The bonds displayed in the 3D crystal view do not correspond to those defined in objcryst - they are automatically added by 3dmol.js based on atomic distances and element radii, with quite strict limits.
It may be necessary to switch to a different intermediate format than CIF to show the bonds which are defined in objcryst, because 3dmol.js can't extract the bonds from a CIF.
The bonds displayed in the 3D crystal view do not correspond to those defined in objcryst - they are automatically added by 3dmol.js based on atomic distances and element radii, with quite strict limits.
It may be necessary to switch to a different intermediate format than CIF to show the bonds which are defined in objcryst, because 3dmol.js can't extract the bonds from a CIF.
Maybe use a CIF model to define the unit cell, and use a different model to define the atoms and mods. See https://github.com/3dmol/3Dmol.js/blob/master/3Dmol/parsers.js