Command: altlocs

The altlocs command lists and manages alternate locations, where an atomic structure contains multiple different positions for the same set of atoms. In PDB format, for example, alternate locations are indicated by a character identifier in column 17 of ATOM and HETATM records. Most of the command capabilities are also available in the Altloc Explorer graphical interface.

Within a given atomic model, ChimeraX uses only one of the alternate locations at a time for display and for any calculations. For each contiguous (through-bond) set of atoms with alternate locations, the location used initially is that with the highest average atomic occupancy, then as a tie-breaker, the lowest average atomic B-factor, and if a tie-breaker is still needed, by alphabetical order of the alternate location ID.

The altlocs command controls which alternate location is used within a given model. It also allows viewing multiple alternate locations simultaneously by opening them as separate submodels.

See also: swapaa, swapna, torsion, build, dockprep, attributes

• altlocs list – list alternate locations and report which is being used
• altlocs change – specify which alternate location to use
• altlocs clean – delete all but the currently used alternate location
• altlocs show/hide – view multiple alternate locations at the same time

In the Log, report any alternate locations of the specified residues, and for each residue with alternate locations, which location is being used. For example, to list all residues in chain A that have alternate locations:

altlocs list /A

Use the indicated alternate location for all specified residues that contain it. Even if only part of a residue is specified (e.g., a single atom), the same alternate location will be used for any other atoms in that residue and any contiguous (through-bond) set of atoms for which the same alternate location identifier is available, including atoms in other residues. For example, to use alternate location C of residue 171 in chain A:

altlocs change C /A:171

Delete all but the currently used alternate location for the specified residues and remove their alternate location IDs. Examples:

altlocs clean /A:171
altlocs clean /A
altlocs clean

The last example deletes all unused alternate locations.

The altlocs show command allows viewing multiple alternate locations at the same time. A separate submodel is generated for each alternate location of each specified residue that has alternate locations. All alternate locations are included unless limited to a subset with altloc-ID-list, a series of altloc identifiers separated by commas only. As per the usual ChimeraX convention, a blank residue specification indicates all residues. The altlocs hide command has the same options as altlocs show and simply allows hiding one or more of the alternate-location submodels. Altlocs show and altlocs hide do not affect the original atomic model, only the additional alternate-location submodels.