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ChimeraX Change Log
This log includes new features of interest to users. Minor feature improvements and minor bug fixes are usually not included. Dates are approximate.
May 15, 2024 Missing-segment labels - missing-structure pseudobonds are labeled by the number of missing residues that they represent; these labels can be hidden/shown using the Preferences
May 8, 2024: Release 1.8 branch made
April 12, 2024: view docking results from MOE - ViewDockX recognizes molecular docking results in Mol2 format from MOE
April 12, 2024: Select by attribute GUI - Render/Select by Attribute set to its Select tab can be opened from the Select menu
April 9, 2024: surface-surface contact area - measure contactarea command to report the area of one surface within a cutoff distance of another surface
March 21, 2024: PDB-REDO fetch - fetch atomic structures from the PDB-REDO database using Fetch by ID or the open command
March 12, 2024: Worms - create specialized cartoons in which "worm" fatness shows values of an attribute (bfactor, seq_conservation, ...) with Render by Attribute or commands worm or cartoon byattribute
February 22, 2024: Save tables as comma- or tab-separated values - various sortable-table dialogs now have a context menu option to Save CSV or TSV File... (e.g. Rotamers, Check Waters, Axes/Planes/Centroids table of objects)
February 15, 2024: Join models generalized to any covalent bond - build join bond allows joining models in the general case (bonds other than peptide); this feature is also available in the Build Structure GUI
February 2, 2024: Label models - label command models option
February 2, 2024: Segmentations tool applies to any volume data - the Segmentations tool for manual plane-by-plane segmentation can be used on any type of volume data (previously only medical images)
January 29, 2024: Combine models without changing chain IDs - combine command option retainIds true
January 11, 2024: View multiple alternate locations at the same time - altlocs show command
January 10, 2024: Fetch/read PDB NMR-STAR format - NMR-STAR restraints can be shown as pseudobonds on associated structures (details...)
January 2, 2024: Model Panel capabilities for rapidly flipping through models - context menu allows adding Next/Previous/Skip controls
November 14, 2023: Command to create pseudobonds - pbond command
November 10, 2023: Show attribute values with atomic radii - command size byattribute, Radii section in Render by Attribute
November 7, 2023: Release 1.7 branch made; released: December 20, 2023
November 7, 2023: Customize initial map colors - colors to use for newly opened maps can be customized with the initialColors option of volume defaultvalues
October 24, 2023: Designate map as difference map - open command option difference true to specify automatically showing a map with negative and positive contours
October 15, 2023: Specify model number when opening data - open command id option
October 12, 2023: A File→Fetch By ID menu item has been added to conveniently fetch atomic structures, density maps, and protein sequences from online sources.
September 29, 2023: Fetch EMDB map + fit structures - if the EMDB map metadata refers to fit models, the corresponding atomic structures can be fetched in the same open command with fits true or by specifying the fetch source as "emdb_fits"
September 22, 2023: Combine sessions - opening a session with the open command option combine true (e.g.,"open session-file.cxs combine true") merges the incoming session with the current session instead of closing it first. Model IDs in the incoming session may be changed to avoid duplicate ID numbers. Please report any bugs you encounter with this feature, since some tools may need further enhancements to work correctly when combining sessions.
September 9, 2023: Z-translation with mouse - additionally pressing the Ctrl key when using a translation mouse mode (translate selected models, move picked model, etc.) switches to Z-translation
September 6, 2023: Rotate view to Z-align centroids of two sets of atoms - view zalign option can take two sets of atoms separated by inFrontOf keyword to align their geometric centers front to back (previously required exactly 2 atoms)
August 29, 2023: Adjust default settings for new maps - volume defaultvalues command allows setting user defaults for subsequently opened maps
August 24, 2023: ViewDockX starts automatically - by default, opening a file recognized as ligand docking results shows the ViewDockX tool
August 23, 2023: Better separation of trackpad multitouch zoom and rotate - pinch-zoom and twist can no longer occur simultaneously; the gesture will be interpreted as one or the other rather than both
June 23, 2023: mmCIF reader - memory leak fixed
June 22, 2023: Fetch by IUPAC name - IUPAC name translation to SMILES using a web service provided by the Centre for Molecular Informatics (University of Cambridge) followed by the existing SMILES fetch process; available in the open command and Build Structure tool
June 22, 2023: Invert selection in selected models - option to invert the selection but only within the selected models added to the Select menu and available as right/left arrow shortcut (Shift-right/left arrow to invert in all models)
June 15, 2023: Centering mouse mode - mousemode function added to center the view on the clicked item
June 10, 2023: Easy selection inversion - the left/right arrow keys will invert the selection (same as Selection→Invert menu item)
June 6, 2023: Save Blast results to TSV file - button added to save all Blast Protein results as a tab-separated values file
June 1, 2023: Map Filter tool - Map Filter graphical interface to several kinds of map filtering and transformation (Gaussian, Laplacian, etc.)
May 25, 2023: Copy settings from one atomic structure to another - mcopy command implemented
May 15, 2023: Save GLTF options - new options for saving GLTF: whether to cull surface backfaces, omit per-vertex colors when an entire object is a single color, and omit normal vectors (show triangles as facets instead of smooth-shaded)
April 21, 2023: Bond angle GUI - the Adjust Angles section of Build Structure can be used to modify bond angles and other angles defined by three atoms
April 10, 2023: Save info to file - saveFile option added to the info command file (e.g., one can save a list of the selected atoms to a file)
March 31, 2023: Bond rotation GUI - the Adjust Torsions section of Build Structure can be used to modify torsion angles; one way to add a torsion to this interface is by control-double-clicking a bond and choosing "Adjust Torsion" from the resulting pop-up menu
March 23, 2023: Release 1.6 branch made; released: May 9, 2023
March 8, 2023: Palette and color-key support in Render by Attribute - Render by Attribute allows choosing from a menu of the available palettes, as well as clicking a button to create a Color Key that matches the current coloring (regardless of whether a named palette is used)
March 5, 2023: Read NRRD files - support for reading .nrrd files (Nearly Raw Raster Data) often used for medical images
February 20, 2023: Fetch medical images from The Cancer Imaging Archive - the new Download DICOM tool allows browsing TCIA medical image collections and fetching image series of interest
February 14, 2023: Invert chiral center - swap substituents of an atom with the Invert section of Build Structure or the command build invert
February 10, 2023: Read NIfTI files - support for reading .nii files (NIfTI format developed by the Neuroimaging Informatics Technology Initiative) often used for medical images
February 3, 2023: SwissDock format - docking results from SwissDock can be read by adding "format swissdock" to the open command, or by switching from "All files" to "SwissDock" in the main File→Open dialog.
