Viewing orbitals and charge distributions
Hello All! I am a CHIMERA newbie and I would like to know how could I create a module in order to read orbitals and/or charge distributions from molecular orbitals programs such as GAUSSIAN, GAMESS, etc. Thanks in advance, .................................................................João -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm
Hi João, Chimera can read several volumetric data formats and create isosurfaces. The formats are listed in the Chimera User's Guide under Tools/Volume Viewer, or you can look at the File types menu of the File/Open... dialog. The types are BRIX or DSN6, CCP4 or MRC, CNS or XPLOR, DelPhi or GRASP, DOCK grids, NetCDF, PRIISM, and SPIDER. Maybe GAUSSIAN or GAMESS can output one of these formats. It is possible to add a new volume file format reader to Chimera by writing some Python code. This is described in the Chimera User's Guide under Tools/Volume Viewer. It says: "ADDING A FILE TYPE A new file format can be added using Python code. The code must read the desired file type into a Numeric Python array and specify how to map data indices into Chimera XYZ positions by giving an XYZ origin (position for index 0,0,0) and XYZ step size (spacing between grid points). In the chimera/share/VolumeData directory, look at dsn6/dsn6_format.py and dsn6/dsn6_grid.py for an example using single-component data. Look at priism/priism_format.py and priism/priism_grid.py for an example with multiple-component data. The *_format.py file is the file reader, and the *_grid.py wraps the data in a grid object suitable for the Volume Viewer user interface. The last step is to add an entry to the list of known file types in fileformats.py." If you are not familiar with Python I may be able to add a volume file reader for you if you provide documentation and example files for the file format. Tom
participants (2)
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João Otávio
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Thomas Goddard