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
