id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 679 Crash tab completing pseudobonds collection methods in Python shell tic20@… Eric Pettersen "open 3loh # In shell p = session.models.list()[1] # Pseudobond group pb = p.pseudobonds pb. crashes because tab completion attempts to get the Pseudobonds._ses_ids property which causes the crash. Tristan's report of this follows: Begin forwarded message: From: Tristan Croll <> Subject: Pseudobonds question (and crash) Date: May 18, 2017 at 1:32:07 AM PDT To: Tom Goddard Hi Tom, Apologies for sending the below crash info directly to you rather than through the ticket system, but the server is playing up. Apparently plato wants me to update my password, but its password server is offline so I can't. Upshot is that I can't log in to the Wiki right now. Anyway, I'm working through the list of different restraints / scripted manipulations I want to add to ISOLDE (from an MD perspective, the code needed to restrain a segment to a specific location or conformation is exactly the same as the code needed to drive it there in the first place). I have working restraints to force/maintain secondary structures, force/maintain specific rotamers, restrain distances between key atoms, and restrain individual atoms to (x,y,z) points. All pretty fun to work work with, but now I want to include visualisations of the distance/xyz restraints in particular (to make it easier for the user to keep track of what's actually being restrained, for a start). Pseudobonds seem like they should be a neat fit for this job, and implementing them for atom-atom distance restraints should be very straightforward. But, it would be nice to also be able to use them for visualising restraints to arbitrary spatial points - but a Pseudobond from an atom to an arbitrary xyz point doesn't seem to be possible right now. I could of course fudge it by creating dummy Atom objects to sit at the target points, but I'm wondering how hard it would be to add the (atom - fixed coordinate) option to the Pseudobond class? While trying to look into the architecture of Pseudobonds, I ran into the crash below. Looks fairly similar to the bug from the other day when querying an empty AtomicStructure. Thanks, Tristan (loaded model 3loh) pseudbondgroup = session.models.list()[-1] pseudobonds = pseudobondgroup.pseudobonds pseudobonds. Thread 0x00007f918d421700 (most recent call first): File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/zmq/utils/garbage.py"", line 47 in run File ""/home/tic20/apps/chimerax/lib/python3.6/threading.py"", line 916 in _bootstrap_inner File ""/home/tic20/apps/chimerax/lib/python3.6/threading.py"", line 884 in _bootstrap Thread 0x00007f918dc22700 (most recent call first): File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/iostream.py"", line 207 in _really_send File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/iostream.py"", line 199 in File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/iostream.py"", line 105 in _handle_event File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/tornado/stack_context.py"", line 277 in null_wrapper File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py"", line 414 in _run_callback File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py"", line 472 in _handle_recv File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/zmq/eventloop/zmqstream.py"", line 440 in _handle_events File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/tornado/stack_context.py"", line 277 in null_wrapper File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/tornado/ioloop.py"", line 888 in start File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/zmq/eventloop/ioloop.py"", line 177 in start File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/iostream.py"", line 72 in _thread_main File ""/home/tic20/apps/chimerax/lib/python3.6/threading.py"", line 864 in run File ""/home/tic20/apps/chimerax/lib/python3.6/threading.py"", line 916 in _bootstrap_inner File ""/home/tic20/apps/chimerax/lib/python3.6/threading.py"", line 884 in _bootstrap Current thread 0x00007f9275397740 (most recent call first): File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/core/atomic/molc.py"", line 126 in get_prop File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/evaluate/compiled/__init__.py"", line 328 in get File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/cache.py"", line 121 in wrapper File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/evaluate/compiled/__init__.py"", line 345 in values File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/api/completion.py"", line 210 in _trailer_completions File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/api/completion.py"", line 169 in _get_context_completions File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/api/completion.py"", line 96 in completions File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/jedi/api/__init__.py"", line 179 in completions File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/IPython/core/completer.py"", line 1231 in _jedi_matches File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/IPython/core/completer.py"", line 1839 in _complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/IPython/core/completer.py"", line 1774 in complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/IPython/core/interactiveshell.py"", line 1958 in complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/ipkernel.py"", line 257 in do_complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/kernelbase.py"", line 434 in complete_request File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/kernelbase.py"", line 235 in dispatch_shell File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/inprocess/client.py"", line 170 in _dispatch_to_kernel File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ipykernel/inprocess/client.py"", line 110 in complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/qtconsole/frontend_widget.py"", line 774 in _complete File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/qtconsole/frontend_widget.py"", line 325 in _tab_pressed File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/qtconsole/console_widget.py"", line 1320 in _event_filter_console_keypress File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/qtconsole/frontend_widget.py"", line 381 in _event_filter_console_keypress File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/qtconsole/console_widget.py"", line 412 in eventFilter File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/chimerax/core/ui/gui.py"", line 167 in event_loop File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ChimeraX_main.py"", line 572 in init File ""/home/tic20/apps/chimerax/lib/python3.6/site-packages/ChimeraX_main.py"", line 663 in File ""/home/tic20/apps/chimerax/lib/python3.6/runpy.py"", line 85 in _run_code File ""/home/tic20/apps/chimerax/lib/python3.6/runpy.py"", line 193 in _run_module_as_main " defect closed major Core fixed goddard@… all ChimeraX