Opened 6 days ago

Closed 5 days ago

#19439 closed defect (fixed)

Chain integrity in PDB format

Reported by: kgf4@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
We are trying to isolate specific chains from a Model Angelo .cif file for further refinement. We open the model, select the desired chains (18 total), invert the selection, delete the selected atoms and bonds, rename the remaining chains to single-letter names, and save a PDB file using the hybrid-36 format. Upon opening the new PDB file, we see many broken chains in the model. Inspection of the PDB file in a text editor shows many LINK and CONECT lines have been added relative to the original file. If these are deleted, the revised PDB model looks OK in ChimeraX. Note that this problem is system-agnostic (happens on both the Mac and Windows versions of 1.10) and could NOT be reproduced on a Mac running version 1.9. 

I am attaching PDB file from Model Angelo here, and the log is included in the report. We appreciate your help with figuring what is going wrong in our workflow!

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/J126_MA.cif"

Summary of feedback from opening
C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail tube/J126_MA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for J126_MA.cif #1  
---  
Chain | Description  
AAQa | No description available  
AGOa | No description available  
AHDa | No description available  
ANUa | No description available  
AWQa | No description available  
DCa | No description available  
DMa | No description available  
DXa | No description available  
FHa FHb | No description available  
HCa | No description available  
JI0 JI1 JI2 JI4 JIw JIx JIz | No description available  
JI3 | No description available  
JI5 | No description available  
JI6 JI7 | No description available  
JI8 | No description available  
JI9 JIaa | No description available  
JIa | No description available  
JIab JIac | No description available  
JIad | No description available  
JIae | No description available  
JIaf | No description available  
JIag | No description available  
JIah | No description available  
JIai | No description available  
JIaj | No description available  
JIak | No description available  
JIal | No description available  
JIam | No description available  
JIan | No description available  
JIao | No description available  
JIap | No description available  
JIaq | No description available  
JIar | No description available  
JIas | No description available  
JIat | No description available  
JIau | No description available  
JIav | No description available  
JIb JIc JId JIe JIf JIg JIh JIi JIj JIk JIl JIm JIn JIo JIp JIq JIr JIs JIt JIu JIv | No description available  
JIy | No description available  
JNa | No description available  
KGa | No description available  
KXa | No description available  
PQa | No description available  
RTa | No description available  
VVa | No description available  
YWa | No description available  
  

Cannot find consistent set of bond orders for ring system containing atom CG1
in residue VAL /JIai:76  

> hide atoms

> show cartoons

Computing secondary structure  

> select
> /JIa/JId/JIe/JI1/JIk/JIs/JIf/JI5/JIl/JIj/JIg/JIz/JIi/JIu/JI2/JIq/JIn/JIv

26966 atoms, 27885 bonds, 3521 residues, 1 model selected  

> select ~sel & ##selected

46818 atoms, 48923 bonds, 108 pseudobonds, 6114 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> select #1/JI5

1497 atoms, 1542 bonds, 195 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel A

