Match→Align associating to alignment: numpy error

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.8.3-x86_64-i386-64bit
ChimeraX Version: 1.12rc202605070126 (2026-05-07 01:26:37 UTC)
Description
ui tool show Match→Align
msa3d #2/A#3/A
Match→Align cutoff: 5.0, in column if within cutoff of: any 82 residue pairs aligned 110 fully populated columns 
Pairwise RMSDs across all fully populated columns
Model
2
3
2
0.000
28.811
3
28.811
0.000
Overall RMSD: 28.811 Sequence lengths: 110 522 SDM (cutoff 5.0): -247.145 Q-score: 0.002 Alignment identifier is MA-1 Showing conservation header ("seq_clustal_conservation" residue attribute) for alignment MA-1 Traceback (most recent call last):   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/tool.py", line 259, in match_align     run(self.session, "msa3d " + ' '.join(args))   File "/Applications/ChimeraX-1.12-rc2026.05.07.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-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3245, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_align/cmd.py", line 225, in make_alignment     alignment.associate(orig, seq=aligned, silent=True)   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 386, in associate     do_assoc()   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 305, in do_assoc     self.prematched_assoc_structure(best_match_map, best_errors, reassoc)   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 742, in prematched_assoc_structure     self._set_residue_attributes(match_maps=[match_map])   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 1071, in _set_residue_attributes     values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 1071, in <listcomp>     values = [100.0 * self.most_common(col)[1] / num_seqs for col in range(len(self._seqs[0]))]                       ^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 691, in most_common     chars, counts = self.column_counts()[col_index]                     ^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 485, in column_counts     data = numpy.array([list(seq.characters) for seq in self._seqs])            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. File "/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 485, in column_counts data = numpy.array([list(seq.characters) for seq in self._seqs])

Log:
UCSF ChimeraX version: 1.12rc202605070126 (2026-05-07)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

Log from Sun Jan 25 11:55:12 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

Log from Sun Jan 25 11:18:21 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs" format session

Log from Tue Jan 20 17:12:49 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs" format session

Log from Tue Jan 20 16:53:43 2026UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

Log from Tue Jan 20 16:01:25 2026

> set bgColor light grey

> ui tool show "command line interface"

UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif format mmcif

6His-860_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 6His-860_0.cif #1  
---  
Chain | Description  
A | Entity A  
  
Color 6His-860_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> close session

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"
> format mmcif

850His_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 850His_0.cif #1  
---  
Chain | Description  
A | Entity A  
  
Color 850His_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His_0.cif"
> format mmcif

850His_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 850His_0.cif #2  
---  
Chain | Description  
A | Entity A  
  
Color 850His_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> open /Users/frankseeber/Downloads/6His-860/6His-860_0.cif

6His-860_0.cif title:  
Chai-1 predicted structure [more info...]  
  
Chain information for 6His-860_0.cif #3  
---  
Chain | Description  
A | Entity A  
  
Color 6His-860_0.cif by residue attribute pLDDT_score  
Computing secondary structure  

> ui tool show Matchmaker

> close #1

> ui tool show Matchmaker

> matchmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3),
sequence alignment score = 152.3  
RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs:
14.240)  
  

> ui tool show Matchmaker

> matchmaker #3 to #2 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 850His_0.cif, chain A (#2) with 6His-860_0.cif, chain A (#3),
sequence alignment score = 152.3  
Alignment identifier is 1  
Showing conservation header ("seq_clustal_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 850His_0.cif #2/A,
6His-860_0.cif #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 50 pruned atom pairs is 1.232 angstroms; (across all 105 pairs:
14.240)  
  

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

——— End of log from Tue Jan 20 16:01:25 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #c0c0c0ff

[Repeated 1 time(s)]

> color sel #c0c0c0fa

> color sel #c0c0c0e5

> color sel #c0c0c0d5

> color sel #c0c0c0cf

> color sel #c0c0c0cc

> color sel #c0c0c0c7

> color sel #c0c0c0b8

> set bgColor white

> color sel #c0c0c0b6

> color sel #c0c0c0ac

> color sel #c0c0c0a9

> color sel #c0c0c09b

> color sel #c0c0c099

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> color sel #c0c0c091

> color sel #c0c0c08f

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> color sel #c0c0c088

> color sel #c0c0c081

> color sel #c0c0c079

> color sel #c0c0c072

> color sel #c0c0c071

> color sel #c0c0c0ff

> color sel #ebebebff

> color sel #d6d6d6ff

> color sel #ebebebff

> color sel #d6d6d6ff

> select clear

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #d6d6d6ff

> color sel #d6d6d6f7

> color sel #d6d6d6ec

> color sel #d6d6d6ea

> color sel #d6d6d6cb

> color sel #d6d6d6b1

> color sel #d6d6d6a9

> color sel #d6d6d694

> color sel #d6d6d686

> color sel #d6d6d67d

> color sel #d6d6d67b

> color sel #d6d6d678

> color sel #d6d6d66e

> color sel #d6d6d661

> color sel #d6d6d65a

[Repeated 1 time(s)]

> color sel #d6d6d66a

> color sel #d6d6d672

> color sel #d6d6d67e

> color sel #d6d6d687

> color sel #d6d6d693

> color sel #d6d6d695

> color sel #d6d6d697

> color sel #d6d6d698

> color sel #d6d6d656

> color sel #d6d6d615

> color sel #d6d6d604

> color sel #d6d6d600

> color sel #d6d6d611

> color sel #d6d6d635

> color sel #d6d6d646

> color sel #d6d6d64a

> color sel #d6d6d663

> color sel #d6d6d677

[Repeated 1 time(s)]

