We solved the problem this afternoon. The version of APBS that comes with PyMOL does not work on Tiger (10.4). Neither does the universal binary of apbs-1.2.1b available on sourceforge.
An older version of apbs (0.5) worked. We are in the middle of installing APBS via MacPorts, as it seems like that should work too.
I've added some troubleshooting instructions to both
I download and install macpymol-1_2r2.tgz.
I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up.
Load a pdb file after removing HETATM lines.
Open APBS Tools and set grid:
Maximum number of grid points exceeded. Old grid dimensions were
[129, 97, 129]
Fine grid points rounded down from [117, 87, 117]
New grid dimensions are [97, 65, 97]
APBS Tools: coarse grid: (76.908,61.259,77.489)
APBS Tools: fine grid: (65.240,56.035,65.582)
APBS Tools: center: (-22.620,-1.106,-3.967)
APBS Tools: fine grid points (97,65,97)
Click "Run APBS", see hydrogens appear, see residues being selected
and unselected, then the display says:
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
PowerBook, PPC, 10.4.11
David N. Garboczi, PhD
Head, Structural Biology Section (SBS)
Research Technologies Branch (RTB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
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