Scripts: save.py

# Fit an atomic model in a map and save new coordinates and map to files.

from chimera import runCommand as run, openModels
run('open 1grl')
run('open emdbID:1080')
run('fit #0 #1')

# Get PDB and map Python objects
m, v = openModels.list()

# Save the map using Python function
map_path = "/tmp/mymap.mrc"
from VolumeData import save_grid_data
save_grid_data(v.data, map_path)

# Or save the map using a command
#run('volume #1 save %s' % map_path)

# Save the PDB relative to the volume coordinate system using Python function
pdb_path = "/tmp/fitpdb.pdb"
from Midas import write
write(m, v, pdb_path)

# Or save the pdb using a command
#run('write relative #1 #0 %s' % pdb_path)