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Command: open

Usage:
openfilename | URL | [ prefix:]identifier ) [ coordsets  true | false ]  other-options

Usage:
open formats

The command open reads data in several formats from:

Input files may contain data to be displayed or commands or code to be executed. Local files can browsed interactively by giving browse as the filename in the open command (or by using File... Open in the menu instead of a command, in which case the proper filename suffix is required). Another way to open local files is by drag-and-drop onto the ChimeraX icon or a running instance of ChimeraX. On a Mac, ChimeraX-associated file types can also be opened by double-clicking them in a Finder window or using “open” in a Terminal window. See also: close, save, help, sym, info, File History, Rapid Access , initial colors, automatic styling

Examples:

open ~/Desktop/maps/myfile.mrc name refined3
open 2gbp
open 1plx format pdb coord T
open emdb:3087
open 3237 from emdb name "gamma-secretase complex"
open http://www.rbvi.ucsf.edu/chimerax/features.html

Input Formats

The command open formats command lists the possible formats and databases in the Log. File types can be categorized as:

File Types
format format-name suffix description
Atomic Structures and Related Data
Protein Data Bank (PDB) pdb .pdb
.pdb1
.ent
.pqr
atomic coordinates and associated annotations
PDBx/mmCIF mmcif .cif
.mmcif
atomic coordinates and associated annotations
(see assemblies from mmCIF, H-bonds from mmCIF,
ChimeraX Fast mmCIF Guidelines)
Pseudobond file pseudobonds .pb plain text file with each line specifying a pair of atoms (already open in ChimeraX) to connect with pseudobonds
Trajectory Coordinates
(requires an already-open structure for topology, see the structureModel option)
DCD coordinates (binary) dcd .dcd atomic trajectory
Gromacs compressed coordinates xtc .xtc atomic trajectory
Gromacs full-precision coordinates (binary) trr .trr atomic trajectory
Volume Data and Related (associated tool: Volume Viewer)
Amira mesh amira .am 3D data
Adaptive Poisson-Boltzmann Solver (APBS) potential
(see the APBS interface in UCSF Chimera)
apbs .dx electrostatic potential map
BRIX density map dsn6 .brix density map
CCP4 density map ccp4 .ccp4
.map
density map
DeltaVision map dv .dv light microscopy data
Chimera/ChimeraX map
(based on the hierarchical data format HDF5)
cmap .cmp
.cmap
volume data
Directional FSC (Fourier shell correlation) dres .dres directional resolution to show on a colored globe
(plain text file with four whitespace-separated columns of numbers, an XYZ vector and a resolution or other value to colormap onto the globe)
DSN6 density map dsn6 .omap density map
ImageJ or OME TIFF
(multiple channels and/or time points specified in file header)
.tif, .tiff microscopy data
Image stack
(grayscale image series in multiple files or a single multipage file, in formats supported by PIL)
images .tif, .tiff
.png
.pgm
image stack
Imaris map ims .ims 3D-5D image
(could be time series and/or multichannel)
MRC density map mrc .mrc density map
STochastic Optical Reconstruction Microscopy (STORM) storm .storm super-resolution optical microscopy data
Other 3D Objects
Chimera/ChimeraX BILD bild .bild
.bld
graphical objects
Chimera/ChimeraX markers markers .cmm markers and links
(analogous to atoms and bonds)
COLLADA collada .dae graphical objects
(geometry nodes define surfaces)
GL Transmission Format gltf .glb graphical objects
STereoLithography (binary) stl .stl triangle-based format (binary) native to stereolithography CAD software
Visualization Toolkit (VTK) PolyData vtk .vtk lines, polygons
Wavefront OBJ obj .obj graphical objects
(geometric and texture vertices, vertex normals, faces; no colors)
Sequences (associated tool: Sequence Viewer)
FASTA, aligned FASTA fasta .fasta, .fa
.afasta, .afa
individual sequence(s) or sequence alignment
Multiple Sequence Format (MSF) msf .msf sequence alignment
PIR, aligned PIR pir .pir
.ali
individual sequence(s) or sequence alignment
Composite
ChimeraX session file ses .cxs ChimeraX session
Integrative Hybrid Model (IHM) ihm .ihm integrative hybrid model, potentially including atomic and coarse-grained representations, crosslinks, etc. (examples can be downloaded from the archive)
Miscellaneous
ChimeraX command file cmd .cxc ChimeraX commands
Python py .py
.pyc
.pyo
Python code
HTML, XHTML .html, .htm
.xhtml, .xht, .xml
hypertext to render in the ChimeraX browser

