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; see also Fetch by ID

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, alphafold, 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 https://www.rbvi.ucsf.edu/chimerax/features.html

[back to top: open]

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
• Trajectory Topology
• Volume Data and Related
• Segmentations
• Other 3D Objects
• Sequences
• Composite
• Miscellaneous

[back to top: open]

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 Sequence 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.

alignTo  chain-spec [ trim  true | false ]
When fetching an AlphaFold prediction or ESMFold prediction, superimpose the predicted structure onto the specified chain using matchmaker defaults, and make the chain ID of the prediction the same as the specified chain's. If the trim option is true (default), the predicted structure will be trimmed to start and end with the first and last aligned positions in the sequence alignment calculated by matchmaker as part of the superposition step.

associate  chain-spec
When fetching a sequence from UniProt, associate it with the specified structure chain(s) only. Normally, association will occur automatically; however, this option handles cases in which the desired chain does not associated automatically due to a high number of sequence mismatches, truncations, large insertions, etc., and/or one wishes to exclude some of the associations that would otherwise occur automatically. After a sequence is opened, its associations can also be adjusted with the Sequence Viewer context menu or the sequence associate command.

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 Sequence 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 (details...). The channel option allows manually assigning a channel to a map so that it can be saved along with other data in a single (multichannel) Chimera map file. See also: image stack wildcards, volume channels

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.

colorConfidence  true | false
When fetching an AlphaFold prediction or ESMFold prediction, whether to color it by the pLDDT confidence measure in the B-factor field (default true):

• 90 to 100 – high accuracy expected
• 70 to 90 – expected to be modeled well (a generally good backbone prediction)
• 50 to 70 – low confidence, treat with caution
• 0 to 50 – should not be interpreted, may be disordered

...in other words, using color bfactor palette 0,red:50,orange:70,yellow:90,cornflowerblue:100,blue
The Color Key graphical interface or key command can be used to draw a corresponding color key, for example:

key red:low orange: yellow: cornflower blue: blue:high  [other-key-options]

combine  true | false
When opening a session file, whether to retain the current session (existing models and other data) or to close the current session first (default, combine false). The model numbers of the incoming session will be changed as needed to avoid duplicate model numbers. See also the resizeWindow option.

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.

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

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

difference  true | false
When opening a density map, whether to display it as a difference map, i.e., showing positive and negative contour surfaces and turning off capping at box faces (default false, except true when fetching from edsdiff).

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

fits  true | false
When fetching a map from the EMDB, whether to additionally fetch associated atomic structures, if any, from the PDB. Alternatively, specifying the data source as emdb_fits (rather than emdb) will automatically fetch both types of data without the use of this option.

forEachFile  input-files
The forEachFile option allows processing multiple data files iteratively with the same ChimeraX command file without having to open the command file over and over. The data files over which to iterate are specified in a single pathname using wild cards or globbing, and would typically contain maps or atomic structures. For example:

open myscript.cxc foreach ~/data/*.cif

...would open the first data file, run the script, open the next data file, run the script, etc. Any existing models are closed before each data file is opened. For saving input-specific output files, “$file” can be used within the command file to indicate the base name of each data file. For example, the following command would save 1a0m.png for input file 1a0m.pdb, 2gbp.png for input file 2gbp.pdb, etc.:

save $file.png

Output files will be placed in the same directory as the data files unless the file-saving command gives a different pathname. See also: alias, runscript

height  h
Height in physical units of distance (Å) for the photo (single image) being opened.

id  model-id
A model identifier (model number, as shown in the Model Panel) will be assigned automatically, starting with the lowest available number, unless another identifier is given with the id option. If the same command opens multiple models or the model-id is already “taken,” submodel numbers will be used. Similarly, the name option can be used to specify the model name. The name and/or number of an existing (already open) model can be changed with the rename command.

ident  alignment-ID
When opening sequence data, assign the specified text as the sequence alignment identifier. If this option is not used, an identifier will be generated automatically. This identifier is used to specify the sequence alignment in other commands and appears in the title bar of the Sequence Viewer window, if shown. See also the viewer option.

log  true | false
When opening a ChimeraX command file, whether to echo each command within the file to the Log as it is executed (default true). If false, although the commands themselves will not be logged, any informational outputs they generate will still appear there.

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.

models  model-spec
Limit attribute assignment to the specified models.

name  model-name
The name of a model (as 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. Similarly, the id option can be used to specify the model identifier (model number). The name and/or number of an existing (already open) model 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).

pixelSize  s
Pixel size in physical units of distance (Å) for the photo (single image) being opened.

resizeWindow  true | false
When opening a session, whether to restore its window size along with its contents; overrides the corresponding Window preference. See also the combine option.