> color sel #d6d6d663

> color sel #d6d6d60a

> color sel #d6d6d600

> color sel #d6d6d60a

> color sel #d6d6d62c

> color sel #d6d6d632

> color sel #d6d6d631

> color sel #d6d6d62c

> color sel #d6d6d628

> color sel #d6d6d626

[Repeated 1 time(s)]

> color sel #d6d6d625

> color sel #d6d6d626

> color sel #d6d6d628

> color sel #d6d6d629

> color sel #d6d6d62a

> color sel #d6d6d62e

> color sel #d6d6d630

> color sel #d6d6d632

> color sel #d6d6d633

> color sel #d6d6d634

> color sel #d6d6d636

[Repeated 1 time(s)]

> select clear

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

[Repeated 1 time(s)]

——— End of log from Tue Jan 20 16:53:43 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> color sel #a9a9a942

> color sel #a9a9a944

> color sel #a9a9a947

> color sel #a9a9a948

> color sel #a9a9a949

> color sel #a9a9a94b

> color sel #a9a9a94c

> color sel #a9a9a94d

> color sel #a9a9a94f

> color sel #a9a9a950

> color sel #a9a9a952

> color sel #a9a9a953

> color sel #a9a9a954

> color sel #a9a9a955

> color sel #a9a9a956

> color sel #a9a9a958

[Repeated 1 time(s)]

> color sel #a9a9a959

[Repeated 1 time(s)]

> color sel #a9a9a95b

> color sel #a9a9a95c

> color sel #a9a9a95d

[Repeated 1 time(s)]

> color sel #a9a9a95e

> select clear

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His.cxs"

——— End of log from Tue Jan 20 17:12:49 2026 ———

> view name session-start

opened ChimeraX session  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> "select #3/a:1-177,259-525"

Unknown command: "select #3/a:1-177,259-525"  

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:1-525

3959 atoms, 4022 bonds, 522 residues, 1 model selected  

> color sel #ebebebff

> select clear

> select #3/a:1-177,259-525

3365 atoms, 3419 bonds, 441 residues, 1 model selected  

> select #3/a:181-260

586 atoms, 593 bonds, 80 residues, 1 model selected  

> color sel #dda0ddff

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/6His-860"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His/6His-860  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

——— End of log from Sun Jan 25 11:18:21 2026 ———

> view name session-start

opened ChimeraX session  

> cd "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His"

Current working directory is: /Users/frankseeber/Documents/RKI/2nd LEA
paper/850His  

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

> save /Users/frankseeber/Desktop/model_1.tif width 1800 transparentBackground
> true

[Repeated 3 time(s)]

> save "/Users/frankseeber/Documents/RKI/2nd LEA paper/850His/850His vs
> 860His_1.cxs"

——— End of log from Sun Jan 25 11:55:12 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  

> ui tool show Match→Align

> msa3d #2/A#3/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
82 residue pairs aligned  
110 fully populated columns  
Pairwise RMSDs across all fully populated columns  
---  
Model | 2 | 3  
2 | 0.000 | 28.811  
3 | 28.811 | 0.000  
  
Overall RMSD: 28.811  
Sequence lengths: 110 522  
SDM (cutoff 5.0): -247.145  
Q-score: 0.002  
Alignment identifier is MA-1  
Showing conservation header ("seq_clustal_conservation" residue attribute) for
alignment MA-1  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align  
run(self.session, "msa3d " + ' '.join(args))  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.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-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 225, in make_alignment  
alignment.associate(orig, seq=aligned, silent=True)  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 386, in associate  
do_assoc()  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 305, in do_assoc  
self.prematched_assoc_structure(best_match_map, best_errors, reassoc)  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 742, in
prematched_assoc_structure  
self._set_residue_attributes(match_maps=[match_map])  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 1071, in
_set_residue_attributes  
values = [100.0 * self.most_common(col)[1] / num_seqs for col in
range(len(self._seqs[0]))]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 1071, in <listcomp>  
values = [100.0 * self.most_common(col)[1] / num_seqs for col in
range(len(self._seqs[0]))]  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 691, in most_common  
chars, counts = self.column_counts()[col_index]  
^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 485, in column_counts  
data = numpy.array([list(seq.characters) for seq in self._seqs])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: setting an array element with a sequence. The requested array has
an inhomogeneous shape after 1 dimensions. The detected shape was (2,) +
inhomogeneous part.  
  
ValueError: setting an array element with a sequence. The requested array has
an inhomogeneous shape after 1 dimensions. The detected shape was (2,) +
inhomogeneous part.  
  
File
"/Applications/ChimeraX-1.12-rc2026.05.07.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 485, in column_counts  
data = numpy.array([list(seq.characters) for seq in self._seqs])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-22.5.15
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2094.80.5.0.0 (iBridge: 23.16.13120.0.0,0)
      OS Loader Version: 580.140.1~106

Software:

    System Software Overview:

      System Version: macOS 14.8.3 (23J220)
      Kernel Version: Darwin 23.6.0
      Time since boot: 4 Tage, 4 Stunden und 42 Minuten

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2421E:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2S6N6H3     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        DELL U2421E:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: BPTJBH3     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
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    ChimeraX-Modeller: 1.5.23
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    ChimeraX-Nifti: 1.2
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    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
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    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SeqView: 2.18
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    ChimeraX-Struts: 1.0.1
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    ChimeraX-WebCam: 1.0.2
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[Eric Pettersen]

Something went haywire in this 2-chain pairing. How could the RMSD in the fully populated columns be 28 when the cutoff was 5?