RMSD header using dead residues

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202312190520 (2023-12-19 05:20:12 UTC)
Description
Had sequence alignment from matchmaker between 7rfw and 7dvw, then made crystal unit cell copies for cell size 1 1 2, then switched to cell size 1 1 1 which deleted 4 copies and produced this error.

Log:
UCSF ChimeraX version: 1.8.dev202312190520 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_peptide.cxs format session

Log from Thu Mar 23 18:51:03 2023UCSF ChimeraX version: 1.6.dev202303240108
(2023-03-24)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open C:/cygwin64/home/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_peptide.cxs

Log from Thu Mar 23 17:15:13 2023UCSF ChimeraX version: 1.6.dev202303230058
(2023-03-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_7dvw.cxs format session

Log from Thu Mar 23 17:12:58 2023Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.dev202303230058 (2023-03-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7dvw format mmcif fromDatabase pdb

7dvw title:  
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp5|6 peptidyl substrate [more
info...]  
  
Chain information for 7dvw #1  
---  
Chain | Description | UniProt  
A | 3C-like proteinase | R1AB_SARS2 1-306  
C | nsp5/6 peptidyl substrate | R1AB_SARS2 -3-16  
  
Non-standard residues in 7dvw #1  
---  
DMS — dimethyl sulfoxide  
  
7dvw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> sym #1 assembly 1

Made 2 copies for 7dvw assembly 1  

> view

> color #2.1 salmon

> select #2/C

130 atoms, 124 bonds, 24 residues, 2 models selected  

> color #2/C cornflowerblue

> show #2/C

> hide #2/C ribbons

> color #2/C byhetero

> select ligand

12 atoms, 9 bonds, 3 residues, 3 models selected  

> show #2/C :< 4

> style #2/C ball

Changed 130 atom styles  

> select clear

> select #2/C:7-9

36 atoms, 34 bonds, 6 residues, 2 models selected  

> color #2/C:7-9 green

> color #2/C:7-9 byhetero

> select clear

> show #2/C ribbons

> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_7dvw.cxs

——— End of log from Thu Mar 23 17:12:58 2023 ———

opened ChimeraX session  

> ui tool show "Send to Quest"

> graphics quality atomTriangles 100

> graphics quality bondTriangles 20

> graphics quality ribbonDivisions 5

> graphics quality ribbonSides 4

> graphics quality ribbonSides 8

> style solvent stick

Changed 846 atom styles  

> save /Users/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_7dvw.cxs

——— End of log from Thu Mar 23 17:15:13 2023 ———

opened ChimeraX session  

> save C:/Users/goddard/Desktop/scene.glb

Running command: "C:/Program
Files/Unity/Hub/Editor/2022.2.5f1/Editor/Data/PlaybackEngines/AndroidPlayer/SDK/platform-
tools/adb.exe" push C:/Users/goddard/Desktop/scene.glb
/sdcard/Android/data/com.UCSF.LookieAR/files  

> color #2.1 byhetero

> save C:/cygwin64/home/goddard/ucsf/presentations/paxlovid-vr-
> mar2023/data/mpro_peptide.cxs

——— End of log from Thu Mar 23 18:51:03 2023 ———

opened ChimeraX session  

> close

> open 7rfw

7rfw title:  
Structure of SARS-CoV-2 main protease in complex with a covalent inhibitor
[more info...]  
  
Chain information for 7rfw #1  
---  
Chain | Description | UniProt  
A | 3C-like proteinase | R1AB_SARS2 1-306  
  
Non-standard residues in 7rfw #1  
---  
4WI —
(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
(PF-07321332, bound form; nirmatrelvir, bound form; Paxlovid, bound form)  
  
7rfw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> select ligand

68 atoms, 70 bonds, 1 residue, 1 model selected  

> color sel orange

> color sel magenta

> color sel byhetero

> style sel sphere

Changed 68 atom styles  

> style sel ball

Changed 68 atom styles  

> select clear

> select ligand

68 atoms, 70 bonds, 1 residue, 1 model selected  

> select clear

> surface

> lighting soft

> open 7dvw

7dvw title:  
SARS-CoV-2 Mpro mutant (H41A) in complex with nsp5|6 peptidyl substrate [more
info...]  
  
Chain information for 7dvw #2  
---  
Chain | Description | UniProt  
A | 3C-like proteinase | R1AB_SARS2 1-306  
C | nsp5/6 peptidyl substrate | R1AB_SARS2 -3-16  
  
Non-standard residues in 7dvw #2  
---  
DMS — dimethyl sulfoxide  
  
7dvw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> surface hidePatches

> 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 7rfw, chain A (#1) with 7dvw, chain A (#2), sequence alignment
score = 1600.6  
RMSD between 299 pruned atom pairs is 0.634 angstroms; (across all 306 pairs:
2.810)  
  

> select #2/C:1-9

62 atoms, 62 bonds, 9 residues, 1 model selected  

> color sel orange

> color /C:1-6 yellow

> color /C:1-6 purple

> color /C:1-6 geen

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

> color /C:1-6 green

> show sel atoms

> color sel byhetero

> 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 7rfw, chain A (#1) with 7dvw, chain A (#2), sequence alignment
score = 1600.6  
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: 7rfw #1/A, 7dvw #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 299 pruned atom pairs is 0.634 angstroms; (across all 306 pairs:
2.810)  
  

