Re: [PyMOL] OpenDX files from opendx.org
Hi David, I've saved the files and will look into this. Thanks for bringing this to our attention. I'll let you know when I find something. Cheers, -- Jason On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where loading into pymol gives the error ObjectMap-Error: Error reading map. Any help in what's wrong with these files (or how to patch the VMD plugins that I believe pymol uses to read in dx files) would be appreciated. -David -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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] OpenDX files from opendx.org
Hi David, As far as I know, PyMOL is still using its own DX reading functions (primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious). I don't think it would be too much work to get PyMOL to read regular.dx. As far as I can tell, the only problem is that PyMOL is expecting the line that starts with object 3 to say object 3 class array type double instead of object 3 class array float. As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see e.g. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html), but I'm not sure that PyMOL's DX reader supports them directly. I have not looked into the VMD plugins. If they support non-orthogonal DX maps out of the box, that might be a quick and easy solution. Cheers, -Michael On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where loading into pymol gives the error ObjectMap-Error: Error reading map. Any help in what's wrong with these files (or how to patch the VMD plugins that I believe pymol uses to read in dx files) would be appreciated. -David -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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) -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev___ 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] OpenDX files from opendx.org
Thanks, Clearly my assumption about using the VMD plugins was wrong (and the reader in dxplugin.cpp doesn't appear to even read that line, much less assume it will say double). As a more general question, does pymol use the plugins in contrib/uiuc/plugins/molfile_plugin at all or is that a relic from some earlier time? Since the directory was still being updated in June 2009, I assume it is at least used for some files? -David On Mon, Oct 18, 2010 at 11:49 AM, Michael Lerner mgler...@gmail.com wrote: Hi David, As far as I know, PyMOL is still using its own DX reading functions (primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious). I don't think it would be too much work to get PyMOL to read regular.dx. As far as I can tell, the only problem is that PyMOL is expecting the line that starts with object 3 to say object 3 class array type double instead of object 3 class array float. As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see e.g. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html), but I'm not sure that PyMOL's DX reader supports them directly. I have not looked into the VMD plugins. If they support non-orthogonal DX maps out of the box, that might be a quick and easy solution. Cheers, -Michael On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where loading into pymol gives the error ObjectMap-Error: Error reading map. Any help in what's wrong with these files (or how to patch the VMD plugins that I believe pymol uses to read in dx files) would be appreciated. -David -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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) -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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] OpenDX files from opendx.org
Hi David, Warren placed the VMD molfile plugin code into the open-source PyMOL contrib source tree (honoring any copyright mandates), but didn't integrate it into open-source PyMOL (see setup.py). The Incentive PyMOL build we deliver though, does have working molfile plugin code--one of the perks for those who support the PyMOL project. (A few days ago, I was bug-fixing PyMOL's interaction with the molfile DCD trajectory plugin, and PyMOL could easily handle systems with ~45,000 atoms over 3500 states on my machine.) The VMD molfile plugin is a useful contribution to the scientific community, and I think, the route we'll continue to take with PyMOL. Cheers, -- Jason On Mon, Oct 18, 2010 at 4:12 PM, David Hall li...@cowsandmilk.net wrote: Thanks, Clearly my assumption about using the VMD plugins was wrong (and the reader in dxplugin.cpp doesn't appear to even read that line, much less assume it will say double). As a more general question, does pymol use the plugins in contrib/uiuc/plugins/molfile_plugin at all or is that a relic from some earlier time? Since the directory was still being updated in June 2009, I assume it is at least used for some files? -David On Mon, Oct 18, 2010 at 11:49 AM, Michael Lerner mgler...@gmail.com wrote: Hi David, As far as I know, PyMOL is still using its own DX reading functions (primarily ObjectMapDXStrToMap in layer2/ObjectMap.c if anyone's curious). I don't think it would be too much work to get PyMOL to read regular.dx. As far as I can tell, the only problem is that PyMOL is expecting the line that starts with object 3 to say object 3 class array type double instead of object 3 class array float. As for regularskewed.dx, PyMOL *does* support non-orthogonal maps (see e.g. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05870.html), but I'm not sure that PyMOL's DX reader supports them directly. I have not looked into the VMD plugins. If they support non-orthogonal DX maps out of the box, that might be a quick and easy solution. Cheers, -Michael On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote: I have long been happy reading .dx files produced by apbs and my own programs into pymol. Everything works great. Interestingly, when I save a .dx file from OpenDX (http://opendx.org), pymol seems to not be able to read it. I've attached two files that come from OpenDX's samples directory where loading into pymol gives the error ObjectMap-Error: Error reading map. Any help in what's wrong with these files (or how to patch the VMD plugins that I believe pymol uses to read in dx files) would be appreciated. -David -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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) -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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
[PyMOL] Displaying PDB files that were determined via fiber diffraction
Hello, Does anyone know how to display PDB files that are determined by fiber diffraction? The default just shows a single peptide, when in fact it is supposed be a bunch of peptides interacting with one another to make a fiber. Thanks a lot. Chad *** Chad R. Simmons Researcher Biodesign Institute at Arizona State University P.O. Box 875601 Tempe, AZ 85287 Office: (480) 727-6495 Lab:(480) 727-0428 Fax:(480) 727-0396 -- Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev ___ 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
