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UCSF Chimera Changelog

What's new in UCSF Chimera 1.17.2

Jul 6, 2023
  • Notable Bug Fixes:
  • The FFmpeg program for encoding movies was missing from Mac/Windows builds.
  • The Solvate / Add Ions / Write Prmtop tools now work on Windows installations where the installation path has spaces in it.

New in UCSF Chimera 1.15 (Dec 18, 2020)

  • General Changes:
  • The retirement of legacy RCSB PDB web service APIs impacts the fetching of UniProt sequence annotations and fetching additional information about BLAST hits. Those functions have been revised to use the new APIs that replace the legacy APIs. It also impacts the fetching of PDB and mmCIF entries, and that has been revised as well.
  • Notable Bug Fixes:
  • Support added for Gromacs 2020 trajectories
  • Many user-interface problems on Mac fixed by upgrading the Tk windowing toolkit to version 8.6.10

New in UCSF Chimera 1.14 (May 1, 2020)

  • General Changes:
  • AmberTools updated to version 18
  • Previous/Next buttons added to activation/display button rows below the command line, for quickly cycling through (or toggling between) model display and/or activation
  • Tool Changes:
  • Area/Volume from Web (Surface/Binding Analysis) — removed because the NIH StrucTools server is no longer available
  • Multalign Viewer (Sequence) — option to get annotations from the Conserved Domain Database (CDD) removed due to CDD changes
  • MD Movie preserves PSF segment name as residue attribute segment, and reports the segment names to the Reply Log as the trajectory is read. Therefore a segment named XYZ could be referenced in a command using the atom specifier :/segment=XYZ
  • Notable Bug Fixes:
  • Upgraded Tk windowing toolkit to fix bug on Mac where specifying multiple coordinate files in MD Movie could hang Chimera.
  • Fixed problem at startup with libfontconfig on recent versions of Linux.
  • Fixed problem reading GROMACS trajectories on recent versions of Linux.

New in UCSF Chimera 1.13 Build 41965 (Jun 6, 2019)

  • General Changes:
  • updated CASTp fetch URL (1/5/2018)
  • serial-numbering option for saving very large PDB files (4/2/2018)
  • Tool Changes:
  • Additional Tools menu to facilitate getting third-party plugins, notably the Tangram suite of molecular modeling tools from InsiliChem (JD Maréchal's group, Universitat Autònoma de Barcelona) (4/17/2018)
  • Rotamers (Structure Editing) — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • Command Changes:
  • swapaa — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • tile — label option adds 2D labels showing each tiled model's number and name (2/27/2018)
  • write — serial-numbering option for saving very large PDB files (4/2/2018)
  • Notable Bug Fixes:
  • Modeller input preparation sometimes failed when the template chain contained a modified amino acid (a HETATM residue) (fixed 2/22/2018)
  • Bogus "file does not exist" dialog no longer appears (fixed 10/31/2017)
  • Fixed MD Simulation's "incompatible files" problem when restarting a trajectory computation (fixed 4/2/2018)
  • Notable Bug Fixes:
  • Fixed Align Chain Sequences tool
  • Fixed problem with using rotamers of proline from the Dunbrack 2010 rotamer library
  • Support independent rotation in Animation scenes
  • Fixed problem with mis-identified element types in new Amber trajectories
  • H-bond-guided hydrogen addition was wrongly ignoring certain hydrogen bonds when structures were being treated in isolation
  • On Windows, prevent a possible crash when fetching auxiliary Modeller scores
  • Improve macOS Mojave 10.14 appearance

New in UCSF Chimera 1.13 Build 41780 (Aug 13, 2018)

