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)
