pbond adding group to scene twice

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
If I use the `pbond` command to create a pseudobond between two different models, then subsequent calls on the same or a new inter-model selection fail.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5c3i

Summary of feedback from opening 5c3i fetched from pdb  
---  
note | Fetching compressed mmCIF 5c3i from http://files.rcsb.org/download/5c3i.cif  
  
5c3i title:  
Crystal structure of the quaternary complex of histone H3-H4 heterodimer with
chaperone ASF1 and the replicative helicase subunit MCM2 [more info...]  
  
Chain information for 5c3i #1  
---  
Chain | Description | UniProt  
A E I M Q U | Histone chaperone ASF1A | ASF1A_HUMAN 1-175  
B F J N R V | Histone H3.1 | H31_HUMAN 0-135  
C G K O S W | Histone H4 | H4_HUMAN 0-102  
D H L P T X | DNA replication licensing factor MCM2,MCM2 | MCM2_HUMAN 63-124 63-126  
  
5c3i mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
5| author_and_software_defined_assembly  
6| author_and_software_defined_assembly  
  

> close

> open 7w1y

Summary of feedback from opening 7w1y fetched from pdb  
---  
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain O  
Ignoring microheterogeneity for label_seq_id 2 in chain O  
Ignoring microheterogeneity for label_seq_id 3 in chain O  
Ignoring microheterogeneity for label_seq_id 4 in chain O  
Ignoring microheterogeneity for label_seq_id 5 in chain O  
93 messages similar to the above omitted  
note | Fetching compressed mmCIF 7w1y from http://files.rcsb.org/download/7w1y.cif  
  
7w1y title:  
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]  
  
Chain information for 7w1y #1  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808  
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
O | DNA (49-MER) |   
S | DNA (49-MER) |   
  
Non-standard residues in 7w1y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  
2025 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close

> open 5c3i

5c3i title:  
Crystal structure of the quaternary complex of histone H3-H4 heterodimer with
chaperone ASF1 and the replicative helicase subunit MCM2 [more info...]  
  
Chain information for 5c3i #1  
---  
Chain | Description | UniProt  
A E I M Q U | Histone chaperone ASF1A | ASF1A_HUMAN 1-175  
B F J N R V | Histone H3.1 | H31_HUMAN 0-135  
C G K O S W | Histone H4 | H4_HUMAN 0-102  
D H L P T X | DNA replication licensing factor MCM2,MCM2 | MCM2_HUMAN 63-124 63-126  
  
5c3i mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
5| author_and_software_defined_assembly  
6| author_and_software_defined_assembly  
  

> cartoon

> hide

> select /D,H,L,P,T,X

2627 atoms, 2638 bonds, 1 pseudobond, 335 residues, 2 models selected  

> usage rain

rainbow [objects] [level] [target a text string] [transparency a number]
[palette a colormap]  
— color residues and chains sequentially  
objects: an objects specifier or nothing  
level: one of chains, polymers, residues, or structures  

> rainbow sel level chains

> select clear

> open 7w1y

Summary of feedback from opening 7w1y fetched from pdb  
---  
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain O  
Ignoring microheterogeneity for label_seq_id 2 in chain O  
Ignoring microheterogeneity for label_seq_id 3 in chain O  
Ignoring microheterogeneity for label_seq_id 4 in chain O  
Ignoring microheterogeneity for label_seq_id 5 in chain O  
93 messages similar to the above omitted  
  
7w1y title:  
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]  
  
Chain information for 7w1y #2  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808  
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
O | DNA (49-MER) |   
S | DNA (49-MER) |   
  
Non-standard residues in 7w1y #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  
2025 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select #2/2

5624 atoms, 5726 bonds, 9 pseudobonds, 709 residues, 3 models selected  

>

Unknown command: sequence #2/2  

> sequence chain #2/2

Alignment identifier is 2/2  

> rainbow sel

> select clear

> cartoon #2

> hide #2&protein

> rainbow #2/A

> select #2/D,H,L,P,T,X:124-126

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/D,H,L,P,T,X:120-126

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select #2/D,H,L,P,T,X:100-126

201 atoms, 202 bonds, 27 residues, 1 model selected  

> show sel

> hide sel

> select #1/D,H,L,P,T,X:120-126

200 atoms, 195 bonds, 21 residues, 1 model selected  

> show sel

> select #2

66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-49.496,0,1,0,-40.506,0,0,1,-90.403

> lighting simple

> view matrix models #2,1,0,0,-59.603,0,1,0,-64.048,0,0,1,-116.49

> view matrix models
> #2,-0.26403,-0.31933,0.91012,61.022,-0.88443,-0.29631,-0.36054,474.87,0.38481,-0.90013,-0.20419,250.78

