MolMol file format for electrostatic potentials

Hi, Is there a way to import into Chimera the results of MolMol's calculation for electrostatic potentials? I like MolMol because it shows the charge without the surface hydrogens (so the results show the same thing as with, the hydrogens, but 'more strongly'), and equally important, the program is very easy to use. Is there a format conversion script, or would it be possible to make one? I can send sample files, if this would be helpful. thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt@bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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 page: http://www.scl.kyoto-u.ac.jp/scl/appli/appli_manual/molmol/help/html/ReadPot... 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 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. Tom
participants (2)
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Esther Bullitt
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Tom Goddard