Opened 18 months ago

Closed 18 months ago

#15122 closed defect (can't reproduce)

Seq viewer: region not in regions list

Reported by: chimerax-bug-report@… 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:        macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/aury/Desktop/Déjà ranger/Post-Doc (Pr Vincent Burrus)/Système
> d'anti-restriction (hde)/Analyse bio-informatique/prédiction d'interaction
> protéine/Hde1-Hde2-Hde3/test_01ceb_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb"

Chain information for
test_01ceb_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> select /A:1-322

2477 atoms, 2527 bonds, 322 residues, 1 model selected  

> color sel bychain

> undo

Alignment identifier is 1/A  

> log metadata #1

The model has no metadata

> log chains #1

Chain information for
test_01ceb_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> color sel red

> select /B:1-425

3354 atoms, 3406 bonds, 425 residues, 1 model selected  

> color sel yellow

> select /C:1-598

4530 atoms, 4596 bonds, 598 residues, 1 model selected  

> select /C:1-598

4530 atoms, 4596 bonds, 598 residues, 1 model selected  

> color sel cyan

> select /A:1-322

2477 atoms, 2527 bonds, 322 residues, 1 model selected  

> sequence chain #1/A

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

> sequence chain #1/A

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

> sequence chain #1/A

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

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #1/C

Alignment identifier is 1/C  

> select
> /C:3-18,52-68,79-99,101-117,129-146,149-165,168-183,187-209,294-308,312-314,319-332,352-381,399-404,431-434,443-459,490-496,506-519,538-550,564-567,578-597

2250 atoms, 2262 bonds, 292 residues, 1 model selected  

> interfaces select /A & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

7 contacting residues  

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> show sel cartoons

> style sel ball

Changed 249 atom styles  

> style sel stick

Changed 249 atom styles  

> show sel atoms

> set bgColor white

> set bgColor black

> lighting simple

> color sel blue

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> label sel attribute label_one_letter_code

> undo

[Repeated 2 time(s)]

> color sel white

> label sel attribute label_one_letter_code

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> style sel ball

Changed 249 atom styles  

> style sel stick

Changed 249 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> cartoon sel

> style sel ball

Changed 249 atom styles  

> show sel target ab

> undo

> show sel cartoons

> show sel atoms

> style sel stick

Changed 249 atom styles  

> style sel ringFill thick

Changed 30 residue ring styles  

> undo

> style sel sphere

Changed 249 atom styles  

> undo

No Surface models open  

> label sel attribute label_specifier

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> label sel attribute label_one_letter_code

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> color sel light gray

> label sel attribute label_one_letter_code

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> style sel ball

Changed 280 atom styles  

> style sel stick

Changed 280 atom styles  

> undo

[Repeated 2 time(s)]

> select /A:1-322

2477 atoms, 2527 bonds, 322 residues, 1 model selected  

> color sel white

> select /B:1-425

3354 atoms, 3406 bonds, 425 residues, 1 model selected  

> color sel white

> select /C:1-598

4530 atoms, 4596 bonds, 598 residues, 1 model selected  

> color sel white

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> color sel red

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> style sel ball

Changed 280 atom styles  

> show sel cartoons

> cartoon sel

> show sel target ab

> style sel stick

Changed 280 atom styles  

> color sel medium blue

> hbonds sel reveal true

40 hydrogen bonds found  

> undo

> hbonds sel reveal true

40 hydrogen bonds found  

> hide sel surfaces

> color sel blue

> ~hbonds

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select /A

2477 atoms, 2527 bonds, 322 residues, 1 model selected  

> ui tool show "Color Actions"

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> color bfactor sel

2477 atoms, 322 residues, atom bfactor range 39.9 to 97  

> undo

> color sel bypolymer

> undo

> rainbow sel

> undo

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> undo

> style sel sphere

Changed 2477 atom styles  

> style sel ball

Changed 2477 atom styles  
No Surface models open  

> select

10361 atoms, 10529 bonds, 1345 residues, 2 models selected  

> color (#!1 & sel) byhetero

> transparency (#!1 & sel) 20

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> style sel ball

Changed 280 atom styles  

> view sel

> interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

19 contacting residues  

> color (#!1 & sel) cornflower blue

> style sel ball

Changed 149 atom styles  

> undo

[Repeated 1 time(s)]

> color (#!1 & sel) blue

> style sel stick

Changed 149 atom styles  

> style sel ball

Changed 149 atom styles  

> style (#!1 & sel) stick

Changed 149 atom styles  

> style (#!1 & sel) sphere

Changed 149 atom styles  

> style sel sphere

Changed 149 atom styles  

> style sel ball

Changed 149 atom styles  

> show (#!1 & sel) target ab

> color (#!1 & sel) byhetero

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> color (#!1 & sel) byhetero

> color (#!1 & sel) cyan

> color (#!1 & sel) byhetero

> interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

19 contacting residues  

> color (#!1 & sel) cyan

> color (#!1 & sel) byhetero

> style sel stick

Changed 149 atom styles  

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> style sel stick

Changed 280 atom styles  

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> style sel stick

Changed 249 atom styles  

> ui tool show "Color Actions"

> color sel tomato

> color sel coral

> color sel yellow

> color sel orchid

> color sel pale green

> color sel indigo

> color sel deep sky blue

> color sel gold

> color sel green yellow

> color sel brown

> color sel byhetero

> interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

21 contacting residues  

> surface (#!1 & sel)