> view matrix models
> #2,-0.26403,-0.31933,0.91012,67.168,-0.88443,-0.29631,-0.36054,452.34,0.38481,-0.90013,-0.20419,240.83

> view matrix models
> #2,-0.52242,-0.0063509,0.85266,77.317,-0.78019,0.40704,-0.47499,231.94,-0.34405,-0.91339,-0.2176,389.2

> view matrix models
> #2,-0.36984,-0.23746,0.89824,94.825,-0.92154,-0.029313,-0.38718,259.15,0.11827,-0.97096,-0.20798,293.99

> view matrix models
> #2,-0.36984,-0.23746,0.89824,103.94,-0.92154,-0.029313,-0.38718,182.99,0.11827,-0.97096,-0.20798,281.73

> view matrix models
> #2,-0.36984,-0.23746,0.89824,68.873,-0.92154,-0.029313,-0.38718,210.58,0.11827,-0.97096,-0.20798,305.11

> view matrix models
> #2,-0.84183,-0.40931,0.35183,312.7,-0.34391,-0.095608,-0.93412,222.08,0.41598,-0.90737,-0.060281,198.77

> view matrix models
> #2,-0.84183,-0.40931,0.35183,305.29,-0.34391,-0.095608,-0.93412,213.28,0.41598,-0.90737,-0.060281,193.45

> view matrix models
> #2,-0.60233,-0.54426,0.58394,231.25,-0.68102,-0.031246,-0.73159,226.69,0.41642,-0.83834,-0.35183,243.53

> view matrix models
> #2,-0.60233,-0.54426,0.58394,218.59,-0.68102,-0.031246,-0.73159,195.36,0.41642,-0.83834,-0.35183,245.09

> surface #1/B,F,J,N,R,V,C,G,K,O,S,W

> select #1/D,H,L,P,T,X

2627 atoms, 2638 bonds, 1 pseudobond, 335 residues, 2 models selected  

> color sel brown

> select clear

> lighting soft

> cofr centerOfView showPivot true

> select clear

> color #2/O orange

> color #2/S firebrick

> select clear

> select #1/D:138

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select up

35 atoms, 34 bonds, 7 residues, 1 model selected  

> ~cartoon sel

> select #1/D:122@CA

1 atom, 1 residue, 1 model selected  

> select add #1/L:123@CD

2 atoms, 2 residues, 1 model selected  

> select #1/D,H,L,P,T,X

2627 atoms, 2638 bonds, 1 pseudobond, 335 residues, 2 models selected  

> hide sel

> select #1/D:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/A:176

17 atoms, 15 bonds, 2 residues, 2 models selected  

> usage pseudo

"pseudo" is not a command name  

> usage bond

bond atoms [reasonable true or false]  
— add bond(s)

bond length bond [length] [move move]  
— set bond length  
length: a number > 0  
move: one of large or small  

> help help:user

> ui tool show "Bond Editor"

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

2 atoms must be selected  

> select sel&@CA

2 atoms, 2 residues, 2 models selected  

> tsbond sel color rgb(171, 255, 255) radius 0.160 transparency 75

atoms must be on the same structure  

> usage pbond

pbond atoms [color a color] [currentCoordsetOnly true or false] [dashes
dashes] [global] [name a text string] [radius radius] [reveal true or false]
[showDist true or false]  
— Create pseudobond  
dashes: an integer ≥ 0  
radius: a number > 0

pbond delete atoms [global] [name a text string]  
— Delete pseudobond  

> pbond sel dashes 20

> pbond sel dashes 20 radius 0.3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 185, in pbond_cmd  
session.models.add([pbg])  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 749, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model custom #3 to scene twice  
  
ValueError: Attempted to add model custom #3 to scene twice  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 749, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  

> select #1/L:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #2/2:176

17 atoms, 15 bonds, 2 residues, 2 models selected  

> select sel&@CA

2 atoms, 2 residues, 2 models selected  

> pbond sel dashes 20 radius 0.3

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 185, in pbond_cmd  
session.models.add([pbg])  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 749, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model custom #3 to scene twice  
  
ValueError: Attempted to add model custom #3 to scene twice  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 749, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       7.4Gi        12Gi       347Mi        11Gi        22Gi
	Swap:          2.0Gi       1.4Gi       576Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.8
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[Eric Pettersen]

Happens only for pseudobond between different models

[Eric Pettersen]

Fixed in the next daily. Note that running "pbond" twice with the same atoms will create two pseudobonds, not replace the existing one.

Fix: ​https://github.com/RBVI/ChimeraX/commit/b151bae24573450353949998dea6d8fdc6503341