Link

# open a protein and run chimera commands
from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
from chimera import replyobj # for emitting status messages

replyobj.status('Reading 5nsr from pdb.org ...')
rc('open 5nsr')
rc('sel :.C :.D')
rc('del ~sel')
rc('sel :325.C :773.C :1161.C :361.D')
rc('color blue')
rc('color red sel')

Tools -> General Controls -> IDLE

import chimera

# open a protein in Chimera
opened = chimera.openModels.open('3fx2', type="PDB") # a list of opened modules

mol = opened[0] # get the first molecule

# mol.name # pdf file name
# mol.atoms # atoms
# mol.bonds # bonds
# mol.residues # residues

# chimera.colorTable contains getColorByName and getTKColorByName
from chimera.colorTable import getColorByName
red = getColorByName('red') # _chimera.MaterialColor
blue = getColorByName('blue')
yellow = getColorByName('yellow')

mol.color = red # change model color to be red

atoms = mol.atoms
print(len(atoms))
for atom in atoms:
    if atom.name == 'CA':
        atom.color = yellow
    else:
        atom.color = blue
    atom.drawMode = chimera.Atom.Ball
    #coor = atom.xformCoord()
    #print('%10s%10s\n' % (atom.name, atom.residue.id)) # disply stdout to IDLE
    #print(coor.x, coor.y, coor.z)

# ChimeraExtension.py
from  chimera.extension import EMO, manager

# -----------------------------------------------------------------------------
#
class ModelZ_Dialog_EMO ( EMO ):

  def name(self):
    return 'ecsudraft' # extension name displayed in Chimera

  def description(self):
    return "a draft for ecsu validation tool" # description appeared as balloon help

  def categories(self):
    return ['Utilities'] # category in Chimera

  def icon(self):
    return self.path('logo.jpg') # logo

  def activate(self):
    # if no name is supplied, the "__init__.py" module is returned
    self.module('backbone').colorBB() # locate module backbone and call its function colorBB()

# -----------------------------------------------------------------------------
# Register dialogs and menu entry.
#
manager.registerExtension ( ModelZ_Dialog_EMO ( __file__ ) )

# backbone.py
import chimera
from chimera import openModels, Molecule
from chimera.colorTable import getColorByName

def colorBB():

    red = getColorByName('red')
    yellow = getColorByName('yellow')

    # return a list of opened molecules
    for mol in openModels.list(modelTypes=[Molecule]):
        mol.color = red # change model color to be red
        atoms = mol.atoms
        for atom in atoms:
            if atom.name == 'CA':
                atom.color = yellow # change CA atoms to be yellow

Download biopython

python setup.py install --home=/Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/

Enter /Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib, "mv ./python/* ./python2.7", "rm -r ./python", # the default install directory is /python instead of /python2.7

Restart Chimera, open IDLE, type "import Bio"