[Chimera-users] Viewing orbitals and charge distributions
goddard at cgl.ucsf.edu
Fri Apr 23 09:29:20 PDT 2004
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.
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