> undo

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> color (#!1 & sel) byhetero

> interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

19 contacting residues  

> interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

21 contacting residues  

> surface hidePatches (#!1 & sel)

> show (#!1 & sel) target ab

> color (#!1 & sel) magenta

> style sel stick

Changed 178 atom styles  

> show sel surfaces

[Repeated 1 time(s)]

> hide sel surfaces

> color (#!1 & sel) byhetero

> select down

178 atoms, 21 residues, 2 models selected  

> select clear

> interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

21 contacting residues  

> label (#!1 & sel) attribute label_one_letter_code

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel ladder

[Repeated 1 time(s)]

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> show (#!1 & sel-residues & sidechain) target ab

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
test_01ceb_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface #1.3: minimum, -19.95, mean -3.52, maximum 10.42  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic sel

Coulombic values for
test_01ceb_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb_B
SES surface #1.3: minimum, -19.95, mean -3.52, maximum 10.42  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

> hide sel surfaces

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> select
> /B:6-9,28-30,55-57,60-75,87-113,115-125,127-136,140-146,163-196,204-219,221-223,225-243,254-265,268-276,281-292,294-296,350-352,355-360

1628 atoms, 1636 bonds, 198 residues, 1 model selected  

> ui tool show "Selection Inspector"

> help help:user/tools/inspector.html

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> ui mousemode right zoom

> ui mousemode right "link markers"

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> select
> /C:3-18,52-68,79-99,101-117,129-146,149-165,168-183,187-209,294-308,312-314,319-332,352-381,399-404,431-434,443-459,490-496,506-519,538-550,564-567,578-597

2250 atoms, 2262 bonds, 292 residues, 1 model selected  

> select ligand

Nothing selected  

> select sequence MM

32 atoms, 30 bonds, 4 residues, 1 model selected  

> hbonds sel reveal true

4 hydrogen bonds found  

> ~hbonds

> select sidechain

6326 atoms, 5095 bonds, 1345 residues, 1 model selected  

> select disulfide

Nothing selected  

> select protein

10361 atoms, 10529 bonds, 1345 residues, 1 model selected  

> select thiol

9 atoms, 9 residues, 1 model selected  

> select sel @< 5

7884 atoms, 172 bonds, 1023 residues, 1 model selected  

> select clear

> select
> /B:6-9,28-30,55-57,60-75,87-113,115-125,127-136,140-146,163-196,204-219,221-223,225-243,254-265,268-276,281-292,294-296,350-352,355-360

1628 atoms, 1636 bonds, 198 residues, 1 model selected  

> ui dockable false "Sequence Viewer"

> ui tool show Contacts

> contacts ignoreHiddenModels true

7497 contacts  

> undo

> ui tool show Contacts

> contacts ignoreHiddenModels true makePseudobonds false

7497 contacts  

> contacts ignoreHiddenModels true makePseudobonds false

7497 contacts  

> ui tool show H-Bonds

> hbonds twoColors true reveal true

971 hydrogen bonds found  
528 strict hydrogen bonds found  

> ui tool show H-Bonds

> hbonds reveal true

971 hydrogen bonds found  

> hbonds reveal true

971 hydrogen bonds found  

> ~hbonds

> undo

[Repeated 8 time(s)]

> select /A

2477 atoms, 2527 bonds, 322 residues, 1 model selected  

> hide sel atoms

> interfaces select /A & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

30 contacting residues  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> show sel atoms

> select /B

3354 atoms, 3406 bonds, 425 residues, 1 model selected  

> hide sel atoms

> interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

21 contacting residues  

> show sel atoms

> select /C

4530 atoms, 4596 bonds, 598 residues, 1 model selected  

> hide sel atoms

> interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0
> areaCutoff 0

21 contacting residues  

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

33 contacting residues  

> show sel atoms

> interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0
> areaCutoff 0

19 contacting residues  

> show sel atoms

> save "/Users/aury/Desktop/Déjà ranger/Post-Doc (Pr Vincent Burrus)/Système
> d'anti-restriction (hde)/Analyse bio-informatique/prédiction d'interaction
> protéine/Hde1-Hde2-Hde3/Hde1-Hde2-Hde3.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot  
'region browser': self.region_manager.state(),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x303f1d250> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16c7ce390> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x3037aeb10>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16c7ce390> -> <chimerax.seq_view.tool.SequenceViewer object at 0x3037aeb10>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16c7ce390> -> <chimerax.seq_view.tool.SequenceViewer object at
0x3037aeb10>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/tool.py", line 845, in take_snapshot  
'region browser': self.region_manager.state(),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seq_view/region_browser.py", line 1132, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
^^^^^^^^^^^^^^^^^^^^^  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x303f1d250> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery  
self.processed[key] = self.process(obj, parents)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x16c7ce390> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x3037aeb10>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x16c7ce390> -> <chimerax.seq_view.tool.SequenceViewer object at 0x3037aeb10>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x16c7ce390> -> <chimerax.seq_view.tool.SequenceViewer object at
0x3037aeb10>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac14,12
      Model Number: MNH73FN/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 2 jours, 22 heures et 7 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        ASUS VG279Q1A:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 144.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        50S451CA:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Television: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Seq viewer: region not in regions list

comment:2 by Eric Pettersen, 18 months ago

Resolution: → can't reproduce
Status: accepted → closed

If this recurs, may have to catch the exception, print the region, and re-raise the exception.

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