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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March 29, 2018: save command serialNumbering option - how to format output PDB files with too many atoms and/or residues for standard format

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 8, 2018: mmCIF output more complete - includes a subset of mmCIF tables, but all those that ChimeraX uses

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