qindex is an experimental program to do initial screening of 2-D crystals, and perform single-particle style averaging on data from poorly ordered crystals. It was developed in collaboration with Gina Sosinsky (as an end-user). This is not exhaustive documentation, but should be enough to get you started with it:

There are then 5 buttons next to the panning widget. These are basically designed to be used sequentially (except clear)

  1. Pick a good area of your crystal and adjust the unit cell parameters
  2. press 'Avg' (this may take some time depending on the unit cell size)
  3. a new window will appear with an improved contrast average about 2-3 unit cells in size (varies a bit). Hoepfully the real-space crystal will appear very visibly in this window, but how well it works will depend on the contrast a bit...
  4. set a 'ref size' in pixels corresponding to the size of the region you want to 'reconstruct' (in 2d), generally a couple of unit cells, then left-drag in the new window to select your phase origin
  5. click on the 'corr' button. This will cross-correlate the average region you just selected with the entire micrograph, giving you an overview of crystal quality across the image. Of course this will only be accurate within a single crystal. This replaces the original micrograph.
  6. raise the display contrast in the micrograph window to 1.0, then adjust the brightness so you can see a pattern of spots corresponding to good regions of your crystal.
  7. press the 'peak' button, this will apply a peak filter to the correlation map. Readjust the brightess. Any peak you see on the screen will be treated as a 'good' region for further processing.
  8. press the 'box' button. The number of selected dots will appear below the panning widget, and a box database fill will be written to disk with the name 'qindex.box'.
  9. quit qindex (or hide it)

{{{batchboxer input=<your micrograph> dbbox=qindex.box output=boxed.hed

proc2d boxed.hed boxed.avg.hed average v2 boxed.avg.hed}}}

Contact me (Steve Ludtke) if you need more assistance.

EMAN1/Programs/QIndex (last edited 2008-11-26 04:42:28 by localhost)