December 22, 2022: Blast from Sequence Viewer - start the Blast Protein tool from the Sequence Viewer context menu
December 22, 2022: Nucleic acid virtual mutation - with the swapna command
December 7, 2022: Blast Protein sequence input - Blast Protein tool and command allow specifying the query sequence by UniProt ID/name, or as plain text pasted into the dialog or command line
November 28, 2022: ESMFold GUIs - ESMFold and ESMFold Error Plot for getting and evaluating ESMFold-predicted protein structures (tool equivalents of the esmfold command)
November 24, 2022: Coulombic ESP map - coulombic command option to create a volume model from the computed electrostatic potential (ESP)
November 23, 2022: Dock Prep GUI - tool equivalent of dockprep command
November 17, 2022: CIF format reader - initial support for reading (uncomplicated) small-molecule CIF files, as well as fetching from the Crystallography Open Database and Predicted Crystallography Open Database
November 10, 2022: Add Charges GUI - tool equivalent of addcharge command
November 9, 2022: ESMFold protein structure prediction - added esmfold command to predict protein structures from sequence or to fetch pre-computed structures from the ESM Metagenomic Atlas.
October 26, 2022: Surface smoothing - smoothing options added to surface and segmentation surfaces commands (the latter also in the 1.5 release branch)
October 14, 2022: Bare-bones Render by Attribute tool - only does coloring based on attribute values, not setting atomic radii, changing tube thickness, or selecting (unlike Chimera version of the tool). The tool will be enhanced over the coming weeks and months.
October 13, 2022: Release 1.5 branch made; released: November 23, 2022
November 12, 2022: Alphafold database version 4 - updated alphafold database searches to use database version 4 which fixes 4% of entries that were mis-computed in database version 3.
October 12, 2022: DICOM Browser and Metadata - clicking the Info button on the Model Panel for a DICOM model opens a DICOM Browser showing the associated patient, study, and series hierarchy, with option to show full details in the Metadata Browser
September 13, 2022: Show channels from MOLEonline - opening JSON downloaded from the MOLEonline server displays channels, with a slider interface for flipping between them
September 8, 2022: Altloc Explorer tool enhanced to show/update H-bonds when altloc changed.
September 7, 2022: Dock prep - dockprep command
August 30, 2022: Alphafold database version 3 - updated alphafold database searches to use database version 3 with over 200 million entries
August 30, 2022: Add Hydrogens GUI - tool equivalent of addh command
August 25, 2022: Assign atomic partial charges and Amber/GAFF types - addcharge command looks up Amber force field charges for standard residues, uses Antechamber to assign GAFF types and calculate charges for nonstandard residues
August 25, 2022: Axes/Planes/Centroids GUI - Axes/Planes/Centroids tool includes interactive table of objects and dialogs to define them
August 24, 2022: Set location of AlphaFold results - AlphaFold tool and alphafold predict command allow specifying name and location of directory containing prediction results
August 11, 2022: Align view with axis or plane object - view command zalign option allows specifying previously defined axis or plane
August 8, 2022: Closing session reverts more settings - close session command improved to restore more settings to startup values (background color, silhouettes, clipping, camera mode, etc.)
August 8, 2022: Closing tiled models reverts to single rotation - closing tiled models turns off independent rotation mouse mode
July 18, 2022: AlphaFold predictions ten times faster - tool and GUI now run predictions using ColabFold, an open-source, optimized version of AlphaFold2; see video. ChimeraX 1.3 and 1.4 also now use ColabFold.
July 12, 2022: Change Chain IDs GUI - tool for changing chain IDs
July 8, 2022: Change chain IDs - changechains command
June 17, 2022: Alignment reference sequence - the Sequence Viewer context menu allows using the numbering of a particular sequence in the alignment (the "reference" sequence) as the overall numbering across the top. It also allows showing/hiding that overall numbering as well as individual sequence numberings on the left and/or right.
June 30, 2022: Fix UniProt fetch - UniProt changed the API for fetching sequence information from their website, requiring corresponding changes to ChimeraX.
June 16, 2022: Renumber Residues GUI - tool for renumbering residues
June 10, 2022: Colored lines show AlphaFold residue-residue error - alphafold contacts command to draw pseudobonds colored by AlphaFold PAE value
June 9, 2022: Renumber residues - renumber command
June 7, 2022: Crosseye and walleye stereo - crosseye and walleye modes added to camera command
June 7, 2022: Surface invertShown - surface invertShown command to show only the dust (smallest blobs) after hiding dust
June 3, 2022: Surface transform - surface transform command to scale, rotate, and/or shift surface coordinates
May 5, 2022: Release 1.4 branch made; released: June 10, 2022
April 26, 2022: Join models - two models can be joined through a peptide bond using the build join peptide command or by using the "Join Models" section of the Build Structure tool.
