Resources

• ​Programmer's Guide (​http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/)
• ​Example scripts (​http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts)
• IDLE (Tools > General Controls): help(object), dir(object)
• ​Chimera developer mailing list (​http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev)
• Source code:
  • ​subversion browser (​http://plato.cgl.ucsf.edu/trac/chimera/browser)
  • ​download (​http://www.cgl.ucsf.edu/chimera/sourcecode.html)
  • C++ headers are available in distributions (see $CHIMERA/include)
  • Python source code is included with distributions (see $CHIMERA/share)
• ​Python documentation (​http://docs.python.org/)
• ​Numpy examples (​http://www.scipy.org/Numpy_Example_List_With_Doc)

Chimera Molecular Data

# a list of open models
models = chimera.openModels.list()

# restrict list to Molecules
molecules = chimera.openModels.list(modelTypes=[chimera.Molecule])

# a Molecule's residues, atoms, or bonds
if len(molecules):
  r = molecules[0].residues
  a = molecules[0].atoms
  b = molecules[0].bonds

Residues

• type: LYS, HEM, etc.
• id.position / id.chainId / id.insertionCode: number / chain ID / insertion code
• molecule: parent Molecule
• atoms: list of atoms
• atomsMap: dict of {atom-name: [list of atoms]}
• isHelix / isStrand: in helix / strand

Atoms

• name: name
• coord() / xformCoord(): untransformed / transformed coordinates
• residue / molecule: parent Residue / Molecule
• bonds: list of bonds
• neighbors: list of bonded atoms
• primaryBonds() / primaryNeighbors(): same as above but only primary altlocs
• bondsMap: dict of {bonded-atom: bond}
• color: Color
• display: True if shown
• drawMode: one of chimera.Atom.X with X being Dot, Sphere, EndCap, or Ball
• element: chemical element (type chimera.Element, settable with string or number)
• label: label shown in graphics window
• radius: VdW radius

Bonds

• atoms: 2-tuple of atoms
• otherAtom(a): [a is one of the bond's atoms] other atom in bond
• drawMode: one of chimera.Bond.X with X being Wire or Stick
• label: label shown in graphics window
• molecule: parent Molecule
• length(): length

Molecular Measurements

chimera module functions use Points, which are returned by Atom's coord() or xformCoord() methods

• distance / sqdistance
• also: a1.coord().[sq]distance(a2.coord()) [similar for xformCoord]
• angle (in degrees)
• dihedral (in degrees)

Molecular Editing

Look in $CHIMERA/share/BuildStructure/__init__.py for examples of creating new molecules and residues.

Using the chimera.molEdit module:

• addAtom
  • if adding in bulk, make sure to specify optional serialNumber keyword
• addBond
• addDihedralAtom -- add atom given a bond length / angle / dihedral

Setting or Querying Selections

Using the chimera.selection module:

• currentAtoms / currentBonds / currentResidues / currentMolecules: currently selected Atoms / Bonds / Residues / Molecules
• setCurrent: set current selection to given items
• addCurrent / addImpliedCurrent: add given items to current selection
• the "implied" version also selects endpoint Atoms of added Bonds and connecting Bonds of added Atoms
• removeCurrent: remove items from current selection, if present

Miscellaneous

• chimera.runCommand: execute any command-line command (arg is a string)
  • direct Python equivalent usually in Midas module
• chimera.colorTable module:
  • getColorByName: get a Color by name
• OpenSave module:
  • osOpen: open a file or HTTP URL, with or without compression
• chimera.extension module
  • manager.instances: running dialogs listed at end of Tools menu