Command: open

Usage:
open ( filename | URL | [ prefix:]identifier ) [ maxModels  M ] [ coordsets  true | false ]  options 

Usage:
open formats

The command open reads data in several input formats from:

• local files
• URLs
• online sources

Input files may contain data to be displayed or commands or code to be executed.

For some types of files, associated information is automatically shown in the Log when the file is read. See also: runscript, close, save, help, sym, info, File History, Rapid Access , initial colors, automatic styling, ChimeraX Fast mmCIF Guidelines

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

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Input Formats

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

• Atomic Structures and Related Data
• Trajectory Coordinates
• Volume Data and Related
• Segmentations
• Other 3D Objects
• Sequences
• Composite
• Miscellaneous

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Local Files

Usage: open  filename  [ filename2... ] [ format  format-name ] [ maxModels  M ] [ coordsets  true | false ] [ vseries  true | false ] [ resizeWindow  true | false ]  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). For image stacks only, additional wild cards may be used.

Multiple filenames separated by spaces can also be given, which is equivalent to using the open command multiple times with the same options for each filename.

Substituting the word browse for the filename brings up a file browser window for choosing the name and location interactively.

The file format can be indicated with either the filename suffix or the format option (where format-name can be truncated). Certain formats can be read when compressed (.gz, .bz2, or .xz, see details).

Giving browse as the filename brings up a dialog for browsing the filesystem interactively.

Additional ways to open local files:

• menu File... Open, in which case the proper filename suffix is required
• Toolbar icon
• 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.

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Options

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.

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.

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.

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

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:

• _ch0_
• _0ch_

(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. See also: image stack wildcards

combineSymAtoms  true | false
Nonstandard PDB or mmCIF files may contain duplicate copies of atoms at symmetry positions; this option indicates whether to merge multiple singleton atoms of the same element at the same 3D position into one (default true) to prevent errors in subsequent calculations such as adding hydrogens.

childModels  true | false
When opening a ChimeraX positions file, whether to explicitly apply matrices for submodels rather than simply allowing them to follow their parent models.

contours  true | false
Whether to read the contours from an IMOD segmentation file.

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).

debug  true | false
Whether to send verbose information to the Log when opening a EMDB segmentation file.

ensembles  true | false
Whether to fetch ensembles associated with an IHM dataset (default false, as these can be quite large).

logInfo  true | false
Whether to show available model information (other than structure title) in the Log. See also: log metadata

matchNames  true | false
When opening a ChimeraX positions file, whether to match models by name instead of simply applying the matrices in order of appearance in the file.

maxModels  M
Maximum number of models to keep when opening a multi-model file in mmCIF or PDB format as multiple models in ChimeraX (coordsets false).

maxSurfaces  N
Maximum number of surface models to create when opening an EMDB segmentation file.

meshes  true | false
Whether to read the meshes from an IMOD segmentation file.

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.

newTab  true | false
Whether to open an HTML file in a new tab of the ChimeraX browser (default false, replace any current page).

resizeWindow  true | false
When opening a session, whether to restore its window size along with its contents; overrides the corresponding Window preference. Opening a ChimeraX session automatically runs close session first.

segidChains  true | false
Whether to assign segment IDs in PDB format as the chain IDs in ChimeraX.

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 structureModel #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. This option is also needed to open local MTZ files (details...).

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:

• _stack0012_
• _0012stack_

(and 0012 could be any integer).

verbose  true | false
Whether to show detailed debugging information for DICOM input. If format dicom is specified explicitly, all of the DICOM files in a directory and its subdirectories can be opened with a single open command, for example:

open "~/Desktop/2-CT 5.0 H30s-55580" format dicom

Each stack that is found will be opened as a separate model. Alternatively, the multiple files of a stack can be specified with filename globbing as described above. The option to specify a directory rather than filenames is only available for this format. See also: ChimeraX DICOM Reference

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URLs

Usage: open  URL  [ dataFormat  format-name ] [ maxModels  M ] [ coordsets  true | false ] [ vseries  true | false ] [ resizeWindow  true | false ]  options 

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

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

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Fetch from Online Sources

Usage: open [ source1:]identifier  [[ source2:]identifier2... ] [ fromDatabase  source ] [ format  format-name ] [ maxModels  M ] [ coordsets  true | false ] [ ignoreCache  true | false ] [ maxAssemblies  N ]  options 

Atomic structures, density maps, and protein sequences can be fetched directly into ChimeraX from online sources. A specific compound or entry is specified by an identifier, and its source (database or web service) 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.