April 18, 2022: Centered GLTF - new default for saving GLTF is to center the scene at 0,0,0
April 14, 2022: Blast UniRef - uniref100, uniref90, and uniref50 added to choices of protein sequence database in Blast Protein tool and blastprotein command
March 29, 2022: Percent identity calculation - percent sequence identity calculations available via the Sequence Viewer context menu and sequence identity command
March 25, 2022: AlphaFold predicted aligned error heatmaps - display of Alphafold residue-to-residue errors as PAE plots with menu entry Tools / Structure Prediction / AlphaFold Error Plot or command alphafold pae.
March 21, 2022: Copy sequence - the Sequence Viewer context menu allows copying a sequence to the system text buffer for subsequent paste operations
March 11, 2022: Qt 6 window toolkit - updated window toolkit ChimeraX uses from Qt 5.15.2 to Qt 6.2.3.
March 9, 2022: Updated AlphaFold database - alphafold match and search now use the January 2022 third release of the EBI AlphaFold database adding proteins related to neglected tropical disease and antimicrobial resistance. The AlphaFold database now has 1 million structures.
March 8, 2022: webcam command handles more video camera formats, specifically NV12 encoding which is very common on laptop and desktop web cameras.
February 11, 2022: Alternate residue numberings - biopolymer structures from the wwPDB can be switched between the residue numberings provided by the depositor (author, initial default), used internally by the PDB (canonical), or in the UniProt sequence (uniprot). This can be done by using setattr to change the res_numbering model attribute. Example: setattr #1 structure res_numbering uniprot
February 2, 2022: Read ZDOCK output - ZDOCK quasi-PDB files can be opened with the format zdock option
January 28, 2022: User interface toolkit update - switch to Qt 6, currently available separately as a "technology preview build" on the download page. After an appropriate amount of testing, will be incorporated into the regular daily build.
January 24, 2022: ModBase target-template alignment and model scores - opening a comparative model from ModBase (mmCIF format) automatically shows the target-template sequence alignment in the Sequence Viewer, and model quality scores can be shown with log metadata
January 19, 2022: Independent centers of rotation - added rotate independent mouse mode, automatically assigned by the tile command
December 31, 2021: Align sequences with Clustal Omega or MUSCLE - sequence align command and Sequence Viewer context menu allow (re)aligning sequences with web services hosted by the RBVI
December 16, 2021: Increment/decrement radii - size command allows changing settings relative to their current values by giving a +/-increment
December 14, 2021: AlphaFold Database v2 - the AlphaFold tool and commands alphafold search and alphafold match search the new, larger AlphaFold Database (~800,000 sequences; ChimeraX 1.3 uses database v1 with ~360,000 sequences)
December 7, 2021: Animated PNG - added movie output format apng
December 3, 2021: AlphaFold Multimer - the AlphaFold tool and alphafold predict command can run multimer predictions on Google Colab (albeit with memory limits on total size)
November 17, 2021: Local Modeller execution - The modeller comparative and modeller loops commands now support execution of a locally installed Modeller as an alternative to using the web service ("executableLocation" keyword).
November 15, 2021: Edit model panel names/IDs - Model names and IDs can now be directly edited in the model panel by double clicking on the name or ID and entering a new value.
November 3, 2021: Define axes - define axis command to calculate best-fit axes (shown as cylinders) that can be used in distance and angle measurements and used to specify vectors in other commands (for example, the axis of rotation for roll)
October 6, 2021: Release 1.3 branch made; released: December 8, 2021
October 5, 2021: Blast Protein update - new Blast Protein graphical interface (easier column controls, etc.)
September 22, 2021: Change bond length - graphical interface and bond length command for adjusting bond length
September 15, 2021: Show model info - new Info button on the Model Panel shows model information for atomic structures in the Log
September 15, 2021: Model Loops GUI
August 27, 2021: Model loops - add missing segments or refine existing segments with modeller loops command
August 20, 2021: AlphaFold GUI - tool to fetch predictions from the AlphaFold Database and to run new AlphaFold calculations using Google Colab
August 15, 2021: BLAST AlphaFold - Blast Protein can search the AlphaFold Database
August 10, 2021: Open subset of trajectory - start, end, step options for opening trajectory coordinate files
July 30, 2021: Combine or copy atomic models - combine command
July 29, 2021: AlphaFold fetch - alphafold command to get AI-predicted protein structures from the AlphaFold Database
July 13, 2021: Scale Bar tool and scalebar command
June 30, 2021: List multiple map-fitting solutions - the Fit List dialog enumerates and allows switching among multiple fits from a fitmap global search
June 25, 2021: Altloc Explorer - tool to list residue alternate locations and control which are used (for display, calculations, etc.)
June 24, 2021: GLTF export options - ability to use instancing and texture colors for some models when saving GLTF
May 21, 2021: PSF files - trajectories can now be opened directly as a PSF topology file in conjunction with a coordinates file, e.g. "open PSF file coords coordinate file". If you use the File→Open dialog to open the PSF file or if you omit the coords keyword from the open command, a file browser will be shown for specifying the coordinates file interactively.
May 20, 2021: Map values at atom positions - measure mapvalues command assigns map values as an atom attribute that can then be used for coloring, command-line specification, etc.
May 18, 2021: Relocatable CentOS RPM files - Made the CentOS RPM package files relocatable with "rpm -i --relocate /usr=INSTALL_ROOT ..." Dependencies have to be handled separately.
April 28, 2021: Manage alternate locations - altlocs command to list alternate locations in atomic structures and to control which location is used for display and calculations
April 26, 2021: Command-file opening options - open command options to apply a command file iteratively to multiple data files and/or to suppress logging each command as it is executed
April 15, 2021: Selection Inspector - bare-bones Selection Inspector to inspect/change attributes of selected items. Currently only handles atoms, bonds, and residues. June 28: now includes atomic models, pseudobonds, and pseudobond models. Will eventually include surfaces.
