Re: [PyMOL] OpenDX files from opendx.org

2010-10-18 Thread Jason Vertrees
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

Re: [PyMOL] OpenDX files from opendx.org

2010-10-18 Thread Michael Lerner
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

Re: [PyMOL] OpenDX files from opendx.org

2010-10-18 Thread David Hall
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

Re: [PyMOL] OpenDX files from opendx.org

2010-10-18 Thread Jason Vertrees
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

[PyMOL] Displaying PDB files that were determined via fiber diffraction

2010-10-18 Thread Chad Simmons
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