The command open reads data in several input formats from:
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: close, save, help, sym, info, File History, Rapid Access , initial colors, automatic styling, ChimeraX Fast mmCIF Guidelines
open ~/Desktop/maps/myfile.mrc name refined3
open 1plx format pdb coord T
open 3237 from emdb name "gamma-secretase complex"
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|
|PDB (Protein Data Bank)||pdb||.pdb, .pdb1
|atomic coordinates and associated annotations; if PQR, sets atomic radius|
|atomic coordinates and associated annotations
(see assemblies from mmCIF, H-bonds from mmCIF,
ChimeraX Fast mmCIF Guidelines)
|MMTF (Macromolecular Transmission Format)||mmtf||.mmtf||atomic coordinates and associated annotations|
|Sybyl Mol2||mol2||.mol2||atomic coordinates
(see ViewDockX for analysis of docking results from UCSF DOCK v4-6, DOCK v3.7, or GOLD)
(see ViewDockX for analysis of docking results from AutoDock Vina)
|Pseudobond file||pseudobonds||.pb||list of atom pairs to connect with pseudobonds|
(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|
electrostatic potential map from
Adaptive Poisson-Boltzmann Solver
(see the APBS tool in UCSF Chimera)
|BRIX map||dsn6||.brix||electron density map|
|CCP4 map||ccp4||.ccp4, .map||electron density map|
|Chimera map||cmap||.cmp, .cmap||volume data from Chimera/ChimeraX
(based on the hierarchical data format HDF5)
|CNS or XPLOR map||xplor||.cns, .xplor||unformatted ASCII density map|
|DelPhi or GRASP potential||delphi||.phi||electrostatic potential map from DelPhi (the academic version) or GRASP|
|DeltaVision map||dv||.dv||light microscopy data|
|DICOM map||dicom||.dcm||medical image stack; see the verbose option|
|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)
|DOCK scoring grid||dock||.bmp
UCSF DOCK (versions 4, 5, 6)
bump, contact, and energy scoring grids
(suffixes not interchangeable; gridname.bmp required for reading gridname.cnt and/or gridname.nrg)
|DSN6 map||dsn6||.omap||electron density map|
|EMAN HDF map||emanhdf||.hdf, .h5||electron density map
(based on the hierarchical data format HDF5)
|Gaussian cube grid||cube||.cube, .cub||orbitals, electron densities, other|
|gOpenMol grid||gopenmol||.plt||orbitals, electron densities, other|
|ImageJ or OME TIFF||.tif, .tiff||microscopy data
(multiple channels and/or time points specified in file header)
|Image stack||images||.tif, .tiff
(grayscale image series in multiple files or a single multipage file, in formats supported by PIL)
|Imaris map||ims||.ims||3D-5D image
(could be time series and/or multichannel)
|IMOD map||imodmap||.rec||electron density map
(MRC map with signed 8-bit mode interpreted as unsigned)
|MacMolPlt grid||macmolplt||.mmp||3D surfaces|
|MRC map||mrc||.mrc||electron density map|
|3D light or EM data
(.xyzt is time series)
|PROFEC grid||profec||.profec||interaction free energy grid from PROFEC (in Amber versions 6 and 7)|
|Purdue image format||pif||.pif||electron density map|
|Situs map||situs||.situs, .sit||electron density map|
|SPIDER map||spider||.spi, .vol||electron density map|
|STORM (STochastic Optical Reconstruction Microscopy)||storm||.storm||super-resolution microscopy data|
|TOM toolbox map||tom_em||.em||electron density map|
|UHBD potential (binary)||uhbd||.grd||electrostatic potential map from University of Houston Brownian Dynamics|
|← Other 3D Objects|
|Chimera/ChimeraX BILD||bild||.bild, .bld||graphical objects|
|Chimera/ChimeraX markers||markers||.cmm||markers and links
(analogous to atoms and bonds)
|GL Transmission Format||gltf||.glb||graphical objects|
|STereoLithography (binary)||stl||.stl||triangle-based format native to stereolithography CAD software|
|VTK (Visualization ToolKit) PolyData||vtk||.vtk||lines, polygons [documentation PDF]|
|Wavefront OBJ||obj||.obj||graphical objects
(triangles only: vertices, vertex normals, faces; no colors)
|← Sequences (associated tool: Sequence Viewer)|
|Clustal ALN||aln||.aln, .clustal
|FASTA, aligned FASTA||fasta||.fasta, .fa
|individual sequence(s) or sequence alignment|
|GCG MSF (Multiple Sequence Format)||msf||.msf||sequence alignment|
|GCG RSF (Rich Sequence Format)||rsf||.rsf||sequence alignment|
(other information not read; see HSSP database)
|PIR (NBRF), aligned PIR||pir||.pir, .ali||individual sequence(s) or sequence alignment|
|Selex (Pfam)||pfam||.selex, .slx
|Stockholm||stockholm||.sth, .sto||sequence alignment|
|ChimeraX session file||session||.cxs||ChimeraX session; see the Window preferences|
|IHM (Integrative Hybrid Model)||ihm||.ihm||integrative hybrid model, examples available from PDB-Dev (see database fetch); may create residue attributes|
|ChimeraX command file||cmd||.cxc||ChimeraX commands|
|Python||py||.py, .pyc, .pyo||Python code|
|HTML, XHTML||html||.html, .htm
.xhtml, .xht, .xml
|hypertext to render in the ChimeraX browser|
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). 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.
Giving browse as the filename brings up a dialog for browsing the filesystem interactively.
Additional ways to open local files:
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.
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
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.
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.
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).
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
Maximum number of models to keep when opening a multi-model file in mmCIF or PDB format as multiple models in ChimeraX (coordsets false).
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.
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.
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).
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
Usage: open URL [ format 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, MIME type, or the format option.
Web-fetched data other than those handled by the ChimeraX browser are stored locally as described below.
Usage: open [ source1:]identifier [[ source2:]identifier2... ] [ fromDatabase source ] [ format format-name ] [ maxModels M ] [ coordsets true | false ] [ ignoreCache true | false ] 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.
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.
See also: Web Access preferences
|RCSB Protein Data Bank||pdb||atomic coordinates and associated annotations||mmcif (default) or pdb
(see wwPDB formats)
|Protein Data Bank
in Europe (PDBe)
|pdbe||atomic coordinates and associated annotations||mmcif (default) or pdb|
|PDBe||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||atomic coordinates and associated annotations||mmcif|
|PDBe Electron Density Server (EDS)||eds||(2Fo-Fc) electron density map for a PDB entry;
not available for all PDB entries
|PDBe EDS||edsdiff||(Fo-Fc) electron density difference map for a PDB entry;
not available for all PDB entries
|Electron Microscopy Data Bank
(ftp from wwpdb.org to .edu/.gov hosts, Chinese mirror site to .cn hosts, otherwise from ebi.ac.uk)
|emdb||electron density map||ccp4|
|PDB-Dev||pdbdev||integrative hybrid model;
leading zeroes can be omitted from the identifier, for example, accession code PDBDEV_00000010 can be opened with command:
see cellPACK Chimera instructions for available identifiers
|UniProt||uniprot||protein sequence (associated tool: Sequence Viewer)||uniprot|