## Determining filament widths

The variation in the width of a filament with a long pitch may aid in establishing the cross-overs more accurately. To improve the contrast, the filament image can be smoothed with a moving average function, and by averaging the helical repeats. The requirements are that the filament lies parallel to the y axis and in the center of the image.

Cropped example of a cryoEM image of a filament.

The filament image can be preprocessed to set the image parameters, invert the contrast and smooth along the y axis:

bfilwidth -v 7 -sam 1.5 -ori 128,4000,0 -invert -average 1,30,1 863-crop_ctf_fil000001.pif 863-ccf_avg.pif

The filament with at each y position is then calculated using a moving average window and limits on the expected width of the filament:

bfilwidth -v 7 -period 256,600,1 -width 30 -limits 55,100 -Post 863-ccf_per.ps 863-ccf_avg.pif 863-ccf_per.pif

Periodically averaged filament to determine the widths along the helical axis.

Plot of filament widths along the helical axis.