crazy tube helices after dssp on 4hhb

[Elaine Meng]

open 4hhb
rainbow
dssp
cartoon style modeh tube

(the rainbow isn’t required to show this problem but the dssp is… doesn’t matter if it is before or after changing to the tube mode... guess I will file a ticket and assign to Conrad)

Log:
cartoon style modeHelix tube
/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/sse.py:214: RuntimeWarning: invalid value encountered in true_divide
normal = normal / norm(normal)

Image attached.

[Conrad Huang]

dssp is assigning a single helix ssid for residues /c:4-35 when there are three different helices (two alpha sandwiched around a 3-10). It should assign three different ssids.

[Elaine Meng]

See also #561 cartoon should show abutting helices as separate instead of continuous
https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/561
…in that example, however, dssp is not involved, so either ssId is set wrong initially or the tube calculation ignores it.

[pett]

Okay, DSSP now changes the ss_id for consecutive residues if the helix type changes.

I should note that "cartoon style modeHelix tube" on 4hhb works but yields the following error message:

/Users/pett/src/chimera2/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/sse.py:234: RuntimeWarning: invalid value encountered in true_divide
normal = normal / norm(normal)

Also, selecting that section of residues (/c:4-35) produces a depiction that has gaps in the selection.

[Elaine Meng]

Not sure what you meant about gaps for /c:4-35, or maybe it’s fixed in today’s build.  Before dssp it is two tubes and dssp splits it into three tubes.

[pett]

Using the daily build, selecting /c:4-35 in tube mode, it looks like this:




The selection does not look continuous.  After DSSP, it’s even more so:

[pett]

Added by email2trac

[pett]

Added by email2trac

[Conrad Huang]

Tube selection was not selecting the half-tubes at the end of helices. Fixed in 14af384.