Usage:
sym [ molmodel [ refmodel ] ] [ contact contact-dist | range range-dist ]

Usage:
~sym [ molmodel ]

The sym command generates copies of a molecule at symmetric positions that update automatically as the original molecule is moved.

The primary use of sym is to facilitate symmetrical placement of copies of a structure within related volume data, usually a density map. The symmetry of the data can be specified in either of two ways:

• with BIOMT (PDB REMARK 350) records in the PDB file of the molecule model (example)
• by using the command volume with its symmetry option. This information is retained in files saved in Chimera map format.

• generate the symmetry-related copies of molmodel
• initiate dynamic updating of the molmodel copies when the original molecule is moved. Generally this is done while refmodel (the volume model) is deactivated and thus frozen in place. All copies will be moved using the symmetry matrices applied in the coordinate frame of refmodel.

The keyword contact indicates that only copies with any atom within contact-dist of the original molecule should be generated. The keyword range indicates that only copies with centers within range-dist of the center of the original molecule should be generated. A structure's center is defined as the center of its bounding box. It may be necessary to use one of these options or simply to specify fewer matrices to avoid creating too many atoms.

A secondary use of sym is to generate BIOMT-described copies of a molecule model, where that model is specified as both molmodel and refmodel. Since a model cannot be moved relative to itself, the dynamic updating does not come into play in this situation.

The command ~sym removes the copies of molmodel generated with sym. If the volume refmodel is closed, the copies of molmodel will no longer update to preserve symmetry when the original molecule is moved.

BIOMT matrices can be added to PDB files with a text editor. The image shows twelve copies of myosin arranged helically, as specified by the following twelve matrices for PDB entry 1i84 (the first is simply an identity matrix that does not specify an additional copy):

REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: S, T, U, V, W, Z
REMARK 350   BIOMT1   1  1 0 0 0
REMARK 350   BIOMT2   1  0 1 0 0
REMARK 350   BIOMT3   1  0 0 1 0
REMARK 350   BIOMT1   2  0 -1 0 0
REMARK 350   BIOMT2   2  1 0 0 0
REMARK 350   BIOMT3   2  0 0 1 0
REMARK 350   BIOMT1   3  -1 0 0 0
REMARK 350   BIOMT2   3  0 -1 0 0
REMARK 350   BIOMT3   3  0 0 1 0
REMARK 350   BIOMT1   4  0 1 0 0
REMARK 350   BIOMT2   4  -1 0 0 0
REMARK 350   BIOMT3   4  0 0 1 0
REMARK 350   BIOMT1   5  0.866025 -0.5 0 0
REMARK 350   BIOMT2   5  0.5 0.866025 0 0
REMARK 350   BIOMT3   5  0 0 1 145
REMARK 350   BIOMT1   6  -0.5 -0.866025 0 0
REMARK 350   BIOMT2   6  0.866025 -0.5 0 0
REMARK 350   BIOMT3   6  0 0 1 145
REMARK 350   BIOMT1   7  -0.866025 0.5 0 0
REMARK 350   BIOMT2   7  -0.5 -0.866025 0 0
REMARK 350   BIOMT3   7  0 0 1 145
REMARK 350   BIOMT1   8  0.5 0.866025 0 0
REMARK 350   BIOMT2   8  -0.866025 0.5 0 0
REMARK 350   BIOMT3   8  0 0 1 145
REMARK 350   BIOMT1   9  0.866025 0.5 0 0
REMARK 350   BIOMT2   9  -0.5 0.866025 0 0
REMARK 350   BIOMT3   9  0 0 1 -145
REMARK 350   BIOMT1  10  -0.5 0.866025 0 0
REMARK 350   BIOMT2  10  -0.866025 -0.5 0 0
REMARK 350   BIOMT3  10  0 0 1 -145
REMARK 350   BIOMT1  11  -0.866025 -0.5 0 0
REMARK 350   BIOMT2  11  0.5 -0.866025 0 0
REMARK 350   BIOMT3  11  0 0 1 -145
REMARK 350   BIOMT1  12  0.5 -0.866025 0 0
REMARK 350   BIOMT2  12  0.866025 0.5 0 0
REMARK 350   BIOMT3  12  0 0 1 -145

See also: matrixcopy, volume, Volume Viewer, Multiscale Models, Unit Cell