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
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
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.
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.
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.surfaceOnly true | false
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.