- ChimeraX-announce - RBVI Mailing Lists

ChimeraX 1.7 release!
by Elaine Meng 19 Dec '23

19 Dec '23

UCSF ChimeraX version 1.7 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.6 (May 2023) include: New graphical interfaces: - Fetch By ID - Map Filter - Adjust Torsions (new section in Build Structure) - Adjust Angles defined by three atoms (also in Build Structure) Open command options to: - specify model number - combine incoming session with existing session - designate map as difference map (show +/-contours automatically) - fetch by IUPAC name (also in Build Structure tool) - fetch EMDB map + fit structures Mouse mode updates: - new mouse mode to center the view on the clicked item - better separation of trackpad multitouch zoom and rotate - Z-translation by additionally pressing Ctrl in a translation mouse mode Other: - invert selection with left/right arrow keys - mcopy command to copy settings from one atomic structure to another - save GLTF options to cull backfaces, omit per-vertex colors, omit normals - volume defaultvalues command to set defaults for subsequently opened maps - info command saveFile option (list selection, attribute values, etc.) - opening docking results automatically starts ViewDockX - button to save Blast Protein results to TSV For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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REMINDER: ChimeraX website downtime
by Elaine Meng 15 May '23

15 May '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. Please pardon any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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ChimeraX 1.6.1 release
by Eric Pettersen 10 May '23

10 May '23

UCSF ChimeraX version 1.6.1 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html> Updates since version 1.5 (Nov 2022) include: - ESMFold protein structure prediction and residue-residue error plot - Add Charge GUI - Dock Prep GUI to repair side chains, add hydrogens, etc. - Render by Attribute GUI for coloring by atomic or residue values - swapna command to mutate nucleic acid residues - invert chiral center - read SwissDock docking results - Blast Protein query sequence can be pasted in or specified by UniProt ID - browse/fetch medical images from The Cancer Imaging Archive - read medical images in NIfTI (.nii) and NRRD (.nnrd) formats For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> For those of you who downloaded plain 1.6 while it was briefly available, please upgrade to 1.6.1. It has several bug fixes that 1.6 should have had but didn't. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. Please pardon any inconvenience, --Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX 1.5 release
by Elaine Meng 30 Nov '22

30 Nov '22

UCSF ChimeraX version 1.5 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ Updates since version 1.4 (Jun 2022) include: - AlphaFold search/fetch uses database v4 (fixes ~4% of v3 entries) - show AlphaFold residue-residue errors (PAE) with colored lines - Axes/Planes/Centroids tool to define objects, use in measurements - transform surface models (scale, shift, rotate) - add hydrogens GUI - calculate and assign charges, including for nonstandard residues - dock prep command - renumber residues, change chain IDs - crosseye and walleye stereo - cleaner close session (reverts more settings) - UniProt sequence fetch updated to work with UniProtKB's new API - DICOM browser shows patient-study-series hierarchy in medical image data For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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ChimeraX 1.4
by Eric Pettersen 10 Jun '22

10 Jun '22

UCSF ChimeraX version 1.4 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ This will be the last release to support macOS 10.14 (Mojave). Also, ChimeraX 1.4 is not available for CentOS 7, Ubuntu 16.04 and 18.04 because the Qt 6 window toolkit does not support those older Linux distributions. Updates since version 1.3 (Dec 2021) include: - search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures - display AlphaFold predicted aligned error (PAE) plots - can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR) - AlphaFold prediction of multimers (of limited size) on Google Colab - independent centers of rotation available as mouse mode - join models with Build Structure tool or command - define axes for display and/or use in measurements - increase/decrease VDW radii relative to their current values - switch PDB residue numbering scheme (author/canonical/uniprot) - align sequences with Clustal Omega or MUSCLE - calculate % identity in sequence alignments - window toolkit updated to Qt 6.2.3 from 5.15.2 For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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ChimeraX version 1.2 released!
by Elaine Meng 28 May '21

28 May '21

UCSF ChimeraX version 1.2 has been released! Major changes since v1.1 (Aug 2020) include: - Surface Color tool - Unit Cell tool - Color Key tool and command - Crystal Contacts tool and command - volume tools: Hide Dust, Color Zone, Surface Zone - Meeting panel for multiperson VR - "fly" command for smooth motion along multiple saved views - "rmsd" command for calculating RMSD in current positions (w/o fitting) - nucleic-acid building - bond deletion/addition - UniProt fetch includes sequence feature annotations (domains, mutations, modification sites, etc.) - support for Amber netCDF trajectories - smaller session files - faster saving of sessions with maps - mouse mode for moving a clicked model without having to select it For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog Downloads: https://www.rbvi.ucsf.edu/chimerax/download.html

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ChimeraX 1.1 available
by Eric Pettersen 11 Sep '20

11 Sep '20

UCSF ChimeraX version 1.1 has been released! Updates since version 1.0 (June) include: - fetch biological assemblies - Matchmaker graphical interface - per-model clipping - color protein surfaces by Coulombic electrostatic potential - color protein by conservation from sequence alignment - sequence alignment RMSD header - assign attributes from file (same file format as in Chimera) - define centroids and planes - measure rotation - more input formats: EMDB segmentation files IMOD mesh or contour SWC (e.g. neuron trace) - assign commands to VR hand-controller buttons For more details, see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

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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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