Chimera Commands Index

Usage:
sym [ molmodel ] options

Usage:
~sym [ molmodel ]

(see Quicktime movie)
The sym command generates symmetry-related copies of a molecule model. The command ~sym removes the copies. See also: crystalcontacts, matrixcopy, measure symmetry, fitmap, Unit Cell, Multiscale Models, Cage Builder, the biological unit function in the Model Panel, fetching PQS files

The molecule model to copy (molmodel) is specified by model number, optionally preceded by #. This specification can be omitted from the sym command when there is only one molecule model. If sym-created copies of molmodel already exist, they will be replaced. The ~sym command without arguments closes all sym-created copies.

One application of sym is to facilitate symmetrical placement of copies of a structure (molecule model) within related volume data, usually a density map. In that case, the volume model should be specified as the reference coordinate system. After the structure has been placed approximately as desired in the density, sym can be used with update true to create copies that update automatically when the original model is moved. For example, see a Quicktime movie of myosin copies moving symmetrically.

For memory and display efficiency, the copies can be generated as low-resolution surfaces (from Multiscale Models) instead of atomic coordinates by specifying surfaces true. This may be helpful for large multimers. See also: play, msc

Options

Option keywords (but not their arguments) can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive options, and default settings are indicated with bold.
group symmetry
Specifications of symmetry are case-independent, and most types have additional sub-options or parameters:
axis axis
Specify axis of symmetry (default z), where axis can be:
center center
Specify center of symmetry (default 0,0,0), where center can be:
coordinateSystem N
Specify a reference model (default is the original molecule model, molmodel) by model number N preceded by #. The reference coordinate system is used for dynamic updating and for interpreting coordinate specifications such as of axis and center of symmetry.
biomtSet  true | false
Whether to generate BIOMT matrices for molmodel according to the specified symmetry, replacing any pre-existing BIOMT information. The BIOMT matrices will be included if molmodel is subsequently saved as PDB.

The accelerator mB (command ac mB) sets BIOMT matrices for molecule models associated with the currently selected multiscale chains to only the symmetries represented by those chains. This allows writing only a subset of the original BIOMT matrices (or symmetries assigned with sym).

update true | false
Whether to dynamically update the positions of the copies to preserve symmetry when the original model is moved relative to the reference coordinate system. If the reference model is closed, the copies will cease to update.
modelId N
Open the copy or copies as model number N (an integer, optionally preceded by #). The default is the lowest unused number. When multiple copies are loaded, they will be opened as submodels of the specified model. When only a single copy is loaded, it will not receive a submodel number unless a specification of the form #N.N (# required) is given instead of N.
contact contact-dist
Only generate copies with any atom within contact-dist of the original molecule model.
range range-dist
Only generate copies with centers within range-dist of the center of the original molecule model. A model's center is defined as the center of its bounding box.
occupancy  f
Only generate copies at a fraction of the positions that would otherwise be filled. Random number generation is used to fill each position at a probability f (a value ranging from 0 to 1). This approach may yield different overall fractions filled for multiple uses of the same command, but distributed about f.
surfaces  all | true | false  [ resolution r ]
Whether to generate the additional copies as low-resolution surfaces (from Multiscale Models) instead of atomic coordinates. The surfaces may be preferred for large multimers because they require much less memory and are more efficient to display than atomic coordinates. The keyword all indicates making a surface for the original structure as well as for the additional copies. A low-resolution surface is created by counting the atoms in each cell of a 3D grid and then making an isosurface of this occupancy map. The resolution r is the grid spacing (default 8 Å). The isosurface is smoothed to reduce artifacts associated with using an arbitrarily aligned grid.

BIOMT Matrices

BIOMT matrices are included in some Protein Data Bank (PDB) entries, for example, 1fav. (The corresponding information in mmCIF format can also be used.) BIOMT matrices can be added to PDB files using a text editor or the command sym with biomtSet true.

The image shows twelve copies of myosin arranged helically, as specified by the following twelve matrices added to 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