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, Unit Cell, Fit in Map, Multiscale Models, 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. However, automatic updating does not apply to these surfaces.

group symmetry
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 of molmodel (details...)
• cyclic symmetry Cn around axis and center
  • Example: C3
• dihedral symmetry Dn around axis and center
  • Example: d7
• icosahedral symmetry I[,orientation] around center
  • Example: i,n25
  where orientation can be:
  • 222 (default) - with two-fold symmetry axes along the X, Y, and Z axes
  • 2n5 - with two-fold symmetry along X and 5-fold along Z
  • n25 - with two-fold symmetry along Y and 5-fold along Z
  • 2n3 - with two-fold symmetry along X and 3-fold along Z
  • 222r - same as 222 except rotated 90° about Z
  • 2n5r - same as 2n5 except rotated 180° about Y
  • n25r - same as n25 except rotated 180° about X
  • 2n3r - same as 2n3 except rotated 180° about Y
  
  
• helical symmetry H,repeat,rise[,angle[,n]] around axis and center
  • Example: h,13,43.5
  where repeat defines a number of subunits, rise is the translation along the axis per repeat subunits, angle is the rotation in degrees per repeat subunits (default 360), and n is how many copies total (including the original) the resulting segment of infinite helix should contain (default same as repeat) prior to any filtering by contact or range.
  
  
• translational symmetry T,n,distance along axis – or – T,n,x,y,z
  • Example: t,3,26.7
  where n is 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 a distance along the axis or as a vector x,y,z in the reference coordinate system.

axis axis
Specify axis of symmetry (default z), where axis can be:

• x - X-axis
• y - Y-axis
• z - Z-axis
• x,y,z (three values separated by commas only) - an arbitrary vector in the reference coordinate system
• an atom-spec of 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 word selected, sel, or picked; any atoms also selected at the time will be ignored.

center center
Specify center of symmetry (default 0,0,0), where center can be:

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

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.

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. Updating only works with atomic copies, not the low-resolution surfaces generated with surfaces true.

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.

surfaces true|false
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 update true setting does not work with these surfaces.

BIOMT matrices are included in some Protein Data Bank (PDB) entries, for example, 1fav. For structures lacking such information, 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 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