April 15, 2021: New hotkeys to hide/show floating tool windows and cycle through which window is in the front (details...)
April 14, 2021: Release 1.2 branch made; released: May 28, 2021
May 23, 2021: Relocatable CentOS RPM files - backport from daily builds
March 18, 2021: Surface Color tool - GUI for coloring by map value or distance (radial, etc.)
March 13, 2021: Fly along multiple views - fly command to smoothly traverse a series of named views for animation purposes
March 11, 2021: Color Key tool for interactive placement and adjustment of a color key
March 8, 2021: Crystal Contacts tool and command to check for clashes between symmetry-related copies of a structure
March 5, 2021: Unit Cell tool and command to generate crystallographic unit cells
March 2, 2021: Measure Volume and Area tool (GUI) to report the total area and enclosed volume of a surface model
February 26, 2021: Volume tool GUIs - graphical interfaces for Hide Dust, Color Zone, and Surface Zone
February 22, 2021: Map toolbar improvements including new icons for volume zone, color zone, and hide dust
February 12, 2021: Structure building starting from ring-system fragments implemented
February 10, 2021: Color key command - key command to draw a color key, GUI to come later
January 28, 2021: Window-fill command - the icon at the bottom right of the ChimeraX window that hides docked tools to show a larger graphics area now has a command equivalent: ui windowfill toggle. This is most useful for assigning to a function key via the functionkey command for situations where using the icon might be tedious (e.g. a laptop with a track pad).
January 27, 2021: Auto-float tools - if the "Start tool windows undocked" preference is turned on, any tool launched after ChimeraX startup will start out floating (undocked) and undockable. Sometimes useful with laptops or smaller screens. A tool can be made dockable again by using its "Dockable Tool" context menu entry.
January 26, 2021: Nucleic-acid building - the Build Structure tool and build start nucleic command can be used to construct RNA, DNA, or RNA/DNA hybrids from scratch.
January 15, 2021: Maestro reader included - the daily build can read .mae files (such as Glide docking output) without installation of a separate plugin
December 21, 2020: Read Gromo87 (.gro) files as structures (not as a trajectories).
December 21, 2020: UniProt features - fetching a sequence from UniProt will not only show the sequence but also bring up a browser-like interface for showing features on the sequence such as transmembrane regions, sequence variants, etc.
December 1, 2020: Faster map session save - saving session files that include map files is much faster with slightly larger file size, relying on lz4 compression instead of gzip.
November 16, 2020: Meetings - user interface panel allows hosting ChimeraX meetings, with virtual reality or screen display.
November 9, 2020: Rainbow coloring - can now color parts of a chain with rainbow command.
November 4, 2020: Smaller session files - compress ChimeraX session files (*.cxs) with LZ4 for 4 times smaller file size.
November 2, 2020: Icosahedral cages - added new icosahedral cage modes to hkcage command contributed by Colin Brown and Antoni Luque.
October 30, 2020: Open command reads attribute files - will deprecate the defattr command now that open fills its role
October 26, 2020: Volume series marker display - markers on volume series data are assigned a frame attribute for synchronized display
October 19, 2020: Save attributes - attribute values (e.g., per-residue surface areas from measure sasa) can be saved to a file
October 12, 2020: Mark surface blobs - marker connected command to place a marker in the center of each connected surface blob, for microscopy.
October 7, 2020: ChimeraX on macOS Big Sur - released ChimeraX 1.1.1 fixing a problem that made older versions fail to start on the new macOS Big Sur operating system.
October 1, 2020: Move specific model w/o selection - move picked model mouse mode for moving the clicked model without having to select it first
October 1, 2020: Open flat image as a model - new input type for *.jpg files, photo (useful, for example, to show a paper figure within a shared VR session)
September 24, 2020: Python 3.8 - ChimeraX daily builds have been updated from Python 3.7 to Python 3.8. Next official release will use Python 3.8.
September 23, 2020: Amber trajectories - The default Amber netCDF coordinate format (.nc suffix) is now supported in the exact same way as other trajectory formats.
September 18, 2020: Calculate RMSD without fitting - rmsd command to measure RMSD using the current atomic positions
September 15, 2020: Read V3000 SDF - support for reading the V3000 variant of SDF files
September 14, 2020: ChimeraX source code on GitHub - moved ChimeraX source code repository from UCSF to GitHub.
September 10, 2020: New ChimeraX recipes website gives examples command scripts and Python scripts.
September 9, 2020: Measure angles between 3 atoms and/or centroids, or two planes, with the angle command.
September 3, 2020: Add/delete bonds - The bond and ~bond commands can be used to add and delete bonds, as well as the new "Adjust Bonds" tab in the Build Structure tool.
August 25, 2020: Release 1.1
August 24, 2020: Improved Update mechanism - a dialog is shown if there are updates
August 22, 2020: Color by Coulombic electrostatic potential - preliminary coulombic command for coloring a surface by electrostatic potential without requiring an input map. Currently limited to surfaces containing only standard residues. This limitation will be removed in the future, but that will take some time.
August 21, 2020: Matchmaker tool - graphical user interface for matchmaker command
August 18, 2020: Read attributes from file - defattr command and associated file format for assigning atom/residue/etc. attribute values in bulk
August 18, 2020: Wobble rotation - figure-eight rotation with wobble command
August 5, 2020: Fetch biological assemblies - use open command to load biological assemblies from rcsb_bio or from pdbe_bio
July 29, 2020: Color by sequence conservation - values in Sequence Viewer header lines are assigned as residue attributes of associated structures, allowing coloring by attribute "seq_conservation" (or "seq_rsmd")
July 29, 2020: Linux installation - worked around startup failure due to anaconda's changes to LD_LIBRARY_PATH.
July 28, 2020: RMSD header - sequence alignments can show the RMSD between associated chains as a header line.
