[Chimera-users] MolMol file format for electrostatic potentials
goddard at cgl.ucsf.edu
Wed Jan 16 13:34:29 PST 2008
Chimera does not know how to read the MolMol potential file header.
But the MolMol format is very simple and you could edit it to a similar
format the APBS electrostatic potential format and use that file in
Chimera to color a molecular surface.
Here's the MolMol potential format as described in the ReadPot manual
x0 xSize xInc
y0 ySize yInc
z0 zSize zInc
val val val ....
and here is an example APBS file:
# 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 ....
I believe if you replaced the first lines of the MolMol file with:
object 1 class gridpositions counts xSize ySize zSize
origin x0 y0 z0
delta xInc 0 0
delta 0 yInc 0
delta 0 0 zInc
val val val .....
and make the file suffix ".dx", then this would be read in Chimera as an
APBS potential file and could be used for coloring.
The MolMol format could be added into Chimera so this file editing is
not needed but I wonder if enough people would use that to make it worth
writing code for. I'll add it to our list of requested features.
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