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

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# ----------------------------------------------------------------------------- # 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)