FYI, that worked for me. I just copied the binary to /usr/local/lib. -- Jason
-- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner <mgler...@gmail.com> wrote: > 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 <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 >> >> >> 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) > > ------------------------------------------------------------------------------ > 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 (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 > ------------------------------------------------------------------------------ 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 (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