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

transferMethod  https | ftp
Method to use when fetching a map from a specific EMDB mirror site.

showTool  true | false
Whether to show the ViewDockX tool when opening a file of molecular docking results (certain files in the formats swissdock, pdbqt, mae, and mol2; default showTool true). If the file is not found to contain molecular docking results, however, ViewDockX will not be shown. Alternatively, one or more files of docking results can be opened with showTool false, and subsequently (in a separate step) the ViewDockX tool started from the Tools menu or by using the viewdockx command.

transparency  percent
Assign the specified percent transparency to MOLEonline channels read from JSON format (default 0, not transparent). See also the transparency command.

viewer  true | false
Whether to show the Sequence Viewer when opening sequence data. See also the ident option.

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

width  w
Width in physical units of distance (Å) for the photo (single image) being opened.

[back to top: open]

Trajectory Options

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.

Only multi-model mmCIF or PDB files provide all of the trajectory information in a single file. The coordsets option indicates reading the file as a trajectory instead of as multiple models, for example:

• open 1plx.cif coordsets true

Otherwise, the trajectory topology and coordinates come from two different files, either:

• a trajectory coordinate file with topology provided by an already-open atomic model specified with the structureModel option, for example:
  open myfile.trr structureModel #1
• a PSF trajectory topology file with the corresponding trajectory coordinate file specified with the coords option, for example:
  open myfile.psf coords myfile.dcd

Option details:

coordsets  true | false [ missingCoordsets  fill | ignore | renumber ]
Whether to open a multi-model file in mmCIF or PDB format as a trajectory. By default (coordsets false), 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).

The missingCoordsets sub-option indicates how to treat gaps in MODEL numbering when reading a PDB multi-model file as a trajectory with coordsets true. In PDB format, MODEL records are typically numbered consecutively. The numbers from these records are used as the frame numbers of the coordinate sets in the trajectory. When gaps in the numbering are detected, options are to:

• fill – generate duplicate coordinate sets (additional trajectory frames) to fill in the gaps
• ignore – use the MODEL numbers without filling gaps
• renumber (default) – renumber the coordinate sets consecutively

For example, if the first coordinate set MODEL 1 is immediately followed in the file by another coordinate set MODEL 6, fill would create four additional copies of the first coordinate set as frames 2-5, ignore would give trajectory frame 1 immediately followed by trajectory frame 6, and renumber would renumber the MODEL 6 coordinate set as trajectory frame 2.

structureModel  model-spec
To provide the topology information needed to open a trajectory coordinate file as a trajectory, the structureModel option is used to specify an existing model with the same set of atoms (for example: open myfile.trr structureModel #1). This model can itself be a trajectory. If the structureModel option is omitted and only one atomic model is present, that model will be used; if more than one is present, a dialog will appear for specifying which to use. The model coordinates will be replaced with those in the incoming coordinate file unless replace false is used to indicate appending the new frames instead. The structureModel option is also needed to open local MTZ files (details...).

replace  true | false
Whether to replace the coordinates of the existing structure model (which could be a trajectory with multiple frames) with those from the incoming trajectory coordinate file. If replace false is given, the new frames will be appended to the existing frames.

coords  trajectory-coordinate-file 
As an alternative to opening a trajectory coordinate file and supplying the topology with the structureModel option, one can open a PSF trajectory topology file and use the coords option to supply the corresponding trajectory coordinate file. Any of the trajectory coordinate formats may be used. The trajectory-coordinate-file is specified by pathname, or by the word browse to specify it interactively in a file browser window. Omitting this option also raises a file browser window for specifying the file interactively.

start  start
end  end
step  step
The start, end and step options allow loading a subset of the coordinate sets from a trajectory coordinate file, starting with frame number start and proceeding with steps of step but not exceeding the specified end. For example, start 2 end 25 step 5 would read in coordinate sets 2 (the second one in the file), 7 (the seventh), 12, 17, and 22. These options take integer values only, and they do not apply to reading trajectories from multi-model mmCIF or PDB files.

slider  true | false
Whether to show a graphical interface for trajectory playback (default true). The slider can be dragged or a frame number entered directly. The interface also includes a play/pause button, a    value to increase for slower playback, and a button for recording a movie (). The movie will start at the current slider position, so to include the whole trajectory, place the slider at the far left before clicking the record button. See also: coordset slider

[back to top: open]

