Unit Cell Unit Cell icon

Unit Cell builds crystallographic unit cells using symmetry information from the input coordinate file (PDB or mmCIF). A crystallographic unit cell consists of a unique set of coordinates, duplicated and transformed according to the crystallographic and (if present) noncrystallographic symmetries in the crystal. Unit Cell can be used to regenerate the full unit cell, or only those parts defined by crystallographic symmetry or noncrystallographic symmetry. See also: Crystal Contacts, Multiscale Models, sym, the biological unit function in the Model Panel, fetching PDB-biounit and PQS files

There are several ways to start Unit Cell, a tool in the Higher-Order Structure category.

Unit Cell dialog

After a PDB or mmCIF file has been opened in Chimera, Unit Cell can generate symmetry-related copies if the file contains sufficient information. In the dialog, Molecule can be set to any open molecule model. The space group, unit cell parameters, and numbers of transformation matrices for the current Molecule are shown, if available.

The copies can be saved. Close simply dismisses the dialog, while Help opens this page in a browser window.

Clicking Options reveals additional settings (clicking the close button on the right hides them again). The descriptions below refer to PDB files, but the corresponding mmCIF information can also be used:

Changes in cell origin or number can be applied by pressing Enter (return) or clicking the Make copies button.


Many problems are due to information that is missing from (or incorrect within) the input file. One way to validate symmetry information is to identify steric clashes with the Crystal Contacts tool.

Unit Cell does not generate multimers defined by BIOMT matrices, but this can be done with Multiscale Models or the command sym.

Only the following CIF unit cell fields are used:

cell_length_a, cell_length_b, cell_length_c
cell_angle_alpha, cell_angle_beta, cell_angle_gamma

UCSF Computer Graphics Laboratory / June 2014