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Avogadro 1.95 Release

We are pleased to announce the latest release of Avogadro, including piles of bug fixes and feature enhancements.

Thanks to many for suggestions, bug reports, and discussions.

This release includes many new features, including new protein ribbon / cartoon renderings and the new “Layer” system as part of Google Summer of Code by Marc Masó

Draft developer documentation can be found at https://two.avogadro.cc

If you have comments or suggestions, please join us at https://discuss.avogadro.cc and as always, help and contributions in many forms are very welcome, particularly if you’d like to help update user documentation.

We anticipate several more releases over fall 2021 as we finish up our 2.0 release.

:sparkles: Features

  • New “Layer” system, including custom rendering, locking and hiding parts of the molecule @serk12 (#709)
  • Atom and residue labels @serk12 (#715)
  • New protein cartoon / ribbon display @serk12 (#660 #694 #716)
  • Update render options for Wireframe and Ball-and-Sticks @ghutchis (#700 #720)
  • Use MMTF downloads - more efficient than PDB format @ghutchis (#699)
  • Add back support for importing crystals @ghutchis (#658 #659)
  • Add CJSON support for save/load residues and atom colors @ghutchis (#646)
  • Refactor of Python command and input generators, including tabs @ghutchis (#667)
  • New View => Apply Colors menu @ghutchis (#640 #723)
  • Apply color schemes for residues @ghutchis (#638 #688)
  • Add more selection commands, including select by residue @ghutchis (#632 #634)
  • Render selected atoms in VdW and licorice modes @ghutchis (#702)
  • Detect secondary structure from residues / backbones @ghutchis (#685)
  • Save enabled / disabled state of scene / rendering plugins on quit @ghutchis
  • Should now download and install translations for @ghutchis

:bug: Bug Fixes

  • Fix Mac builds by turning off COORDGEN library @ghutchis (#606)
  • Fix Windows installer to include all needed files @ghutchis
  • Save projection type on close #682 @ghutchis
  • Add a pass to fix OB plugin library paths on Mac @ghutchis (#627 #628)
  • Fix odd behavior on ‘Center’ command @serk12 (#728)
  • Fix several crashes with proteins @ghutchis (#724 #726 #727)
  • Fix crash in CJSON reading file without labels @ghutchis (#722)
  • Fix bug deleting selected atoms #650 @ghutchis (#672 #677)
  • Fix “delete last atom” bug @ghutchis (#691)
  • When dragging to create a new atom, use starting coords @ghutchis (#690)
  • Fix #679 - incorrect PDB unit cells @ghutchis (#689)
  • Fixed problems inserting SMILES without coordinates @ghutchis (#661)
  • Fix for transparent widgets @ghutchis (#656)
  • Fix #602 - use Molden order for f-orbitals @ghutchis (#649)
  • If a chain ID is missing / invalid, skip (to read non-standard PDB) @ghutchis (#647)
  • Make sure to reset colors when changing elements @ghutchis (#708)

:toolbox: Maintenance

  • Make sure to install crystals directory even when it exists @ghutchis (#613)
  • Replace NULL/0 with nullptr @e-kwsm (#617)
  • Add support for reading partial charge models from obabel @ghutchis (#626)
  • Replace obsolescent LINK_(PRIVATE|PUBLIC) with (PRIVATE|PUBLIC) @e-kwsm (#629)
  • Refactor Molecules class @serk12 (#648)
  • Don’t install cclib script - which was removed @ghutchis (#662 #663)

:books: Translations

  • Fix fuzzy entry for Nihonium (not Zirconium!) @e-kwsm (#618)
  • Fix all incorrect fuzzy entries #619 @e-kwsm (#643)
  • Remove wrong entries which were fuzzy @e-kwsm (#644)
  • Translations update from Weblate @weblate (#625)
  • Add a workflow which should update the translation template continuously @ghutchis (#624)

Credits

Thanks to many contributors, including: @12emin34, @GicoProgram, @LihanzUpenn, @NathanBnm, @San4ito, @acunm, @alexrsoares, @danialk03, @dillonschultz93, @e-kwsm, @ghutchis, @grsousajunior, @psavery, @rezaalmanda, @serk12, @tacitcoast, @weblate, Eisuke Kawashima, Jacque Fresco and phlostically

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A few new images made possible in 1.95:



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