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#14774 assigned defect

Nucleotide undo after deletion throws traceback

Reported by:	chimerax-bug-report@…	Owned by:	Greg Couch
Priority:	normal	Milestone:
Component:	Undo/Redo	Version:
Keywords:		Cc:	Eric Pettersen
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403070144 (2024-03-07 01:44:19 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.8.dev202403070144 (2024-03-07)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1d86 fromDatabase pdb format mmcif

1d86 title:  
Structural consequences of A carcinogenic alkylation lesion on DNA: effect of
O6-ethyl-guanine on the molecular structure of D(CGC[E6G]aattcgcg)-netropsin
complex [more info...]  
  
Chain information for 1d86 #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')  
  
Non-standard residues in 1d86 #1  
---  
NT — netropsin  
  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> select C

250 atoms, 159 bonds, 25 residues, 1 model selected  

> color sel white

> select solvent

74 atoms, 74 residues, 1 model selected  

> hide sel target a

> select ::name="DA"

84 atoms, 94 bonds, 4 residues, 1 model selected  

> color sel blue

> select ::name="DC"

146 atoms, 154 bonds, 8 residues, 1 model selected  

> color sel cyan

> select ::name="DG"

176 atoms, 192 bonds, 8 residues, 1 model selected  

> color sel yellow

> select ::name="DT"

80 atoms, 86 bonds, 4 residues, 1 model selected  

> color sel magenta

> style sel sphere

Changed 80 atom styles  

> select /A

283 atoms, 272 bonds, 52 residues, 1 model selected  

> style sel sphere

Changed 283 atom styles  

> select /A

283 atoms, 272 bonds, 52 residues, 1 model selected  

> style sel ball

Changed 283 atom styles  

> select clear

> style ball

Changed 591 atom styles  

> style stick

Changed 591 atom styles  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> show target ab

> hide target a

> undo

[Repeated 2 time(s)]

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> cartoon style xsection oval modeHelix default

> hide (protein|nucleic) target a

> cartoon hide

> show ((protein&@ca)|(nucleic&@p)) target ab

> undo

[Repeated 9 time(s)]

> nucleotides sel stubs

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab

> nucleotides sel slab

> nucleotides sel fill

> nucleotides sel tube/slab

> close

> open 1d86 format mmcif fromDatabase pdb

1d86 title:  
Structural consequences of A carcinogenic alkylation lesion on DNA: effect of
O6-ethyl-guanine on the molecular structure of D(CGC[E6G]aattcgcg)-netropsin
complex [more info...]  
  
Chain information for 1d86 #1  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')  
  
Non-standard residues in 1d86 #1  
---  
NT — netropsin  
  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> select C

250 atoms, 159 bonds, 25 residues, 1 model selected  

> color sel white

> select solvent

74 atoms, 74 residues, 1 model selected  

> hide sel target a

> select ::name="DA"

84 atoms, 94 bonds, 4 residues, 1 model selected  

> color sel blue

> select ::name="DC"

146 atoms, 154 bonds, 8 residues, 1 model selected  

> color sel cyan

> select ::name="DG"

176 atoms, 192 bonds, 8 residues, 1 model selected  

> color sel yellow

> select ::name="DT"

80 atoms, 86 bonds, 4 residues, 1 model selected  

> color sel magenta

> style sel sphere

Changed 80 atom styles  

> select /A

283 atoms, 272 bonds, 52 residues, 1 model selected  

> style sel ball

Changed 283 atom styles  

> style sel ball

Changed 283 atom styles  

> select clear

> style stick

Changed 591 atom styles  

> cartoon

> cartoon style xsection rectangle modeHelix default

> cartoon style xsection oval modeHelix default

> nucleotides tube/slab

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 486 atom styles  

> nucleotides slab

> style nucleic stick

Changed 486 atom styles  

> color bynucleotide

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> nucleotides stubs

> nucleotides ladder

> nucleotides tube/slab shape ellipsoid

[Repeated 1 time(s)]

> nucleotides tube/slab shape box

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides tube/slab shape ellipsoid

> nucleotides slab

> style nucleic stick

Changed 486 atom styles  

> nucleotides tube/slab shape box

> nucleotides tube/slab shape ellipsoid

[Repeated 9 time(s)]

> nucleotides slab

> style nucleic stick

Changed 486 atom styles  

> nucleotides tube/slab shape ellipsoid

> help help:user/preferences.html#startup

> select /A

283 atoms, 272 bonds, 52 residues, 1 model selected  

> nucleotides sel slab

> style nucleic & sel stick

Changed 243 atom styles  

> nucleotides sel ladder

[Repeated 6 time(s)]

> distance style symbol false

[Repeated 1 time(s)]

> distance style symbol true

[Repeated 1 time(s)]

> distance style radius 0.09

[Repeated 1 time(s)]

> distance style radius 0.1

[Repeated 1 time(s)]

> distance style radius 0.11

[Repeated 1 time(s)]

> distance style radius 0.12

[Repeated 1 time(s)]

> distance style radius 0.13

[Repeated 1 time(s)]

> distance style radius 0.14

[Repeated 1 time(s)]

