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Opened 4 years ago
Closed 4 years ago
#6606 closed defect (duplicate)
'Sequence' object has no attribute 'structure'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.13.0-39-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/pierre/Téléchargements/7dte.pdb
7dte.pdb title:
Sars-cov-2 RDRP catalytic complex with T33-1 RNA [more info...]
Chain information for 7dte.pdb #1
---
Chain | Description
A | NSP12
B D | NSP8-1
C | NSP7
F | RNA (57-mer)
G | RNA (33-mer)
Non-standard residues in 7dte.pdb #1
---
ZN — zinc ion
> show atoms
> style stick
Changed 12130 atom styles
> style ball
Changed 12130 atom styles
> show cartoons
> hide atoms
> ui tool show "Modeller Comparative"
No alignments chosen for modeling
> ui tool show "Blast Protein"
> toolshed show
> ui tool show "Show Sequence Viewer"
> toolshed show
> ui tool show Toolbar
> select sequence
> SKDSNFLNRVRGSIVNARIEPCSSGLSTDVVFRAFDICNYKAKVAGIGKYYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQNSEVLKAILVKYGCCDVTYFENKLWFDFVENPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIEWPLTEYDFTDYKVQLFEKYFKYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNAFLDLRTSCFSVAALTTGLTFQTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFNKFGKARVYYESMSYQEQDELFAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMPNMCRIFASLILARKHGTCCTTRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYAFLNKHFSMMILSDDGVVCYNSDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAYPLTKHEDIEYQNVFWVYLQYIEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQ
Nothing selected
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show Matchmaker
> ui tool show Matchmaker
> matchmaker # to #1
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> sequence chain /A
Destroying pre-existing alignment with identifier 1/A
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/show_sequences/tool.py", line 64, in show_seqs
run(self.session, "seq chain %s" % " ".join([chain.atomspec for chain in
chains]))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/cmd.py", line 141, in seqalign_chain
auto_associate=None, intrinsic=True)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 220, in new_alignment
self.destroy_alignment(self._alignments[identify_as])
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 109, in destroy_alignment
alignment._destroy()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 587, in _destroy
self._notify_observers(self.NOTE_DESTROYED, None)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 636, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 464, in alignment_notification
self.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 502, in delete
ToolInstance.delete(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 321, in remove_tool
self.main_window.remove_tool(tool_instance)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 706, in remove_tool
tw._destroy()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1974, in _destroy
self.__toolkit.destroy()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2109, in destroy
sbar.destroy()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/statusbar.py", line 50, in destroy
v.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 390, in delete
self.make_current()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 430, in make_current
return self._opengl_context.make_current()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 128, in make_current
qc = self._initialize_context()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 149, 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/python3.7/site-
packages/chimerax/graphics/opengl.py", line 149, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> ui tool show Matchmaker
> ui tool show "Blast Protein"
> ui tool show "Modeller Comparative"
No alignments chosen for modeling
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2807, in _update_current_size
int(100.0 * window_width / screen_width),
ZeroDivisionError: float division by zero
Error processing trigger "resized":
ZeroDivisionError: float division by zero
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2807, in _update_current_size
int(100.0 * window_width / screen_width),
See log for complete Python traceback.
> sequence chain #1/A
Alignment identifier is 1/A
> ui tool show "Modeller Comparative"
> save "/home/pierre/Téléchargements/test alignement seq sars2" format aln
> alignment 1/A
> save "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS.cxs"
> ui tool show "Modeller Comparative"
> ui tool show "Fit to Segments"
> ui tool show Matchmaker
> open /home/pierre/Téléchargements/7ed5.pdb
7ed5.pdb title:
A dual mechanism of action of At-527 against sars-cov-2 polymerase [more
info...]
