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.

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December 16, 2019: Toolbar - button corresponding to current right mouse mode is highlighted

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)

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May 22, 2019: Release 0.9 release candidate

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)

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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

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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

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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

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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.

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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

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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

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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)

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March 28, 2017: Alpha 1 release

December 2016: Daily builds -- first builds for public

August 2016: Daily builds -- for friends and family