Error restoring session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-71-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/iwe28/Dieter/AR3A_iGL.cxs

Log from Sun Feb 26 14:18:57 2023UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/iwe28/Dieter/HCV/ProteinMPNN/NoAbTest/HEPC3/iGL_HEPC3_6UYG_HEPC3_0003.pdb
> format pdb

Summary of feedback from opening
/home/iwe28/Dieter/HCV/ProteinMPNN/NoAbTest/HEPC3/iGL_HEPC3_6UYG_HEPC3_0003.pdb  
---  
warnings | Ignored bad PDB record found on line 6340  
Residues missing H-bonds:  
  
Ignored bad PDB record found on line 6341  
Residue Chain Atom  
  
Ignored bad PDB record found on line 6342  
30 H N  
  
Ignored bad PDB record found on line 6343  
30 H H  
  
Ignored bad PDB record found on line 6344  
31 H N  
  
486 messages similar to the above omitted  
  
Chain information for iGL_HEPC3_6UYG_HEPC3_0003.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> select /H

1863 atoms, 1888 bonds, 126 residues, 1 model selected  

> select sel @< 5

2414 atoms, 2406 bonds, 183 residues, 1 model selected  

> select sel @< 5

3130 atoms, 3116 bonds, 240 residues, 1 model selected  
Alignment identifier is 1/H  
Alignment identifier is 1/L  
Alignment identifier is 1/A  

> set selection sel, 5A

Expected keyword "selectionColor" or "selectionWidth"  

> set sel, 5A

Expected a keyword  

> set sel, 5A

Expected a keyword  

> select sel ~/H

Expected a keyword  

> select ~/H

4456 atoms, 4528 bonds, 298 residues, 1 model selected  

> ~select sel /H

> select subtract sel /H

Expected a keyword  

> ~select /H

551 atoms, 518 bonds, 57 residues, 1 model selected  

> ~select /L

252 atoms, 238 bonds, 25 residues, 1 model selected  

> rename sel, 5A

Missing or invalid "models" argument: only initial part "sel" of atom
specifier valid  

> rename sel 5A

> hide target m

> show target m

> select /A:96

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:4-96

1356 atoms, 1379 bonds, 93 residues, 1 model selected  

> undo

> undo

> select /A:16-32,34-37,44,70,96,98

398 atoms, 398 bonds, 25 residues, 1 model selected  

> select /A:16-32,34-37,44,70,96,98

398 atoms, 398 bonds, 25 residues, 1 model selected  

> select /A:16-32,34-37,44,70,96,98

398 atoms, 398 bonds, 25 residues, 1 model selected  

> select /A:16-32,34-37,44,70,96,98

398 atoms, 398 bonds, 25 residues, 1 model selected  

> select /A:16-32,34-37,44,70,96,98

398 atoms, 398 bonds, 25 residues, 1 model selected  

> delete /H

> delete /L

> surface

> color sel red

> lighting soft

> close session

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 932, in <lambda>  
close_action.triggered.connect(lambda *, s=self, sess=session:
s.file_close_cb(sess))  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 652, in file_close_cb  
run(session, 'close session')  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 252, in reset_state  
alignment._destroy()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 603, in _destroy  
self._notify_observers(self.NOTE_DESTROYED, None)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 474, in alignment_notification  
self.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 512, in delete  
ToolInstance.delete(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete  
self.session.ui.remove_tool(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 345, in remove_tool  
self.main_window.remove_tool(tool_instance)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 725, in remove_tool  
tw._destroy()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 2049, in _destroy  
self.__toolkit.destroy()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 2189, in destroy  
sbar.destroy()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> open
> /home/iwe28/Dieter/HCV/NNK_scan/iGL/iGL_6UYG_6bkb_renum_0002_0001_0006.pdb
> format pdb

Summary of feedback from opening
/home/iwe28/Dieter/HCV/NNK_scan/iGL/iGL_6UYG_6bkb_renum_0002_0001_0006.pdb  
---  
warnings | Ignored bad PDB record found on line 6304  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 6305  
#BEGIN_POSE_ENERGIES_TABLE iGL_6UYG_6bkb_renum_0002_0001_0006.pdb  
  
Ignored bad PDB record found on line 6306  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 6307  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 6308  
pose -2247.41 299.212 1235.82 4.10507 65.1474 -55.9984 -623.008 5.33292
-69.9029 -155.517 -76.4317 -50.1244 -9.29635 69.8945 401.696 -115.129 0.92558
204.694 21.2368 -1094.76  
  
426 messages similar to the above omitted  
  
Chain information for iGL_6UYG_6bkb_renum_0002_0001_0006.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> select /H