Chain information for 7ed5.pdb #2
---
Chain | Description
A | RNA-directed RNA polymerase
B D | NSP8
C | NSP7
I | RNA (5'-
R(P*GP*CP*up*ap*up*GP*up*GP*ap*GP*ap*up*up*ap*ap*GP*up*up*ap*U*(AT9) )-3')
J | RNA (5'-
R(P*CP*CP*CP*CP*ap*up*ap*ap*CP*up*up*ap*ap*up*CP*up*CP*ap*CP*ap*up*ap
*GP*C)-3')
Non-standard residues in 7ed5.pdb #2
---
AT9 —
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogenphosphate (At-9010)
MG — magnesium ion
ZN — zinc ion
> style sel stick
Changed 7473 atom styles
> show sel atoms
> hide sel atoms
> hide sel cartoons
> style sel stick
Changed 7473 atom styles
> hide sel atoms
> hide #!2 models
> show sel atoms
> show sel cartoons
> hide sel atoms
> show #!2 models
> hide #!1 models
> select #2
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#2) with 7dte.pdb, chain A (#1), sequence
alignment score = 4536.3
RMSD between 914 pruned atom pairs is 0.534 angstroms; (across all 926 pairs:
0.655)
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#2) with 7dte.pdb, chain A (#1), sequence
alignment score = 4536.3
RMSD between 914 pruned atom pairs is 0.534 angstroms; (across all 926 pairs:
0.655)
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#2) with 7dte.pdb, chain A (#1), sequence
alignment score = 4536.3
RMSD between 914 pruned atom pairs is 0.534 angstroms; (across all 926 pairs:
0.655)
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> show sel atoms
> close session
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 914, in <lambda>
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 633, in file_close_cb
run(session, 'close session')
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/std_commands/close.py", line 60, in close_session
session.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open /home/pierre/Téléchargements/7ed5.pdb
7ed5.pdb title:
A dual mechanism of action of At-527 against sars-cov-2 polymerase [more
info...]
Chain information for 7ed5.pdb #1
---
Chain | Description
A | RNA-directed RNA polymerase
B D | NSP8
C | NSP7
I | RNA (5'-
R(P*GP*CP*up*ap*up*GP*up*GP*ap*GP*ap*up*up*ap*ap*GP*up*up*ap*U*(AT9) )-3')
J | RNA (5'-
R(P*CP*CP*CP*CP*ap*up*ap*ap*CP*up*up*ap*ap*up*CP*up*CP*ap*CP*ap*up*ap
*GP*C)-3')
Non-standard residues in 7ed5.pdb #1
---
AT9 —
[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-
oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogenphosphate (At-9010)
MG — magnesium ion
ZN — zinc ion
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> ~select #1
Nothing selected
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> show sel atoms
> show sel cartoons
> show sel atoms
> select ::name="ZN"
2 atoms, 2 residues, 1 model selected
> select ::name="MG"
3 atoms, 3 residues, 1 model selected
> select ::name="ZN"
2 atoms, 2 residues, 1 model selected
> select ::name="AT9"
86 atoms, 92 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> color sel magenta
> color sel magenta
> color sel magenta
> color sel magenta
> color sel magenta
> save "/home/pierre/ownCloud/Construction model/NSP12_SARS2_AT9_NIRAN.cxs"
> open /home/pierre/Téléchargements/MERS_NSP12_current_best_1.pdb
Chain information for MERS_NSP12_current_best_1.pdb #2
---
Chain | Description
A | No description available
> ui tool show "Modeller Comparative"
> select #2
7508 atoms, 7700 bonds, 933 residues, 1 model selected
> select #1
11402 atoms, 11732 bonds, 18 pseudobonds, 1354 residues, 2 models selected
> ui tool show "Modeller Comparative"
> modeller comparative 1/A:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [28-239] RMSD: 1.131
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [37-39] RMSD: 2.420
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [64-68] RMSD: 2.673
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [107-109] RMSD: 0.816
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [121-122] RMSD: 0.637
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [165] RMSD: 3.700
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [187] RMSD: 1.866
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [186-189] RMSD: 0.997
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [31-43] RMSD: 2.173
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [48-54] RMSD: 1.434
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [61-69] RMSD: 1.859
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [74-81] RMSD: 0.968
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [671-675] RMSD: 0.906
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [697-702] RMSD: 1.930
Alignment identifier is 1/A
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [242-244] RMSD: 0.827
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [242] RMSD: 0.450
> color sel yellow
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [250] RMSD: 0.818
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [251-260] RMSD: 0.685
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [262-267] RMSD: 0.511
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [31-41] RMSD: 2.373
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [42-58] RMSD: 1.095
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [91-93] RMSD: 0.769
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [64-67] RMSD: 2.754
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [63-67] RMSD: 2.299
> color sel yellow
> open /home/pierre/Téléchargements/7cyq.pdb
7cyq.pdb title:
Cryo-em structure of an extended sars-cov-2 replication and transcription
complex reveals an intermediate state In cap synthesis [more info...]
Chain information for 7cyq.pdb #3
---
Chain | Description
A | RNA-directed RNA polymerase
B D | non-structural protein 8
C | non-structural protein 7
E F | helicase
G | non-structural protein 9
I | primer
J | template
Non-standard residues in 7cyq.pdb #3
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
> save "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS.cxs"
> ui tool show Matchmaker
> matchmaker #2#!3 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Matchmaker 7ed5.pdb, chain A (#1) with 7cyq.pdb, chain A (#3), sequence
alignment score = 4626.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7ed5.pdb #1/A, 7cyq.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 909 pruned atom pairs is 0.528 angstroms; (across all 926 pairs:
0.663)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> select #3
21841 atoms, 22412 bonds, 44 pseudobonds, 2717 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> matchmaker #2#!3 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Matchmaker 7ed5.pdb, chain A (#1) with 7cyq.pdb, chain A (#3), sequence
alignment score = 4626.9
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: 7ed5.pdb #1/A, 7cyq.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 909 pruned atom pairs is 0.528 angstroms; (across all 926 pairs:
0.663)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> matchmaker #2#!3 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7ed5.pdb, chain A (#1) with MERS_NSP12_current_best_1.pdb, chain A
(#2), sequence alignment score = 3478.5
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: 7ed5.pdb #1/A,
MERS_NSP12_current_best_1.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 666 pruned atom pairs is 0.923 angstroms; (across all 924 pairs:
3.800)
Matchmaker 7ed5.pdb, chain A (#1) with 7cyq.pdb, chain A (#3), sequence
alignment score = 4626.9
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: 7ed5.pdb #1/A, 7cyq.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 909 pruned atom pairs is 0.528 angstroms; (across all 926 pairs:
0.663)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> select ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> select ::name="GDP"
28 atoms, 30 bonds, 1 residue, 1 model selected
> show sel atoms
> save "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs"
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [62-70] RMSD: 1.861
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [25-40] RMSD: 3.291
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [41-42] RMSD: 1.432
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [48-49] RMSD: 1.059
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [61-68] RMSD: 1.986
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [72] RMSD: 0.896
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [73] RMSD: 0.965
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [74-76] RMSD: 1.152
Seqview [ID: 1] region 7ed5.pdb, chain A..MERS_NSP12_current_best_1.pdb, chain
A [61-76] RMSD: 1.489
> show sel atoms
> style sel stick
Changed 239 atom styles
> ui tool show Rotamers
> swapaa interactive sel ALA rotLib Dunbrack
> swapaa sel ALA rotLib Dunbrack
Using Dunbrack library
Swapping 7ed5.pdb #1/A ASP 36 to ALA
Swapping 7ed5.pdb #1/A ILE 37 to ALA
Swapping 7ed5.pdb #1/A TYR 38 to ALA
Swapping 7ed5.pdb #1/A ASN 39 to ALA
Swapping 7ed5.pdb #1/A ASP 40 to ALA
Swapping 7ed5.pdb #1/A LYS 41 to ALA
Swapping 7ed5.pdb #1/A VAL 42 to ALA
Swapping 7ed5.pdb #1/A ALA 43 to ALA
Swapping 7ed5.pdb #1/A GLY 44 to ALA
Swapping 7ed5.pdb #1/A PHE 45 to ALA
Swapping 7ed5.pdb #1/A ALA 46 to ALA
Swapping 7ed5.pdb #1/A LYS 47 to ALA
Swapping 7ed5.pdb #1/A PHE 48 to ALA
Swapping 7ed5.pdb #1/A LEU 49 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ASP 36 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ILE 37 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A CYS 38 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ASN 39 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A TYR 40 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A LYS 41 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ALA 42 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A LYS 43 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A VAL 44 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ALA 45 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A GLY 46 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A ILE 47 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A GLY 48 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A LYS 49 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A TYR 50 to ALA
Swapping MERS_NSP12_current_best_1.pdb #2/A TYR 51 to ALA
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/alignment_headers/rmsd.py", line 202, in _atomic_changes_cb
if chain.structure in changes.modified_structures():
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "changes":
AttributeError: 'Sequence' object has no attribute 'structure'
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 69, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> undo
Undo failed, probably because structures have been modified.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer
cxcmd(session, topic)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
> open "/home/pierre/ownCloud/Construction model/Test 1 model NSP12
> SARS2_VS_MERS_vs_7CYQ.cxs" format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/core/session.py", line 649, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-packages/chimerax/ui/gui.py",
line 629, in customEvent
func(*args, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer
cxcmd(session, topic)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 691, in restore
self.reset()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/session.py", line 502, in reset
sm.reset_state(container, self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/tools.py", line 292, in reset_state
tool_inst.delete()
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/seq-
view/tool.py", line 497, in delete
self.alignment.detach_viewer(self)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, 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/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 367, in detach_viewer
self.viewers.remove(viewer)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 510.54
OpenGL renderer: Quadro RTX 3000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7550
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz
Cache Size: 16384 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 13Gi 7.2Gi 200Mi 10Gi 17Gi
Swap: 30Gi 3.0Mi 30Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics [8086:9bc4] (rev 05)
DeviceName: Onboard - Video
Subsystem: Dell Device [1028:09c3]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
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: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
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: 0.29.20
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: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
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: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 'Sequence' object has no attribute 'structure' |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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