Usage:
open [ noprefs ] [ model | pdb | object ] [ model_number ] [ filename ]

Usage:
( close | ~open ) model_number

Usage:
( close | ~open ) ( all | session )

Open reads local files or fetches by ID over the Web.

Input files may contain structures to be displayed, commands or code to be executed, or other data. A file of data to be displayed in the graphics window is opened as model model_number. Model_number should not be preceded by #. If model_number is omitted, the lowest available number is used.

The noprefs keyword indicates that a user's New Molecules preferences should not be applied. This prevents inconsistent behavior of command files and demos potentially caused by the different preferences settings of different users.

The filename is generally a pathname to a local file, absolute or relative to the current working directory (which can be changed with cd). If filename is omitted, a dialog for specifying the name and location will appear. Any of the registered file types can be opened.

If the keyword model or pdb is given, 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 can be specified by a suffix that is part of the filename or by prefix:filename, where prefix is not part of the filename. Prefixes and suffixes are overridden by the model, pdb, or object keyword. If a prefix and a suffix are both given, the prefix overrides the suffix. Filenames, prefixes, and suffixes are case-sensitive. Unrecognizable prefixes are assumed to be part of the filename. For many of the registered file types, files that are gzipped (as indicated by .gz following the regular filename) are recognized and opened. Similarly, compressed files (as indicated by .Z) can be recognized and opened for many input types if gzip is on the user's execution path (can be run by entering gzip at the system command line). PDB format is the default input type.

Other than a local file, filename can be the database identifier of a file to be retrieved over the Web and opened:

• the prefix pdbID: indicates a PDB ID to be used to fetch a PDB-format file from the Protein Data Bank. Chimera will first attempt to find the file within a local installation of the Protein Data Bank; if the file is not found locally, Chimera will try to retrieve it from the Protein Data Bank web site (by default; this can be turned off in the PDB preferences).
• any input specified as PDB format (which is the default) will be fetched in the same way if filename resembles a PDB ID and is not found in the current working directory or any personal PDB directories
• the prefix cifID: indicates a PDB ID to be used to fetch an mmCIF-format file from the Protein Data Bank
• the prefix modbase: indicates a SwissProt, TrEMBL, GenPept or PIR accession code for which to fetch modeled protein structure(s) in PDB format from ModBase. The structures are comparative models created with MODELLER. The MODELLER error profile is placed in the column normally used for B-factors (higher values imply lower reliability). If multiple modeled structures are available for the sequence, they will be opened as submodels of a single model number.
• the prefix ndb: indicates an NDB ID to be translated into a PDB ID and used to fetch the corresponding structure from the Protein Data Bank
• the prefix scop: indicates a SCOP domain ID to be used to fetch a domain structure from the ASTRAL Compendium
• the prefix viperID: indicates an identifier in the Virus Particle Explorer database of icosahedral virus capsid structures (the capsid will be constructed automatically with Multiscale Models)
• the prefix pqsID: indicates a PDB ID to be used to fetch the predicted biological unit from the Protein Quaternary Structure server (predictions are not available for all PDB entries; some entries have multiple predictions, and for those, multiple files will be retrieved)
• the prefix edsID: indicates a PDB ID to be used to fetch an electron density map from the Electron Density Server (not all PDB entries have maps available; Volume Viewer will be used to show the map)
• the prefix edsdiffID: indicates a PDB ID to be used to fetch an electron density difference map (fo-fc) from the Electron Density Server (not all PDB entries have maps available; Volume Viewer will be used to show the map)

The command close or ~open closes (removes) structures and other data. Models and submodels can be specified for closing by model_number. The keyword all can be used to close all open models (all data with associated model numbers; everything listed in the Model Panel). The keyword session additionally specifies data without associated model numbers, such as 2D labels and sequence alignments.

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.

See also: load, read, source, delete, split, start, the Open File dialog, Fetch by ID, the close function in the Model Panel