'StrandPlank' object has no attribute '_straight_tilt'

[samo.lesnik@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-164-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
I tried to make strands in cartoons as planks with the command: cartoon style protein modeS plank. 

Log:
> select @area

Nothing selected  

> select @area 5

Expected a keyword  

> select @alt_loc

Nothing selected  

> select @alt_loc=A

Expected an objects specifier or a keyword  

> select @\alt_loc=A

Expected an objects specifier or a keyword  

> select \@alt_loc=A

Expected an objects specifier or a keyword  

> select /@alt_loc=A

Expected an objects specifier or a keyword  

> select @/alt_loc=A

Expected an objects specifier or a keyword  

> select @@alt_loc=A

Nothing selected  

> select @@charge

Nothing selected  

> select @@charge>2

Nothing selected  

> select @@charge>0

Nothing selected  

> select @@charge>-1

Nothing selected  

> select @@idatm_type=Car

724 atoms, 684 bonds, 125 residues, 1 model selected  

> select @@segname

Nothing selected  

> select @@segname=PROA

Nothing selected  

> select @@segname=A

Nothing selected  

> select @@segname=proa

Nothing selected  

> select ::segname=proa

Nothing selected  

> select ::segname=PROA

Nothing selected  

> select ##segname=PROA

Nothing selected  

> select @@segname=GPRA

Nothing selected  

> select @@segname=MUOR

Nothing selected  

> select ::segname=MUOR

Nothing selected  

> select ##segname=MUOR

Nothing selected  

> select ##segment=MUOR

Nothing selected  

> select ::segment=MUOR

Nothing selected  

> select @@segment=MUOR

Nothing selected  

> select ::segment=MUOR

Nothing selected  

> select ::segment=MUOR

Nothing selected  

> select ::segment=*

Nothing selected  

> select ::segname=*

Nothing selected  

> select @@segname=*

Nothing selected  

> select @@segment=*

Nothing selected  

> select ::segment=*

Nothing selected  

> select ##segment=*

Nothing selected  

> select ##segname=*

Nothing selected  

> select ::segname=*

Nothing selected  

> select ##segname=*

Nothing selected  

> select clear

[Repeated 1 time(s)]

> select add /?:217

178 atoms, 172 bonds, 5 residues, 1 model selected  

> select add /?:212

365 atoms, 355 bonds, 10 residues, 1 model selected  

> select up

745 atoms, 741 bonds, 34 residues, 1 model selected  

> select clear

Drag select of 5 residues  

> select up

190 atoms, 189 bonds, 12 residues, 1 model selected  

> hide sel cartoons

> select clear

Drag select of 15 atoms, 54 residues, 20 bonds  

> select up

717 atoms, 717 bonds, 43 residues, 2 models selected  

> select up

737 atoms, 739 bonds, 43 residues, 2 models selected  

> select up

971 atoms, 973 bonds, 57 residues, 2 models selected  

> select up

5652 atoms, 5701 bonds, 352 residues, 2 models selected  

> select clear

Drag select of 9 residues  

> select up

304 atoms, 302 bonds, 20 residues, 1 model selected  

> select up

5063 atoms, 5110 bonds, 335 residues, 1 model selected  

> select clear

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> select clear

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> select protein zr<3.5

Expected a keyword  

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> select sel :< 3.5 & ~sel

12304 atoms, 10236 bonds, 2058 residues, 1 model selected  

> select sel :< 3.5 & ~sel

30759 atoms, 27704 bonds, 3780 residues, 1 model selected  

> select intersect ::name="TIP"

8655 atoms, 5770 bonds, 2885 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 8655 atom styles  

> style sel ball

Changed 8655 atom styles  

> select clear

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> select clear

> select :MOR|:GDP

81 atoms, 87 bonds, 2 residues, 1 model selected  

> show sel surfaces

> style sel sphere

Changed 81 atom styles  

> hide sel surfaces

> select clear

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> select :POPC

54672 atoms, 53756 bonds, 408 residues, 1 model selected  

> show sel surfaces

> select :POPC

54672 atoms, 53756 bonds, 408 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> clip front 1 axis z position :MOR

