VIDA 4.3.0

August 2014

New Features

  • “Drag and Drop” is now supported for rearranging items in the List Window.

  • Advanced depiction options, including atom property maps from the Grapheme TK, substructure highlighting, and 2D structure alignment, are available for depiction in the 2D window and spreadsheet.

  • Improved surface rendering using the new “atom splitting” feature from the Spicoli TK.

  • Atom-based selection of surfaces.

  • Atom and surface selection is now indicated using bright outlines instead of atom coloring.

  • A new “Select” menu provides a wide range of ways to select atoms. The menu also allows creation and manipulation of named sets of atoms.

  • A surface hydrophobicity coloring scheme based on atomic XLogP contributions was added.

  • A new surface “curvature” coloring scheme was added that combines the previous “concavity” and “curvature” schemes.

  • An additional VIDA extension for coloring molecules by SD data is included.

  • An example “Cluster Browsing” script, for viewing clustered molecule data, is included.

  • Many enhancements were made to the Extensions Manager dialog, to allow better handling of extension subscriptions. Other extension improvements include the ability to specify the order in which extensions are loaded, and the ability to use the VIDA_EXTENSIONS_URL environment variable to specify multiple auto-subscriptions.

  • Molecular surfaces can now be created over sets of selected atoms, and can be regenerated via the Style Control.

  • The VIDA spreadsheet can now include generic data stored on molecules and conformers.

  • The List Window now allows clicking on column headers to show/hide, mark, and lock all items in the list.

  • The builder now issues a warning (and opportunity to cancel) if a protein molecule has been put into Edit mode.

  • Extension authoring was made easier by allowing local filenames in .pyx and .pyxs files.

Major Bug Fixes

  • A crash from undoing conformer deletion has been fixed.

  • A number of stability issues and strange window behavior under OS X 10.8+ have been resolved.

  • A crash while creating C-alpha traces for some proteins was fixed.

  • Several operations in the sketcher could create radicals unexpectedly. This has been corrected.

Minor Bug Fixes

  • Fixed a warning message when opening .cdx files.

  • A problem with state files not preserving child object visibilities was corrected.

  • SMILES (.smi) files now contain stereochemical information by default.

  • Installation of some extensions caused reading of large files to slow down significantly.

  • The save dialog was very slow to initialize for large files.

  • New lists created (e.g., from “Marked” molecules) now become the current active list.

  • Switching to stereo during a telemodeling session would lose synchronization between the connected sessions.

  • B-Factor labels can now be shown on any atoms, not just C-alpha atoms.

  • Files opened via the command line now appear in the “Recents” list.

  • Fixed an issue with extension updates requiring an extra VIDA restart to take effect.

  • A problem with exiting fullscreen mode was fixed.

  • A crash on exit when using certain extensions on Linux machines was fixed.

  • Grids rendered from CCP4 files now use the statistics embedded in the file, rather than statistics generated within VIDA.

Platform Support

  • Support for Ubuntu 14 was added.

  • Support for RedHat v7 was added.

  • Support for Mac OS X 10.8 and 10.9 was added.

  • Mac OS X 10.6 is no longer supported.

  • RedHat v4 is no longer supported.

  • Windows XP is no longer supported.

Other

Vivant is being retired, and no longer ships with VIDA. Existing versions of Vivant will continue to function and remain compatible with VIDA’s current state files.