After refining structures from crystallographic diffractions or cryo-EM data, yet these PDB files don’t have pre-defined structural structure regions. I sometimes found ChimeraX doesn’t display same helices or sheets as PyMOL or Coot does.
In ChimeraX, if we are certain of the secondary structural regions, a simple command called “setattr” lets users manually define helices or sheets, like PyMOL’s “alter”.
Here is a good and short explanation provided by ChimeraX team.
argument: setattr res ss_type 0
setattr :10-30, 50-56, 90-94 res ss_type 1 (define helices)
setattr /B:23-30 res ss_type 2 (Define B chain, aa 23-30 as sheet)
The ss_type is numerical :
0 = coil
1 = helix
2 = sheet
*update title on Aug. 9. (was wrong title)