Unit Cell

Unit Cell builds crystallographic unit cells using information in PDB files. There are several ways to start Unit Cell, a tool in the Utilities category.

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.

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.

Make unit cell loads copies of the coordinates from the same source as the originally opened model (a local file or a file fetched from the web) and transforms them using the symmetry information specified by the checkbox settings. Pressing the button a second time will create a new set of copies without deleting the first set. Close unit cell deletes all open copies of the molecule, except for the original. All copies will be deleted, not just the ones specified by the current checkbox settings.

The checkbox settings control which matrix information is used to determine the number of copies and their transformations:

• Use SMTRY records in PDB header - The SMTRY1, SMTRY2, and SMTRY3 records found in REMARK 290 contain the rows of transformation matrices defining the crystallographic symmetry. These records are not present in all PDB entries.
  
  
• Use CRYST1 record if SMTRY records are missing - The CRYST1 record contains the unit cell size in angstroms, the cell angles, and the name of the space group. The transformations defining the crystallographic symmetry can be looked up in a table by space group name. Some PDB entries contain nonstandard space group names that are not in the table. When this occurs, the number of space group symmetries is reported as zero; if the SMTRY matrices are also missing, then the crystal packing is unknown.
  
  
• Use MTRIX records for non-crystallographic symmetry - The MTRIX1, MTRIX2, and MTRIX3 records contain the rows of transformation matrices defining the noncrystallographic symmetry. Only a small fraction of PDB entries have MTRIX records (~10% in 2003). Most of these describe how to transform the coordinates of one chain to match closely the coordinates of another chain already present in the PDB file. In a few cases (~0.25% of PDB entries), the MTRIX records describe a transformation that produces a new copy whose coordinates are not already in the file. These two cases are distinguished by the contents of column 60 in the MTRIX records. A "1" means that the transformation yields coordinates that are already given (these MTRIX records are ignored by Unit Cell), whereas a blank space means that the transformation will produce a new copy. MTRIX column 60 is set incorrectly in some files; for example, it is "1" in 2btv even though the MTRIX records define coordinates not present in the file. Further, MTRIX records are sometimes missing. For example, 1cd3 has no MTRIX records, but the remarks describe how to produce them from the BIOMT records. Of course, this cannot be handled by Unit Cell.
  
  MTRIX records do not describe crystallographic symmetries, but define additional symmetries of the asymmetric unit of the crystal. 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. MTRIX records are often used for icosahedral virus particles, where the PDB file will include the coordinates of one molecule in the shell and MTRIX records describing how to place copies that are not crystallographically equivalent. The size of the virus particle precludes independent refinement of coordinates for each copy of a molecule in the shell.
  
  
• Pack close - The transformation matrices frequently specify copies that are spread out in space rather than tightly packed. Any copy can be shifted along a crystal axis by an integral multiple of the cell size along that axis, which can result in a more tightly packed (but equally valid) unit cell. Pack close indicates that copies should be shifted to increase compactness the next time Make unit cell is pressed. To perform close packing, the center of the bounding box of the original molecule is calculated. The center is copied to the new positions along with the atomic coordinates. Each copy is then shifted so that its center is within half a unit cell length of the center of the original molecule along each axis. The unpacked positions are often symmetrically located, while the packed positions may not be.

Limitations

As mentioned above, many problems are due to information that is missing from or incorrect in the PDB file.

Unit Cell does not generate multimers defined by BIOMT records, but this can be done with Multiscale Models.

There is little control over which part of the crystal packing is shown. Given an X-ray density map, for example, there is no way to make only the copies that intersect the map. There is no way to force specific copies to be adjacent so that their packing interface can be examined (one copy may be one cell-width away from the desired position). However, Multiscale Models can generate a 3 by 3 by 3 block of unit cells, which may allow the interface of interest to be examined when the two monomers are shown in atomic detail.