> distance style radius 0.15

[Repeated 1 time(s)]

> distance style radius 0.16

[Repeated 1 time(s)]

> distance style radius 0.17

[Repeated 1 time(s)]

> distance style radius 0.18

[Repeated 1 time(s)]

> distance style radius 0.19

[Repeated 1 time(s)]

> distance style radius 0.2

[Repeated 1 time(s)]

> distance style radius 0.21

[Repeated 1 time(s)]

> distance style radius 0.22

[Repeated 1 time(s)]

> distance style radius 0.23

[Repeated 1 time(s)]

> distance style radius 0.24

[Repeated 1 time(s)]

> distance style radius 0.25

[Repeated 1 time(s)]

> distance style radius 0.26

[Repeated 1 time(s)]

> distance style radius 0.27

[Repeated 1 time(s)]

> distance style radius 0.28

[Repeated 1 time(s)]

> distance style radius 0.29

[Repeated 1 time(s)]

> distance style radius 0.3

[Repeated 2 time(s)]

> distance style radius 0.1

[Repeated 1 time(s)]

> distance style radius 0.11

[Repeated 1 time(s)]

> distance style radius 0.12

[Repeated 1 time(s)]

> distance style radius 0.13

[Repeated 1 time(s)]

> distance style radius 0.14

[Repeated 1 time(s)]

> distance style radius 0.15

[Repeated 1 time(s)]

> distance style radius 0.16

[Repeated 1 time(s)]

> distance style radius 0.17

[Repeated 1 time(s)]

> distance style radius 0.18

[Repeated 1 time(s)]

> distance style radius 0.19

[Repeated 1 time(s)]

> distance style radius 0.2

[Repeated 1 time(s)]

> distance style radius 0.21

[Repeated 1 time(s)]

> distance style radius 0.22

[Repeated 1 time(s)]

> distance style radius 0.23

[Repeated 1 time(s)]

> distance style radius 0.24

[Repeated 1 time(s)]

> distance style radius 0.25

[Repeated 1 time(s)]

> distance style radius 0.26

[Repeated 1 time(s)]

> distance style radius 0.27

[Repeated 1 time(s)]

> distance style radius 0.28

[Repeated 1 time(s)]

> distance style radius 0.29

[Repeated 1 time(s)]

> distance style radius 0.3

[Repeated 1 time(s)]

> distance style radius 0.1

[Repeated 1 time(s)]

> distance style radius 0.3

[Repeated 1 time(s)]

> delete atoms sel

> delete bonds sel

> undo

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 124, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 124, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
^^^^^^^^^^^^  
File "atomic_cpp\\\cymol.pyx", line 986, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "atomic_cpp\\\cymol.pyx", line 982, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\undo.py",
line 196, in undo  
inst.undo()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\undo.py",
line 533, in undo  
a.undo()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\nucleotides\cmd.py", line 202, in undo  
NA.NucleotideState.restore_snapshot(self.session, self.before_state)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 508, in restore_snapshot  
new_residues = Residues(info.keys())  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 1190, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 129, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'dict_keys'>"  
  
undo failed: Collection items of unrecognized type "":  
ValueError: Collection items of unrecognized type ""  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 129, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  

> undo

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 124, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 124, in <listcomp>  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
^^^^^^^^^^^^  
File "atomic_cpp\\\cymol.pyx", line 986, in
chimerax.atomic.cymol.CyResidue._c_pointer.__get__  
File "atomic_cpp\\\cymol.pyx", line 982, in
chimerax.atomic.cymol.CyResidue.cpp_pointer.__get__  
RuntimeError: Residue already deleted  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\undo.py",
line 196, in undo  
inst.undo()  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\core\undo.py",
line 533, in undo  
a.undo()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\nucleotides\cmd.py", line 202, in undo  
NA.NucleotideState.restore_snapshot(self.session, self.before_state)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 508, in restore_snapshot  
new_residues = Residues(info.keys())  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 1190, in __init__  
Collection.__init__(self, residue_pointers, molobject.Residue)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 129, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type "<class 'dict_keys'>"  
  
undo failed: Collection items of unrecognized type "":  
ValueError: Collection items of unrecognized type ""  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molarray.py", line 129, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4502
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: tr_TR.cp1254
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: HUAWEI
Model: MCLF-XX
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 16,890,716,160
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12450H
OSLanguage: tr-TR

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.54.5
    ChimeraX-AtomicLibrary: 14.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    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: 1.8.dev202403070144
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.9
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.2
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.2.1
    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-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.36.1
    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
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.8
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.49.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
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Change History (2)

comment:1 by Eric Pettersen, 20 months ago

Component:	Unassigned → Undo/Redo
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Multiple errors when undoing after deletion

comment:2 by Eric Pettersen, 20 months ago

Cc:	Eric Pettersen added
Owner:	changed from Eric Pettersen to Greg Couch
Status:	accepted → assigned
Summary:	Multiple errors when undoing after deletion → Nucleotide undo after deletion throws traceback

Nucleotide undo code needs to either skip residues whose 'deleted' attribute is True, or throw a (probably) UserError saying that nucleotide state cannot be undone/restored because residues have been deleted.

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