(see Quicktime movie) |

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**

groupsymmetry

Specifications ofsymmetryare case-independent, and most types have additional sub-options or parameters:

biomt(default) - use biological unit information, if any, in themolmodelinput file- symmetry of model
#- use biomt information from another molecule model or the symmetry assignment of a volume modelN

- Example:
#4- cage model polygon symmetry
#orN,pM#- place copies at equivalent positions relative to each M-sided polygon in the cage model with ID numberN,pnMN. Thepform places one copy per M-sided polygon, whereasMpnplaces M copies per M-sided polygon using CMMsymmetry about the center of the M-sided polygon nearest the original copy.

- Examples:
#2,p6or#2,pn5(more...)- cyclic symmetry
Caround axis and centern

- Example:
C3- dihedral symmetry
Daround axis and centern

- Example:
d7- tetrahedral symmetry
T[,around centerorientation]where

- Example:
t,z3orientationcan be:

222(default) - with two-fold symmetry axes along the X, Y, and Z axes, a three-fold along axis (1,1,1)z3- a three-fold symmetry axis along Z, another three-fold axis in the YZ plane such that rotation about the X axis by ~110° is a symmetry operation (EMAN convention)- octahedral symmetry
Oaround center- icosahedral symmetry
I[,around centerorientation]where

- Example:
i,n25orientationcan be:

222(default) - with two-fold symmetry axes along the X, Y, and Z axes2n5- with two-fold symmetry along X and 5-fold along Zn25- with two-fold symmetry along Y and 5-fold along Z2n3- with two-fold symmetry along X and 3-fold along Z222r- same as 222 except rotated 90° about Z2n5r- same as 2n5 except rotated 180° about Yn25r- same as n25 except rotated 180° about X2n3r- same as 2n3 except rotated 180° about Y- helical symmetry
H,around axis and centerrise,angle,n[,offset]where

- Example:
h,43.5,21,6,-2riseis the translation along the axis per subunit,angleis the rotation in degrees per subunit, andnis how many copies total (including the original) the resulting segment of infinite helix should contain prior to any filtering by contact or range. The integeroffset(default0) allows extending the helix in both directions. The example above would given= 6 copies total, with two copies in the negative axis direction, one at the identity position, and three in the positive axis direction.- translational symmetry
shift,along axis – or –n,distanceshift,n,x,y,zwhere

- Example:
shift,3,26.7nis how many copies total (including the original) the result should contain prior to any filtering by contact or range. The translation can be expressed as adistancealong the axis or as a vectorx,y,zin the reference coordinate system.- the product of symmetry groups, each specified as described above and separated by
*to indicate multiplying each symmetry matrix of one group with each symmetry matrix of another; can be generalized to multiple symmetry groups (not just two)

- Example:
c2*h,42,21,9,-4

axisaxis

Specify axis of symmetry (defaultz), whereaxiscan be:

x- X-axisy- Y-axisz- Z-axisx,y,z(three values separated by commas only) - an arbitrary vector in the reference coordinate system- an
atom-specof exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the wordselected,sel, orpicked; any atoms also selected at the time will be ignored.

centercenter

Specify center of symmetry (default0,0,0), wherecentercan be:

x,y,z(three values separated by commas only) - an arbitrary point in the reference coordinate system- an
atom-specof any combination of atoms and surface pieces. The center of the bounding sphere of the specified items will be used.

coordinateSystemN

Specify a reference model (default is the original molecule model,molmodel) by model numberNpreceded by #. The reference coordinate system is used for dynamic updating and for interpreting coordinate specifications such as of axis and center of symmetry.

biomtSettrue| false

Whether to generate BIOMT matrices formolmodelaccording to the specified symmetry, replacing any pre-existing BIOMT information. The BIOMT matrices will be included ifmolmodelis subsequently saved as PDB.The accelerator

mB(commandac 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 withsym).

updatetrue |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.

modelIdN

Open the copy or copies as model numberN(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 ofN.

contactcontact-dist

Only generate copies with any atom withincontact-distof the original molecule model.

rangerange-dist

Only generate copies with centers withinrange-distof the center of the original molecule model. A model's center is defined as the center of its bounding box.

occupancyf

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 probabilityf(a value ranging from 0 to 1). This approach may yield different overall fractions filled for multiple uses of the same command, but distributed aboutf.

surfacesall | true |false[resolutionr]

Whether to generate the additional copies as low-resolution surfaces (fromMultiscale 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 keywordallindicates 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. Theresolutionris the grid spacing (default8Å). The isosurface is smoothed to reduce artifacts associated with using an arbitrarily aligned grid.

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