  • General Changes:
  • updated CASTp fetch URL (1/5/2018)
  • serial-numbering option for saving very large PDB files (4/2/2018)
  • Tool Changes:
  • Additional Tools menu to facilitate getting third-party plugins, notably the Tangram suite of molecular modeling tools from InsiliChem (JD Maréchal's group, Universitat Autònoma de Barcelona) (4/17/2018)
  • Rotamers (Structure Editing) — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • Command Changes:
  • swapaa — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • tile — label option adds 2D labels showing each tiled model's number and name (2/27/2018)
  • write — serial-numbering option for saving very large PDB files (4/2/2018)
  • Notable Bug Fixes:
  • Modeller input preparation sometimes failed when the template chain contained a modified amino acid (a HETATM residue) (fixed 2/22/2018)
  • Bogus "file does not exist" dialog no longer appears (fixed 10/31/2017)
  • Fixed MD Simulation's "incompatible files" problem when restarting a trajectory computation (fixed 4/2/2018)

New in UCSF Chimera 1.13 Build 41754 RC (Jun 4, 2018)

  • General Changes:
  • updated CASTp fetch URL (1/5/2018)
  • serial-numbering option for saving very large PDB files (4/2/2018)
  • Tool Changes:
  • Additional Tools menu to facilitate getting third-party plugins, notably the Tangram suite of molecular modeling tools from InsiliChem (JD Maréchal's group, Universitat Autònoma de Barcelona) (4/17/2018)
  • Rotamers (Structure Editing) — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • Command Changes:
  • swapaa — Dunbrack backbone-dependent rotamer library updated to 2010 version (4/26/2018)
  • tile — label option adds 2D labels showing each tiled model's number and name (2/27/2018)
  • write — serial-numbering option for saving very large PDB files (4/2/2018)
  • Notable Bug Fixes:
  • Modeller input preparation sometimes failed when the template chain contained a modified amino acid (a HETATM residue) (fixed 2/22/2018)
  • Bogus "file does not exist" dialog no longer appears (fixed 10/31/2017)
  • Fixed MD Simulation's "incompatible files" problem when restarting a trajectory computation (fixed 4/2/2018)

New in UCSF Chimera 1.11.2 Build 41376 (Sep 15, 2017)

  • Notable Bug Fixes:
  • works with changes in NCBI Blast and associated databases
  • updated SCOP domain fetch to use new URLs
  • CATH domain fetch removed (service discontinued for now)

New in UCSF Chimera 1.11.1 (Sep 15, 2017)

  • Notable Bug Fixes:
  • speed up opening of large non-molecule structures with no bonds
  • suppress excessive warnings when opening PDB files
  • make sure output goes to right place when opening mmCIF files
  • NCBI URLs have to use https now
  • rainbow helix recognizes abutting helices as distinct
  • fix Join Models tab in Build Structure so the setting of the phi angle never moves the "non-moving" side
  • fix ion parameter in APBS
  • handle plots with closed models more gracefully in RRDistMaps
  • Enhancements:
  • User's Guide includes attribute assignment file for Moon-Fleming hydrophobicity scale
  • put Chimera version in X3D output
  • struts command takes into account the currently displayed pseudobonds (H-bonds, distance monitors) and ignores bonds that are hidden
  • surface command warnLarge false option to bypass having to confirm a large calculation

New in UCSF Chimera 1.10.2 Build 40686 (Jul 31, 2015)

  • Updated URL for CASTp fetch
  • Got minimization working again on structures with disulphide bonds or glycosylations involving standard residues
  • Opening structures with duplicate chain IDs works again
  • Various mda bug fixes
  • Improved mda performance when displaying sequences in Multalign Viewer and associating sequences with structures
  • Prevent surface-generation failure from preventing session restoration
  • Prevent running web services from messing up session saving
  • Fixed R 3 and R 3 2 and H 3 and H 3 2 space groups
  • Added IMAGIC file reader
  • Fonts on Linux are now in points, not pixels, so they scale with the screen's dots per inch
  • Fixed another case of chimera crashing on dual-display Macs

New in UCSF Chimera 1.10 Build 40219 (Oct 20, 2014)

