Open reads the contents of the file filename into Chimera. If filename is omitted, a dialog for specifying the name and location will appear. Input files may contain structures to be displayed, commands or code to be executed, or other data; Chimera can read any input types that have been registered. Data to be displayed is opened and shown as model model_number (if model_number is omitted, the lowest available model number is automatically assigned). Model_number should not be preceded by #.
The optional specification of input type as model, pdb, or object guides interpretation of filename. If the keyword model or pdb is used, filename will be read as a PDB-format file; if the keyword object is used, filename will be read as a VRML file.
Alternatively, file type may be specified by a suffix that is part of the filename or by prefix:filename (where the prefix is not part of the filename). Prefixes and suffixes are overridden by the keyword model, pdb, or object. If a prefix and an suffix are both given, the prefix overrides the suffix. Unrecognizable prefixes are assumed to be part of the filename. PDB format is the default when no recognized prefix or suffix is supplied.
Files that are gzipped (as indicated by .gz following the regular filename) are recognized and opened. If a tool-specific type of file is opened, the associated tool will be executed or started, if it has not been started already.
Filename is generally a pathname to a file or the name of a file in the current working directory. To change the working directory, use cd. Alternatively, filename can be a database identifier. If the file type is PDB and filename resembles a PDB identifier, the corresponding file will be retrieved from the Protein Data Bank, as described for Fetch by ID. The prefix ndb: indicates an NDB identifier and the prefix scop: indicates a SCOP domain identifier; in either case, the file will be retrieved from the appropriate database as described for Fetch by ID.
Filenames, prefix and suffix types, and PDB identifiers are case-sensitive and (except for filenames) must be in lower case.
The command close or ~open with the keyword all closes all open models. Giving a model or submodel number (instead of all) closes the specified model(s). A single number can specify multiple models because a molecule model can share a numbeee with one or more molecular surface models and/or objects (any of the other model types). Models sharing a number can be closed separately with the Model Panel function close.
Various attributes of newly opened molecules can be customized in the New Molecules preferences (see also set autocolor).
If a model is closed and another model opened with the same model number, none of the transformations applied to the previous model are applied to the newly opened model. The transformation matrix of one model can be applied to another model using matrixcopy.