VIDA 4.1.0

August 2011

New Features

  • Simultaneous 2D and 3D editing of small molecules.

  • Ability to rotate and translate molecules independently in the builder.

  • Simplified authoring of extensions, and inclusion of a number of new example extension scripts.

  • Ability to add annotations to existing objects, and have those annotations appear in the List Window.

  • Adjustment of torsion angles within rings to change ring puckers and interconvert axial and equatorial substitutions.

  • Option to use the MMFF94s force field when building molecules.

  • Improved set of fragment templates in the sketcher

Major Bug Fixes

  • Fixed a crash when saving state files after loading a large number of proteins.

  • Fixed a crash when editing cells in a spreadsheet.

  • Centering on selected atoms would sometimes require a change in visibility before taking effect. This has been fixed.

  • Fixed a bug which caused rows to sometimes disappear when cells in a spreadsheet were edited.

  • Spreadsheet depictions are now being updated as molecules are edited.

  • An issue which caused the view to occasionally jump unexpectedly during molecule rotations was fixed.

  • Fixed a problem which sometimes caused crashes while creating measurements in the “All” scope.

  • Changing colors/styles of grids now operates on the proper scope, rather than on all visible grids.

  • Addressed issues with the builder and sketcher which sometimes caused fragments to be joined incorrectly.

  • Fixed a bug which sometimes caused right-click menus to become inoperative.

Minor Bug Fixes

  • Hotkeys for Marked/Locked/Visible now work on selected rows in the spreadsheet, not just the active molecule.

  • Fixed a bug where changes to the spreadsheet cell formats weren’t being propagated immediately to the spreadsheet.

  • Fixed a bug to have VIDA remember the hidden/visible state of depictions in a spreadsheet from one session to another.

  • Fixed an issue with the spreadsheet so that users can’t edit non-editable cells, such as computed values (e.g., molecular weight, number of rotors) and user-defined python expressions.

  • Fixed a sizing problem with the 2D Sketcher window, which had caused some tools in its toolbar to be hidden.

  • When a spreadsheet is created from a list, it is now made the current spreadsheet.

  • Fixed an issue which would cause blank entries to sometimes appear in the List Window.

  • Fixed a rendering problem which caused circles to be displayed incorrectly.

  • Corrected an issue in which text would be incorrectly wrapped within labels.

  • Display of symmetry-related molecules now updates automatically as the view is translated.

  • Surface created in the FRED View are now added to the List Window and can be deleted individually.

  • Grid contours are now contoured by default at the original resolution of the grid file.

  • Contours of a grid can now be temporarily shown, similarly to conformers, by clicking on their names in the List Window.

  • All child objects of grids now show in the List Window. Previously only the contours would show.

  • Corrected an issue which sometimes caused incorrect hydrogen geometries during building.

  • Addressed several issues affecting performance and behavior of spreadsheets.

  • Fixed an issue that could sometimes cause incorrect stereochemistries to appear in 2D depictions.

  • Fixed a bug which caused stereochemistry to be omitted from molecules when copying to the clipboard.

  • Corrected strange lasso behavior in the sketcher.

Platform support

Support for Ubuntu 10 (x64) and RedHat Enterprise v6 (x64) was added. RedHat Enterprise v3 is no longer supported.