== 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. ---- August 27, 2021: **Model loops** - add missing segments or refine existing segments with [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/modeller.html#loops modeller loops] command August 10, 2021: **Open subset of trajectory** - start, end, step options for opening [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory trajectory coordinate files] July 30, 2021: **Combine or copy atomic models** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html combine] command July 29, 2021: **Fetch !AlphaFold predictions** - fetch AI-predicted protein structures ([https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html details...]) July 13, 2021: **Scale Bar** tool and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/scalebar.html scalebar] command June 30, 2021: **List multiple map-fitting solutions** - the [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html#fitlist Fit List] dialog enumerates and allows switching among multiple fits from a [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html fitmap] global search June 25, 2021: **Altloc Explorer** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/altlocexplorer.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#gltf 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 Fileā†’Open dialog to open the PSF file or if you omit the [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coords coords] keyword from the [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local open] command, a file browser will be shown for specifying the coordinates file interactively. May 20, 2021: **Map values at atom positions** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#mapvalues measure mapvalues] command assigns map values as an atom attribute that can then be used for [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute coloring], command-line [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes 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 ** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html 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** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html open] command options to apply a [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files command file] iteratively [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile to multiple data files] and/or to [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#log suppress logging] each command as it is executed April 15, 2021: **Selection Inspector** - bare-bones [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html 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 ([https://www.rbvi.ucsf.edu/chimerax/docs/user/window.html#hotkeys details...]) ---- April 14, 2021: **Release 1.2 branch made; released: May 28, 2021** 23 May, 2021: **Relocatable CentOS RPM files** - backport from daily builds March 18, 2021: **Surface Color tool** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html GUI] for coloring by map value or distance (radial, ''etc.'') March 13, 2021: **Fly along multiple views** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/fly.html fly] command to smoothly traverse a series of named views for animation purposes March 11, 2021: **Color Key** [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/colorkey.html tool] for interactive placement and adjustment of a color key March 8, 2021: **Crystal Contacts** [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/crystalcontacts.html tool] and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/crystalcontacts.html command] to check for clashes between symmetry-related copies of a structure March 5, 2021: **Unit Cell** [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/unitcell.html tool] and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/unitcell.html command] to generate crystallographic unit cells March 2, 2021: **Measure Volume and Area** [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/measurevolume.html tool] (GUI) to report the total area and enclosed volume of a surface model February 26, 2021: **Volume tool GUIs** - graphical interfaces for [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/hidedust.html Hide Dust], [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/colorzone.html Color Zone], and [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/surfacezone.html Surface Zone] February 22, 2021: **Map toolbar improvements** including new icons for volume zone, color zone, and hide dust February 12, 2021: [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start Structure building] starting from **ring-system fragments** implemented February 10, 2021: **Color key command** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/key.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start Build Structure] tool and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start 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 [https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#uniprot 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/meeting.html ChimeraX meetings], with virtual reality or screen display. November 9, 2020: ** Rainbow coloring ** - can now color parts of a chain with [https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential 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 [https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html 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 ** - [http://www.cgl.ucsf.edu/chimerax/docs/user/markers.html markers] on [http://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html#vseries volume series] data are assigned a [http://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#atom frame attribute] for synchronized display October 19, 2020: ** Save attributes ** - attribute values (e.g., per-residue surface areas from [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa measure sasa]) can be [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes saved to a file] October 12, 2020: ** Mark surface blobs ** - [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html#connected 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 ** - [http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions 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, [http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#miscellaneous 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 [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory exact same way] as other trajectory formats. September 18, 2020: **Calculate RMSD without fitting** - [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/rmsd.html 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 [https://github.com/RBVI/ChimeraX on GitHub]** - moved ChimeraX source code repository from UCSF to !GitHub. September 10, 2020: **New [https://rbvi.github.io/chimerax-recipes/ 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 [http://www.cgl.ucsf.edu/chimerax/docs/user/commands/angle.html angle] command. September 3, 2020: **Add/delete bonds** - The [https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html bond] and [https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html ~bond] commands can be used to add and delete bonds, as well as the new "Adjust Bonds" tab in the [https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html 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 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html matchmaker] command August 18, 2020: **Read attributes from file** - [https://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html defattr] command and associated [https://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html#attrfile file format] for assigning atom/residue/''etc.'' attribute values in bulk August 18, 2020: **Wobble rotation ** - figure-eight rotation with [https://rbvi.ucsf.edu/chimerax/docs/user/commands/wobble.html wobble] command August 5, 2020: **Fetch biological assemblies** - use [https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch open] command to load biological assemblies **from rcsb_bio** or **from pdbe_bio** July 29, 2020: **Color by sequence conservation** - values in **Sequence Viewer** [https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers header lines] are assigned as residue attributes of associated structures, allowing [https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute 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 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/clip.html#model clip model] command July 23, 2020: **Neuron trace** SWC file reader. July 22, 2020: **Leap Motion hand tracking** command [https://rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#leapmotion leapmotion], discussion [https://www.rbvi.ucsf.edu/chimerax/data/leap-july2020/ here], and [https://twitter.com/UCSFChimeraX/status/1285435087236915201 video]. July 16, 2020: **!LookingGlass** a 3D display without glasses, command [https://rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#lookingglass lookingglass], example uses [https://www.rbvi.ucsf.edu/chimerax/data/lookingglass-july2020/ 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 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#webcam webcam] command as shown in [https://www.rbvi.ucsf.edu/chimerax/data/sbgrid-july2020/ SBGrid webinar]. July 1, 2020: **Centroids** and **planes** can be created with the [https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html 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 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb save] command only) June 16, 2020: **Blast** protein sequence directly from [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html Sequence Viewer] context menu. June 16, 2020: **Open EMDB segmentations** - [https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html open] EMDB segmentation file format (.sff, .hff) files. June 16, 2020: **Open IMOD models** - [https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html open] mesh or contour IMOD model files. June 15, 2020: **Save model positions** - [https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html save model position matrices] to a text file. June 8, 2020: **VR button commands** - new [https://rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#vr-button vr button] option allows assigning any command to a button press. June 3, 2020: **Measure rotation** - added [https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation 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 [https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#image 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** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html shape] command to create geometric shapes as surface models: sphere, ellipsoid, cylinder, cone, triangle, ''etc.'' April 8, 2020: **Peptide building** - the [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start Build Structure] tool and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start 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 ([https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#appearance details...]) February 27, 2020: **More Medical Image icons** - icons for tilted-slab mode and brain CT preset added to [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/medicalimage.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/2dlabels.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/undo.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch open] command January 21, 2020: **!PubChem** compound structures can be fetched using the [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch open] command January 22, 2020: **Dome projection mode** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/camera.html camera] command can set ''dome'' mode January 21, 2020: **[https://en.wikipedia.org/wiki/Chemical_table_file 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#realsense 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 [http://gdcm.sourceforge.net/wiki/index.php/Main_Page GDCM] which allows reading lossless jpeg 16-bit images. November 22, 2019: **Rotamers tool** - graphical user interface for [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html swapaa] command November 21, 2019: **!Clashes/Contacts tools** - graphical user interfaces for [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html clashes] and [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html contacts] commands October 28, 2019: **Tape measure** - added mouse mode and VR hand controller mode to [https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#tapemeasure 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session ChimeraX session files] October 18, 2019: **Assign commands to function keys** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey 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 [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html 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) - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#vr-roomCamera 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** - [https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/device.html#vr-button 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** - [https://www.ncbi.nlm.nih.gov/pubmed/11524371 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