3D surfaces from MacMolPlt or Gamess
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 ********************************************** 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@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)
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
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. Tom 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
participants (2)
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David Chenoweth -
Tom Goddard