Tool: Unit Cell

Unit Cell builds crystallographic unit cells using symmetry information from the input coordinate file (PDB or mmCIF, but not small-molecule CIF). It can regenerate the full unit cell, multiple unit cells, or only those parts defined by crystallographic symmetry or noncrystallographic symmetry. See also: Crystal Contacts, sym

The Unit Cell tool can be opened from the Higher-Order Structure section of the Tools menu and manipulated like other panels (more...). It is also implemented as the command unitcell.

The Atomic structure of interest should be chosen from the list of current atomic models. The space group, unit cell parameters, and numbers of transformation matrices (if available from the input file) are shown in the dialog. Buttons:

• Make Copies – create additional copies of the atomic structure and transform them as specified by the options
• Outline – show/hide a white outline box of the unit cell
• Delete Copies – remove the additional copies of the structure
• Options – show/hide the options
• Help – open this page in the Help Viewer

Option descriptions are for PDB symmetry records, but the equivalent information from mmCIF is used in the same way:

• Use crystal symmetries from file – apply crystallographic symmetry described by SMTRY1, SMTRY2, and SMTRY3 matrices in REMARK 290 lines of a PDB file
  
  
• Use space group if symmetries are missing – for files without crystallographic symmetry matrices, use the space group name in the CRYST1 record of a PDB file to look up the crystallographic symmetry. Space group names are the full Hermann-Mauguin symbols, e.g., P 1 21 1 rather than P 21 (see lists of names).
  
  
• Use non-crystallographic symmetry – apply noncrystallographic symmetry described by MTRIX1, MTRIX2, and MTRIX3 matrices in a PDB file. However, most MTRIX records describe how to transform one chain to match closely another chain that is already present in the PDB file, as indicated by a “1” in column 60; these MTRIX records are ignored. Conversely, a blank space in column 60 indicates that the transformation will produce a new copy. There may be errors in MTRIX records, or they may be missing entirely. For example, 1cd3 has no MTRIX records, but the remarks describe how to produce them from the BIOMT records. This is not handled by Unit Cell.

  MTRIX records give coordinate transformations that are needed to make a complete asymmetric unit from the coordinates contained in the file. These are not crystallographic symmetries. Because the copies of the molecule occupy nonequivalent positions in the crystal, they usually have small structural differences due to differing crystal contacts. Thus, an independent set of coordinates is usually included for these copies, and MTRIX records are not needed. However, they are often used for icosahedral virus particles, where the size of the virus particle precludes independent refinement of coordinates for each subunit.

• Pack structures in unit cell – whether to pack the structures so that their centers fall within one unit cell box

• Cell origin coordinates (default 0 0 0) are in unit cell lengths and describe translations of the unit cell along its axes. Values of a coordinate that differ by integer amounts are equivalent; e.g., (0.3 0 0) is equivalent to (-0.7 0 0) and (4.3 0 0). Changing the origin may rearrange the copies and shift the outline (if present). The shift will occur in the direction that maintains the center of the original copy within the box.
  
  
• Number of cells (default 1 1 1, a single unit cell) offset (default 0 0 0) allows generating a block of multiple unit cells. The first three values specify dimensions in number of cells along the unit cell axes; the second three values specify the placement of the block relative to the cell containing the original structure. For example, number of cells 3 1 1 and offset –1 0 0 would give a 3x1x1 block of cells with the original structure in the middle cell along the first axis.

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Limitations

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 the sym command.

ChimeraX does not read small-molecule CIF files, and Unit Cell does not handle them.

Only the following mmCIF tables are used:

cell
symmetry
struct_ncs_oper
pdbx_struct_oper_list
atom_sites