Local Files

Usage: open  filename  [ filename2... ] [ format  format-name ] [ coordsets  true | false ] [ vseries  true | false ] [ channel  N ] [ alignment  true | false ] [ structureModel  model-spec ] [ atomic  true | false ] [ ensembles  true | false ] [ newTab  true | false ]  general-options 

The filename is generally a pathname to a local file, either absolute or relative to the current working directory as reported by pwd. The working directory can be changed with cd. A pathname may start with “~” to indicate the user's home directory. One or more files can be specified with a single filename by including * (wild card), ? (single-character wild card), and/or square-bracketed character ranges (Unix-style pathname expansion or globbing). Substituting the word browse for the filename brings up a file browser window for choosing the name and location interactively. Specifying multiple filenames is equivalent to using the open command multiple times with the same options for each filename.

The file format can be indicated with either the filename suffix or the format option (where format-name can be truncated). Files that are gzipped, as indicated by their additional .gz suffix, can also be read.

Opening a Chimera session file automatically runs close session first.

Further command options:

coordsets  true | false
Whether to open a multi-model file in mmCIF or PDB format as a trajectory and show a slider graphical interface. Only one frame (coordinate set) of a trajectory can be viewed at a time; different frames can be accessed or played back sequentially with the coordset command or the slider interface. By default, the multiple models in the file will be opened not as a trajectory but as separate submodels that can be shown/hidden/specified independently (for example, using #1.1, #1.2, #1.3...) or collectively (for example, using #1).
vseries  true | false
When multiple maps with the same grid dimensions are opened in a single command (multiple files specified with wild cards or globbing, or a single multi-map file), this option can be used to enforce loading them as a volume series for playback with vseries or the associated slider (if true), or as independent models (if false). If the option is not used, 3D TIFF images and Chimera map files containing five or more same-sized maps are automatically interpreted as series, if possible. When multiple maps are opened in a single command (multiple files specified with wild cards or globbing), time ordering is automatically discerned from the filenames, if possible: for example, a file will be identified as time point 12 if its name contains either of the following: (and 0012 could be any integer).
channel  N
Assign channel number N to map; typically used for light microscopy data. When multiple maps are opened in a single command (multiple files specified with wild cards or globbing), channel numbers are automatically discerned from the filenames, if possible: for example, a file will be identified as channel 0 if its name contains either of the following: (and 0 could be any whole number). Multichannel data opened from a single file or from multiple files in a single command (as described above) are automatically grouped, in that changing the display style, step size, or plane for one channel in Volume Viewer changes it for all of the channels in the group. The channel option allows manually assigning a channel to data so that it can be saved along with other datasets in a single (multichannel) Chimera map file.
alignment  true | false
Whether to interpret a multi-sequence file as an alignment (default, all sequences in one Multalign Viewer window). Otherwise, each sequence will be opened in a separate window. If the sequences (including any gap characters) are of differing lengths, the option must be set to false.
structureModel  model-spec
A trajectory coordinate file is automatically opened as trajectory, but to provide topology information, this option must be used to specify an existing model with the same set of atoms (for example: open myfile.trr struct #1). The coordinates of the existing model will be replaced with the new, unless replace false is used to indicate appending the new frames instead.
atomic  true | false
Whether to interpret coordinates read from mmCIF or PDB format as an atomic model (true, default). Setting the option to false is appropriate for data such as SAXS models that are simply collections of points (possibly with connecting “bonds”) rather than realistically spaced atoms; it classifies the models as Structure rather than atomicStructure, bypassing chemical perception steps like identifying atom types.
ensembles  true | false
Whether to fetch ensembles associated with an IHM dataset (default false, as these can be quite large).
newTab  true | false
Whether to open an HTML file in a new tab of the ChimeraX browser (default false, replace any current page).

