List of molecular modeling software supporting crystolecules

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NanoEngineer-1 — no longer maintained
Avogadro — https://avogadro.cc (docs>>manipulate-tool)
Samson — https://www.samson-connect.net
atomCAD — https://github.com/atomCAD/atomCAD/
...

Related

Software
For bulk limit: Constructive solid geometry
List of programmatic 3D modelling tools

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