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 <[email protected]>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: [email protected]
>
>
> 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 ([email protected])
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/[email protected]
>
--
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)
------------------------------------------------------------------------------
Join us December 9, 2009 for the Red Hat Virtual Experience,
a free event focused on virtualization and cloud computing.
Attend in-depth sessions from your desk. Your couch. Anywhere.
http://p.sf.net/sfu/redhat-sfdev2dev
_______________________________________________
PyMOL-users mailing list ([email protected])
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/[email protected]
