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Helical Straightening

Straightening LogoWe have made a number of changes to the Tkir and Tkll GUI applications in SUPRIM (image viewer and layerline viewer, respectively).  One of the most significant in our view was the inclusion of a plugin architecture, a means of extending and adding functionality of the core programs by means of external plugins.  These plugins allow developers to add new functions while retaining all the core benefits of the original applications.


Here we present a helical boxing and straightening plugin for Tkir.  The user can display a micrograph containing one or more helical features of interest.  Although Tkir has a boxing mode which can select regions of an image, it does directly not allow for boxing curved features.  Instead, with this plugin, the user selects points along the curved filament which will then be boxed out.  Unlike other boxing GUIs, this plugin provides a real-time element.  Each time a new point is selected, a preview of the boxed-out and straightened filament is displayed, along with a fourier transform of that straightened filament.  This allows the user to extract the optimal section of further processing with the Burnham-Brandeis Helical Package, Phoelix or EMAN while significantly reducing the trial-and-error element.



The plugin consists of a tcl script which is a plugin for Tkir.  The plugin is not executable in it's own right, but a script which can be loaded and executed by Tkir.  To do this, the plugin should be installed in either ~/.tkir/plugins/Tkir/ (for the current user only) or $SUPRIM_TK_LIB/plugins/Tkir (for all users).  It can then be invoked by calling Tkir as usual but with an additional "-str" flag, e.g.:

tkir -f input_file.mrc -str


tkstraighten version 0.3-alpha is now available for download!  Please take note of the version number, 0.3-alpha.  While much more stable than the previous 0.2-alpha release, this remains for now pre-release plugin for Tkir and should not yet be considered ready for production use.  Also, check out the Helical Straightening FAQ.