(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.

groupsymmetry

Several types of symmetry are available, and most types have additional sub-options or parameters; specifications are case-independent:

biomt(default) - use BIOMT records, if any, in the PDB file ofmolmodel(details...)- cyclic symmetry
Caround axis and centern

- Example:
C3- dihedral symmetry
Daround axis and centern

- Example:
d7- 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 centerrepeat,rise[,angle[,n]]where

- Example:
h,13,43.5repeatdefines a number of subunits,riseis the translation along the axis perrepeatsubunits,angleis the rotation in degrees perrepeatsubunits (default360), andnis how many copies total (including the original) the resulting segment of infinite helix should contain (default same asrepeat) prior to any filtering by contact or range.

- translational symmetry
T,along axis – or –n,distanceT,n,x,y,zwhere

- Example:
t,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.

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.

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.

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.

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