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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

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

2 Answers 2

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

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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

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