[Chimera-users] 3D surfaces from MacMolPlt or Gamess
goddard at cgl.ucsf.edu
Fri Jun 13 15:59:17 PDT 2008
I added a MacMolPlt grid file reader to Chimera. Works with the
example files you sent. It will be in tonight's daily builds if they
succeed. I made the automatically recognized file suffix ".mmp". Tell
me if there is a standard file suffix for these files and I will make
Chimera recognize it. Otherwise you have to choose the file type each
time you open such a file in Chimera.
David Chenoweth wrote:
> Hi Tom,
> I agree that it would be better to just read from the Gamess file
> directly but I think MacMolPlt3D is calculating the electron density
> map and electrostatic potential map from the Gamess file not just
> reading it in. I am sending you the Gamess file Imidazole_321g_jag.log
> that I open in MacMolPlt3D to create the surfaces. I am also sending
> you two exported surface files for imidazole that were made from
> MacMolPlt3d and they are called Im_Dens_Gamess and Im_EPot_Gamess
> (they are zipped into Example_Gemess_file.zip). Maybe the modified
> Gaussian cube file reader will work with these files.
> Thanks for all the help,
> Dave Chenoweth
Tom Goddard wrote:
> Hi David,
> What is the format of the grid data from the Gamess DFT calculation?
> It seems like it would be better to read the Gamess file instead of the
> grid file produced by MacMolPlt.
> The MacMolPlt 3D surface export would be simple to read in Chimera
> using a modified version of the Gaussian cube file reader (Python code
> chimera/share/VolumeData/gaussian/gaussian_format.py). I would need an
> example file to test with.
David Chenoweth wrote:
> 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,
More information about the Chimera-users