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

Tom Goddard goddard at cgl.ucsf.edu
Fri Jun 13 15:59:17 PDT 2008

Hi Dave,

  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.
>     Tom

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,
> Dave

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