[Chimera-users] 3D surfaces from MacMolPlt or Gamess
David Chenoweth
dchen at caltech.edu
Thu Jun 12 19:08:07 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 with an exported density file and
electrostatic potential map. 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,
Dave
**********************************************
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:
http://www.scl.ameslab.gov/~brett/MacMolPlt
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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