== 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 16, 2019: **ViewDockX** - when ViewDockX table has the focus, up/down arrow keys will select the next/previous compound. New commands "viewdockx up" and "viewdockx down" will 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 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** - [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