[Chimera-users] MolMol file format for electrostatic potentials

Tom Goddard goddard at cgl.ucsf.edu
Wed Jan 16 13:34:29 PST 2008

Hi Esther,

  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
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
data follows
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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