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.

Multiple biological assemblies are defined for many entries in the PDB. By default, fetching from rcsb_bio or pdbe_bio will return every assembly available for that entry in that database. The maxAssemblies option limits fetching to the first N assemblies. A single assembly from pdbe_bio will be opened as a single model, but even a single assembly from rcsb_bio may be composed of multiple models (opened as submodels of the assembly model).

See also: Web Access preferences

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Image Stack Wildcards

For image stacks only, special wildcards {t}, {c}, {z} can be used in the open command file pathname to specify the stack collectively. These wildcards indicate the parts of the filename with time, channel, and Z-indices, respectively. For example, to open a stack where each file is a 3D volume (each file contains all Z planes for one channel at one timepoint):

open "/Volumes/data/micro/cell8_3 stars/cell8_{c}ch_{t}stack_*msec.tif"

cell8_0ch_0000stack_000000msec.tif
cell8_0ch_0001stack_001383msec.tif
cell8_0ch_0002stack_002766msec.tif
cell8_0ch_0003stack_004149msec.tif
cell8_1ch_0000stack_000000msec.tif
cell8_1ch_0001stack_001383msec.tif
cell8_1ch_0002stack_002766msec.tif
cell8_1ch_0003stack_004149msec.tif
[...]

open ~/Desktop/latest/r12c09f01p{z}-ch{c}sk{t}fk1fl1.tiff

r12c09f01p01-ch1sk01fk1fl1.tiff
r12c09f01p01-ch1sk02fk1fl1.tiff
r12c09f01p01-ch1sk03fk1fl1.tiff
r12c09f01p01-ch1sk04fk1fl1.tiff
[...]

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Compressed Files

Certain file types can be read when compressed, as indicated with a suffix for the type of compression (.gz, .bz2, or .xz following the usual suffix for the type of file). For example, myfile.pdb.gz is a gzipped PDB file.

The file types that can be read by ChimeraX in compressed form (as well as uncompressed) are ALN, BILD, Collada, compiled Python code, directional FSC, FASTA, glTF, HSSP, MMTF, MSF, PDB, Pfam, PIR, pseudobonds, Python code, RSF, STL, Stockholm, STORM, VTK PolyData, and Wavefront OBJ.

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Open/Save Options from Clipper

The Clipper bundle from the ChimeraX Toolshed allows opening and saving crystallographic reflection files in MTZ format.

Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option. Structure factors can also be fetched along with the corresponding atomic structure from the RCSB Protein Data Bank by specifying structureFactors true, for example:

open 6cmn structureFactors t

Saving: Only previously fetched structure factors or those from a previously opened MTZ file can be saved as MTZ, with additional save command options:

preserveInput  true | false
Whether to pass through the original, unmodified structure factors as well as those actually used by Clipper (which may have been modified).

saveMapCoeffs  true | false
Whether to save the current amplitudes and phases for all maps generated by Clipper. If false, just save the experimental data.

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Generic HDF File Reader

If EMAN HDF format is expected, but that file reader fails, a generic HDF file reader is tried instead. This generic reader does not look for any metadata; it simply looks for 3-dimensional arrays and tries to open them as volume models with grid spacing of 1. The following open command option can be used to limit which 3D arrays are read:

arrayName  name
In HDF5 format, each array has a directory path within the file and a name (the last part of the pathname). This option indicates reading only arrays with the specified name. Example:

open Cam_long_00003.h5 arrayName Data