[PyMOL] APBS plugin woes
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
Re: [PyMOL] APBS plugin woes
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.govwrote: 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
Re: [PyMOL] APBS plugin woes
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
