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#7814 closed defect (fixed)

SEQCROW: substitute: list.remove(x): x not in list

Reported by:	ichcharisma@…	Owned by:	Tony Schaefer
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Custom presets folder '/Users/ich/Charisma/S-PRED' does not exist  
  

> color name ocean #005493

Color 'ocean' is opaque: rgb(0%, 32.9%, 57.6%) hex: #005493

  

> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6

> alias cylinders cartoon style protein modeh tube rad 2 sides 24

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ich/Charisma/DSIM/luigi/dna_no_mutated.pdb format pdb

Chain information for dna_no_mutated.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "Build Structure"

> ~select

Nothing selected  

> select sel

Nothing selected  

> select all

1142 atoms, 1280 bonds, 56 residues, 1 model selected  

> nucleotides sel stubs

> ribbon sty x oval w 1 t 1

> color sel dark seagreen

> ~select

Nothing selected  

> ui tool show "Change Substituents"

> select /A:12

19 atoms, 20 bonds, 1 residue, 1 model selected  

> nucleotides

Missing or invalid "representation" argument: Expected one of 'atoms', 'fill',
'ladder', 'slab', 'stubs', or 'tube/slab'  

> nucleotides atoms

> select all

1142 atoms, 1280 bonds, 56 residues, 1 model selected  

> nucleotides stubs radius 0.3

> nucleotides stubs rode 0.3

Expected a keyword  

> nucleotides stubs

> ~select

Nothing selected  

> select /A:12

19 atoms, 20 bonds, 1 residue, 1 model selected  

> nucleotides sel atoms

> select /A:12,17

38 atoms, 40 bonds, 2 residues, 1 model selected  

> nucleotides sel atoms

> color sel byhetero

> color sel & C yellow

> color sel & C grey

> color sel & C gold

> ~select

Nothing selected  

> ui mousemode right bond

> select /A:12@C5

1 atom, 1 residue, 1 model selected  

> ui mousemode right substitute

> ui mousemode right "select fragment"

> select clear

> select /A:12@C5

1 atom, 1 residue, 1 model selected  

> ui mousemode right bond

> ui mousemode right tsbond

> ui mousemode right "change element"

> ui mousemode right bond

> select clear

> select /A:12@C5

1 atom, 1 residue, 1 model selected  

> ui mousemode right substitute

> substitute /A:12@C5 substituents Me minimize true newResidue false
> useRemoteness false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/mouse_modes.py", line 914, in mouse_up  
run(  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/commands/substitute.py", line 184, in substitute  
rescol.substitute(  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 563, in substitute  
residue.substitute(sub, target, *args, attached_to=attached_to,
minimize=False, **kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 376, in substitute  
return super().substitute(sub, target, *args, attached_to=attached_to,
**kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 4056, in substitute  
geom -= old  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
ValueError: list.remove(x): x not in list  
  

Populating font family aliases took 318 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

ValueError: list.remove(x): x not in list  
  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
  
See log for complete Python traceback.  
  

> substitute /A:12@C5 substituents Me minimize true newResidue false
> useRemoteness false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/mouse_modes.py", line 914, in mouse_up  
run(  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/commands/substitute.py", line 184, in substitute  
rescol.substitute(  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 563, in substitute  
residue.substitute(sub, target, *args, attached_to=attached_to,
minimize=False, **kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 376, in substitute  
return super().substitute(sub, target, *args, attached_to=attached_to,
**kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 4056, in substitute  
geom -= old  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
  
See log for complete Python traceback.  
  

> substitute /A:12@C5 substituents Me minimize true newResidue false
> useRemoteness false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/mouse_modes.py", line 914, in mouse_up  
run(  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/commands/substitute.py", line 184, in substitute  
rescol.substitute(  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 563, in substitute  
residue.substitute(sub, target, *args, attached_to=attached_to,
minimize=False, **kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 376, in substitute  
return super().substitute(sub, target, *args, attached_to=attached_to,
**kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 4056, in substitute  
geom -= old  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
  
See log for complete Python traceback.  
  

> substitute /A:12@C5 substituents Me minimize true newResidue false
> useRemoteness false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 637, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 531, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/mouse_modes.py", line 914, in mouse_up  
run(  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/commands/substitute.py", line 184, in substitute  
rescol.substitute(  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 563, in substitute  
residue.substitute(sub, target, *args, attached_to=attached_to,
minimize=False, **kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 376, in substitute  
return super().substitute(sub, target, *args, attached_to=attached_to,
**kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 4056, in substitute  
geom -= old  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
  
See log for complete Python traceback.  
  

