[Chimera-users] 3D surfaces from MacMolPlt or Gamess

David Chenoweth dchen at caltech.edu
Fri Jun 13 11:57:18 PDT 2008

Dear Chimera team,

I am having a bit of trouble reading a file into Chimera.  Currently I  
am using Gamess to run DFT calculations and I can open these files in  
MacMolPlt which allows me to display orbitals or plot electrostatic  
potential surfaces. I can export the 3D surface data however I can't  
get Chimera to read the 3D grid files. Can you help me?  I attached  
the file format info below and I can send you example files if you  
need. I am really trying to use Chimera for all my graphics needs  
wether it be viewing surfaces or orbitals from DFT calculations or  
looking at electron density maps from crystal structure data. If I  
could convert the 3D surface data files below into ccp4 or cns  
formated files that should also work for Chimera I just haven't found  
a way to do this yet.

Thanks in advance,

David M. Chenoweth
California Institute of Technology
Division of Chemistry and Chemical Engineering
Mail Code: 164-30
1200 California Boulevard, 91125 Pasadena
California, USA

Phone: 626-395-6074
Email: dchen at caltech.edu

File format data info:

2D and 3D Surfaces (Import and Export)

MacMolPlt implements a simple format for importing and exporting 2D  
and 3D surface data. To export a surface first create a surface and  
make sure that the surface is updated so that the grid data is  
available for export. Then choose the Export menu command and the  
Surface export format. MacMolPlt will then export the surface grid  
data to the file you specify (this is useful to check the input format  
as well). To import a 2D or 3D surface create a new General 2D or 3D  
surface. From the surface dialog you can then choose the file  
containing the grid data. The format for the 2D and 3D files are  
similar but there are a couple of differences. Floating point numbers  
may be given in a variety of formats and the grid data may contain any  
number of values per line. The units for the coordinate system should  
normally be angstroms.

For 2D planes the format is:

1Line Label
30 # grid points
-4.165882 -4.306789 0.839681 //Origin of the 2D grid
0.297019 0.000000 0.000000 //X inc vector
0.000000 0.297019 0.000000 //Y inc vector
-0.000018 -0.000021... (# of grid points squared grid values)

For 3D surfaces:

1 Line label
35 12 41 //nx ny nz
-4.687880 -1.587537 -5.059790 //Origin of the 3D grid
0.280144 0.288642 0.275207 //x increment, y inc, z inc/ grid(x(y(z)))
0.000000 0.000000... (nx*ny*nz grid values)
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