Crystallography operations are activated by selecting the "Micrograph/Crystallography" menu item or the Crystallography tool (Dot array icon). This brings up a new window with a menu "Crystallography" and parameters:

Setup for crystallography

The image of a crystal is read into bshow, and its Fourier transform calculated with the "Image/Fourier transform" menu item. The Fourier transform is then shifted to center the origin with the menu item, "Image/Center origin".

Structure factors and unit cell parameters

To activate picking reflections, select the crystallography tool icon (dot array) from the tools window. Click on a reflection and then set its indices with the "Crystallography/Set indices" menu item. Repeat this with at least one more reflection. Generate the unit cell vectors using the "Crystallography/Calculate unit cell vectors" menu item. Finally, generate all reflections within a given resolution by selecting the "Crystallography/Generate spots" menu item.



With the structure factors defined, they can be masked using the "Crystallography/Mask spots" menu item. The "Structure factor radius" in the crystallography window is used to determine the mask radius.


The Fourier transform can then be backtransformed to produce a new filtered image.


Mouse controls for picking reflections

Clicking the left or middle mouse button in an empty region on the image creates a new reflection.
To delete a reflection, hold down the shift key and click the left or middle button on the reflection.


Reading and saving crystallographic parameters

The "Micrograph/Read parameters" and "Micrograph/Write parameters" menu items are used to read and write parameter files (usually in the STAR format).