Opened 4 weeks ago

Closed 4 weeks ago

#20176 closed defect (fixed)

"sym" command: tflist is None

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Documentos/Sonia/Curso
> ChimeraX_2026/EjercicioExtra/Groel/emd_8750.map"

Opened emd_8750.map as #1, grid size 240,240,240, pixel 1.23, shown at level
0.0402, step 1, values float32  

> open "C:/Documentos/Sonia/Curso
> ChimeraX_2026/EjercicioExtra/Groel/5w0s_monomerA.pdb"

5w0s_monomerA.pdb title:  
Groel using cryoem [more info...]  
  
Chain information for 5w0s_monomerA.pdb #2  
---  
Chain | Description | UniProt  
A | 60 kda chaperonin | Q6Q099_ECOLX 2-525  
  

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,32.401,0,1,0,-4.2034,0,0,1,-63.295

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93646,-0.3505,0.013596,93.168,0.098463,0.29988,0.94888,-52.033,-0.33666,-0.88725,0.31534,222.54

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,226.33,0.99603,-0.032476,-0.082906,209.91,-0.022606,-0.99284,0.11733,281.9

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,372.62,0.99603,-0.032476,-0.082906,242.94,-0.022606,-0.99284,0.11733,232.59

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,380.96,0.99603,-0.032476,-0.082906,232.4,-0.022606,-0.99284,0.11733,271.16

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,381.78,0.99603,-0.032476,-0.082906,187.71,-0.022606,-0.99284,0.11733,271.06

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,391.3,0.99603,-0.032476,-0.082906,175.98,-0.022606,-0.99284,0.11733,273.21

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,392.06,0.99603,-0.032476,-0.082906,175.29,-0.022606,-0.99284,0.11733,271.96

> view matrix models
> #2,-0.086122,-0.11499,-0.98963,400.37,0.99603,-0.032476,-0.082906,185.19,-0.022606,-0.99284,0.11733,274.12

> select clear

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01426, steps = 88  
shifted from previous position = 1.8  
rotated from previous position = 6.27 degrees  
atoms outside contour = 3245, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
0.01606642 -0.11326973 -0.99343437 401.49776610  
0.99796578 -0.05948827 0.02292246 172.23684464  
-0.06169412 -0.99178179 0.11208355 273.69217599  
Axis -0.57330587 -0.52643137 0.62784584  
Axis point 280.60879584 352.83867193 0.00000000  
Rotation angle (degrees) 117.75353674  
Shift along axis -149.01540911  
  

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,283.26,0.85357,-0.47821,-0.20672,289.88,-0.52022,-0.76099,-0.38763,319.84

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,281.57,0.85357,-0.47821,-0.20672,288.06,-0.52022,-0.76099,-0.38763,320.8

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.028054,0.43842,-0.89833,271.99,0.85357,-0.47821,-0.20672,286.49,-0.52022,-0.76099,-0.38763,312.21

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.23373,0.73372,-0.63798,166.94,0.69099,-0.33627,-0.63989,339.52,-0.68404,-0.5904,-0.4284,286.98

> view matrix models
> #2,-0.4608,0.84252,-0.27898,77.933,0.45205,-0.047703,-0.89072,331.08,-0.76375,-0.53656,-0.35888,263.39

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 116  
shifted from previous position = 3.91  
rotated from previous position = 12.7 degrees  
atoms outside contour = 3098, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53383562 0.74403247 -0.40179002 118.19507626  
0.58297715 -0.02033986 -0.81223392 314.19580887  
-0.61250076 -0.66783379 -0.42289579 304.63717083  
Axis 0.47818483 0.69777419 -0.53333896  
Axis point -28.69975753 0.00000000 268.91180194  
Rotation angle (degrees) 171.31582617  
Shift along axis 113.28194823  
  

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 48  
shifted from previous position = 0.00321  
rotated from previous position = 0.00712 degrees  
atoms outside contour = 3098, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53393407 0.74396549 -0.40178322 118.20407305  
0.58296564 -0.02027077 -0.81224391 314.18705575  
-0.61242589 -0.66791051 -0.42288306 304.65184338  
Axis 0.47813643 0.69780062 -0.53334777  
Axis point -28.68472024 0.00000000 268.91359090  
Rotation angle (degrees) 171.31898471  
Shift along axis 113.27221771  
  

> select clear

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.01777, steps = 60  
shifted from previous position = 0.0198  
rotated from previous position = 0.0294 degrees  
atoms outside contour = 3097, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.53385021 0.74401227 -0.40180805 118.19585852  
0.58269374 -0.02065750 -0.81242924 314.28420126  
-0.61275767 -0.66784655 -0.42250328 304.54798237  
Axis 0.47816493 0.69765414 -0.53351381  
Axis point -28.71734716 0.00000000 268.95609821  
Rotation angle (degrees) 171.30439704  
Shift along axis 113.29823517  
  

