Opened 8 years ago

Closed 8 years ago

#745 closed defect (fixed)

"hbonds" doesn't like ensembles, I guess

Reported by: Elaine Meng Owned by: Eric Pettersen
Priority: major Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

I tried 2 different ensembles, seemingly unrelated: 1g1p and 2nbk

Open either one of those, and try hbonds on even just the first submodel:

hb spec #1.1

hbonds spec #1.1
75 hydrogen bonds found
Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py", line 178, in execute
cmd.run(cmd_text)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py", line 2366, in run
result = ci.function(session, kw_args)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/hbonds/cmd.py", line 133, in cmd_hbonds
sqdist = h.scene_coord.sqdistance(acc.scene_coord)
AttributeError: 'numpy.ndarray' object has no attribute 'sqdistance'

Change History (3)

comment:1 by Elaine Meng, 8 years ago

I also get this error if I open the ensemble as a trajectory instead, e.g.

open 2nbk coord true
hb

comment:2 by Eric Pettersen, 8 years ago

Status: assignedaccepted

comment:3 by Eric Pettersen, 8 years ago

Resolution: fixed
Status: acceptedclosed
Note: See TracTickets for help on using tickets.