July 27, 2020: Per-model clipping - the rotatable clip planes (front/back) can be limited to specific models with the clip model command
July 23, 2020: Neuron trace SWC file reader.
July 22, 2020: Leap Motion hand tracking command leapmotion, discussion here, and video.
July 16, 2020: LookingGlass a 3D display without glasses, command lookingglass, example uses here.
July 12, 2020: PDB 2-character chain IDs. Column 21 in a PDB file, normally blank, is now treated as the second character of the chain ID if appropriate. Previously, non-blanks in that column were treated as the fourth character of the residue name (needed in some Amber files). Now, that column is treated as part of the chain ID as long as it is consistent across all the residues in the chain, otherwise it is treated as part of the residue name. This works for both input and output of PDB files.
July 9, 2020: Offscreen rendering now works for 2D and 3D labels.
July 8, 2020: Video backgrounds for creating augmented reality videos can be created with the webcam command as shown in SBGrid webinar.
July 1, 2020: Centroids and planes can be created with the define command and used in distance measurements.
June 30, 2020: Tabbing information now also saved when Save Tool Position context-menu item used.
June 27, 2020: Save PDB options in dialog opened from File menu, including selected-only, displayed-only, and relative to another model (previously available via save command only)
June 16, 2020: Blast protein sequence directly from Sequence Viewer context menu.
June 16, 2020: Open EMDB segmentations - open EMDB segmentation file format (.sff, .hff) files.
June 16, 2020: Open IMOD models - open mesh or contour IMOD model files.
June 15, 2020: Save model positions - save model position matrices to a text file.
June 8, 2020: VR button commands - new vr button option allows assigning any command to a button press.
June 3, 2020: Measure rotation - added measure rotation command that measures angle and shift of one model relative to another.
June 11, 2020: Release 1.0
May 19, 2020: Show image on surface - added color image command that colors a surface from an image file.
May 6, 2020: Version 1.0 Release Candidate - the daily build process has been switched to building version 1.0 release candidates!
May 6, 2020: Chemical Component Dictionary - CCD entries can be opened as structures (in addition to their previous use as residue templates)
April 18, 2020: Show chain sequence - convenience tool to show chain sequences, in the same way that a structure's chain table in the log shows them.
April 16, 2020: Create shape surfaces - shape command to create geometric shapes as surface models: sphere, ellipsoid, cylinder, cone, triangle, etc.
April 8, 2020: Peptide building - the Build Structure tool and build start peptide command can be used to construct peptides from scratch.
April 3, 2020: Release 0.93
April 2, 2020: Faster cartoons - the generation of cartoons is up to 6X faster
April 1, 2020: Uncompressed sessions - session files are now saved uncompressed for 20X faster save, 3X faster restore (but 2X bigger files)
March 31, 2020: Command speedups - Sped up commands (show, hide, color, select, style, size, transparency...) when acting on all objects
March 31, 2020: New open/save infrastructure - try the open2 and save2 commands, will replace open and save in next release. Open and Save dialogs use the new code paths
March 30, 2020: Toolshed updated - the toolshed web site is now based on Python 3 and supports the ~= compatible release operator in dependencies
March 19, 2020: Auto-compression of saved files - save a file with a compression suffix (i.e., .gz) and it is compressed
March 10, 2020: Log restored - restoring a session restores the corresponding log contents, under a dated disclosure triangle
March 7, 2020: Release 0.92
March 5, 2020: Common Linux ABI - use CentOS 7 compiled bundles for all Linux variations
February 27, 2020: Custom presets for map image display - users can define presets of thresholds/colors for image-style maps with the nameAppearance option of the volume command (details...)
February 27, 2020: More Medical Image icons - icons for tilted-slab mode and brain CT preset added to Medical Image toolbar
February 25, 2020: 2D arrows - similar to 2D text labels, 2D arrows can be placed on the scene to annotate it, and can be moved by dragging either end with the move label mouse mode; see 2dlabels
February 19, 2020: Undo mouse movements that change relative positions - relative (but not global) motions with mouse modes to rotate/translate selected models or atoms can be undone
February 3, 2020: Toolbar Home-tab customization - choose Settings in the Toolbar context menu to get a dialog for rearranging the icons and/or adding them from other tabs
February 3, 2020: Trajectory playback mouse mode -play coordinates mode and corresponding Right Mouse toolbar icon
January 27, 2020: SMILES strings can be translated into 3D structures (courtesy of NCI or Indiana University web services) using the open command
January 21, 2020: PubChem compound structures can be fetched using the open command
January 22, 2020: Dome projection mode - camera command can set dome mode
January 21, 2020: MDL SDF files (.sdf, .mol suffixes) can now be opened
December 23, 2019: Release 0.91
December 16, 2019: Toolbar - button corresponding to current right mouse mode is highlighted
December 12, 2019: Multiple sequence alignment from Blast Protein results - checkboxes allow designating one or more hits to show in the Sequence Viewer as a query-anchored multiple alignment
December 10, 2019: Medical Image icons - new toolbar tab with an application-specific collection of icons
December 4, 2019: Augmented reality video capture - new device realsense command allows recording augmented reality videos that show a person interacting with molecules or other 3d data.
December 2, 2019: DICOM reader - now use Grassroots DICOM library GDCM which allows reading lossless jpeg 16-bit images.
November 22, 2019: Rotamers tool - graphical user interface for swapaa command
November 21, 2019: Clashes/Contacts tools - graphical user interfaces for clashes and contacts commands
October 28, 2019: Tape measure - added mouse mode and VR hand controller mode to measure distances between points or atoms.