> ~clip

> clip front 5 axis z position :MOR

> clip front 3 axis z position :MOR

> ~clip

> hide sel surfaces

> clip front 3 axis z position :MOR

> ~clip

> clip front 0 axis z position :MOR

[Repeated 1 time(s)]

> ~clip

> clip front 0 axis z position :MOR

> ~clip

> clip front 0.5 axis z position :MOR

> ~clip

> clip front -0.5 axis z position :MOR

> ~clip

> clip front -1.5 axis z position :MOR

> ~clip

> clip front -2.5 axis z position :MOR

[Repeated 3 time(s)]

> clip front -3.5 axis z position :MOR

> clip front -4.5 axis z position :MOR

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> clip model #!protein false

Missing or invalid "models" argument: invalid models specifier  

> clip #protein false

Expected a keyword  

> clip protein false

Expected a keyword  

> clip plane

Expected a keyword  

> clip plane x

Expected a keyword  

> clip axis z

> ~clip

> ~clip !protein

Expected fewer arguments  

> clip near

Missing "near" keyword's argument  

> clip near plane

Invalid "near" argument: Expected 'off' or a number  

> clip near 5

[Repeated 4 time(s)]

> ~clip

[Repeated 1 time(s)]

> clip position :MOR

[Repeated 2 time(s)]

> clip position :MOR offset

Expected a keyword  

> clip position :MOR offset 5

Expected a keyword  

> clip model !protein position :MOR

Missing or invalid "models" argument: invalid models specifier  

> clip model !protein True position :MOR

Missing or invalid "models" argument: invalid models specifier  

> clip model #1!protein True position :MOR

Missing or invalid "models" argument: only initial part "#1" of atom specifier
valid  

> clip model #0!protein True position :MOR

Missing or invalid "models" argument: only initial part "#0" of atom specifier
valid  

> clip model #0 true position :MOR

Expected a keyword  

> clip model #0 true

> clip model #0!proteinž true

Missing or invalid "models" argument: only initial part "#0" of atom specifier
valid  

> clip model #0!protein true

Missing or invalid "models" argument: only initial part "#0" of atom specifier
valid  

> clip model #0protein true

Missing or invalid "models" argument: only initial part "#0" of atom specifier
valid  

> clip model #0&protein true

> clip model #0&!protein true

Missing or invalid "models" argument: only initial part "#0" of atom specifier
valid  

> clip model #0&protein true

> clip model #0&protein false

> ~clip

> clip model #0&protein false

> clip model #0&protein true

> ~clip

> clip plane z position :MOR

Expected a keyword  

> clip axis z position :MOR

[Repeated 3 time(s)]

> clip axis z position :MOR offset

Expected a keyword  

> clip axis z position :MOR offset on

Expected a keyword  

> clip axis z position :MOR offset 2

Expected a keyword  

> clip model protein false

> clip axis z position :MOR

[Repeated 1 time(s)]

> select !protien

Expected an objects specifier or a keyword  

> select not protien

Expected an objects specifier or a keyword  

> select ~protien

Expected an objects specifier or a keyword  

> select protien

Expected an objects specifier or a keyword  

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> select !protein

Expected an objects specifier or a keyword  

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> select ~protein

307721 atoms, 223248 bonds, 84113 residues, 1 model selected  

> clip protein ~protein

Expected a keyword  

> split protein ~protein

Expected a keyword  

> split atoms protein atoms ~protein

Split step5_input.pdb (#1) into 2 models  
Chain information for step5_input.pdb 1 #1.1  
---  
Chain | Description  
? | No description available  
  

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> interfaces ~solvent

1 buried areas: #1.2/ #1.1/ 8014  

> interfaces ~solvent

1 buried areas: #1.2/ #1.1/ 8014  

> ui mousemode right clip

[Repeated 1 time(s)]

> ui tool show "Model Panel"