  • General Changes:
  • AmberTools updated to version 14 (new force field, etc.)
  • Fetch by ID now includes PDB biounit, CATH domain
  • “ligand” definition expanded to include residues that are bonded to a chain but not in the chain's main sequence (e.g., retinal in rhodopsin, glycosylations)
  • protein SSE (helix, strand, or other) inserted into ↑↓ selection cascade between residue and connected set of atoms
  • keyboard shortcuts rn, rp, ri to shift selection to next residue in chain, previous residue in chain, and to include intervening residues, respectively
  • New Molecules preferences:
  • option to show/hide atoms added
  • reorganization, graying-out to clarify which settings are overridden by smart initial display
  • Reply Log shows more information about accessed web services (software version, etc.)
  • structure-derived amino acid substitution matrices SDM, HSDM added (more choices for MatchMaker and Multalign Viewer alignment scoring and AL2CO sum-of-pairs conservation calculations)
  • added green-magenta (trioscopic) stereo mode
  • new input format: COLLADA (.dae)
  • New Tools:
  • RR Distance Maps (Structure Comparison) — create a protein contact map color-coded by distance (and/or standard deviation, if comparing multiple structures)
  • Tool Changes:
  • Add Charge (Structure Editing) — force field options changed, new default: Amber ff14SB (same charges as ff12SB, but different sidechain dihedral restraints, thus mainly affects any subsequent minimization)
  • Axes/Planes/Centroids (Structure Analysis) — can center and align chosen axis or chosen plane's normal vector along X,Y, or Z
  • Modeller comparative modeling interface (called from Multalign Viewer) —
  • new options: thorough optimization, specify distance restraints file
  • Multalign Viewer (Sequence) —
  • RMSD header renamed “RMSD: ca”, additional headers “RMSD: backbone” and “RMSD: full” available
  • can map feature annotations from the NCBI Conserved Domain Database (CDD) onto a sequence
  • regions can be included/excluded from the Region Browser listing based on data source (UniProt, CDD, Chimera built-in)
  • shortcut to associate all members of a structural ensemble with the same sequence (supplants tedious one-by-one approach)
  • searching by full or partial sequence name added to Edit menu
  • Command Changes:
  • addcharge — force field options changed, new default: Amber ff14SB (same charges as ff12SB, but different sidechain dihedral restraints, thus mainly affects any subsequent minimization)
  • mda (MultiDomain Assembler) —
  • assigns attributes for custom-coloring BLAST hits (potential templates) by BLAST score, %ID, etc.
  • shows the BLAST sequence alignment and the Modeller dialog
  • provides additional options for limiting hits
  • open —
  • PDB biological assembly fetch, prefix biounitID:
  • CATH domain fetch, prefix cath:
  • rainbow — can assign a unique color to each helix and/or strand in a protein chain
  • set —
  • set echo (new) echoes command-file lines in the Reply Log and status line as they are executed, along with line numbers
  • sop —
  • sop smooth (new) smooths surfaces by moving each vertex toward the average position of its neighbors
  • volume —
  • dumpHeader option to write MRC or CCP4 file header contents to the
  • Reply Log
  • toggle to show volume models that are hidden, hide those that are shown
  • vop —
  • vop gaussian can use different half-widths along X,Y,Z
  • vop mininum (new) takes the mininum values pointwise from two or more input maps
  • vop ridges (new) skeletonizes a map by emphasizing ridges or filamentous structures in the density
  • vop scale normalization options:
  • rms - scale to give the specified root-mean-square
  • sd - shift to zero mean, then scale to give the specified root-mean-square
  • vseries —
  • vseries measure (new) tracks volume series surface area, enclosed volume, centroid position
  • Notable Bugfixes:
  • surfaces read from STL files are saved in sessions

New in UCSF Chimera 1.8.1 Build 39231 (Dec 9, 2013)

  • Major Bugs Fixed:
  • Add workaround for Mac OS X 10.9 (Mavericks) graphics driver crash
  • Fix slow text entry on 64-bit Mac OS X 10.9 systems shows notes (as in Notepad) from sessions saved with pre-1.8 versions of Chimera