I have a pdb file of some solvent molecules in a box of 20 Angstroms I have built using Tinker. I have opened the file with Chimera, Molden, Pymol and Avogadro... but I would like to see, and maybe generate a figure with, the proper limits of the box if there is any tool for doing so.

Has anyone succeded before? I do not mind getting used to another visualization program or tool.

Thank you in advance

  • $\begingroup$ I know VMD can show the box of surfaces, but I'm not sure about this specific case. Have you tried it yet? $\endgroup$ Commented Mar 24, 2022 at 17:02

2 Answers 2


In pymol the cell can be displayed by typing show cell into the command line.


Atomic simulation environment is useful for a lot of other manipulations you might want to do and it comes with a GUI that is capable of doing this (given that you define the cell, it will also behave if you do not define a cell though since it works for periodic and non-periodic systems).

pip install --user ase
ase gui structure.pdb

Visual of the GUI in Atomic Simulation Environment


You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .