Opened 3 years ago

Closed 3 years ago

#7288 closed defect (fixed)

Bad sequence pointer

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\Users\Philip Shaw\Documents\PhD 2021-2025\Ferritin NPs\ChimeraX
> model building\Final\Final.pdb" format pdb

Final.pdb title:  
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
[more info...]  
  
Chain information for Final.pdb #1  
---  
Chain | Description | UniProt  
A B C D E | ferritin | FTN_HELPJ  
F | ferritin | FTN_HELPJ  
  
Non-standard residues in Final.pdb #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> select #1

13548 atoms, 12981 bonds, 2146 residues, 1 model selected  
Alignment identifier is 1  
Alignment identifier is 1/F  

> close session

> open 3BVE format mmcif fromDatabase pdb

3bve title:  
Structural basis for the iron uptake mechanism of Helicobacter pylori ferritin
[more info...]  
  
Chain information for 3bve #1  
---  
Chain | Description | UniProt  
A B C D E F | Ferritin | FTN_HELPJ  
  
Non-standard residues in 3bve #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3bve mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> select #1

9310 atoms, 8699 bonds, 1850 residues, 1 model selected  
Alignment identifier is 1  

> select
> /A-D:0-2,1001,1002,1003,1004,1005,1006/E-F:0-2,1001,1002,1003,1004,1005

436 atoms, 452 bonds, 52 residues, 1 model selected  

> select sel

436 atoms, 452 bonds, 52 residues, 1 model selected  

> delete sel

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> cd "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX model
> building"

Current working directory is: C:\Users\Philip Shaw\Documents\PhD
2021-2025\Ferritin NPs\ChimeraX model building  

> save "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX
> model building/his-tag removed_3bve.pdb" relModel #1

> hide solvent

> save "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX
> model building/his-tag removed_3bve.pdb" relModel #1

> close session

> open "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX
> model building/his-tag removed_3bve.pdb"

Chain information for his-tag removed_3bve.pdb #1  
---  
Chain | Description  
A B C D E | No description available  
F | No description available  
  

> hide solvent

> select #1:7

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select #1:7

48 atoms, 42 bonds, 6 residues, 1 model selected  
Alignment identifier is 1  
Alignment identifier is 1/F  

> open "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX
> model building/3bve.pdb"

3bve.pdb title:  
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
[more info...]  
  
Chain information for 3bve.pdb #2  
---  
Chain | Description | UniProt  
A B C D | ferritin | FTN_HELPJ  
E | ferritin | FTN_HELPJ  
F | ferritin | FTN_HELPJ  
  
Non-standard residues in 3bve.pdb #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> close session

> open "C:/Users/Philip Shaw/Documents/PhD 2021-2025/Ferritin NPs/ChimeraX
> model building/3bve.pdb"

3bve.pdb title:  
Structural basis for the iron uptake mechanism of helicobacter pylori ferritin
[more info...]  
  
Chain information for 3bve.pdb #1  
---  
Chain | Description | UniProt  
A B C D | ferritin | FTN_HELPJ  
E | ferritin | FTN_HELPJ  
F | ferritin | FTN_HELPJ  
  
Non-standard residues in 3bve.pdb #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  

> select #1

9310 atoms, 8699 bonds, 1850 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

Alignment identifier is 1  
Alignment identifier is 1/E  
Alignment identifier is 1/F  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

[Repeated 1 time(s)]

> ui tool show "Build Structure"

> build start peptide "custom built" S -57.0,-47.0 rotLib Dunbrack

> select #1/A

1542 atoms, 1450 bonds, 299 residues, 1 model selected  
Alignment identifier is 1/A  

> select #1/F

1556 atoms, 1450 bonds, 312 residues, 1 model selected  

> select #1/F:180

Nothing selected  

> select #1/F:170

Nothing selected  

> select #1/F:150

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/F:160

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/F:168

Nothing selected  

> select #1/F:167

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/A:167

Nothing selected  

> select #1/A:166

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:166#2

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:166@C#2@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Could not find second C atom for phi angle  

> select #1/A:166@C#2@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Could not find second C atom for phi angle  

> close #2

> build start peptide "custom built" SS -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #2  
---  
Chain | Description  
A | No description available  
  

> select add #2

14 atoms, 12 bonds, 3 residues, 2 models selected  

> close #2

> build start peptide "custom built" SG -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #2  
---  
Chain | Description  
A | No description available  
  

> select #1/A:166@C#2:1@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> build start peptide "custom built" SG -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #2  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" SG -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #3  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" SG -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #4  
---  
Chain | Description  
A | No description available  
  

> build start peptide "custom built" SG -57.0,-47.0 -57.0,-47.0 rotLib
> Dunbrack

Chain information for custom built #5  
---  
Chain | Description  
A | No description available  
  

> select #1/B:166@C#2:1@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select #1/C:166@C#3:1@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select #1/D:166@C#4:1@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select #1/E:166@C#5:1@N

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select #1

9365 atoms, 8754 bonds, 1860 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #1/F

1556 atoms, 1450 bonds, 312 residues, 1 model selected  

> select #1/A

1553 atoms, 1461 bonds, 301 residues, 1 model selected  

> select #1/A

1553 atoms, 1461 bonds, 301 residues, 1 model selected  
Alignment identifier is 1/A  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

> select #1

9365 atoms, 8754 bonds, 1860 residues, 1 model selected  
Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 310, in run  
f(shortcut_atoms(s))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1046, in show_sequence  
run(session, 'sequence chain %s' % seq_chain_spec, log = False)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 241, in seqalign_chain  
alignment.associate(chain, keep_intrinsic=True)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 253, in associate  
est_len, segments, gaps = estimate_assoc_params(sseq)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1233, in estimate_assoc_params  
return f(sseq._c_pointer)  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1233, in estimate_assoc_params  
return f(sseq._c_pointer)  
  
See log for complete Python traceback.  
  

> color sel bychain

> select #1/F

1556 atoms, 1450 bonds, 312 residues, 1 model selected  

> select #1

9365 atoms, 8754 bonds, 1860 residues, 1 model selected  
Alignment identifier is 1  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 310, in run  
f(shortcut_atoms(s))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1046, in show_sequence  
run(session, 'sequence chain %s' % seq_chain_spec, log = False)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 241, in seqalign_chain  
alignment.associate(chain, keep_intrinsic=True)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 253, in associate  
est_len, segments, gaps = estimate_assoc_params(sseq)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1233, in estimate_assoc_params  
return f(sseq._c_pointer)  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
OSError: exception: access violation reading 0xFFFFFFFFFFFFFFFF  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1233, in estimate_assoc_params  
return f(sseq._c_pointer)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 511.81
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_BE.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Inspiron 16 7610
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 34,085,838,848
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Attachments (1)

test.cxc​ (1.5 KB ) - added by Eric Pettersen 3 years ago.

Download all attachments as: .zip

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Bad sequence pointer

Can reproduce with attached cxc script followed by clicking "Show Sequence" toolbar icon.

by Eric Pettersen, 3 years ago

Attachment: test.cxc​ added

comment:2 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Fix: ​https://github.com/RBVI/ChimeraX/commit/d05223220f84749d4824c8972ab1f7e267bc6bff

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