Hi again,
I've gotten the code much closer to working. Also, I think it's factored
well enough that most of it should be non-GPL-contaminated. After I
actually get it working completely, I'll email the APBS folks to see if
they care about licensing issues.
Right now, I can generate isomeshes and isosurfaces for methanol that look
reasonable (yay!). But I can't get the surface coloring to work. If I do
this:
load methanol.pdb
show surface, methanol
run cleanerDxMap.py # loads up my APBS-generated map
ramp_new e_lvl, map, [-10,0.00,10]
set surface_color, e_lvl, methanol
isosurf surfneg, map, -0.1
isomesh meshpos, map, 0.1
color red, surfneg
color blue, meshpos
I get a good looking mesh, a good looking isosurface, and a completely
white surface around methanol. dragging the limits on the map around to
really small things or really large things doesn't seem to help either.
Any quick guesses?
In case you have a little bit of spare time, I have two dumb sounding
questions:
1) What exactly is supposed to go into ObjectMapState-Dim?
At first, I thought it was just a list of three integers giving the map
dimensions (in grid points), but that doesn't seem to be the answer. When
I take a map that PyMOL generates for me (e.g. with
cmd.map_new(map,gaussian,0.1,methanol)) and print it out as a
Python list (using ObjectMapAsPyList, etc.), I get different results each
time the program is run.
2) What exactly is supposed to go into ObjectMapState-Field-Points?
I think it's just the x,y,z coordinates of the points starting at
minCorner and working up through maxCorner by incrementing z then y then x
([x1,y1,z1,x1,y1,z2,...]. But, when I first tried to set points myself, I
got a few things wrong .. it looks like n_dim is supposed to be 4. I had
guessed 3. It also looks like Dim should be four ints, the grid
dimensions followed by the number 3. Finally, it looks like stride should
be the normal stride followed by the base_size. What am I missing here?
Why is points a four-dimensional thing while data is a three-dimensional
thing?
thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Thu, 11 Dec 2003, Warren L. DeLano wrote:
Michael,
Impressive! I think you're one of the few people to delve into
PyMOL's source like this.
Obviously I'd be the best person to look at your code, but I'm
crunched right now getting ready for this upcoming trip. Also, if the
code is GPL-contaminated, then it can't be useful in the main version,
but perhaps we can rewrite this cleanly later on. I can probably help
you in January. What you've written sounds right...
One thing I'd suggest for debugging in the meantime is that you
use the isomesh or isosurface routines to explore what data is ending up
in the Map, before trying to use the color ramps. There may also be
some code in the chempy brick stuff which could serve as an example for
populating the list.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
