ProDy 0.2 Series

0.2 (Nov 16, 2010)

Important Changes:

  • Single word keywords not followed by “and” logical operator are not accepted, e.g. “protein within 5 of water” will raise a SelectionError, use “protein and within 5 of water” instead.

  • findMatchingChains() is renamed to matchChains().

  • showOverlapMatrix() is renamed to showOverlapTable().

  • Modules are reorganized.

New Features:

  • Atomic for easy type checking.

  • Contacts for faster intermolecular contact identification.

  • Select can identify intermolecular contacts. See contacts for an examples and details.

  • sampleModes() implemented for sampling conformations along normal modes.

Improvements:

  • proteins.compare functions are improved. Now they perform sequence alignment if simple residue number/identity based matchin does not work, or if user passes pwalign=True argument. This impacts the speed of X-ray ensemble analysis.

  • Select can cache data optionally. This results in speeds up from 2 to 50 folds depending on number of atoms and selection operations.

  • Implementation of showProjection() is completed.

Normal Mode Wizard

Release 0.2.3

  • For each mode a molecule for drawing arrows and a molecule for showing animation is formed in VMD on demand. NMWiz remembers a color associated with a mode.

  • Deselecting a residue by clicking on a plot is possible.

  • A bug causing incorrect parsing of NMD files from ANM server is fixed.

Release 0.2.2

  • Selection string option allows user to show a subset of arrows matching a VMD selection string. Optionally, this selection string may affect protein and animation representations.

  • A bug that caused problems when over plotting modes is removed.

  • A bug affecting line width changes in plots is removed.

  • Selected residue representations are colored according to the color of the plot.

Release 0.2.1

  • Usability improvements.

  • Loading the same data file more than once is prevented.

  • If a GUI window for a dataset is closed, it can be reloaded from the main window.

  • A dataset and GUI can be deleted from the VMD session via the main window.

Release 0.2

  • Instant documentation is improved.

  • Problem with clearing selections is fixed.

  • Plotting options frame is populated.

  • Multiple modes can be plotted on the same canvas.