Important Changes:
- Single word keywords not followed by "and" logical operator are not accepted, e.g. "protein within 5 of water" will raise a :class:`.SelectionError`, use "protein and within 5 of water" instead.
- :func:`findMatchingChains` is renamed to :func:`.matchChains`.
- :func:`showOverlapMatrix` is renamed to :func:`.showOverlapTable`.
- Modules are reorganized.
New Features:
- :class:`.Atomic` for easy type checking.
- :class:`.Contacts` for faster intermolecular contact identification.
- :class:`.Select` can identify intermolecular contacts. See :ref:`contacts` for an examples and details.
- :func:`.sampleModes` implemented for sampling conformations along normal modes.
Improvements:
- :mod:`.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=Trueargument. This impacts the speed of X-ray ensemble analysis.- :class:`.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 :func:`.showProjection` is completed.
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.