October 23, 2019: VR status and settings in sessions - VR status, model positions in the room, and hand-controller button assignments are saved in ChimeraX session files
October 18, 2019: Assign commands to function keys - functionkey command to define function-key actions
October 18, 2019: Restricted-motion mouse modes - new options to rotate z selected models and translate xy selected models
October 11, 2019: H-Bonds tool - graphical user interface for hbonds command
October 9, 2019: Several VR improvements:
- ChimeraX tools shown as individual panels in VR that can be moved collectively or independently
- pop-up menus and panels work
- icon layout on cones reflects hand-controller button positions (different for Oculus vs. Vive)
- vr roomCamera command to define a separate camera view in VR, useful for making videos
September 9, 2019: Command to assign VR hand-controller functions - vr button command, scriptable alternative to clicking icons to assign modes interactively
September 4, 2019: Maestro file reader available from Toolshed - enables reading .mae files (such as from GLIDE docking) for analysis with ViewDockX
August 16, 2019: ViewDockX up/down arrow controls - when the ViewDockX table has the focus, up/down arrow keys will select the next/previous compound. New commands viewdockx up and viewdockx down simulate pressing the arrow keys.
August 7, 2019: 2D labels simplified - 2dlabels command no longer needs create or change keywords, and the 2D labels are now models (have ID numbers, are listed in Model Panel, etc.)
August 2, 2019: Move 3D labels with mouse - the "move labels" mouse mode works on both "3D" labels and 2D labels (previously 2D labels only)
July 30, 2019: Improved MLP parameters - mlp command for showing protein hydrophobicity uses an updated set of atomic values with symmetrically hydrophilic carboxylate oxygens, and covers a few more residue types than before
July 24, 2019: Rotamer libraries - amino acid sidechain rotamer libraries available for virtual mutation with the swapaa command
July 23, 2019: Markers toolbar - icons and associated mouse modes for creating and modifying markers and links
July 1, 2019: Fit in Map - graphical interface for fitting atoms or maps into maps
July 1, 2019: Segger tools - Segment Map for watershed segmentation and interactive (un)grouping, Fit to Segments for fitting structures into the resulting segmentation regions
June 29, 2019: Map Coordinates tool - specify placement and scaling of map in x,y,z coordinates (origin index, voxel size, etc.)
June 27, 2019: Measure symmetry command - identify map symmetry from a limited set of possibilities in standard orientations
June 12, 2019: Reverse color palettes - putting ^ right before the palette name reverses the order of the colors
June 6, 2019: Web site authentication - users may log into web sites in the help viewer
June 6, 2019: Custom presets - users may create their own presets by writing files of ChimeraX commands and/or Python code and then setting the Startup->Custom presets folder preference to tell ChimeraX where to find them. Files directly in the folder will be in category "Custom" and those in first-level subfolders will have the same category as the folder name.
June 5, 2019: 2D label animation - the 2dlabels change command now takes a frames argument to animate the changes over the given number of frames.
June 1, 2019: Aliases saved in sessions - command aliases (created with the alias command) included in session files
May 30, 2019: Map Eraser - tool and mouse mode for interactively erasing parts of maps (also command volume erase)
May 29, 2019: Measure and Color Blobs - tool and mouse mode for measuring individual disconnected surface blobs (also command measure blob)
May 22, 2019: Release 0.9
May 17, 2019: Control sequence-structure association - dialog and sequence command options to manually control sequence-structure association
May 15, 2019: BLAST query from sequence alignment - the blastprotein command can use a sequence (regardless of whether a structure is open) as the query; previously only the sequences of open structures could be used
May 8, 2019: Fetch UniProt sequence - the open command can be used to fetch a UniProt sequence by prefixing the UniProt accession code or identifier with "uniprot:" or by adding the "fromDatabase uniprot" arguments to the command (e.g. "open uniprot:NGF_HUMAN" or "open P01138 from uniprot")
May 2, 2019: View Autodock Vina docking results - the ViewDockX tool can be used with pdbqt output from Autodock Vina
April 29, 2019: Tabbed toolbar - existing icon toolbars combined into a new tabbed interface; icon improvements underway
April 25, 2019: Settings code change - some settings code got moved from the ChimeraX core into appropriate tool bundles. Settings that moved (Clipping, Distances Labels, Log, Startup, Trackpad, and Window) will revert to their initial default values. However, for recovery purposes (copying into new version), the previous values can still be seen by running an older build. This may be particularly helpful for the startup commands.
April 22, 2019: View GOLD docking results - the ViewDockX tool can be used with Mol2 output from GOLD
April 18, 2019: Modeller comparative modeling - tool and command for comparative (homology) modeling of single- and multiple-chain protein structures with Modeller
March 18, 2019: More presets - presets for cartoon styles, molecular surfaces, etc. (preset API improved, but still in progress)
March 13, 2019: Faster reading TIFF volumes - Reading TIFF volume data is 2 to 5 times faster now, using tifffile.py instead of Pillow.
March 9, 2019: Report volume settings - new volume settings command lists the current settings of volume models
February 25, 2019: AL2CO conservation - AL2CO conservation scoring available as a sequence-alignment header
February 21, 2019: Volume GPU rendering - GPU rendering options for maps in the transparent solid style improve both performance (significant in VR) and appearance
January 25, 2019: Measure center - implemented measure center command
January 25, 2019: Attribute coloring - color byattribute (color by for short) for coloring based on structure, residue, or atom attribute values
January 24, 2019: Mouse modes for volume data - added "windowing" (changing all thresholds simultaneously), made "crop volume" separate from "move planes" (previously combined into a single mode)
January 23, 2019: Volume 3D projection - solid-rendering 3D projection mode avoids large changes in apparent brightness during rotation
January 16, 2019: Save sequences as CLUSTAL ALN - sequences can be saved as ALN format in addition to the already available PIR (NBRF) and FASTA formats
January 7, 2019: DICOM reader - initial version (will continue to improve) for importing medical imaging datasets
December 14, 2018: Chain table revamp - in the table of chains shown in the Log when a structure is opened, links in the lefthand column select the corresponding chains (those in the righthand column still show the chain sequence, as before)
December 17, 2018: Release 0.8
December 14, 2018: Named selections in sessions - named selections and other targets defined with the name command are saved in session files
December 14, 2018: Select sequence - select biopolymer segments by exact sequence match or using ambiguity codes or regular expressions (Select menu and select command options)
December 4, 2018: Filled rings - ringfill options in style command
November 29, 2018: Right drag to move models - Changed right mouse drag to move models instead of zoom. Zooming can be done by scrolling.
