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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

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.

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:

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.

Copy Representation Options

copies  true | false
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.
newModel  true | false
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).

surfaceOnly  true | false
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:

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2022