URLs

Usage: open  URL  [ format  format-name ] [ coordsets  true | false ] [ vseries  true | false ] [ channel  N ] [ alignment  true | false ] [ structureModel  model-spec ] [ atomic  true | false ] [ ensembles  true | false ] [ newTab  true | false ]  general-options 

Uniform Resource Locators (URLs) starting with http:, https:, and ftp: are handled. File types and command options are as described above for local files. The file type can be indicated by suffix, MIME type, or the format option.

Web-fetched data other than those handled by the ChimeraX browser are stored locally as described below.

Fetch from Online Databases

Usage: openprefix:]identifier  [[ prefix2:]identifier2... ] [ fromDatabase  source ] [ format  format-name ] [ coordsets  true | false ] [ ignoreCache  true | false ]  general-options

An entry can be fetched from a database if its identifier is supplied. The source database can be indicated with either a prefix before the identifier or the fromDatabase option. The default database for a 4-character identifier without prefix is the RCSB Protein Data Bank; the default format for that database is mmcif, although pdb or mmtf can be specified with the format option. Specifying multiple identifiers is equivalent to using the open command multiple times with the same options for each identifier.

Opening a structure in mmCIF format automatically shows a clickable table of assembly information in the Log. See also: ChimeraX Fast mmCIF Guidelines

Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory), with subdirectories PDB for atomic coordinates from the Protein Data Bank, EMDB for density maps from the Electron Microscopy Data Bank, etc. For caching, no distinction is made among the different Protein Data Bank sites. If a data file specified for opening is not found in this local cache or ignoreCache is set to true, the file will be fetched and cached.

Fetch Sources
database prefix source description format-name
RCSB Protein Data Bank pdb: pdb atomic coordinates and associated annotations mmcif (default) or pdb
(see wwPDB formats)
or mmtf
Protein Data Bank
in Europe (PDBe)
pdbe: pdbe atomic coordinates and associated annotations mmcif (default) or pdb
PDBe pdbe_updated: pdbe_updated atomic coordinates and associated annotations,   updated to include small-molecule connectivity and binding-site information as described in Velankar et al., Nucleic Acids Res 44:D385 (2016) mmcif
Protein Data Bank Japan (PDBj) pdbj: pdbj atomic coordinates and associated annotations mmcif
PDBe Electron Density Server (EDS) eds: eds (2Fo-Fc) electron density map for a PDB entry; not available for all PDB entries ccp4
PDBe EDS edsdiff: edsdiff (Fo-Fc) electron density difference map for a PDB entry; not available for all PDB entries ccp4
Electron Microscopy Data Bank
  (ftp from wwpdb.org to .edu/.gov hosts, Chinese mirror site to .cn hosts, otherwise from ebi.ac.uk) 
emdb: emdb density map ccp4
cellPACK cellpack: cellpack hierarchical model; see cellPACK Chimera instructions for available identifiers cellpack

General Options

name  model-name
The name of the model (shown in the Model Panel) will be generated automatically from the input filename or database identifier unless another name is given with the name option. If model-name contains spaces, it should be enclosed in quotation marks. Model number is also assigned automatically, starting with the lowest available number. Model name and number can be changed with the rename command.
autoStyle  true | false
Setting autoStyle to false bypasses automatic styling, i.e., automatically adjusting the appearance of a newly opened atomic model based on its contents. Bypassing this calculation shows all atoms as white spheres, and may be useful in rare cases where generating the rule-based representation is slow (such as drawing cartoons for very large numbers of models) or when chemical perception is inappropriate (such as for a SAXS bead model). See also: markers and links
autoAssociate  true | false
Whether structure-chain sequences should be compared to sequences in Multalign Viewer and automatically associated if the number of mismatches is no more than 1/10 the number of residues in the structure chain. Unlike the other options of open, this sets a state that persists within the ChimeraX session unless explicitly changed. The initial setting is true.

For automatic association, the sequence and structure files can be opened in either order. Gaps in the structure sequence relative to the sequence in the alignment file can only occur where residues are missing from the structure (for example, a flexible loop with insufficient density to determine coordinates). Associations are reported in the status line and the Log. A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure. If more than one sequence matches a given structure chain, the single best-matching sequence is associated.


UCSF Resource for Biocomputing, Visualization, and Informatics / November 2017