VIDA 4.4.0

February 2018

New Features

  • A new ribbon style has been introduced into Spicoli TK and is now being used to render ribbons within VIDA. The new style produces ribbons with a smoother appearance.

  • Various improvements to the Builder/Sketcher behavior have been made, including:

    • closing the Sketcher window now prompts for Save, Save as New, Discard, or Cancel

    • closing the Builder now closes the Sketcher window

    • an additional Save As New option appears in the toolbar and Builder context menu

    • hitting Return now finishes adding typed-in molecules from the Sketcher

  • An Unhide Atoms option was added to the Select Menu.

  • Extensions can now be deactivated centrally by appending -remove to the extension’s entry in a PYXS subscription file. Various other improvements to the Extension Manager behavior were also made.

  • 3D renderings of OEAnnotation objects are now selectable.

  • Several improvements have been made to the Scripting window, including to the Paste and Drag/Drop behavior.

Major Bug Fixes

  • A bug that caused waters to not show as hydrogen bond acceptors has been fixed.

  • An issue that caused bond torsions to rotate atoms on the wrong end of the bond has been fixed.

  • A crash caused by excessive memory use while centering a large number of molecules in All Scope mode has been rectified.

  • A bug that could sometimes cause a crash when changing the font size in the 3D Window has been fixed.

  • A memory leak that occurred when switching screenshots or switching layouts has been fixed.

  • A crash that could occur when adding large number of grids has been fixed.

  • A crash that could occur when shift-selecting surfaces on proteins has been fixed.

  • A crash that occurred when clicking the List Window’s visibility header button when a grid and many molecules were loaded has been fixed.

  • Coloring proteins using the Alternate Locations coloring scheme no longer crashes the program when applied to molecules without alternate locations specified.

  • A conflict between the Qt libraries installed with VIDA and the Qt libraries included in Kubuntu would cause a “Cannot mix incompatible Qt libraries” error message when starting VIDA. This error has been corrected by including some additional Qt libraries in the VIDA distribution.

Minor Bug Fixes

  • The Save dialog had been performing very slowly when a large number of molecules were loaded. This has been fixed.

  • Screenshots made from the 2D Viewer are no longer saved with a border.

  • An issue that caused a complete molecular surface to appear during operations on molecules with partial surfaces has been fixed.

  • A problem with synchronizing selections between atoms in the 2D/3D Viewers and atoms in the SMILES display in the 3D Viewer has been fixed.

  • Aromaticity of certain molecules with tetravalent sulfur atoms had previously displayed inconsistently between the sketcher and the 3D Viewer. This has been fixed

  • A bug that could cause electrostatic grids generated using AM1BCC charges to generate incorrect contours has been fixed.

  • The default electrostatic surface grid spacing has been increased.

  • In certain cases, rounding errors were causing incorrect sorting behavior for very large numbers in the spreadsheet. This was fixed by changing the internal representation for spreadsheet numbers from floats to doubles.

  • Changing the application layout no longer hides visible extension windows.

  • A problem with setting bookmark animation timings has been fixed.

  • Minor fixes to the Extensions Manager dialog have been made.

  • Behavior of the AtomLabelSetScoped function has been fixed to make long label-type arguments (e.g., “residue info (ca)”) work as described in the documentation.

  • A bug that made hyperlinks in the spreadsheet case insensitive has been fixed.

  • Some geometry issues with the Attach and Fuse operations in build mode have been fixed.

  • A Donor option had been missing from the Select Within Focused dialog. This has been fixed.

  • A bug that affected the preferences for depicting superatoms in 2D renderings has been fixed. In addition, a new dialog for specifying which functional groups to render as superatoms has been added.

  • The Show Axes preference under the 3D Display General preferences now displays the axes at the center of the 3D view.

Platform Support

  • Support for 64-bit Windows has been added.

  • 32-bit Windows is no longer supported.

  • Support for Ubuntu 16 has been added.

  • Support for RedHat v7 has been added.

  • RedHat v5 is no longer supported.

  • Support for Mac OS X 10.10 Yosemite has been added.

  • Support for Mac OS X 10.11 El capitan has been added.

  • Support for macOS 10.12 Sierra has been added.

  • Support for macOS 10.13 High Sierra has been added.

Other

  • Version 4.4.0 will be the last version of VIDA supporting Python 2.7. Future versions will be based on Python 3.