cartoon linker problems with contiguous helices

[Elaine Meng]

PDB 5CHZ protein chain A has some contiguous helices:

HELIX 5 AA5 ASP A 495 LYS A 504 1 10
HELIX 6 AA6 PRO A 505 GLY A 507 5 3
HELIX 7 AA7 LEU A 508 LYS A 526 1 19

There is a problem with the cartoon linkers between these three helices. Regardless of whether "cartoon style ssEnds" are short or long, there should be three helices separated by 2 coil-like linker segments (helix--helix--helix). The difference should only be in whether the coil-like segments are a half residue long (ssEnds long) or a full residue long (ssEnds short). However, when I specify long ssEnds there are no coil-like segments at all (helixhelixhelix), and when I specify short ssEnds there are four coil-like segments(helix--he--lix--he--lix)! ???

[Conrad Huang]

Fixed in 0281404/chimerax to not use same variable name for two different cases.