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.



On Fri, Oct 15, 2010 at 5:51 PM, David Hall <lists@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


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!
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)