Open reads the contents of the file filename into Chimera. Input files may contain structures to be displayed, Python commands 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 command ~open or close followed by the model number closes a specific model; using the keyword all instead of a model number indicates that all open models should be closed.
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 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). If a tool-specific type of file is opened, the associated tool will be executed or started, if it has not been started already.
PDB is the default when no recognized prefix or suffix is supplied. If a prefix and an suffix are both given, the prefix overrides the suffix. Prefixes and suffixes are overridden by the keyword model, pdb, or object. Filenames, prefix and suffix types, and PDB identifiers are case-sensitive and (except for filenames) must be in lower case. Unrecognizable prefixes are assumed to be part of the filename.
In most cases, filename is a pathname to a file or the name of a file in the current working directory. To change the current working directory, use cd. If the file type is identified as PDB and the filename resembles a PDB identifier, but the file is not found in the working directory, Chimera will attempt to find it within a local installation of the Protein DataBank in /usr/mol/pdb/. If the file is not found locally, Chimera will then try to retrieve it from the Protein DataBank web site (by default; this can be turned off in the PDB preferences). If the filename is a SCOP domain identifier, it is necessary to use the prefix scop; Chimera will then try to retrieve the SCOP domain structure from the ASTRAL Compendium.
While display is used to selectively control display of molecules or parts of molecules, objdisplay is used to control display of entire objects. Objects and molecules may share a model_number.
If the autocolor option has been set, then each newly opened model without color definitions will be given a unique color so that different models can be easily distinguished.
Various visual properties of newly opened molecules can be customized in the New Molecules preferences.
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.
See also: display, modeldisplay, objdisplay, surface, the Model Panel