Chimera Commands Index

combine  atom-spec  options

The combine command combines multiple molecule models into a single model without repositioning the models or adding bonds. It can also be used to make a copy of a single molecule model. By contrast, the Join Models section of Build Structure merges two models while repositioning one model to form a bond with the other. Combine is the command-line implementation of the copy/combine function in the the Model Panel.

Although a narrower atom-spec may be supplied, the entire model(s) containing the specified atoms will be included in a new model. The colors, labels, and display settings of the input model(s) will be copied to the new model. To copy settings from one existing molecule model to another without creating a new model, use the command mcopy. See also: split


Option keywords for combine can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

refSpec  ID
Which model's coordinate system to use for the new model (default is the lowest-numbered model involved in the combination). The reference model's untransformed coordinates (if part of the combination) and its current transformation will be carried over into the new model. The coordinates of any other model in the combination will be transformed relative to the reference model. ID is the number of the reference model preceded by #.
newchainids  true | false
Whether to allow changes in chain identifiers to make each residue in the new model uniquely specifiable; otherwise, residues may be renumbered to make them uniquely specifiable. Even when newchainids is true, residues in chains water and het may be renumbered.
name  new-model-name
Name for the new model (default combination). Model names are shown in the Model Panel and other model lists.
modelId  N
Open the new structure as model number N (an integer, optionally preceded by #). The default is the lowest unused number.
close  true | false
Whether to close the original model(s).
log  true | false
Whether to report changes in chain identifiers or residue numbering in the Reply Log.