> sequence header conservation show

Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  

> select #1/A:41

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:41 #2/A:41

15 atoms, 14 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 7rfw, chain A..7dvw, chain A [42] RMSD:
0.303  
  

> hide #2 models

> preset "initial styles" "original look"

Using preset: Initial Styles / Original Look  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> show #2 models

> select #2/C:1-9

62 atoms, 62 bonds, 9 residues, 1 model selected  

> color sel orange

> color /C:1-6 red

> hide #2 models

> color ligand magenta

> color ligand byhetero

> ui tool show "Unit Cell"

> unitcell #1

Associated 7rfw #1 (3.1) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #2 (3.2) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #3 (3.3) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #4 (3.4) chain A to 7rfw, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 7rfw #1/A, 7dvw #2/A, 7rfw #1
#3.1/A, 7rfw #2 #3.2/A, 7rfw #3 #3.3/A, 7rfw #4 #3.4/A  

> unitcell #1 cells 2,1,1

Associated 7rfw #5 (3.5) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #6 (3.6) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #7 (3.7) chain A to 7rfw, chain A with 0 mismatches  
Associated 7rfw #8 (3.8) chain A to 7rfw, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 7rfw #1/A, 7dvw #2/A, 7rfw #1
#3.1/A, 7rfw #2 #3.2/A, 7rfw #3 #3.3/A, 7rfw #4 #3.4/A, 7rfw #5 #3.5/A, 7rfw
#6 #3.6/A, 7rfw #7 #3.7/A, 7rfw #8 #3.8/A  

> unitcell #1 cells 1,1,2

> rainbow #3 model

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> rainbow #3 structures

> measure buriedarea #3.4 #3.7

Missing required "with_atoms2" argument  

> measure buriedarea #3.4 withAtoms2 #3.7

Buried area between #3.4 and #3.7 = 1856.9  
area #3.4 = 14028, area #3.7 = 14028, area both = 24343  

> measure buriedarea #3.4 withAtoms2 #3.8

Buried area between #3.4 and #3.8 = 466.71  
area #3.4 = 14028, area #3.8 = 14028, area both = 27123  

> unitcell outline #1

> unitcell #1

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 182, in _atomic_changes_cb  
self.reevaluate()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 134, in reevaluate  
super().reevaluate(pos1, pos2)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/header_sequence.py", line 218, in
reevaluate  
self.append(self.evaluate(pos))  
^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 81, in evaluate  
for coords in self._gather_coords(pos):  
^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 170, in _gather_coords  
a = r.find_atom(bb_name)  
^^^^^^^^^^^^^^^^^^^^  
File "atomic_cpp/cymol.pyx", line 1645, in
chimerax.atomic.cymol.CyResidue.find_atom  
RuntimeError: Residue already deleted  
  
Error processing trigger "changes":  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1645, in
chimerax.atomic.cymol.CyResidue.find_atom  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 884, in _rmsd_atomic_cb  
self._notify_rmsd_change()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 835, in _notify_rmsd_change  
self._notify_observers(self.NOTE_RMSD_UPDATE, None)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 823, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 53, in
alignment_notification  
self.reevaluate()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 127, in reevaluate  
new_eval_chains = self.alignment.rmsd_chains  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 660, in rmsd_chains  
by_struct.setdefault(chain.structure, []).append(chain)  
^^^^^^^^^^^^^^^  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Error processing trigger "changes":  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 660, in rmsd_chains  
by_struct.setdefault(chain.structure, []).append(chain)  
^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Max
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: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 4 days, 11 hours, 38 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    alphashape: 1.3.1
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.13.1
    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: 3.4.2
    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: 1.51
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.10.5
    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: 1.4
    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: 1.8.dev202312190520
    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
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    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
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    ChimeraX-Markers: 1.0.1
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    ChimeraX-MCopy: 1.0
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    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
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    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: 1.0.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-PDB: 2.7.3
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    ChimeraX-PDBLibrary: 1.0.3
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    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
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    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: 1.14.2
    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: 1.33.4
    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
    click: 8.1.7
    click-log: 0.4.0
    colorama: 0.4.6
    comm: 0.2.0
    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: 4.45.1
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    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: 5.5.0
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.7
    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: 4.0.0
    prompt-toolkit: 3.0.41
    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
    pynmrstar: 3.3.2
    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: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.1
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    Rtree: 1.1.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    shapely: 2.0.2
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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
    trimesh: 4.0.8
    typing-extensions: 4.8.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[pett]

As per Tom's general outline, the minimal commands to reproduce are:

open 7rfw 7dww
matchmaker #2 to #1 showAlignment true
unitcell #1 cells 1,1,2
unitcell #1

[pett]

Fixed on 1.8 and 1.7 branches: ​https://github.com/RBVI/ChimeraX/commit/42e09e91e3a7af321d4a3bb2f5f856c46713e32d