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
http://pymolwiki.org/index.php/APBS
and
http://pymolwiki.org/index.php/User:Mglerner
On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dgarbo...@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)
> Twinbrook 2/Room 110
> 12441 Parklawn Drive
> Rockville, Maryland 20852-1742
> Fax: 301-402-0284
> Email: dgarbo...@niaid.nih.gov
>
>
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--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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