Creating Molecules

Molecules may be created using only Python code. The following example shows how to create a single water molecule.

Example CreateMolecule.py

Function createWater creates a water molecule.
def createWater():


Import the object that tracks open models and several classes from the chimera module.
from chimera import openModels, Molecule, Element, Coord


Create an instance of a Molecule
m = Molecule()


Molecule contains residues. For our example, we will create a single residue of HOH. The four arguments are: the residue type, chain identifier, sequence number and insertion code. Note that a residue is created as part of a particular molecule.
r = m.newResidue("HOH", " ", 1, " ")


Now we create the atoms. The newAtom function arguments are the atom name and its element type, which must be an instance of Element. You can create an Element instance from either its name or atomic number.
atomO = m.newAtom("O", Element("O"))
atomH1 = m.newAtom("H1", Element(1))
atomH2 = m.newAtom("H2", Element("H"))


Set the coordinates for the atoms so that they can be displayed.
from math import radians, sin, cos
bondLength = 0.95718
angle = radians(104.474)
atomO.setCoord(Coord(0, 0, 0))
atomH1.setCoord(Coord(bondLength, 0, 0))
atomH2.setCoord(Coord(bondLength * cos(angle), bondLength * sin(angle), 0))


Next, we add the atoms into the residue.
r.addAtom(atomO)
r.addAtom(atomH1)
r.addAtom(atomH2)


Next, we create the bonds between the atoms.
m.newBond(atomO, atomH1)
m.newBond(atomO, atomH2)


Finally, we add the new molecule into the list of open models.
openModels.add([m])


Call the function to create a water molecule.
createWater()


Code Notes

If multiple water molecules were needed, they should probably be created as multiple residues (with different sequence numbers) in the same molecule.

Running the Example

You can execute the example code by downloading the linked Python script and opening it with the File→Open menu item or with the open command. Note that the .py extension is required for the open dialog/command to recognize that the file is a Python script.