== 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. ---- 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