> transparency 50

> ui mousemode right "translate selected models"

> select add #2

3870 atoms, 3879 bonds, 543 residues, 1 model selected  

> view matrix models
> #2,-0.53385,0.74401,-0.40181,119.61,0.58269,-0.020658,-0.81243,316.45,-0.61276,-0.66785,-0.4225,302.55

> view matrix models
> #2,-0.53385,0.74401,-0.40181,155.35,0.58269,-0.020658,-0.81243,376.56,-0.61276,-0.66785,-0.4225,318.52

> view matrix models
> #2,-0.53385,0.74401,-0.40181,141.21,0.58269,-0.020658,-0.81243,351.18,-0.61276,-0.66785,-0.4225,309.96

> view matrix models
> #2,-0.53385,0.74401,-0.40181,141.81,0.58269,-0.020658,-0.81243,348.23,-0.61276,-0.66785,-0.4225,301.14

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.59355,0.63071,-0.4999,180.12,0.47521,-0.22664,-0.85018,391.73,-0.64952,-0.74218,-0.16519,266.44

> view matrix models
> #2,-0.61875,0.50352,-0.603,222.25,0.6016,-0.18991,-0.77589,372.51,-0.50519,-0.84285,-0.18542,290.06

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.61875,0.50352,-0.603,225.02,0.6016,-0.18991,-0.77589,387.82,-0.50519,-0.84285,-0.18542,315.4

> view matrix models
> #2,-0.61875,0.50352,-0.603,201.79,0.6016,-0.18991,-0.77589,343.17,-0.50519,-0.84285,-0.18542,294.63

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.05266, steps = 80  
shifted from previous position = 5.27  
rotated from previous position = 8.09 degrees  
atoms outside contour = 1603, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.62786285 0.39081539 -0.67309106 238.56749641  
0.66540920 -0.17908472 -0.72467873 328.84863044  
-0.40375593 -0.90287983 -0.14761152 301.81944619  
Axis -0.42037588 -0.63536080 0.64776599  
Axis point 195.98712664 328.22817834 0.00000000  
Rotation angle (degrees) 167.76308568  
Shift along axis -113.71717867  
  

> fitmap #2 inMap #1

Fit molecule 5w0s_monomerA.pdb (#2) to map emd_8750.map (#1) using 3870 atoms  
average map value = 0.05266, steps = 60  
shifted from previous position = 0.0195  
rotated from previous position = 0.0344 degrees  
atoms outside contour = 1610, contour level = 0.040152  
  
Position of 5w0s_monomerA.pdb (#2) relative to emd_8750.map (#1) coordinates:  
Matrix rotation and translation  
-0.62771733 0.39092638 -0.67316233 238.57161894  
0.66526053 -0.17964756 -0.72467591 328.93878596  
-0.40422690 -0.90271996 -0.14730000 301.71479671  
Axis -0.42048960 -0.63514932 0.64789956  
Axis point 195.98378971 328.11807717 -0.00000000  
Rotation angle (degrees) 167.77739501  
Shift along axis -113.76124344  
  

> select clear

> sym #2 symetry #1

Expected a keyword  

> sym #2 symmetry #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\sym.py", line 100, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 510, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 520, in parse_symmetry  
ops = ops * group_symmetries(session, g, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in group_symmetries  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in <listcomp>  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> sym #2 symmetry #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 322, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\std_commands\sym.py", line 100, in sym  
transforms = symmetry.positions(center, axis, coordinate_system,
structures[0])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 510, in positions  
return parse_symmetry(self.session, self.group, c, a, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 520, in parse_symmetry  
ops = ops * group_symmetries(session, g, molecule)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in group_symmetries  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 636, in <listcomp>  
mslist = [model_symmetry(m) for m in models]  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\args.py", line 681, in model_symmetry  
if len(tflist) <= 1:  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 750x609+825+410 (frame:
768x656+816+372) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x601+826+417 (frame: 766x648+817+379)
margins: 9, 38, 9, 9 minimum size: 600x333 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=463)))  

> volume #1 level 0.04185




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: es_ES.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: LENOVO
Model: 81WE
OS: Microsoft Windows 11 Home (Build 26200)
Memory: 8,319,787,008
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
OSLanguage: es-ES

Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2026.1.4
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    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: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    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: 1.1.4
    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: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    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-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    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: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    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: 6.7.0
    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
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    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: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 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: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    WMI: 1.5.1
    yarl: 1.22.0

Change History (2)

comment:1 by Eric Pettersen, 4 weeks ago

Component: Unassigned → Higher-Order Structure
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "sym" command: tflist is None

comment:2 by Tom Goddard, 4 weeks ago

Resolution: → fixed
Status: assigned → closed

Fixed.

User tried to apply symmetry to an atomic model using an EMDB map that had no symmetry info. The code didn't properly handle the case where the map has no symmetry.

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