Hi Scott,

An APBS OpenDX file is just a text file which lists the values at the grid points (x-axis varying fastest, z axis varying slowest).  So you could probably write a script to convert it to this other text format easily enough.  A Chimera Python script could do the same thing but it isn't any easier.  Still if you wanted to try it using Chimera Python here is a basic example of accessing volume data in Chimera

https://www.rbvi.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py

Below is the start of an APBS OpenDX file to give you an idea of how you would write a script to read it and reformat it how you want.

By the way, we haven't developed Chimera for about 8 years and our new program ChimeraX is much more capable, but would still need a similar Python script to output values in the format you want.

  Tom

# Data from APBS 0.3.2
# 
# POTENTIAL (kT/e)
# 
object 1 class gridpositions counts 65 97 97
origin -8.064450e+00 -4.768105e+01 -4.266980e+01
delta 3.779047e-01 0.000000e+00 0.000000e+00
delta 0.000000e+00 4.098240e-01 0.000000e+00
delta 0.000000e+00 0.000000e+00 4.099125e-01
object 2 class gridconnections counts 65 97 97
object 3 class array type double rank 0 items 611585 data follows
8.921700e-01 9.000006e-01 9.078676e-01 
9.157664e-01 9.236924e-01 9.316403e-01 
9.396046e-01 9.475795e-01 9.555586e-01 
9.635354e-01 9.715027e-01 9.794531e-01 
9.873788e-01 9.952714e-01 1.003122e+00 
...

(65 * 97 * 97 values in the file).


On Mar 4, 2024, at 3:46 PM, Scott Bembenek via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:


Is it possible to use Chimera to convert an APBS OpenDX grid to coordinates: x,y,x, grid point value?
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