Command: sym

The sym command generates symmetry copies of an atomic model. See also: open, close, fitmap, view, surface, crystalcontacts, unitcell, Cage Builder, fetching biological assemblies

Assemblies from mmCIF
User-Specified Symmetry
Copy Representation Options

The command sym clear removes all graphical clones from the specified model(s), but not any copies that were opened as full atomic models:

Usage: sym clear  model-spec

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Assemblies from mmCIF

Usage: sym  model-spec
Usage: sym  model-spec   assembly  identifier   copy-options

Given without options, sym reports any assemblies read from mmCIF for the specified model as a table in the Log. Similar information is shown automatically when the structure is first opened. The table gives a brief description of each assembly and a character-string identifier, usually a number, that can be clicked to generate the assembly (with default options) and adjust the view to encompass it.

By default, when the assembly contains more than 12 copies of the asymmetric unit (as in a viral capsid), the copies are added as graphical clones for efficient visualization. However, for any subsequent analyses that require atomic coordinates, full atomic models should be added instead by creating the assembly with copies true (details...).

Alternatively, the full atomic coordinates of a biological assembly can be fetched from online sources instead of generated with sym. The assembly of interest is specified with the identifier mentioned above.

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User-Specified Symmetry

Usage: sym  model-spec   sym-type  [ axis  vector-spec ] [ center  point-spec ] [ coordinateSystem  model-spec ] [ contact  contact-dist ] [ range  range-dist ] [ addMmcifAssembly  true | false ]  copy-options

Alternatively, symmetry information can specified explicitly in the command. The sym-type can be:

• biomt – use “biological assembly” information from the atomic model containing the specified atoms
  (currently this information is only read from PDB format, not mmCIF)
• symmetry #N – use the biological assembly information from another atomic model or the symmetry assignment of a volume model (such as from volume symmetry or measure symmetry), where N is the model number
  • Example: symmetry #4
• symmetry #N,pM or symmetry #N,pnM – use cage model (from Cage Builder) polygon symmetry; place copies at equivalent positions relative to each M-sided polygon in the cage with model number N. The pM form places one copy per M-sided polygon, whereas pnM places M copies per M-sided polygon using CM symmetry about the center of the M-sided polygon nearest the original copy.
  • Examples: symmetry #2,p6 or symmetry #2,pn5
• cyclic symmetry Cn around axis and center
  • Example: C3
• dihedral symmetry Dn around axis and center
  • Example: d7
• tetrahedral symmetry T[,orientation] around center
  • Example: t,z3
  where orientation can 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 O around center
• 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,rise,angle,n[,offset] around axis and center
  • Example: h,43.5,21,6,-2
  where rise is the translation along the axis per subunit, angle is the rotation in degrees per subunit, and n is how many copies total (including the original) the resulting segment of infinite helix should contain. The integer offset (default 0) allows extending the helix in both directions. The example above would give n = 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,n,distance along axis – or – shift,n,x,y,z
  • Example: shift,3,26.7
  where n is how many copies total (including the original) the result should contain. The translation can be expressed as a distance along the axis or as a vector x,y,z in 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

The axis option specifies a vector to use as the axis of symmetry (default z).

The center option specifies a point to use as the center of symmetry (default 0,0,0).

The coordinateSystem option specifies a reference model for interpreting axis and center coordinates. If no reference model is specified, the scene coordinate system is used.

Copies can be filtered by their distance from the original atomic model. The contact option removes copies without any atom within contact-dist of the original model, and the range option removes copies with centers farther than range-dist from the center of the original model. A model's center is defined as the center of the bounding box of all of its atoms, regardless of whether they are displayed.

The addMmcifAssembly option (default false) specifies whether to add the user-defined assembly to the structure metadata so that it will be included when the structure is saved as mmCIF. The new assembly will be named author defined assembly and will be added without removing any previously existing assemblies for that structure. Subsequently opening the saved mmCIF file will allow recreating the assembly as described above. The information is added to the model on which the sym command was run, and to a new model if created with graphical clones (newModel true and copies false), but not to any copies added as full atomic models with copies true.

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Copy Representation Options

The copies option indicates whether the additional copies needed to reconstitute the assembly should be opened as full atomic models (true, default for assemblies with 12 or fewer copies) or as graphical clones (false, default for assemblies of more than 12 copies). Graphical clones allow memory-efficient visualization of very large assemblies such as viral capsids. However, full atomic models are needed for any subsequent analyses that use atomic coordinates: distance and other measurements, hydrogen bonds, contacts, superposition and RMSD calculations with matchmaker and align, etc. Full atomic models are also needed to show the copies in different styles or colors from one another.

The newModel option indicates whether to open the assembly as a new model (default true for assemblies from mmCIF, default false for user-specified symmetry). In addition, copies true automatically sets newModel true. When an assembly is opened as a new model, the original atomic model is hidden but not closed; the original state can be restored by closing the new model and showing (with target m) the original model. An advantage of opening the assembly as a new model is that any parts of the original asymmetric unit that are not part of the specified assembly will be deleted from that model, not merely hidden as they would be with newModel false. Parts that are merely hidden could be displayed inadvertently and cause confusion later.

With newModel true but copies false, the new model will contain at least one full atomic copy, but the remainder will be graphical clones. The command sym clear removes all graphical clones from the specified model(s),

Even when both copies and newModel are false, one or more copies of the full atomic model may be added, namely when the assembly specifies different sets of matrices for different chains. In that case, restoring the original state may require not only using sym clear but also closing the added model(s) and showing all chains of the original copy (some chains may have been hidden when the assembly was shown).

For a simple appearance and economical use of memory, surfaceOnly true (default false) indicates calculating per-chain surfaces for the original structure and then showing only surfaces for the copies. The surfaces can be created as graphical clones, or if copies is also used, as molecular surface models that can be displayed and colored independently of one another (along with their underlying full atomic data). The surface calculation is the same as for the surface command with default parameters:

• If resolution is not specified, solvent-excluded surfaces (SES) will be calculated (probe radius 1.4 Å).
• If resolution is specified, low-resolution Gaussian surfaces will be calculated instead. For each biopolymer chain, a pseudo-density map is generated by summing over atoms, where each atom is described as a Gaussian distribution of width proportional to the resolution r and amplitude equal to the atomic number. An isosurface is displayed and the pseudo-density map discarded.
• The gridSpacing s is the spacing of the grid used to calculate either type of surface. The default spacing is 0.5 Å for an SES, 0.1r (one-tenth the resolution) for a Gaussian surface. A smaller spacing gives a smoother, more finely triangulated surface, but uses more memory.