[Chimera-users] Python script for reading volume values at atom positions

[Terry Lang]

Thanks!  I'll try to test it out tomorrow!

Terry


Tom Goddard wrote:
> Hi Terry,
>
>  Here is a Python script to read a volume map and a PDB file and print 
> the values of the map interpolated at the atom positions.  It will 
> work without the Chimera graphical user interface.  I tested it in 
> Chimera 1.2415.
>
>    Tom
>
> ------------------------------------------------------------------------
>
> # -----------------------------------------------------------------------------
> # Script that opens PDB and map files and prints the map values interpolated
> # at each atom position.  Can be run without graphical user interface:
> #
> #       chimera --nogui avalnogui.py
> #
> def map_values_at_atoms(pdb_path, map_path):
>
>     # Open map file.
>     # File name has to have file suffix indicating volume format.
>     from VolumeData import open_file
>     data = open_file(map_path)
>     from VolumeViewer import Data_Region, full_region, Rendering_Options
>     ro = Rendering_Options()
>     map = Data_Region(data, full_region(data.size), '', ro)
>     attribute_name = data.name.split('.')[0]
>     
>     # Open PDB model(s).
>     from chimera import openModels
>     molecules = openModels.open(pdb_path, 'PDB')
>
>     # Interpolate map values at atom positions.
>     from AtomDensity import set_atom_volume_values
>     for mol in molecules:
>         set_atom_volume_values(mol, map, attribute_name)
>
>     # Print values.
>     for mol in molecules:
>         for a in mol.atoms:
>             v = getattr(a, attribute_name)
>             print '%-15s %12.4g' % (a.oslIdent(), v)
>
> # -----------------------------------------------------------------------------
> #
> map_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.omap'
> pdb_path = '/usr/local/src/chimera-demos/volume/examples/1a0m.pdb'
> map_values_at_atoms(pdb_path, map_path)
>   

-- 
P. Therese Lang
Postdoctoral Scholar
Alber Lab, UC Berkeley