- ChimeraX-announce - RBVI Mailing Lists

ChimeraX version 1.0 release!
by Elaine Meng 18 Jun '20

18 Jun '20

The UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI) is pleased to announce the release of UCSF ChimeraX version 1.0! ChimeraX includes full user documentation and is free for noncommercial use. Download for Windows, Linux, and Mac OS X from: www.rbvi.ucsf.edu/chimerax/ Compared to Chimera, ChimeraX brings together: (A) significant performance and graphics enhancements - interactive display of very large atomic structures and maps - interactive ambient-occlusion lighting and/or directional shadows - fast and robust molecular surfaces - fast mmCIF reader (B) new implementations of Chimera’s most highly used tools - map fitting, segmentation, volume eraser, volume filtering - morph maps or atomic structures - play back volume series or atomic trajectories - view ligand-receptor docking results - find H-bonds, find contacts and clashes - virtual mutation, amino acid sidechain rotamers - radial coloring, coloring by map value - coloring by molecular lipophilicity potential, B-factor, etc. - animatable 2D labels and arrows - shape command to draw spheres, cylinders, etc. - sequence viewer with sequence-structure crosstalk - interface to Modeller comparative modeling (C) entirely new features - tube (curved cylinder) helices in cartoons - chain-chain contact diagram - H-bond or crosslink length histogram - built-in HTML browser with mechanism for click-to-execute commands (D) support for new areas - virtual reality - light-sheet microscopy - medical imaging data (E) major ease-of-use advances - toolbar with icons to perform actions with a single click - basic "undo" - more logical commands and more powerful command-line specification (F) a web repository (ChimeraX Toolshed) for developers to contribute plugins

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preview ChimeraX 1.0!
by Elaine Meng 07 May '20

07 May '20

The ChimeraX 1.0 (!!) release candidate is now available: <http://www.rbvi.ucsf.edu/chimerax/download.html> Please, please try it out and report any issues that you find, as we plan to make the production release by the end of the month. To report issues, use the ChimeraX menu: Help... Report a Bug <http://www.rbvi.ucsf.edu/chimerax/docs/contact.html> For what's new, see the Change Log: <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Thanks! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Tool autostart
by Eric Pettersen 19 Jul '17

19 Jul '17

You can now control which tools are auto-started when ChimeraX starts by bringing up a context menu over the tool (typically by right clicking) and toggling “Start this tool at ChimeraX startup” on/off. This works for all tools/toolbars. It’s a little tricky for the Python shell tool in that that tool’s builtin context menu is pretty handy so we didn’t want to replace it. To control that tool’s autostart you have to position the mouse on the thin border that surrounds the type-in area and bring up a context menu there. That menu will have the autostart entry in it. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Saving PDB files
by Eric Pettersen 18 Jul '17

18 Jul '17

ChimeraX can now save PDB files. See the documentation for the ‘save’ command <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html> for details. You can also save PDB files from the File->Save dialog, but since the dialog does not yet display the command options, they will have their default values. That may be good enough in some cases. —Eric Eric Pettersen UCSF Computer Graphics Lab

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H bonds
by Eric Pettersen 30 Jun '17

30 Jun '17

ChimeraX can now find hydrogens bonds. The “hbonds” command is very similar to the same command in Chimera 1. The principal difference is that since ChimeraX uses cylinders instead of lines to depict the hydrogen bonds, the “lineType” and “lineWidth” keywords have been replaced with “dashes” and “radius” (and the hydrogen bonds are now dashed by default). Full details are available with “help hbonds” or at this link: http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html <http://www.cgl.ucsf.edu/chimerax/docs/user/commands/hbonds.html> Unfortunately, the hydrogen bond computation is also slower than in Chimera 1. We are working on that. —Eric Eric Pettersen UCSF Computer Graphics Lab

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"Rapid Access"
by Eric Pettersen 07 Apr '17

07 Apr '17

Hi all, In the latest builds, your file history will be shown in the main graphics area if there are no models open (e.g. usually at startup). Otherwise, you can hide/show the file list with the lightning bolt icon at the lower right of the main window. —Eric Eric Pettersen UCSF Computer Graphics Lab

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