VIDA 4.2.0

September 2012

New Features

  • A “telemodeling” feature has been introduced (as an included VIDA extension), and allows interactive sharing of VIDA sessions over a network.

  • 3D graphics shading calculations have been redone, to provide much nicer looking rendering of 3D objects.

  • Solid-rendered 3D objects now include edge outlines to improve clarity.

  • VIDA’s spreadsheet has been updated with several new features:

    • Depictions now use the new OEDepict TK, and can be displayed in color.

    • Atom selection is reflected in the spreadsheets.

    • Structures from SMILES strings can now be displayed in spreadsheet cells. Just put the string “(smiles)” anywhere in the column name.

    • URL’s in the spreadsheet are now treated as active hyperlinks.

    • Row heights can be adjusted all at once, to interactively scale (and hide) molecular depictions.

    • The VIDA Name column has been removed.

    • New columns can be added via a “+” button in the spreadsheet headers

  • Spreadsheets can now be exported directly to PDF files.

  • Filenames of files opened within VIDA now show in the title bar of VIDA’s main window.

  • The behavior of the “Recents” menu has been changed, so that it now displays both recently opened and recently saved files, including VIDA state (.oes) files. In addition, a “Recent Directories” menu has been added.

  • A “protein sequence” coloring scheme has been added which colors protein molecules using a gradient from N-terminus (blue) to C-terminus (red).

  • The Extension Manager has been rewritten to simplify the user interface.

  • VIDA can now automatically subscribe to sets of VIDA Extensions pointed to by the environment variable, VIDA_EXTENSIONS_URL.

  • Several rarely-used icons have been removed from VIDA’s main window, and the “Style Toolbar” at the top of the 3D window is now empty by default.

  • An example docking extension is now provided, to allow docking of molecules against a pre-prepared receptor for customers with an OEDocking TK license.

  • New commands for disabling and clearing VIDA’s “Undo” stack have been added to the scripting API. These can be used to prevent repeated operations from building up large amounts of “undo” memory unnecessarily.

  • VIDA can now read MTZ crystallographic reflection files from several common refinement programs and generate regular and difference maps from them.

  • A new preference setting allows molecules without 3D coordinates to be displayed in the 3D window.

  • Monitors (for distances, torsions, etc.) can now be deleted from within the “Measure” option in the Mouse Toolbar.

  • VIDA now incorporates the released versions of OpenEye toolkits, including the newer OEDocking TK, OEDepict TK, and Grapheme TK.

  • The Preferences dialog behavior has been modified to allow updating of preferences without dismissing the dialog.

  • The installer for Windows now allows association of user-selectable file types with VIDA.

  • Load times have been significantly improved for files containing large numbers of molecules.

Major Bug Fixes

  • Under certain conditions, working with a protein with alternate conformations could cause corruption of state files. This has been corrected.

  • A problem causing failure of molecule check-ins after deleting and re-adding hydrogens has been fixed.

  • A severe graphics slowdown on Windows machines with Intel HD Graphics video has been addressed by new OpenGL rendering methods.

  • A bug which caused atom names to sometimes be lost when merging molecules has been fixed.

  • Stereochemistry is now preserved when pasting structures from ChemDraw or reading .cdx files.

  • A graphics bug which made all 3D labels show up in black on certain video cards has been corrected.

Minor Bug Fixes

  • Molecules created by typing a name in the builder would be named with a SMILES string instead of the type-in name, unless a valid Lexichem TK license was found.

  • MoleculeColorByScope() and related functions have been fixed to work properly with molecule keys in the Scratch Scope.

  • Molecule surfaces are now automatically updated when the molecule is edited.

  • On machines with desktops spanning multiple monitors, VIDA could sometimes place the main window and Preferences dialog offscreen.

  • The VIDA icon now shows correctly when the application is pinned to the taskbar in Windows.

  • Disabled inner contours from FRED receptor files are no longer displayed.

  • Previously, users could see very slow performance in the File/Save dialog, when trying to select all molecules with the topmost checkbox. This problem has been eliminated.

Platform support

Support for Ubuntu 12 (x64) and Mac OS X 10.7 has been added.