Opened 2 days ago

Closed 45 hours ago

#20456 closed defect (duplicate)

msa3d not skipping None residues

Reported by: kklee@… 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202604220250 (2026-04-22 02:50:42 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12.dev202604220250 (2026-04-22)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2C36 fromDatabase pdb format mmcif

Summary of feedback from opening 2C36 fetched from pdb  
---  
note | Fetching compressed mmCIF 2c36 from http://files.rcsb.org/download/2c36.cif  
  
2c36 title:  
Structure of unliganded HSV gD reveals a mechanism for receptor- mediated
activation of virus entry [more info...]  
  
Chain information for 2c36 #1  
---  
Chain | Description | UniProt  
A B | GLYCOPROTEIN D HSV-1 | VGLD_HHV1P 23-307  
  
Non-standard residues in 2c36 #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CL — chloride ion  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  
2c36 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open 3U82 fromDatabase pdb format mmcif

Summary of feedback from opening 3U82 fetched from pdb  
---  
note | Fetching compressed mmCIF 3u82 from http://files.rcsb.org/download/3u82.cif  
  
3u82 title:  
Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell
adhesion [more info...]  
  
Chain information for 3u82 #2  
---  
Chain | Description | UniProt  
A | Envelope glycoprotein D | GD_HHV11 1-285  
B | Poliovirus receptor-related protein 1 | PVRL1_HUMAN 30-335  
  
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
4164 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> ui mousemode right "translate selected models"

> select add #2

4164 atoms, 4276 bonds, 531 residues, 1 model selected  
Drag select of 1 residues  

> select add #2

4173 atoms, 4276 bonds, 532 residues, 2 models selected  

> view matrix models
> #1,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333,#2,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333

> view matrix models
> #1,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648,#2,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648

Drag select of 38 residues  

> select add #2

4164 atoms, 4276 bonds, 531 residues, 1 model selected  

> view matrix models #2,1,0,0,10.913,0,1,0,-5.4823,0,0,1,72.473

> select clear

> select add #2

4164 atoms, 4276 bonds, 531 residues, 1 model selected  

> view matrix models #2,1,0,0,49.396,0,1,0,10.72,0,0,1,74.14

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.36377,0.23781,0.90062,93.031,0.2102,0.92097,-0.32808,-4.3201,-0.90746,0.30866,0.28503,95.517

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.36377,0.23781,0.90062,60.161,0.2102,0.92097,-0.32808,39.017,-0.90746,0.30866,0.28503,92.057

> select #2/B

2350 atoms, 2405 bonds, 300 residues, 1 model selected  

> select #1/B

2378 atoms, 2211 bonds, 1 pseudobond, 511 residues, 2 models selected  

> cartoon hide (#!1 & sel)

> hide (#!1 & sel) target a

Drag select of 61 atoms, 63 bonds  

> hide sel target a

Drag select of 15 atoms, 13 bonds  
Drag select of 17 atoms, 15 bonds  

> hide sel target a

> select add #1

4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected  

> view matrix models #1,1,0,0,-1.9223,0,1,0,-10.557,0,0,1,-11.522

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.9967,0.07801,-0.022516,-2.9128,-0.077916,0.99695,0.005019,-6.3853,0.022839,-0.003248,0.99973,-12.683

> view matrix models
> #1,-0.94293,-0.29197,-0.16012,135,0.33274,-0.84487,-0.4189,79.3,-0.012978,-0.44828,0.8938,16.082

> view matrix models
> #1,-0.98397,0.14482,-0.10409,115.23,-0.14104,-0.98908,-0.042846,80.216,-0.10915,-0.027479,0.99364,-3.6143

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.98397,0.14482,-0.10409,116.77,-0.14104,-0.98908,-0.042846,34.526,-0.10915,-0.027479,0.99364,-7.383

> view matrix models
> #1,-0.98397,0.14482,-0.10409,129.19,-0.14104,-0.98908,-0.042846,34.931,-0.10915,-0.027479,0.99364,8.2471

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.65912,-0.68076,-0.31957,161.67,0.51961,-0.10506,-0.84792,30.444,0.54366,-0.72493,0.42297,47.06

