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 <renderea...@gmail.com> Date: Mon, Jun 7, 2010 at 7:07 PM Subject: Help setting apbs tools2 on Mac To: supp...@delsci.com 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) ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ 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
