id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4418 Shell sluggish Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14 ChimeraX Version: 1.2.dev202103230345 (2021-03-23 03:45:30 UTC) Description Bug found while trying to debug another bug :) Every time I enter a line in the shell, there's a hang of about 5 seconds and an error gets raised in the log. While there is no error message in the shell itself, it looks like it's at least partially non-functional: a = 1 a (returns None) m = session.isolde.selected_model m.atoms.selected=True (successfully selects atoms) Log: > alias preview_toolshed toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu; toolshed reload available > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu; > toolshed reload available > alias st isolde step $* > alias aw isolde add water $* > alias awsf isolde add water sim false > alias al isolde add ligand $* > alias so setattr sel atoms occupancy $* UCSF ChimeraX version: 1.2.dev202103230345 (2021-03-23) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.2.dev15-cp38-cp38-manylinux_2_17_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /home/tic20/.cache/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.2.dev15-cp38-cp38-manylinux_2_17_x86_64.whl Requirement already satisfied: ChimeraX-AtomicLibrary~=2.1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.dev15) (2.1) Requirement already satisfied: ChimeraX-Clipper~=0.15.0 in /home/tic20/.local/share/ChimeraX/1.2/site-packages (from ChimeraX- ISOLDE==1.2.dev15) (0.15.0) Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.dev15) (1.0) Requirement already satisfied: ChimeraX-Core~=1.2.dev202103230345 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.dev15) (1.2.dev202103230345) Requirement already satisfied: ChimeraX-Atomic~=1.12.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-ISOLDE==1.2.dev15) (1.12) Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-PDB~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.3) Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.3) Requirement already satisfied: ChimeraX-Graphics~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0) Requirement already satisfied: ChimeraX-Geometry~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.1) Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.0) Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.1) Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.0) Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.4) Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.5) Requirement already satisfied: ChimeraX-IO~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX- Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0.1) Requirement already satisfied: ChimeraX-Surface~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.0) Requirement already satisfied: ChimeraX-UI~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (1.7) Requirement already satisfied: ChimeraX-MapData~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.3) Requirement already satisfied: ChimeraX-Map~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX- Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0.2) Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.1) Requirement already satisfied: ChimeraX-MapFit~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX- Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX- ISOLDE==1.2.dev15) (2.0) Requirement already satisfied: ChimeraX-Dssp~=2.0 in /run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX- Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0) Installing collected packages: ChimeraX-ISOLDE Attempting uninstall: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.2.dev14 Uninstalling ChimeraX-ISOLDE-1.2.dev14: Successfully uninstalled ChimeraX-ISOLDE-1.2.dev14 Successfully installed ChimeraX-ISOLDE-1.2.dev15 > isolde demo crystal_intro > set selectionWidth 4 /home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/validation/ramaplot.py:347: MatplotlibDeprecationWarning: shading='flat' when X and Y have the same dimensions as C is deprecated since 3.3. Either specify the corners of the quadrilaterals with X and Y, or pass shading='auto', 'nearest' or 'gouraud', or set rcParams['pcolor.shading']. This will become an error two minor releases later. pcolor_plot = self.axes.pcolormesh(*grid, logvalues, cmap = 'Greys') before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.2/A | predicted microcompartment protein Done loading forcefield WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing ""(dataset) FOBS, SIGFOBS"". Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at level 0.303, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at level -0.0572,0.0572, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723, shown at level 0.602, step 1, values float32 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723, shown at level 0.366, step 1, values float32 Loaded crystallographic demo: PDB ID 3io0 > select clear Updating bulk solvent parameters... > select clear Updating bulk solvent parameters... Updating bulk solvent parameters... > usage isolde Subcommands are: * isolde add ligand * isolde add water * isolde adjust distances * isolde adjust torsions * isolde cisflip * isolde demo * isolde ignore * isolde ~ignore * isolde jumpto * isolde pepflip * isolde release distances * isolde release torsions * isolde remote rest info * isolde remote rest start * isolde remote rest stop * isolde remote xmlrpc * isolde replace ligand * isolde report * isolde reset forcefield * isolde restrain distances * isolde restrain ligands * isolde restrain single distance * isolde restrain torsions * isolde set * isolde sim * isolde start * isolde stepto * isolde tutorial > isolde sim start #1 Updating bulk solvent parameters... > select clear > isolde sim start #1 Updating bulk solvent parameters... Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/cmd_line/tool.py"", line 275, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/cmd.py"", line 88, in isolde_sim isolde.start_sim() File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2727, in start_sim sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel, File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 576, in __init__ mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode) File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 968, in expand_mobile_selection sel = selections.expand_selection_along_chains(core_atoms, File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/selections.py"", line 40, in expand_selection_along_chains raise TypeError('Selected atoms must all be in the same model!') TypeError: Selected atoms must all be in the same model! TypeError: Selected atoms must all be in the same model! File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/selections.py"", line 40, in expand_selection_along_chains raise TypeError('Selected atoms must all be in the same model!') See log for complete Python traceback. > isolde sim start #1 > select clear > isolde report > isolde set timeStepsPerGuiUpdate 50 > isolde set timeStepsPerGuiUpdate 100 > isolde set timeStepsPerGuiUpdate 20 Updating bulk solvent parameters... > select #1 3348 atoms, 3371 bonds, 229 residues, 30 models selected > select clear > isolde report > isolde set timeStepsPerGuiUpdate 50 > usage isolde rep isolde report [report] [interval an integer] — Report the current simulation performance to the status bar report: true or false > isolde report false > isolde report interval 50 Updating bulk solvent parameters... Updating bulk solvent parameters... > select clear Updating bulk solvent parameters... > isolde restrain distances #1 > isolde restrain torsions #1 > select #1 3348 atoms, 3371 bonds, 229 residues, 30 models selected Updating bulk solvent parameters... > select #1 3348 atoms, 3371 bonds, 229 residues, 30 models selected > select clear Updating bulk solvent parameters... > select #1 3348 atoms, 3371 bonds, 229 residues, 30 models selected Updating bulk solvent parameters... > select clear > isolde sim start #1 Updating bulk solvent parameters... Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/cmd_line/tool.py"", line 275, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/cmd.py"", line 88, in isolde_sim isolde.start_sim() File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2727, in start_sim sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel, File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 576, in __init__ mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode) File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 968, in expand_mobile_selection sel = selections.expand_selection_along_chains(core_atoms, File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/selections.py"", line 40, in expand_selection_along_chains raise TypeError('Selected atoms must all be in the same model!') TypeError: Selected atoms must all be in the same model! TypeError: Selected atoms must all be in the same model! File ""/home/tic20/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/selections.py"", line 40, in expand_selection_along_chains raise TypeError('Selected atoms must all be in the same model!') See log for complete Python traceback. > select clear > ui tool show Shell /opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") ERROR:tornado.general:Uncaught exception in ZMQStream callback Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket ERROR:tornado.general:Uncaught exception in zmqstream callback Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 451, in _handle_events self._handle_recv() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 480, in _handle_recv self._run_callback(callback, msg) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(150, 1) handle: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/asyncio/events.py"", line 81, in _run self._context.run(self._callback, *self._args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/tornado/platform/asyncio.py"", line 189, in _handle_events handler_func(fileobj, events) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 451, in _handle_events self._handle_recv() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 480, in _handle_recv self._run_callback(callback, msg) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/zmq/eventloop/zmqstream.py"", line 434, in _run_callback callback(*args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 120, in _handle_event event_f() File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 214, in self.schedule(lambda : self._really_send(*args, **kwargs)) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 222, in _really_send self.socket.send_multipart(msg, *args, **kwargs) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/socket.py"", line 62, in send_multipart self.message_sent += 1 File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 604, in __set__ self.set(obj, value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 593, in set obj._notify_trait(self.name, old_value, new_value) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1217, in _notify_trait self.notify_change(Bunch( File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1227, in notify_change return self._notify_observers(change) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/traitlets/traitlets.py"", line 1264, in _notify_observers c(event) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/inprocess/ipkernel.py"", line 130, in _io_dispatch ident, msg = self.session.recv(self.iopub_socket, copy=False) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/jupyter_client/session.py"", line 807, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site- packages/ipykernel/iostream.py"", line 246, in __getattr__ warnings.warn(""Accessing zmq Socket attribute %s on BackgroundSocket"" % attr, DeprecationWarning: Accessing zmq Socket attribute recv_multipart on BackgroundSocket OpenGL version: 3.3.0 NVIDIA 455.32.00 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 10G 32G 370M 20G 51G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia Locale: ('en_GB', 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.4 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.12 ChimeraX-AtomicLibrary: 2.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202103230345 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.dev15 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.3 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}} " defect closed normal General Controls can't reproduce chimera-programmers all ChimeraX