> view matrix models
> #1,-0.76831,0.43248,-0.47187,136.7,0.060618,0.78305,0.61899,-103.46,0.6372,0.44698,-0.62785,84.674

> view matrix models
> #1,-0.98248,0.025355,-0.18463,140.71,-0.16057,0.38766,0.90771,-99.638,0.094587,0.92145,-0.3768,75.622

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.98248,0.025355,-0.18463,135.13,-0.16057,0.38766,0.90771,-59.244,0.094587,0.92145,-0.3768,70.638

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.99193,-0.062378,0.1104,114.02,0.080803,0.36003,0.92944,-73.872,-0.097723,0.93085,-0.35208,79.212

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.99193,-0.062378,0.1104,107.05,0.080803,0.36003,0.92944,-72.704,-0.097723,0.93085,-0.35208,82.111

> view matrix models
> #1,-0.99193,-0.062378,0.1104,114.49,0.080803,0.36003,0.92944,-93.699,-0.097723,0.93085,-0.35208,57.904

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.9571,0.28849,0.027023,105.65,0.26877,0.84906,0.45481,-83.486,0.10827,0.44256,-0.89018,111.31

> view matrix models
> #1,-0.94424,0.30785,-0.11683,116.4,0.29468,0.94837,0.11729,-60.158,0.1469,0.076325,-0.9862,131.83

> view matrix models
> #1,-0.94238,0.31033,-0.12494,116.89,0.2985,0.94864,0.10481,-59.325,0.15105,0.061479,-0.98661,132.21

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.94238,0.31033,-0.12494,117.63,0.2985,0.94864,0.10481,-30.747,0.15105,0.061479,-0.98661,147.91

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.94444,0.32578,-0.043662,110.21,0.27276,0.85091,0.44895,-54.711,0.18341,0.4121,-0.89249,124.11

> view matrix models
> #1,-0.94484,0.32551,-0.036316,109.62,0.27314,0.84426,0.46112,-55.505,0.18076,0.42576,-0.8866,123.21

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.94484,0.32551,-0.036316,107.15,0.27314,0.84426,0.46112,-64.24,0.18076,0.42576,-0.8866,119.63

> view matrix models
> #1,-0.94484,0.32551,-0.036316,106.11,0.27314,0.84426,0.46112,-64.181,0.18076,0.42576,-0.8866,125.67

> ui tool show Match→Align

> msa3d #1/A#2/A

Match→Align cutoff: 5.0, in column if within cutoff of: any  
24 residue pairs aligned  
285 fully populated columns  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 199, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args, ma=self.match_align:
ma(apply=True))  
^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 155, in make_alignment  
coords[seq] = column_atoms(seq, full_cols).scene_coords  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'principal_atom'  
  
AttributeError: 'NoneType' object has no attribute 'principal_atom'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select #2/B

2350 atoms, 2405 bonds, 300 residues, 1 model selected  

> cartoon hide sel

> select add #2

4164 atoms, 4276 bonds, 531 residues, 1 model selected  

> select add #1

9076 atoms, 8825 bonds, 6 pseudobonds, 1601 residues, 5 models selected  

> select subtract #2

4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected  

> view matrix models
> #1,-0.94484,0.32551,-0.036316,78.784,0.27314,0.84426,0.46112,-98.282,0.18076,0.42576,-0.8866,101.33

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.89216,0.34963,-0.28601,96.076,0.30726,0.93384,0.18313,-80.114,0.33111,0.075506,-0.94057,111.2

> view matrix models
> #1,-0.8876,-0.11044,-0.44717,127.82,0.45344,-0.38012,-0.80616,47.982,-0.080945,-0.91832,0.38747,61.2

> view matrix models
> #1,-0.72558,-0.22625,-0.64988,140.38,0.61137,-0.64542,-0.45789,19.765,-0.31585,-0.72955,0.60662,48.529

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.72558,-0.22625,-0.64988,154.97,0.61137,-0.64542,-0.45789,58.622,-0.31585,-0.72955,0.60662,76.034

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.78266,-0.3287,-0.52858,151.99,0.44768,-0.88726,-0.11113,48.09,-0.43246,-0.32362,0.84158,46.59

