Hi,
I don't remember the details, but I do remember that I had some
troubles using bricks when I was writing the APBS plugin. The DX file
format is really simple, though, especially for this sort of thing.
http://apbs.sourceforge.net/doc/user-guide/index.html#opendx-format
If I recall correctly, my problems with bricks were mostly that I
wasn't using them correctly, but I didn't figure out how to use them
correctly until after I'd already converted everything to DX.
-Michael Lerner
On 2/19/07, BuzB <bmb...@gmail.com> wrote:
Hi All,
Thanks to everyone and for the responses to and encouragement about my
query on visualizing molecular orbitals in pymol.
I'm using PyMol 0.99rc6.
I feel like I'm quite close to a solution. I've developed a routine to
compute a 3 dimensional matrix containing the probability amplitudes
of the orbitals, which I can load into a PyMol brick object.
Then, things start to go wrong....
When I use the load_brick function in the cmd module;
cmd.load_brick(brik, "Brick")
or alternatively,
cmd.load_object(loadable.brick, brik, "Brik")
PyMol returns the message;
ObjectMap: Map Read. Range = 0.000 to 0.000
but it does display the object "Brick" in the objects menu. I can then
create an isomesh or surface with the command;
cmd.isosurface("BrikSurf", "Brick", 0.1)
But no surface is displayed on screen.
The example file brick01.py that is included in examples/devel does
something almost identical to what I'm trying to do, it displays an
exponentially decaying density, but also with no success in PyMol
0.99rc6. Is there a bug somewhere in the load_brick function that I'm
running into?
Thanks a lot!
bmb197
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Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner http://lernerclan.net