1878 atoms, 1902 bonds, 128 residues, 1 model selected  

> select /H,L

3477 atoms, 3520 bonds, 234 residues, 1 model selected  

> select sel @< 5

3668 atoms, 3688 bonds, 253 residues, 1 model selected  

> select sel @< 5

3998 atoms, 4026 bonds, 285 residues, 1 model selected  

> ~select /H,L

191 atoms, 168 bonds, 19 residues, 1 model selected  

> color sel brown

> undo

> color sel darkbrown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel brown

> color /H lightblue

> color /L magenta

> ~select

Nothing selected  

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting soft

> lighting simple

> lighting soft

> view orient

> select /H

1878 atoms, 1902 bonds, 128 residues, 1 model selected  

> select /H,L,sel

3477 atoms, 3520 bonds, 234 residues, 1 model selected  

> show sel target ab

> hide sel target a

> ~select

Nothing selected  

> save /home/iwe28/Dieter/AR3A_iGL_5A.png width 1979 height 1191 supersample 3
> transparentBackground true

> select /H,L

3477 atoms, 3520 bonds, 234 residues, 1 model selected  

> select sel @< 8

3903 atoms, 3927 bonds, 277 residues, 1 model selected  

> ~select /H,L

426 atoms, 407 bonds, 43 residues, 1 model selected  

> ~select @<5

> select subtract @<5

Expected an objects specifier or a keyword  

> ~select @< 5

> select subtract @< 5

Expected an objects specifier or a keyword  

> ~select (select@< 5)

> select subtract (select@< 5)

Expected an objects specifier or a keyword  

> ~select [select@< 5]

> select subtract [select@< 5]

Expected an objects specifier or a keyword  

> ~select [select @< 5]

> select subtract [select @< 5]

Expected an objects specifier or a keyword  

> color sel forest green

> undo

> color sel light sea green

> select /H,L

3477 atoms, 3520 bonds, 234 residues, 1 model selected  

> select @< 5

Expected an objects specifier or a keyword  

> select sel @< 5

3668 atoms, 3688 bonds, 253 residues, 1 model selected  

> ~select /H,L

191 atoms, 168 bonds, 19 residues, 1 model selected  

> color sel lightbrown

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color sel brown

> ~select

Nothing selected  

> save /home/iwe28/Dieter/AR3A_iGL_5A_8A.png width 1979 height 1191
> supersample 3

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Alignment identifier is 1/H  
Alignment identifier is 1/L  

> select /A:16

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:16-17

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A:16

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:16-17

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A:17

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:16-17

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select /A:16

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:16

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:16

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select /A:16,19

33 atoms, 31 bonds, 2 residues, 1 model selected  

> select /A:16,19,24

47 atoms, 44 bonds, 3 residues, 1 model selected  

> select /A:16,19,24-25

54 atoms, 51 bonds, 4 residues, 1 model selected  

> select /A:16,19,24-25,32

75 atoms, 72 bonds, 5 residues, 1 model selected  

> select /A:16,19,24-25,32,40

82 atoms, 78 bonds, 6 residues, 1 model selected  

> select /A:16,19,24-25,32,40,160

106 atoms, 103 bonds, 7 residues, 1 model selected  

> color sel orange

> undo

> color sel orange

> save /home/iwe28/Dieter/AR3A_iGL_5A_8A_Mut.png width 1979 height 1191
> supersample 3

> save /home/iwe28/Dieter/AR3A_iGL.cxs

——— End of log from Sun Feb 26 14:18:57 2023 ———

opened ChimeraX session  

> open /home/iwe28/Dieter/HEPC3_iGL.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 385, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 106, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1/A'  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 385, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/manager.py", line 106, in destroy_alignment  
del self._alignments[alignment.ident]  
KeyError: '1/A'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 552, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  

> open /home/iwe28/Dieter/HCV/Keystone23/AR3A_iGL_binding.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 679, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 552, in dropEvent  
_open_dropped_file(self.session, p)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 422, in collated_open  
return func(*func_args, **func_kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 982, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 721, in restore  
self.reset()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/session.py", line 529, in reset  
sm.reset_state(container, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/tools.py", line 292, in reset_state  
tool_inst.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 507, in delete  
self.alignment.detach_viewer(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 379, in detach_viewer  
self.viewers.remove(viewer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 530.30.02
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: bluechip Computer AG
Model: bluechip BUSINESSline Workstat
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        34Gi        13Gi       697Mi        14Gi        27Gi
	Swap:         2.0Gi        44Mi       2.0Gi

Graphics:
	07:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2488] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:404c]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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: 2.5.2
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    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: 1.2.1
    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: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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: 1.3.1
    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: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 5.0.9
    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: 2.0.1
    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: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    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