id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20390 Save MD analysis GUI info in sessions alexandra.zahradnikova@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-6.8.0-111-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.12.dev202604290127 (2026-04-29 01:27:48 UTC) Description The session file that was originally saved on May 18, 2025 can be opened but cannot be saved again. The Log shows: save /home/bmcuser/Documents/2026_SKBS/Devana/hwfs1delta_Vm100_1_10_closed_V2.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/std_commands/coordset_gui.py"", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/md_crds/gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , , , , ] -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 1048, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 731, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/std_commands/coordset_gui.py"", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/md_crds/gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , , , , ] -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 133, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 144, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 68, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 1048, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 731, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( Log: UCSF ChimeraX version: 1.12.dev202604290127 (2026-04-29) © 2016-2026 Regents of the University of California. All rights reserved. > open /home/bmcuser/Documents/2026_SKBS/Devana/ions_Vm100_closed.cxs Log from Tue Apr 8 21:23:47 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > F:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs Log from Tue Apr 8 15:09:48 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > J:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs Log from Sun Apr 6 18:08:17 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918/step7_1.gro Chain information for Title #1 --- Chain | Description ? | No description available The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 2 time(s)] > hide atoms > show cartoons > select ::name=""POPC"" 95006 atoms, 94297 bonds, 709 residues, 1 model selected > show sel atoms > select clear > select /?:880 51 atoms, 46 bonds, 5 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define plane sel Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal [1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 56.0 > close #1.1 > define plane sel padding 10 Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal [1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 66.0 > close #1.1 > define plane sel padding 20 Plane 'plane' placed at [89.96647059 88.81803922 93.73862745] with normal [1.20792666e-01 2.40905629e-04 9.92677729e-01] and radius 76.0 > select /?:453 59 atoms, 58 bonds, 5 residues, 1 model selected > define plane sel padding 20 Plane 'plane' placed at [92.58932203 87.80084746 69.83813559] with normal [ 0.02232547 -0.03596117 0.99910378] and radius 90.8 > select ::name=""POPC"" 95006 atoms, 94297 bonds, 709 residues, 1 model selected > hide sel atoms > select clear > select /?:549 79 atoms, 74 bonds, 5 residues, 1 model selected > select /?:502 47 atoms, 42 bonds, 5 residues, 1 model selected > close #1.1 > define plane sel padding 20 Plane 'plane' placed at [ 86.63914894 89.11744681 100.26212766] with normal [-0.01808296 -0.06450767 0.99775336] and radius 89.5 > close #1.1 > select /?:502@ca 4 atoms, 4 residues, 1 model selected > define plane sel padding 20 Plane 'plane' placed at [87.2475 87.685 97.065 ] with normal [-0.03181081 -0.02363679 0.99921438] and radius 88.5 > select /?:477@ca 4 atoms, 4 residues, 1 model selected > close #1.1 > define plane sel padding 20 Plane 'plane' placed at [ 87.8975 87.455 105.9725] with normal [ 0.0178131 0.01799464 -0.99967939] and radius 91.0 > hide sel cartoons > undo > select clear > hide cartoons > select ::name=""CLA"" 403 atoms, 403 residues, 1 model selected > style sel ball Changed 403 atom styles > show sel atoms > color sel yellow > select clear > select ::name=""POT"" 387 atoms, 387 residues, 1 model selected > show sel target ab > style sel ball Changed 387 atom styles > color sel orange > select clear > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_1.xtc Replaced existing frames of Title #1 with 11 new frames > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_2.xtc replace false Added 11 frames to Title #1 > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_3.xtc replace false Added 11 frames to Title #1 > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_4.xtc replace false Added 11 frames to Title #1 > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_5.xtc replace false Added 11 frames to Title #1 > ui tool show ""Side View"" > save F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918/hwfs1delta_Vm100_1_5.cxs > lighting shadows false > select @@serial_number=47366 6 atoms, 6 residues, 1 model selected > style sel sphere Changed 6 atom styles > select clear > select @@serial_number=47366 6 atoms, 6 residues, 1 model selected > style sel ball Changed 6 atom styles > select clear > select @@serial_number=47237 6 atoms, 6 residues, 1 model selected > style sel sphere Changed 6 atom styles > style sel ball Changed 6 atom styles > select clear > select @@serial_number=47349 6 atoms, 6 residues, 1 model selected > select clear > select @@serial_number=47408 6 atoms, 6 residues, 1 model selected > select @@serial_number=47404 6 atoms, 6 residues, 1 model selected > select clear > select @@serial_number=47293 6 atoms, 6 residues, 1 model selected > select #1.2 1 model selected > select @@serial_number=47215 6 atoms, 6 residues, 1 model selected > show sel cartoons > select clear > show cartoons > select clear > ui tool show ""Side View"" > select ::name=""TIP3"" 419976 atoms, 279984 bonds, 139992 residues, 1 model selected > style sel stick Changed 419976 atom styles > select ::name=""TIP3"" 419976 atoms, 279984 bonds, 139992 residues, 1 model selected > style sel stick Changed 419976 atom styles > show sel atoms > select clear > show atoms > style stick Changed 567948 atom styles > select ::name=""TIP3"" 419976 atoms, 279984 bonds, 139992 residues, 1 model selected > hide sel atoms [Repeated 1 time(s)] > select clear > hide atoms > show cartoons > select ::name=""CLA"" 403 atoms, 403 residues, 1 model selected > style sel ball Changed 403 atom styles > show sel atoms > select ::name=""POT"" 387 atoms, 387 residues, 1 model selected > show sel atoms > style sel ball Changed 387 atom styles > select clear > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_6.xtc replace false Added 11 frames to Title #1 > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_7.xtc replace false Added 11 frames to Title #1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 2 time(s)] > save F:/Simulations_F/Devana_F/hwfs1_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918/hwfs1delta_Vm100_1_5.cxs The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 2 time(s)] > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918\step7_8.xtc replace false Added 11 frames to Title #1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. [Repeated 2 time(s)] > open F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc > replace false No such file/path: F:\Simulations_F\Devana_F\hwfs1_gromJob_737764\hwfs1delta_charmm- gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc > open > F:\Simulations_F\Devana_F\hwfs1_closed_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_9.xtc > replace false Added 11 frames to Title #1 > open > F:\Simulations_F\Devana_F\hwfs1_closed_gromJob_737764\hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982\step7_10.xtc > replace false Added 11 frames to Title #1 > save > F:/Simulations_F/Devana_F/hwfs1_closed_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm100_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs ——— End of log from Sun Apr 6 18:08:17 2025 ——— opened ChimeraX session > select ::name=""CLA"" 403 atoms, 403 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define centroid sel radius 10 Centroid 'centroid' placed at [85.24901131 86.62201386 93.5061334 ] > close #1.3 > select clear > select @@serial_number=47570 6 atoms, 6 residues, 1 model selected > select clear > select @@serial_number=47570 6 atoms, 6 residues, 1 model selected > select subtract /?:605 5 atoms, 5 residues, 1 model selected > style sel sphere Changed 5 atom styles > ui tool show ""Side View"" > select clear > select add @@serial_number=47906 6 atoms, 6 residues, 1 model selected > style sel sphere Changed 6 atom styles > style sel ball Changed 6 atom styles > select add @@serial_number=47570 12 atoms, 12 residues, 1 model selected > style sel ball Changed 12 atom styles > select @@serial_number=47237 6 atoms, 6 residues, 1 model selected > select clear [Repeated 1 time(s)] > select : 1654 4 atoms, 2 bonds, 2 residues, 1 model selected > style sel sphere Changed 4 atom styles > select @@serial_number=47408 6 atoms, 6 residues, 1 model selected > select : 1825 4 atoms, 2 bonds, 2 residues, 1 model selected > style sel sphere Changed 4 atom styles > select : 1722 4 atoms, 2 bonds, 2 residues, 1 model selected > style sel sphere Changed 4 atom styles > select clear > save > J:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/hwfs1delta_Vm100_1_10.cxs ——— End of log from Tue Apr 8 15:09:48 2025 ——— opened ChimeraX session > save > F:/Simulations_F/Devana_F/hWFS1delta_closed_gromJob_737764/hwfs1delta_charmm- > gui-2837532676_gromacs_Vm200_gromJob_740764_743918_744982/ions.cxs ——— End of log from Tue Apr 8 21:23:47 2025 ——— > view name session-start opened ChimeraX session > set bgColor white > ui tool show ""Side View"" > select ::name=""TIP3"" 419976 atoms, 279984 bonds, 139992 residues, 1 model selected > show sel atoms > turn z 45 > turn z -45 > turn y -45 > turn x -1 > turn x 1 [Repeated 1 time(s)] > turn y -1 [Repeated 1 time(s)] > turn y 1 [Repeated 1 time(s)] > turn x 5 > turn x -5 > turn z -5 > turn z 5 [Repeated 1 time(s)] > turn z -1 [Repeated 2 time(s)] > turn z .5 > hide sel atoms > select ::name=""POT"" 387 atoms, 387 residues, 1 model selected > style sel ball Changed 387 atom styles > select protein 52176 atoms, 52832 bonds, 3232 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark gray > help help:user > transparecy cartoons 50 Unknown command: transparecy cartoons 50 > transparency cartoons 50 Missing or invalid ""percent"" argument: Expected a number > transparency sel 50 > transparency 50 ribbons > transparency 0 ribbons > hide sel cartoons > select ::name=""POT"" 387 atoms, 387 residues, 1 model selected > style sel sphere Changed 387 atom styles > color sel orange > select ::name=""TIP3"" 419976 atoms, 279984 bonds, 139992 residues, 1 model selected > select ::name=""CLA"" 403 atoms, 403 residues, 1 model selected > style sel sphere Changed 403 atom styles > color sel cornflower blue > select clear > select @@serial_number=47544 6 atoms, 6 residues, 1 model selected > select clear > save > /home/bmcuser/Documents/2026_SKBS/Devana/hwfs1delta_Vm100_1_10_closed_V2.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/std_commands/coordset_gui.py"", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/md_crds/gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , , , , ] -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 1048, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 731, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 322, in process data = sm.take_snapshot(obj, session, self.state_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/std_commands/coordset_gui.py"", line 112, in take_snapshot from chimerax.md_crds.gui import get_session_info ImportError: cannot import name 'get_session_info' from 'chimerax.md_crds.gui' (/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/md_crds/gui.py) The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 297, in discovery self.processed[key] = self.process(obj, parents) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 329, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> [, , , , , , , ] -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 133, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 144, in show_save_file_dialog _dlg.display(session, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/dialog.py"", line 68, in display run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/save_command/cmd.py"", line 101, in provider_save saver_info.save(session, path, **provider_kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core_formats/__init__.py"", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 1048, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 731, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> ValueError: error processing: 'tools' -> [, , , , , , , ] -> : Error while saving session data for 'tools' -> [, , , , , , , ] -> File ""/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- packages/chimerax/core/session.py"", line 301, in discovery raise ValueError( See log for complete Python traceback. OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3 OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits) OpenGL vendor: Mesa Python: 3.11.13 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP= XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:10.0 Manufacturer: Micro-Star International Co., Ltd. Model: Desktop MPG Z890 Infinite X3 AI 2nd OS: Ubuntu 22.04 Architecture: 64bit ELF Virtual Machine: none CPU: 20 Intel(R) Core(TM) Ultra 7 265KF Cache Size: 30720 KB Memory: total used free shared buff/cache available Mem: 62Gi 9.5Gi 44Gi 152Mi 8.2Gi 51Gi Swap: 2.0Gi 979Mi 1.0Gi Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2c05] (rev a1) Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5310] Kernel modules: nvidiafb, nouveau Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2026.4.22 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202604290127 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.4 ChimeraX-LightingGUI: 1.0 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.5 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.3 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 DateTime: 6.0 debugpy: 1.8.20 decorator: 5.2.1 distro: 1.9.0 docutils: 0.21.2 et_xmlfile: 2.0.0 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.20.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.4.0 OpenMM-CUDA-12: 8.4.0 openpyxl: 3.1.5 openvr: 1.26.701 packaging: 25.0 pandas: 3.0.2 ParmEd: 4.2.2 parso: 0.8.6 pathlib: 1.0.1 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.9.6 plotly: 6.7.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.3 pydantic-settings: 2.14.0 pydantic_core: 2.46.3 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pytz: 2026.1.post1 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.1 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.46.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 zope.interface: 8.4 }}} " defect closed normal Sessions duplicate all ChimeraX