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> clip #1.2

Expected a keyword  

> clip model #1.2

Model #1.2 clipping True  

> clip axis y

> clip model #1.2

Model #1.2 clipping True  

> clip model #1.1 false

> close session

> open /home/samo/vol/opioid_dynamics/M_D_S/namd/step5_input.pdb format pdb

Summary of feedback from opening
/home/samo/vol/opioid_dynamics/M_D_S/namd/step5_input.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
224022 messages similar to the above omitted  
  
Chain information for step5_input.pdb #1  
---  
Chain | Description  
? | No description available  
  

> clip

> ~clip

> split atoms protein|:MOR|:GDP atoms :POPC|:TIP

Split step5_input.pdb (#1) into 3 models  
Chain information for step5_input.pdb 1 #1.1  
---  
Chain | Description  
? | No description available  
  

> hide #1.1 models

> show #1.1 models

> hide #1.3 models

> hide #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 cartoons

> hide #1.1 surfaces

> hide #1.1 atoms

> show #1.1 cartoons

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.3 models

> hide #1.3 models

> show #1.1 models

> select :MOR|:GDP

81 atoms, 87 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide #1.1 models

> show #1.1 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> style sel sphere

Changed 81 atom styles  

> select clear

> select add #1.2

304299 atoms, 220174 bonds, 83617 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> select TIP

Expected an objects specifier or a keyword  

> select :TIP

249627 atoms, 166418 bonds, 83209 residues, 1 model selected  

> hide sel atoms

> ui mousemode right clip

> hide #1.2 models

> show #1.2 models

> clip model #1.1 false

> ui mousemode right clip

> hide #1.2 models

> show #1.2 models

> select :SOD

226 atoms, 226 residues, 1 model selected  

> select :SOD|:CLA|CHLO

Expected an objects specifier or a keyword  

> select :SOD|:CLA|:CHLO

454 atoms, 454 residues, 1 model selected  

> select :SOD|:CLA|:CHL1

2970 atoms, 2602 bonds, 488 residues, 1 model selected  

> hide #1.1-2 atoms

> show #1.1-2 atoms

> select add #1.2/?:271@C217

2971 atoms, 2602 bonds, 489 residues, 2 models selected  

> select clear

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> select clear

> hide #1.1-2 atoms

> show #1.1-2 atoms

> select POPC

Expected an objects specifier or a keyword  

> select :POPC

54672 atoms, 53756 bonds, 408 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> style sel stick

Changed 54672 atom styles  

> style sel stick

Changed 54672 atom styles  

> style sel stick

Changed 54672 atom styles  

> style sel stick

Changed 54672 atom styles  

> style sel stick

Changed 54672 atom styles  

> hide sel atoms

> show sel surfaces

> hide #1.1 models

> show #1.1 models

> show sel atoms

> hide sel atoms

> select #1.1

16387 atoms, 16552 bonds, 1030 residues, 1 model selected  

> hide #!1.2 models

> show #!1.2 models

> hide #1.1 models

> show #1.1 models

> hide sel atoms

> hide sel cartoons

> show sel cartoons

> select clear

> select TIP

Expected an objects specifier or a keyword  

> select :TIP

249627 atoms, 166418 bonds, 83209 residues, 1 model selected  

> hide sel atoms

> select clear

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> select :MOR

41 atoms, 45 bonds, 1 residue, 1 model selected  

> show sel atoms

> select :GDP

40 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

[Repeated 1 time(s)]

> hide #1.1#!1.2 cartoons

> show #1.1#!1.2 cartoons

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> ui mousemode right clip

[Repeated 1 time(s)]

> clip model #1.1 false

> save /home/samo/vol/opioid_dynamics/forFigures/whole_system.cxs

> cartoon style pipe helix

Expected an atoms specifier or a keyword  

> cartoon

> cartoon style protein mode

Expected keyword "modeHelix" or "modeStrand"  

