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:

- Crystallography
  - Set spot indices - open a dialog box called "Indices" to set the indices of the currently selected reflection.
  - Calculate unit cell vectors - use the available reflections to calculte unit cell parameters.
  - Generate spots - generate all reflections within a given resolution limit.
  - Mask spots - mask reflections and deletes the background.
  - Delete all spots - delete all reflections in memory (no recovery!).
  - Close - close window and deactivates crystallographic operations.
- Parameters
  - Structure factor radius - sets the radius for drawing circles around reflections and masking.
  - Structure factor count - indicates the number of structure factors.
  - Selected - indicates the currently selected structure factor indices and its figure-of-merit.
  - Radiobuttons to display/hide structure factors and labels.
  - Unit cell - vectors for the unit cell.

## 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.

## Masking

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

- Left/middle button: create a reflection
- Shift - left/middle button: delete a reflection

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).