November 17, 2018: Startup commands - Startup preferences allow specifying command(s) to execute at startup
November 13, 2018: Mac trackpad gestures - trackpad multitouch gestures (2-finger rotation, pinch-zoom etc.) can be used, controlled with Trackpad preferences
November 10, 2018: Wild cards - wild cards * and ? (single-character) can be used in command-line specification of atom and residue names, "start" and "end" (or *) in residue or model number ranges
November 10, 2018: More in Select menu - the Select menu includes residue names, atom types, and structure categories (ligand, solvent, etc.)
November 1, 2018: Measure map statistics, surface-enclosed volumes - measure command new options to report map mean/SD/RMS, isosurface area, and isosurface-enclosed volume
October 30, 2018: Split map by color zone - volume splitbyzone command
October 30, 2018: Mask volumes - volume mask command to mask a map to a surface, volume onesmask to create a map with values of 1 bounded by a surface
October 4, 2018: Initial tool location - Window preferences control whether tool windows should default to being docked on the left or right side of the main window. In addition, each tool's context menu includes a "Save Tool Position" entry. For docked tools/toolbars, only the side can be saved (unlike the preference, this can also be top or bottom). For floating tools, both the size and position relative to the main window can be saved. Due to limitations in the windowing toolkit, toolbars cannot be saved as floating.
October 1, 2018: Move 2D labels interactively - added "move label" mouse mode
September 30, 2018: Improvements for multi-user VR - multi-user sessions instigated with meeting automatically share commands among participants, and more mouse/pointer actions now work via commands
September 28, 2018: Initial window size - ChimeraX now remembers your last-used main window size and starts as that size by default. Other choices available in the ChimeraX 'Window' preferences are fixed size or proportional to screen size.
September 25, 2018: Session files can include map data - save command has "includeMaps" option for sessions
September 6, 2018: Select pseudobonds by length - select command allows selecting pseudobonds (crosslinks, hbonds, etc.) by min and/or max length
September 5, 2018: Select menu - initial Select menu including chain, element, functional group (will continue to expand)
September 1, 2018: Torsion command - torsion command to measure or change torsion angles
August 22, 2018: Label backgrounds - label command "background" option to show a colored rectangle behind the text
August 7, 2018: Release 0.7
August 1, 2018: H-bond guided hydrogen addition - "hbond true" (default) flag of addh command implemented
July 31, 2018: Tug/minimize structures containing nucleic acids, water - tug and minimize mouse modes work on structures with standard nucleic acids and water (previously handled only standard amino acids)
July 23, 2018: Bug reporter - added one-button submission of bug reports when an error occurs
June 28, 2018: Presets menu - initial version of Presets menu including "original look" and "stick" (all atoms)
May 21, 2018: Save sequence file - sequence(s) can be saved to PIR (NBRF) format with the save command (June 11 also FASTA, and also from the Sequence Viewer context menu)
April 25, 2018: Surface zone updating - surface zone near atoms and hiding dust now auto-update when surface changes shape
April 25, 2018: Color auto-updating - coloring by distance, map values, or to match nearby atoms now auto-updates when surface changes shape
April 19, 2018: B-factor coloring - coloring by B-factor using color bfactor command
April 18, 2018: Radial coloring - added color commands for radial, cylindrical, topological height coloring
April 17, 2018: Distance context menu - selecting two atoms while double-clicking the second one will bring up a context menu with "Distance" in it. Clicking that will show the distance. The menu will contain more items in the future, and will work for other numbers of atoms (i.e. like Chimera).
April 12, 2018: More sequence formats - reads same eight formats as Chimera: added aln, rsf, hssp, selex, stockholm (previously fasta, msf, pir)
April 10, 2018: Named selections - name command for creating user-defined targets including named selections
April 7, 2018: Distance mouse mode - allows clicking two atoms to show distance between them
April 6, 2018: Release 0.6
April 5, 2018: Developer API and tutorials - first draft of developers tutorials are included with distribution. See documentation index under Help.
April 5, 2018: Basic Actions tool - simple graphical interface for showing and hiding atoms, cartoons and surfaces
March 29, 2018: improved performance - faster atomic calculations: adding hydrogens, finding H-bonds, detecting clashes and contacts
March 29, 2018: save command serialNumbering option - how to format output PDB files with too many atoms and/or residues for standard format
March 21, 2018: mmCIF reader improved - preserves case for field names
March 15, 2018: mmCIF output improved - includes a subset of mmCIF tables, and interoperates with Phenix, COOT, Rasmol, CCP4mg and JSMol
March 13, 2018: Hbonds toolbar button - compute hydrogen bonds for selected atoms with new toolbar button, equivalent to hbonds command.
March 12, 2018: Minimize energy mouse mode - use OpenMM molecular dynamics on residues in contact with a clicked residue.
March 8, 2018: Swap amino acid mouse mode - click on a residue and drag up or down to change the amino acid to any of 20 standard amino acids.
March 6, 2018: Bond rotation mouse mode - allows click and drag on a bond to rotate atoms on one side.
March 1, 2018: Virtual reality user interface - pressing hand controller button shows desktop user interface in VR allowing mouse clicks and use of mouse modes.
February 15, 2018: Sequence Viewer settings - preferences for character spacing, line wrapping, region colors (selection, missing segments, etc.)
