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
