tube helix with stripes 5cbf

[Elaine Meng]

Another possibly weird case is 5cbf. One of the helix tubes has stripes on it (image attached) and I see this warning in the Log:

cartoon style modeHelix tube
/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/sse.py:223: RuntimeWarning: invalid value encountered in true_divide
normal = normal / norm(normal)

[Elaine Meng]

Maybe they're not related... it is possible to get the tube stripes without the warning, e.g. 5dwe

[Elaine Meng]

I wondered if this was also related to bent helices, like the armadillos. I took a closer look at 5cbf and see there are several tubes with slightly striped or recessed ends, namely near residue 103 in chains A,C,D,F. I didn't see any obvious bending, though. Running "dssp" improved most of these by shortening or extending the helix, but it made the chain C one worse and added a new one at chain C around residue 17.

[Elaine Meng]

Looks like the 5cbf stripes are gone in the daily build!  I didn’t close the the ticket, not sure if you wanted to check something else.  (Cc’ing you directly in case trac isn’t sending you an email automatically)

[Conrad Huang]

Looks like proper sorting fixed the problem.