February 2, 2018: Nucleotide representations in sessions - special representations from the nucleotides command are saved in sessions
January 24, 2018: Surface clipping caps - added surface cap command to turn off caps covering holes where surfaces are clipped, and a preference setting for whether such caps should be shown initially
January 11, 2018: Color modify command to adjust hue, saturation, lightness (etc.) of current colors
December 22, 2017: Release 0.5
December 14, 2017: ViewDockX - initial ViewDockX tool for analysis of molecular docking results (Dock Mol2 format only)
December 14, 2017: Nucleotide representations - nucleotides command to show ladders and other special representations of nucleic acid residues
December 4, 2017: New volume formats - Read 15 more volume formats: delphi, dock, emanhdf, gaussian, gopenmol, imod, macmolplt, priism, profec, pif, situs, spider, tom_em, uhbd, xplor.
November 22, 2017: Distance command - shows and logs distances between atoms (only)
November 21, 2017: BILD file reader - simple text format describing geometric objects, much the same as in Chimera
November 15, 2017: DeltaVision file reader - read multi-channel multi-time 3d light microscopy image data in DeltaVision (suffix ".dv") file format.
November 9, 2017: Bumps command - marks cell protrusions in light microscopy data and sums image signal intensity in protrusions.
November 9, 2017: Alpha release 4
November 3, 2017: Clashes/contacts command - clashes or contacts command for finding interatomic contacts (like Chimera findclash); pre-existing contacts command for plotting chain-chain interfaces renamed interfaces
October 20, 2017: Drop files/folders onto command line - which will insert their path into the command at the current text insertion point. Actually anything with a text equivalent can be dropped (e.g. a text clipping). FYI, the main ChimeraX window already accepts drops of input files.
October 18, 2017: Marker models - added reading and writing of Chimera marker model files with suffix .cmm. Marker note display not yet implemented.
October 17, 2017: Size command - size command with atom- and stick-radius options formerly in style; included in undo/redo
October 12, 2017: Addh command - initial implementation of addh; somewhat slow, lacks H-bond-guided option (requires using hbond false)
October 10, 2017: Undo/redo includes selections
October 4, 2017: Bond labels, click-to-label - label command can show bond lengths; mouse mode allows clicking to label/unlabel atoms, bonds, residues, pseudobonds
October 3, 2017: Alpha release 3
September 28, 2017: Limited undo/redo - Edit menu entries and undo/redo commands for a limited set of changes, from commands: show/hide, color, style, cartoon. Does not include surfaces.
September 27, 2017: Tabs in Help Viewer - the Help Viewer (built-in browser) can show multiple pages in a tabbed interface
September 21, 2017: File browser from command line - in commands, substituting "browse" for a filename or directory opens a file browser window
September 12, 2017: Colorbrewer palettes - palettes from colorbrewer.org available for coloring sequentially (rainbow) or by map value with the color command
September 7, 2017: glTF - added initial glTF 3d scene file writer and reader
August 30, 2017: Zone specifications - command-line atom specification by distance from other atom(s)
August 22, 2017: texture command - added texture command to color surfaces using image files (e.g. jpeg, png, tiff)
August 22, 2017: Wavefront OBJ - added file writing and reading of Wavefront OBJ 3D model files (vertices, normals, faces; no colors)
August 16, 2017: Sequence alignment from matchmaker - implemented showAlignment option of matchmaker command
August 15, 2017: Alpha release 2
August 14, 2017: General attribute-setting command - setattr command to set attribute values of atoms, residues, pseudobonds, various model types
August 9, 2017: Volume display styles - volume viewer display-style menu entries for maximum intensity projection, planes, orthoplanes, and box face
July 20, 2017: Autostart tools - control which tools to show at startup (#761)
July 12, 2017: Write PDB files (#601) - save from File menu or with save command
June 29, 2017: Atom and residue labels - graphics display of labels on atoms, residues and pseudobonds using label command (#615)
June 27, 2017: DCD trajectory format - read and write DCD trajectory coordinate sets
June 26, 2017: Find H-bonds, salt bridges - hbonds command to identify hydrogen bonds (#533)
June 13, 2017: Drag and drop files - allow opening file by dragging onto application or application icon
June 12, 2017: mmCIF coordinate sets - read multimodel mmcif files as coordinate sets using open command coordset option (#460)
June 10, 2017: devel command - create bundles (i.e. plugins) with new devel command
June 5, 2017: Sequential stereo - allow LCD shutter glasses stereo using command-line --stereo option
May 31, 2017: Pick atoms behind surfaces - mouse picking through meshes and transparent surfaces; selection outlines show through transparent surfaces
May 30, 2017: Coordinate-set slider - show slider to play through coordinate sets with coordset slider command
May 24, 2017: Integrative Hybrid Model file reader - improvement to IHM file reader such as reading ensemble coordinates from DCD files
May 23, 2017: Virtual-reality icon panels - enable icons in virtual reality with vr command icons option
May 19, 2017: Model series playback - show a sequence of models in succession with new mseries command
May 16, 2017: Mesh and dot surfaces - show mesh, dot or filled surfaces with surface style command (#675)
April 19, 2017: Chain name table - table of chains and biological names shown in Log when atomic structure is opened, with clickable links to show the corresponding sequences
April 17, 2017: Improved lighting defaults - changed light brightnesses (ambient, key, fill) for better appearance
April 14, 2017: Amira map format - read Amira map files
April 7, 2017: Position command - added view position command to report and set model and camera positions
April 6, 2017: Imaris file reader - read Imaris microscopy 3D image files
April 5, 2017 Color zone - color surfaces to match nearby atoms using color command zone option
April 5, 2017 File history thumbnails - history of open files is shown at startup with thumbnail images (Rapid Access interface)
March 28, 2017: Alpha 1 release
December 2016: Daily builds -- first builds for public
August 2016: Daily builds -- for friends and family
