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 <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)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Fax:    301-402-0284
Email: dgarboczi@niaid.nih.gov


The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient.  If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices.  The National Institute
of Allergy and Infectious Diseases (NIAID) shall not accept liability
for any statement made that are the sender's own and not expressly made
on behalf of the NIAID by one of its representatives.

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now.  http://p.sf.net/sfu/bobj-july
_______________________________________________
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



--
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)