> view matrix models
> #1,-0.93745,-0.34808,0.0054046,116.15,0.33548,-0.90742,-0.25307,67.435,0.092993,-0.23543,0.96743,2.1588

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.93745,-0.34808,0.0054046,134.19,0.33548,-0.90742,-0.25307,62.876,0.092993,-0.23543,0.96743,7.7984

> view matrix models
> #1,-0.93745,-0.34808,0.0054046,134.81,0.33548,-0.90742,-0.25307,63.104,0.092993,-0.23543,0.96743,6.9425

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.89951,-0.31276,0.30507,105.68,0.23313,-0.93413,-0.27028,71.515,0.36951,-0.172,0.91317,-6.847

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.89951,-0.31276,0.30507,101.6,0.23313,-0.93413,-0.27028,72.531,0.36951,-0.172,0.91317,-8.3189

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.89907,-0.3103,0.30885,101.15,0.23415,-0.93688,-0.25966,71.677,0.36993,-0.16114,0.91498,-8.9289

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.89907,-0.3103,0.30885,100.24,0.23415,-0.93688,-0.25966,77.531,0.36993,-0.16114,0.91498,-12.425

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.8404,-0.54186,-0.010584,133.29,0.39205,-0.59435,-0.70217,92.555,0.37419,-0.59426,0.71193,21.838

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.8404,-0.54186,-0.010584,128.48,0.39205,-0.59435,-0.70217,86.68,0.37419,-0.59426,0.71193,20.236

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.89687,-0.44211,-0.012456,127.92,0.31477,-0.61825,-0.7202,93.609,0.31071,-0.64985,0.69365,27.65

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.89687,-0.44211,-0.012456,127.52,0.31477,-0.61825,-0.7202,95.437,0.31071,-0.64985,0.69365,29.561

> view matrix models
> #1,-0.89687,-0.44211,-0.012456,124.44,0.31477,-0.61825,-0.7202,92.625,0.31071,-0.64985,0.69365,32.887

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.65267,-0.75749,-0.015254,123.17,0.48571,-0.40288,-0.77574,78.977,0.58147,-0.51371,0.63087,17.266

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.65267,-0.75749,-0.015254,131.65,0.48571,-0.40288,-0.77574,74.387,0.58147,-0.51371,0.63087,17.936

> view matrix models
> #1,-0.65267,-0.75749,-0.015254,132.85,0.48571,-0.40288,-0.77574,82.595,0.58147,-0.51371,0.63087,11.574

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.63655,-0.75476,0.15853,117,0.67528,-0.64475,-0.35817,45.724,0.37255,-0.12094,0.9201,-16.667

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.63655,-0.75476,0.15853,115.14,0.67528,-0.64475,-0.35817,39.093,0.37255,-0.12094,0.9201,-17.536

> ui tool show Match→Align

> msa3d #2/A#1/A cutoffDistance 10 maxIterations none refChain #1/A

Match→Align cutoff: 10.0, in column if within cutoff of: any  
67 residue pairs aligned  
285 fully populated columns  
285 fully populated columns in at least 3 column stetches  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 129, in make_alignment  
ref_atoms = column_atoms(ref_seq, culled)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'principal_atom'  
  
AttributeError: 'NoneType' object has no attribute 'principal_atom'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in  
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])  
^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.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 Air
      Model Identifier: Mac14,2
      Model Number: Z1610005LLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 10 days, 8 hours, 33 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3.1
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202604220250
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.1
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    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-MatchAlign: 1.1
    ChimeraX-MatchMaker: 2.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.5.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.5
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.12
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.20.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.6
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.3
    pydantic-settings: 2.14.0
    pydantic_core: 2.46.3
    pydata-sphinx-theme: 0.17.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.26
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.3.4
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.6.3
    uvicorn: 0.45.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.23.0

Change History (2)

comment:1 by Eric Pettersen, 45 hours ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → msa3d not skipping None residues

comment:2 by Eric Pettersen, 45 hours ago

Resolution: → duplicate
Status: accepted → closed

Hi Kelly,

Thanks for reporting this problem. It was fixed about 10 days ago, so if you get the current ChimeraX 1.12 release candidate or the daily build then things should work.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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