Can you go to the "Program Locations" tab and find out which version of APBS you're using? There's a problem with the one in /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

I've added instructions for fixing this problem to http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the top of the page, under "APBS Plugin FAQ". Could you try them out and see if they work for you?

Thanks,

-Michael

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dgarboczi@niaid.nih.gov> wrote:
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:
Log:
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:

Log:
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


Help?
PowerBook, PPC, 10.4.11

Dave


--
David N. Garboczi, PhD
Phone: 301-496-4773
Head, Structural Biology Section (SBS)
Research Technologies Branch (RTB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
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Rockville, Maryland 20852-1742
Fax:    301-402-0284
Email: dgarboczi@niaid.nih.gov


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Michael Lerner, Ph.D.
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Laboratory of Computational Biology NIH/NHLBI
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