The analysis of Fourier transforms of images of helical specimens are activated by selecting the
"Micrograph/Helix" menu item or the helix tool (helical diffraction pattern icon).
This brings up a new window with a
menu "Helix" and parameters:
- Helix
- Help - links to on-line help.
- Set layer line index - opens a dialog box called "Indices" to set the indices of the currently selected reflection.
- Generate layer lines - generates all layer lines within a given resolution limit.
- Mask layer lines - masks layer lines and delete the background.
- Delete all layer lines - deletes all layer lines in memory (no recovery!).
- Close - close window and deactivate helix operations.
- Parameters
- Helix axis angle - sets the helix axis direction relative to the x-axis.
- Layer line length - sets the length for drawing layer lines.
- Layer line width - sets the width for masking.
- Layer line count - shows the number of layer lines.
- Selected - indicates the currently selected layer line index and its figure-of-merit.
- Radiobuttons to display/hide layer lines and labels.
Setup for helix processing
The image of a helix 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".
Picking layer lines
To activate picking layer lines, select the helix tool icon (helical diffraction pattern icon) from the tools window. Click on a layer line and then set its index with the "Helix/Set layer line index" menu item. As many layer lines can be picked as needed. The rest of the layer lines can then be generated using the "Helix/Generate layer lines" menu item and setting a resolution limit.
Masking
With any number of defined layer lines, they can be masked using the "Helix/Mask layer lines" menu item. The "Layer line width" in the crystallography window is used to determine the mask width for each layer line. The Fourier transform can then be backtransformed to produce a new image.
Mouse controls for picking reflections
- Left/middle button: create or select a layer line
- Shift - left/middle button: delete a layer line
Clicking the left or middle mouse button in an empty region on the image creates a new reflection. Clicking on an existing layer line selects that layer line, that can then be moved. To delete a layer line, hold down the shift key and click the left or middle button on the layer line.
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).