> cartoon style protein modeHelix

Missing "modeHelix" keyword's argument  

> cartoon style protein modeHelix tube

> cartoon style protein modeHelix tube width 1.5

> cartoon style protein modeHelix tube width 1.0

> cartoon style protein modeHelix tube width 1.6

> cartoon style protein modeHelix tube

> cartoon style protein modeHelix tube radius 2

> cartoon style protein modeHelix tube radius 2 sides 2

Invalid "sides" argument: Must be greater than or equal to 3  

> cartoon style protein modeHelix tube radius 2 sides 3

Invalid "sides" argument: Expected an even integer  

> cartoon style protein modeHelix tube radius 2 sides 5

Invalid "sides" argument: Expected an even integer  

> cartoon style protein modeHelix tube radius 2 sides 6

> cartoon style protein modeHelix tube radius 2

> cartoon style protein mode

Expected keyword "modeHelix" or "modeStrand"  

> cartoon style protein modeStrand

Missing "modeStrand" keyword's argument  

> cartoon style protein modeStrand

Missing "modeStrand" keyword's argument  

> cartoon style protein modeStrand arrow

Invalid "modeStrand" argument: Should be one of 'default' or 'plank'  

> cartoon style protein modeStrand plank

6 oxygens of 105 atoms in 6 residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 1809, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 347, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 651, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 589, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 118, in _make_ribbon_graphics  
_smooth_ribbon(residues, coords, guides, helix_ranges, sheet_ranges,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 928, in _smooth_ribbon  
_arc_strand(rlist, coords, guides, start, end)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/ribbon.py", line 1072, in _arc_strand  
sp = StrandPlank(coords[start:end], oxygens.coords)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/sse.py", line 477, in __init__  
self._straight_optimize()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/sse.py", line 555, in _straight_optimize  
self.width_vector, self.thickness_vector = self._straight_tilt()  
AttributeError: 'StrandPlank' object has no attribute '_straight_tilt'  
  
Error processing trigger "graphics update":  
AttributeError: 'StrandPlank' object has no attribute '_straight_tilt'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/sse.py", line 555, in _straight_optimize  
self.width_vector, self.thickness_vector = self._straight_tilt()  
  
See log for complete Python traceback.  
  

> cartoon style protein

step5_input.pdb 1 #1.1  
\- helix mode=tube xsection=round width=1.6 height=0.4 arrow=False arrow
scale=2  
\- strand mode=plank xsection=square width=1.6 height=0.4 arrow=True arrow
scale=2  
\- coil xsection=round width=0.4 height=0.4  
\- nucleic xsection=square width=0.4 height=2  
\- divisions=20  
\- oval parameters: sides=6  
\- barbell parameters: sides=18 scale=0.5  

> show #1.1#!1.2 atoms

> select clear

> show #1.1#!1.2 cartoons

> hide #1.1 models

> show #1.1 models

> select protein

16306 atoms, 16465 bonds, 1028 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> show sel cartoons




OpenGL version: 3.3.0 NVIDIA 525.125.06
OpenGL renderer: NVIDIA GeForce GTX 1050 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: System manufacturer
Model: System Product Name
OS: Linux Mint 20 Ulyana
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 2600X Six-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           47Gi        10Gi        25Gi       182Mi        11Gi        36Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	08:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd GP107 [GeForce GTX 1050 Ti] [1458:372a]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tom Goddard]

Not sure how you found this modeStrand option of the cartoon style command. It is not documented and is not shown by the "usage cartoon style" command and Google cannot find it. Maybe you looked at the ChimeraX source code.

Apparently modeStrand was an option under development and never fully implemented by Conrad when he retired.

ChimeraX currently does not support strands as planks.

[samo.lesnik@…]

I apologize for the late reply when I was on vacation.

This command is suggested as an expected keyword:

[image: image.png]

Thank you,

Samo


On Fri, Oct 27, 2023 at 8:31 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[samo.lesnik@…]

Added by email2trac

[Tom Goddard]

I see how you found this undocumented and unimplemented option. It should probably be removed from the code since the developer of the cartoon code left years ago. But I inherited his code and there is some small chance in the future I will make that option work. I think almost no one will stumble onto it as you did. Thanks for reporting it though, and if one more person finds it and reports the problem I will take it out so others don't waste their time trying it.