qindex
Experimental 2D-xtal Processing Program
Usage
qindex
Description
qindex is still an experimental program. While it can perform a number of useful tasks as documented below,
it does not yet provide a mechanism for complete 2D crystal processing
qindex was designed to perform the first step in
single particle style 2d xtal analysis, but effectively also
streamlines the initial steps of a normal 2d x-tal analysis.
- run qindex, open a micrograph (real-space image)
- 4 windows will appear
- control panel
- window containing the full micrograph you just opened (pan
using RMB or panning widget in the control panel, middle click as
usual for more controls) Drag with the LMB to select an area of
interest.
- window containing a boxed out section of the micrograph. The
size of the region is specified in the control panel as Size. A grid
corresponding to the current unit-cell spacings is overlaid on this
window.
- window containing the FFT of the boxed out region with an
overlaid unit cell in Fourier space. Enter the A/Pix value in the
control panel, then drag any of the light-blue circles in this
window to define the unit-cell (if you use a higher order circle,
you will get more precise positioning. Unit cell parameters are
shown in the control panel. Note that you can use the middle button
in this window as well...
- You can read out specific peak intensities from the Peak
subwindow in the control panel. There are then 5 buttons next to the
panning widget. These are basically designed to be used sequentially
(except clear)
- Pick a good area of your crystal and adjust the unit cell
parameters
- press 'Avg' (this may take some time depending on the unit cell
size)
- 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...
- 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
- 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.
- 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.
- 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.
- 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'.
- quit qindex (or hide it) batchboxer input=<your micrograph> dbbox=qindex.box
output=boxed.hed
(you can use the newsize= option if you want to change the box size)
(note that batchboxer works only on MRC format images, you will need to use boxer instead for other formats)
proc2d boxed.hed boxed.avg.hed average
v2 boxed.avg.hed
EMAN 1.7, 1997-2006 Steve Ludtke