Usage:
open [ noprefs ] [ nowildcard ] [ model-ID ] [ filename1 filename2 ... ]

Usage:
( close | ~open ) ( model-spec | all | session )

The command open reads local files and fetches data from the Web. Chimera input files may contain structures to be displayed, commands or code to be executed, or other data. Any resulting models in Chimera are assigned the specified model-ID number, or if none is specified, the lowest number(s) available. When multiple models are opened with a single command, model-ID should not be specified unless there is some reason to assign all of the models the same number.

Various attributes of newly opened molecules can be customized in the New Molecules preferences (see also set autoColor). 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.

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.

The command close or ~open removes structures and other data: model(s) specified by number, or all models (everything listed in the Model Panel), or the session (all models, plus data without associated model numbers, such as 2D labels and sequence alignments). Closing a session shows the Rapid Access interface.

See also: read, runscript, split, start, Rapid Access, Fetch by ID, Chimera input file types

A filename is generally a pathname to a local file, either absolute or relative to the current working directory. The working directory can be changed with cd. A pathname may start with "~" to indicate the user's home directory. Multiple files can be specified by including * (wild card), ? (single-character wild card), and/or square-bracketed character ranges in a filename. Such filename expansion or globbing is on by default, but can be turned off with the nowildcard keyword. If no filename is supplied, a dialog for browsing the filesystem will appear.

Any of the registered file types can be opened.

A 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. If a prefix and a suffix are both given, the prefix overrides the suffix. Filenames, prefixes, and suffixes are case-sensitive. Unrecognized 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, a filename can specify data to be retrieved over the Web. Fetched files can be cached locally and reused as needed depending on the Fetch preferences and PDB preferences.

• many registered types can be opened by specifying an URL of the form http://[...] as the filename. Prefix and suffix rules are as described above for local files, but filename globbing and reading compressed or gzipped files are not supported.
• the prefix pdbID: indicates a PDB ID (4-character Protein Data Bank identifier) to be used to fetch a PDB-format file from the Protein Data Bank:
  1. Chimera will first attempt to find the file within a local installation of the Protein Data Bank. The default places to look for a local installation are /usr/mol/pdb/ and then /mol/pdb/ — these can be changed by editing the Python file share/chimera/pdbDir within a Chimera installation.
  2. Next, Chimera will look for the file in any personal PDB directories designated in the PDB preferences.
  3. Next, the PDB subdirectory of the fetch download directory will be checked (unless the use of previously fetched files has been disallowed in the Fetch preferences).
  4. Finally, if not found locally, the file will be fetched from the Protein Data Bank web site (unless fetching has been disallowed in the PDB preferences).
• any input specified as PDB format (which is the default) will be fetched in the same way if the 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 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 biounitID: indicates a PDB ID to be used to fetch biological assemblies from the Protein Data Bank; there may be multiple assemblies for a given entry, and a specific assembly can be designated by appending “.N” to the PDB ID. For example, 1dok specifies all biological assemblies of entry 1dok, 1dok.2 specifies biological assembly 2, and 1dok.1.2 specifies biological assemblies 1 and 2. Each assembly will be opened as a separate main model number, possibly containing submodels.
• 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 viperID: indicates a PDB ID to be used to fetch an entry from the Virus Particle Explorer database of icosahedral virus capsid structures (the capsid will be constructed automatically with Multiscale Models)
• the prefix cath: indicates a CATH domain ID to be used to fetch a domain structure from CATH
• the prefix scop: indicates a SCOP domain ID to be used to fetch a domain structure from the ASTRAL database
• the prefix castp: or CASTp: indicates a PDB ID (with chain ID optionally appended, for example 2gsh.A) to be used to fetch a structure and its precomputed pocket measurements from the Computed Atlas of Surface Topography of proteins (does not include results for all PDB entries; measurements will be displayed in a pocket list)
• the prefix modbase: indicates a SwissProt, TrEMBL, GenPept or PIR accession code for which to fetch PDB-format comparative models from ModBase (associated information will be shown in a list). If multiple modeled structures are available for the sequence, they will be opened as submodels of a single model number.
• the prefix smiles: or SMILES: indicates a SMILES string to be converted to a 3D structure using the smi23d web service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University, or if that does not produce a structure, the SMILES translator provided by the National Cancer Institute CADD group. The smi23d service deploys the same procedure used to populate the Pub3D database (below).
• the prefix pubchem: or PubChem: indicates a PubChem compound identifier (CID) for which to fetch a modeled 3D structure from the Pub3D database using a web service provided by the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University. Pub3D is described in Willighagen et al., BMC Bioinformatics 8:487 (2007). About 99% of the compounds in PubChem are available; the structure generation pipeline generally handles organic compounds, but not inorganic, metallo-, or highly unstable species such as radicals.
• 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 prefix emdbID: indicates a numerical identifier to be used to fetch an electron density map from the Electron Microscopy Data Bank
• the prefix emdbfitID: indicates a numerical identifier to be used to fetch an electron density map from the Electron Microscopy Data Bank, along with any corresponding PDB entries (which may or may not be in the fit positions relative to the map)
• the prefix uniprot: indicates a UniProt accession code or identifier to be used to fetch a protein sequence and its annotations and show them in Multalign Viewer (much as described for PDB/UniProt Info, except independent of structure). This type of fetch is not saved locally even if a download directory has been specified. UniProt's ID mapping service can be used to obtain UniProt identifiers from other sequence database identifiers.