NMR-STAR Options

NMR-STAR files contain distance constraints that will be shown as pseudobonds between atoms. These files can be fetched from the PDB for certain structures determined by nuclear magnetic resonance (NMR), or obtained directly from the PDB website using the Download option “Combined NMR data (NMR-STAR) (.gz).”

structures  model-spec
Specifies the atomic model(s) on which to draw pseudobonds representing constraints read from an NMR-STAR file. If this option is not given, every currently open atomic model that contains all of the atoms associated with constraints in the NMR-STAR file will be used. If an atomic model that does not contain all of the constraint-associated atoms is specified, a warning will be issued, but constraint pseudobonds will still be generated for the atom pairs that are present.

type  type-name
A single NMR-STAR may contain multiple types of constraints, where each type has a name such as “NOE” or “hydrogen bond.” By default, each type will be opened as a separate pseudobond group with the type included in the model name. The type option can be used to limit the input to a specific type. If not specified, all types of constraints are read and each type is placed in a separate pseudobond group.

Examples:

open 8r4w
open 8r4w from pdb_nmr structures #1 type NOE

open ~/Downloads/8r4w_nmr-data.str structures #1

Each restraint has a maximum distance. If the distance in a structure is within the maximum, it is classified satisfied (command-line specifier for the corresponding pseudobonds is nmr-satisfied), otherwise it is long (command-line specifier nmr-long). Examples of using these in commands:

hide satisfied
show satisfied
hide long

NMR-STAR constraints and their maxima are saved in sessions.

[back to top: open]

Photo (Single Image)

A single image file can be opened as a flat model. Although flat, the model exists in 3D and can be rotated and translated like other models. Several image types (filename suffixes .png, .tif, etc.) are accepted, but except for .jpg, require specifying format photo in the open command. Any of the following options can be used to specify the size of the image within the scene:

width  w
height  h
pixelSize  s

Width, height, and pixel size values are specified in physical units of distance (Å). If width or height is given, the other is set according to the aspect ratio of the image. If both are given and their ratio differs from that of the image, the image will be stretched. Width and height values override any pixel size specification. If no width, height, or pixel size is given, a pixel size of 1.0 will be used. Examples:

open ~/Desktop/headshot.png format photo width 5
open figure1.jpg height 30

[back to top: open]

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
[...]

[back to top: open]

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, NIfTI, PDB, Pfam, PIR, pseudobonds, Python code, RSF, STL, Stockholm, STORM, VTK PolyData, and Wavefront OBJ.

[back to top: open]

Attribute Assignments

Usage: open  attr-file  [ format  defattr ] [ models  atom-spec ] [ log  true | false ]

The open command can read and assign attribute values from an attribute assignment file. It is possible to define new attributes or to (re)assign values for existing attributes of atoms, residues, and atomic models. The attr-file is specified by its pathname, or by the word browse to specify it interactively in a file browser window. If the models option is used, assignment will consider only the models containing the specified atoms. Of course, whether attribute values are actually assigned to those models or their parts depends on the contents of the attribute assignment file. The log option indicates whether to report details of the assignments to the Log.

The related command setattr assigns attribute values directly, but is less practical for large-scale assignment since only a single value can be given per command. See also: info, amino acid hydrophobicity

[back to top: open]

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

[back to top: open]

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.

[back to top: open]

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 ] [ resName  name ]  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. As an alternative to the command, Fetch by ID provides a graphical interface to many common fetch types.

See also: Download DICOM, Web Access preferences

Web-fetched data are stored locally in ~/Downloads/ChimeraX/ (where ~ indicates a user's home directory), with subdirectories PDB, EMDB, 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.

The resName option applies only to PubChem3D and SMILES fetches; it assigns a residue name to the compound (default UNL). For compatibility with other programs and PDB format, three-character residue names consisting of uppercase letters and possibly numbers are recommended.

The colorConfidence option (default true) applies only to alphafold or esmfold fetch and specifies whether to color the predicted structures by a confidence value (details...). The alignTo and trim options also apply only to alphafold or esmfold fetch (details...). See also: alphafold, esmfold

[back to top: open]

Open/Save Options from Clipper

The Clipper bundle from the ChimeraX Toolshed allows opening and saving crystallographic reflection files in MTZ format. See also: clipper commands, PDB-REDO fetch

Opening an MTZ file requires specifying an already-open atomic structure with the structureModel option, for example, if that atomic structure is open as model #1:

open myfile.mtz structureModel #1

If the structureModel option is not given in the command, however, a dialog will appear to allow specifying which atomic structure should be used.

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.