AtomicShapeDrawing: AttributeError: 'list' object has no attribute 'selected'

[manjila.bhusalp1@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505100155 (2025-05-10 01:55:54 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.10rc202505100155 (2025-05-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1HYS format mmcif fromDatabase pdb

1hys title:  
Crystal structure of hiv-1 reverse transcriptase In complex with A polypurine
tract RNA:DNA [more info...]  
  
Chain information for 1hys #1  
---  
Chain | Description | UniProt  
A | HIV-1 REVERSE TRANSCRIPTASE | POL_HV1B1 1-553  
B | HIV-1 REVERSE TRANSCRIPTASE | POL_HV1B1 1-425  
C | FAB-28 MONOCLONAL ANTIBODY FRAGMENT LIGHT CHAIN |   
D | FAB-28 MONOCLONAL ANTIBODY FRAGMENT HEAVY CHAIN |   
E | 5'-R(*UP*CP*AP*GP*CP*CP*AP*CP*UP*UP*UP*UP*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3' |   
F | 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*GP*GP*CP*TP*G)-3' |   
  

> sym #1

1hys mmCIF Assemblies  
---  
1| author_defined_assembly| 1 copy of chain A-F  
  

> sym #1 assembly 1

Made 1 copies for 1hys assembly 1  

> view

> ui tool show "Model Panel"

> sym #1 assembly 1

Made 1 copies for 1hys assembly 1  

> view

> sym #1 assembly 1

Made 1 copies for 1hys assembly 1  

> view

> select /A:1-553

17860 atoms, 18332 bonds, 2212 residues, 4 models selected  

> select /B:1-425

13924 atoms, 14332 bonds, 1700 residues, 4 models selected  

> select /C:1-214

6448 atoms, 6608 bonds, 856 residues, 4 models selected  

> ui tool show "Model Panel"

> toolshed show

> ui tool show "Model Panel"

[Repeated 1 time(s)]

> biological unit

Unknown command: biological unit  

> open 1HYS format mmcif fromDatabase pdb

1hys title:  
Crystal structure of hiv-1 reverse transcriptase In complex with A polypurine
tract RNA:DNA [more info...]  
  
Chain information for 1hys #5  
---  
Chain | Description | UniProt  
A | HIV-1 REVERSE TRANSCRIPTASE | POL_HV1B1 1-553  
B | HIV-1 REVERSE TRANSCRIPTASE | POL_HV1B1 1-425  
C | FAB-28 MONOCLONAL ANTIBODY FRAGMENT LIGHT CHAIN |   
D | FAB-28 MONOCLONAL ANTIBODY FRAGMENT HEAVY CHAIN |   
E | 5'-R(*UP*CP*AP*GP*CP*CP*AP*CP*UP*UP*UP*UP*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3' |   
F | 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*GP*GP*CP*TP*G)-3' |   
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 60695 atom styles  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "changes":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "changes":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "changes":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "changes":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "changes":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Preset expands to these ChimeraX commands:

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

  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 559, in rebuild  
_rebuild_molecule('internal', mol)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\nucleotides\\_data.py", line 713, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
AttributeError: 'list' object has no attribute 'selected'  
  
Error processing trigger "new frame":  
AttributeError: 'list' object has no attribute 'selected'  
  
File "C:\Program Files\ChimeraX 1.10rc202505100155\bin\Lib\site-
packages\chimerax\atomic\shapedrawing.py", line 297, in add_shapes  
if atoms is not None and all(atoms.selected):  
^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.5768
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Vivobook_ASUSLaptop X1404VA_X1404VA
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 8,196,866,048
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i5-1335U
OSLanguage: en-GB

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
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    build: 1.2.2.post1
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    cftime: 1.6.4.post1
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    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
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    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
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    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.18
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
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    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-Core: 1.10rc202505100155
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-gltf: 1.0
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    ChimeraX-MapFit: 2.0
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    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[pett]

Hi Manjila,

Thanks for reporting this problem. I have just committed a fix for it, which will be in tomorrow's release candidate and daily build. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Fix: ​https://github.com/RBVI/ChimeraX/commit/c8a85e4475a189624144ac7ab5d318b12f5c4257