Generating an artificial helical map
A simple artificial helical map can be easily calculated using some primitive
shapes and applying helical symmetry:
beditimg -v 7 -create 100,100,100 -ori 50,50,50 -sam 2 -sph 70,50,50,10 -fill 1 -edge 2 sph1.map
beditimg -v 7 -sph 75,60,50,2 -fill 1 -edge 2 sph1.map sph2.map
bhelix -v 7 -helix 8,58 sph2.map helix.map
An artificial helix with a rise per subunit of 8 Å and a rotation per subunit of 58° isosurfaced at a threshold of 1.5 sigma.
Helix with a seam
Some helices have a seam, where protofilaments are shifted. The seam itself is helical, describing the twist of the protofilaments. The seam introduces another orientation requirement: In Bsoft, the seam passes through the positive x-axis (i.e., the vector from the image origin pointing in the x direction). A synthetic helix can be generated as follows:
beditimg -v 7 -create 100,100,100 -ori 50,50,50 -sam 2 -sphere 57,42,47,2 -edge 1 -fill 1 ss1.map
beditimg -v 7 -sphere 57,42,53,3 -edge 1 -fill 1 ss1.map ss2.map
bhelix -v 7 -helix 1.1,33 -seam 0.5 ss2.map h11_s1.map
An artificial helix with a rise per subunit of 1.1 Å, a rotation per subunit of 33° and a seam shifted by 0.5 subunit length, isosurfaced at a threshold of 0.5 sigma.
Map orientation
If a helical map will be used in further processing, it has to be oriented correctly with the helical axis on the z-axis, and if a dyad axis is present, it has to lie on the x-axis.
Generating projections
To generate projections of the helix:
bhelix -v 7 -proj 5 helix.map helix_proj.pif
bproject -v 7 -sym H -ang 5 helix.map helix_proj.pif
Projections of the helical map at 5° intervals.