> substitute /A:12@C5 substituents Me minimize true newResidue false
> useRemoteness false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 639, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/mouse_modes.py", line 914, in mouse_up  
run(  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/commands/substitute.py", line 184, in substitute  
rescol.substitute(  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 563, in substitute  
residue.substitute(sub, target, *args, attached_to=attached_to,
minimize=False, **kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/SEQCROW/residue_collection.py", line 376, in substitute  
return super().substitute(sub, target, *args, attached_to=attached_to,
**kwargs)  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 4056, in substitute  
geom -= old  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
ValueError: list.remove(x): x not in list  
  
ValueError: list.remove(x): x not in list  
  
File "/Users/ich/Library/Application Support/ChimeraX/1.4/site-
packages/AaronTools/geometry.py", line 712, in __sub__  
self.atoms.remove(o)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.48
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.40.8.0.0 (iBridge: 20.16.406.5.1,0)
      OS Loader Version: 564.40.4~15

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A5373b)
      Kernel Version: Darwin 22.1.0
      Time since boot: 20 hours, 5 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        LG HDR WQHD:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 85.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 111NTJJ17772
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: ff.c1


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.5.4
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (4)

comment:1 by Eric Pettersen, 3 years ago

Component:	Unassigned → Third Party
Owner:	set to Tony Schaefer
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → SEQCROW: substitute: list.remove(x): x not in list

Reported by "Charisma"

in reply to: 2 ; follow-up: 2 comment:2 by Tony Schaefer, 3 years ago

My best guess is that the user was using the substitute mouse mode and clicked on an atom in a ring. Modifying substituents only works if there's just one bond connecting the clicked atom to the longest fragment on the clicked atom. The clicked atom and all other groups coming off of it, other than the largest, are deleted and replaced with the new substituent.

I will try to reproduce this for a non-cyclic structure, but it probably just needs a more clear error message.

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, October 19, 2022 12:26 PM
Cc: ichcharisma@gmail.com <ichcharisma@gmail.com>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7814: SEQCROW: substitute: list.remove(x): x not in list (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#7814: SEQCROW: substitute: list.remove(x): x not in list
------------------------------------+---------------------------
          Reporter:  ichcharisma@…  |      Owner:  Tony Schaefer
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+---------------------------
Changes (by pett):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tony Schaefer


Comment:

 Reported by "Charisma"

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7814#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to: 3 ; follow-up: 3 comment:3 by Tony Schaefer, 3 years ago

Apparently there were bugs with replacing a ring with a new substituent and putting it in a new residue. Hard to tell if that's what happened here, as the same error message might've shown up when just trying to substitute an atom in a ring if there are no non-ring atoms connected to that atom. Either way, fixed in SEQCROW 1.5.5

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, October 19, 2022 7:50 PM
To: ichcharisma@gmail.com <ichcharisma@gmail.com>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7814: SEQCROW: substitute: list.remove(x): x not in list

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#7814: SEQCROW: substitute: list.remove(x): x not in list
------------------------------------+---------------------------
          Reporter:  ichcharisma@…  |      Owner:  Tony Schaefer
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Third Party    |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+---------------------------

Comment (by Tony Schaefer):

 {{{
 My best guess is that the user was using the substitute mouse mode and
 clicked on an atom in a ring. Modifying substituents only works if there's
 just one bond connecting the clicked atom to the longest fragment on the
 clicked atom. The clicked atom and all other groups coming off of it,
 other than the largest, are deleted and replaced with the new substituent.

 I will try to reproduce this for a non-cyclic structure, but it probably
 just needs a more clear error message.

 Tony
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: Wednesday, October 19, 2022 12:26 PM
 Cc: ichcharisma@gmail.com <ichcharisma@gmail.com>; Anthony James Schaefer
 <tony.schaefer@uga.edu>
 Subject: Re: [ChimeraX] #7814: SEQCROW: substitute: list.remove(x): x not
 in list (was: ChimeraX bug report submission)

 [EXTERNAL SENDER - PROCEED CAUTIOUSLY]


 #7814: SEQCROW: substitute: list.remove(x): x not in list
 ------------------------------------+---------------------------
           Reporter:  ichcharisma@…  |      Owner:  Tony Schaefer
               Type:  defect         |     Status:  assigned
           Priority:  normal         |  Milestone:
          Component:  Third Party    |    Version:
         Resolution:                 |   Keywords:
         Blocked By:                 |   Blocking:
 Notify when closed:                 |   Platform:  all
            Project:  ChimeraX       |
 ------------------------------------+---------------------------
 Changes (by pett):

  * status:  new => assigned
  * component:  Unassigned => Third Party
  * project:   => ChimeraX
  * platform:   => all
  * owner:  (none) => Tony Schaefer


 Comment:

  Reported by "Charisma"

 --
 Ticket URL:
 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7814#comment:1>
 ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7814#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by Eric Pettersen, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

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