-6.1.3/ccp4i/bin/psize
trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize.py
trying /sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin/psize
trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize.py
trying /sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications/psize
trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize.py
trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/psize
trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize.py
trying /usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386/psize
trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize.py
trying /usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications/psize
trying /usr/local/bin/psize.py
trying /usr/local/bin/psize
trying /opt/local/bin/psize.py
trying /opt/local/bin/psize
trying /sw/bin/psize.py
trying /sw/bin/psize
Could not find default location for file: psize.py
Search dirs ['/sw64/lib/pymol-py26/ext/bin',
'/sw64/lib/pymol-py26/freemol/bin',
'/sw64/lib/pymol-py26/freemol/share/apbs',
'/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
'/sw64/bin/apbs-mpi-openmpi',
'/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
'/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/sw64/lib/pymol-py26/ext/bin', '/sw64/lib/pymol-py26/freemol/bin',
'/sw64/lib/pymol-py26/freemol/share/apbs',
'/sw64/lib/pymol-py26/freemol/share/pdb2pqr',
'/sw64/bin/apbs-mpi-openmpi',
'/sw64/share/apbs-mpi-openmpi/tools/manip/psize.py',
'/sw64/bin/pdb2pqr', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr.py
trying /sw64/lib/pymol-py26/ext/bin/pdb2pqr
trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr.py
trying /sw64/lib/pymol-py26/freemol/bin/pdb2pqr
trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr.py
trying /sw64/lib/pymol-py26/freemol/share/apbs/pdb2pqr
trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr.py
trying /sw64/lib/pymol-py26/freemol/share/pdb2pqr/pdb2pqr
trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr.py
trying /sw64/bin/apbs-mpi-openmpi/pdb2pqr
trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr.py
trying /sw64/share/apbs-mpi-openmpi/tools/manip/psize.py/pdb2pqr
trying /sw64/bin/pdb2pqr/pdb2pqr.py
trying /sw64/bin/pdb2pqr/pdb2pqr
trying /sw/share/pdb2pqr/pdb2pqr.py
trying /sw/share/pdb2pqr/pdb2pqr
trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr.py
trying /usr/local/phenix-dev-403/build/mac-intel-osx/bin/pdb2pqr
trying /sw64/bin/pdb2pqr.py
trying /sw64/bin/pdb2pqr
Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
Could not find default location for file: temp
Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
Could not find default location for file: temp
Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
Could not find default location for file: temp
Search dirs ['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
get_default_location will search the following:
['/usr/local/apbstemp', '/tmp', '.', '/sw/share/pdb2pqr',
'/usr/local/phenix-dev-403/build/mac-intel-osx/bin', '/sw64/bin',
'/sw64/sbin', '/usr/bin', '/bin', '/usr/sbin', '/sbin',
'/usr/local/bin', '/usr/X11/bin', '/usr/libexec', '/Developer/Tools',
'/usr/X11R6/bin', '/sw64/share/xtal/ccp4-6.1.3/etc',
'/sw64/share/xtal/ccp4-6.1.3/bin',
'/sw64/share/xtal/ccp4-6.1.3/ccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/dbccp4i/bin',
'/sw64/share/xtal/ccp4-6.1.3/share/XIAROOT/xia2/Applications',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test',
'/usr/local/xia2-0.3.1.6/xia2core-0.3.1.6/Test/Compiled/mac_386',
'/usr/local/xia2-0.3.1.6/xia2-0.3.1.6/Applications', '/usr/local/bin',
'/opt/local/bin', '/sw/bin']
Could not find default location for file: temp

Also, the default locations are not read, and I get the following
values on the apbs tools2 plugin window:

APBS_BINARY_LOCATION =  /sw64/bin/apbs
APBS_PSIZE_LOCATION = blank
APBS_PDB2PQR_LOCATION = /sw64/bin/pdb2pqr

TEMPORARY PQR FILE = pymol-generated.pqr
TEMPORARY PDB FILE = pymol-generated.pdb
TEMPORARY DX FILE = pymol-generated.dx
APBS INPUT FILE = pymol-generated.in

Is there a fix for this?

Thank you,
Daniel Ra
--
Stop the ACTA. Row, row; fight the power! http://www.eff.org/



-- 
Stop the ACTA. Row, row; fight the power! http://www.eff.org/

Choel Kim Structural Biology Laboratory
Department of Pharmacology, Baylor College of Medicine,
Alkek N510, One Baylor Plaza, Houston, TX 77030
713-798-8687 (Lab)
713-798-3145 (Fax)