By default, py3Dmol loads the content of a PDB entry, which represents the asymmetric unit for structures determined by crystographic methods and some structures determined by 3D electron microscopy. The asymmetric unit contains the unique part of a structure, but may not represent the biologically active form of a structures. See PDB-101 tutorial.
An asymmetric unit may contain:
This example has been copied from py3Dmol tutorial.
import py3Dmol
In this example below (3DEM structure of Zika virus) we load the content of the asymmetric unit. In this case, the asymmetric unit represents a portion of the biological assembly.
view = py3Dmol.view(query='pdb:5ire')
view.setStyle({'cartoon':{'color':'spectrum'}})
view.show()
Using the 'doAssembly' option, the biological assembly will be created using symmetry operations in the PDB entry.
view = py3Dmol.view(query='pdb:5ire',options={'doAssembly':True})
view.setStyle({'cartoon':{'color':'spectrum'}})
view.show()