VIDA 4.0.0

AuguAgust 2009

New Features

  • Added a 1D/2D molecule input dialog which supports SMILES, names, and interactive building.

  • Added a 3D editing mode which enables significant modification of the current molecule including in-vacuo minimization with MMFF94.

  • Added support for DNA/RNA ribbon style visualization

  • Added support for displaying and controlling alternate residue conformations (turn on ALL flavor when reading PDB files to enable this) as well as a number of coloring schemes associated with alternate residues

  • 2D depiction in 3D display is now selectable

  • Add object-type specific tool buttons to the bottom display which provide context sensitive operations such as coloring and style options.

  • Added the ability to import all of OpenEye’s Python toolkits for use within VIDA, provided that the user has a license for those toolkits.

  • Added the ability to transfer molecules, grids, and surfaces between the main application and the bundled OpenEye Python toolkits.

  • Added support for PythonQt scripting within VIDA.

  • Added support for PyQt scripting with VIDA (separate license required from Riverbank computing).

  • Added interactive protein depictions in the spreadsheet.

  • Added many new atom properties to the atom spreadsheet.

  • Added a residue spreadsheet which is capable of controlling alternate residue conformations.

  • Added the ability to load molecules directly from the PDB ( “File > Open Special > From PDB” )

  • Added the following command line arguments:

    -e - Runs the associated file through the Python interpreter and populates the sys.argv variable with the remaining command line arguments

    -eonview - Loads the associated files and processes them using the built in EON view

    -fredview - Loads the associated files and processes them using the built in FRED view

    -rocsview - Loads the associated files and processes them using the built in ROCS view

    -import - Loads the associated files and immediately launches the spreadsheet import dialog

  • PICTO application now ships with VIDA. PICTO requires a valid VIDA license.


  • Significantly increased the speed of searches performed within VIDA.

  • Significantly improved and expanded the scripting examples that come with the distribution.

  • Significantly optimized the loading of OEB molecule files which contain attached grids.

  • When displaying Marked molecules, now only the carbon atoms (as opposed to all) are colored using the Marked color unless the non-carbon atoms are specifically Marked themselves.

  • Optimized the AtomDataGet function when working with multi-conformer molecules.

  • Vastly improved the display and usability of the embedded 3D toolbars

Major Bug Fixes

  • Fixed rendering problems associated with having multiple overlapping transparent surfaces displayed simultaneously.

  • Fixed the handling of triple-quoted strings in the VIDA interpreter.

  • Fixed a bug which was preventing scripts from being aborted while running.

  • Fixed a problem where SD data was being lost on read if one or more conformers in a multiconformer molecule did not have the same SD data fields as the rest.

Minor Bug Fixes

  • Fixed a number of erroneous tooltips.

  • Fixed a few spelling errors in prompts and widgets.

  • Fixed the behavior of the drop-down selections in the constraints and extra molecule buttons in the FRED View controller.

  • Fixed the hybridization, isotope, and symmetry atom labels.

  • Fixed a bug where the ColorSetScoped function did not color selected atoms if SelectedScope was explicitly specified as opposed to BestScope.

  • Fixed the MoleculeMergeScoped function to ensure that residue information is not lost when two molecules are merged together.

  • Fixed the standard deviation function in the spreadsheet.

  • The “Create Spreadsheet” option for list entries in the list windows now works as expected.

  • Fixed the coordinates returned in the AtomData class by the AtomDataGet function when working with multi-conformer molecules.

  • Silenced a large number of annoying and unnecessary warnings that would appear in the scripting window