Unit Cell Unit Cell icon

Unit Cell builds crystallographic unit cells using information in PDB files. 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, fetching PQS files

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

Unit Cell dialog

Once a PDB file has been opened in Chimera, Unit Cell can generate symmetry-related copies if the PDB header 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 available for the current Molecule are shown. If the PDB file has no CRYST1 record, the space group and cell parameters fields will be blank. If the PDB file also lacks SMTRY and MTRIX information, or if the model was not read from a PDB file, it will not be possible to build a unit cell.

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):

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 PDB 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 records, but this can be done with Multiscale Models or the command sym.

UCSF Computer Graphics Laboratory / September 2009