Chain IDs of 195 residues changed  

> select #1/JIf

1501 atoms, 1552 bonds, 196 residues, 1 model selected  

> changechains sel B

Chain IDs of 196 residues changed  

> select #1/JIe

1501 atoms, 1548 bonds, 196 residues, 1 model selected  

> changechains sel C

Chain IDs of 196 residues changed  

> select #1/JIg

1501 atoms, 1556 bonds, 196 residues, 1 model selected  

> changechains sel D

Chain IDs of 196 residues changed  

> select #1/JIj

1501 atoms, 1552 bonds, 196 residues, 1 model selected  

> changechains sel E

Chain IDs of 196 residues changed  

> select #1/JIl

1501 atoms, 1550 bonds, 196 residues, 1 model selected  

> changechains sel F

Chain IDs of 196 residues changed  

> select #1/JIs

1501 atoms, 1549 bonds, 196 residues, 1 model selected  

> changechains sel G

Chain IDs of 196 residues changed  

> select #1/JIv

1501 atoms, 1556 bonds, 196 residues, 1 model selected  

> changechains sel H

Chain IDs of 196 residues changed  

> select #1/JIa

1474 atoms, 1524 bonds, 193 residues, 1 model selected  

> changechains sel I

Chain IDs of 193 residues changed  

> select #1/JI1

1494 atoms, 1543 bonds, 195 residues, 1 model selected  

> changechains sel J

Chain IDs of 195 residues changed  

> select #1/JId

1501 atoms, 1553 bonds, 196 residues, 1 model selected  

> changechains sel K

Chain IDs of 196 residues changed  

> select #1/JIk

1501 atoms, 1558 bonds, 196 residues, 1 model selected  

> changechains sel L

Chain IDs of 196 residues changed  

> select #1/JI2

1494 atoms, 1539 bonds, 195 residues, 1 model selected  

> changechains sel M

Chain IDs of 195 residues changed  

> select #1/JIu

1501 atoms, 1550 bonds, 196 residues, 1 model selected  

> changechains sel N

Chain IDs of 196 residues changed  

> select #1/JIi

1501 atoms, 1555 bonds, 196 residues, 1 model selected  

> changechains sel O

Chain IDs of 196 residues changed  

> select #1/JIz

1494 atoms, 1544 bonds, 195 residues, 1 model selected  

> changechains sel P

Chain IDs of 195 residues changed  

> select #1/JIn

1501 atoms, 1546 bonds, 196 residues, 1 model selected  

> changechains sel Q

Chain IDs of 196 residues changed  

> select #1/JIq

1501 atoms, 1549 bonds, 196 residues, 1 model selected  

> changechains sel R

Chain IDs of 196 residues changed  

> changechains sel R

Chain IDs of 0 residues changed  

> select #1/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R

26966 atoms, 27885 bonds, 3521 residues, 1 model selected  

> select subtract #1

Nothing selected  

> save "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/Fionn_TailTube_3rings_TEST3.pdb" relModel #1

> open "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/Fionn_TailTube_3rings_TEST3.pdb"

Chain information for Fionn_TailTube_3rings_TEST3.pdb #2  
---  
Chain | Description  
A | No description available  
B C D E F G H K L N O Q R | No description available  
I | No description available  
J M P | No description available  
  

> hide atoms

> show cartoons

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> close #1-2

> open "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/J126_MA.cif"

Summary of feedback from opening
C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail tube/J126_MA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for J126_MA.cif #1  
---  
Chain | Description  
AAQa | No description available  
AGOa | No description available  
AHDa | No description available  
ANUa | No description available  
AWQa | No description available  
DCa | No description available  
DMa | No description available  
DXa | No description available  
FHa FHb | No description available  
HCa | No description available  
JI0 JI1 JI2 JI4 JIw JIx JIz | No description available  
JI3 | No description available  
JI5 | No description available  
JI6 JI7 | No description available  
JI8 | No description available  
JI9 JIaa | No description available  
JIa | No description available  
JIab JIac | No description available  
JIad | No description available  
JIae | No description available  
JIaf | No description available  
JIag | No description available  
JIah | No description available  
JIai | No description available  
JIaj | No description available  
JIak | No description available  
JIal | No description available  
JIam | No description available  
JIan | No description available  
JIao | No description available  
JIap | No description available  
JIaq | No description available  
JIar | No description available  
JIas | No description available  
JIat | No description available  
JIau | No description available  
JIav | No description available  
JIb JIc JId JIe JIf JIg JIh JIi JIj JIk JIl JIm JIn JIo JIp JIq JIr JIs JIt JIu JIv | No description available  
JIy | No description available  
JNa | No description available  
KGa | No description available  
KXa | No description available  
PQa | No description available  
RTa | No description available  
VVa | No description available  
YWa | No description available  
  

Cannot find consistent set of bond orders for ring system containing atom CG2
in residue VAL /JIai:76  

> hide atoms

> show cartoons

Computing secondary structure  

> select
> /JIa/JId/JIe/JI1/JIk/JIs/JIf/JI5/JIl/JIj/JIg/JIz/JIi/JIu/JI2/JIq/JIn/JIv

26966 atoms, 27885 bonds, 3521 residues, 1 model selected  

> select ~sel & ##selected

46818 atoms, 48923 bonds, 108 pseudobonds, 6114 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> ui tool show "Change Chain IDs"

> changechains JI1 A

Chain IDs of 195 residues changed  

> changechains JI2 B

Chain IDs of 195 residues changed  

> changechains JI5 C

Chain IDs of 195 residues changed  

> changechains JIa D

Chain IDs of 193 residues changed  

> changechains JId E

Chain IDs of 196 residues changed  

> changechains JIe F

Chain IDs of 196 residues changed  

> changechains JIf G

Chain IDs of 196 residues changed  

> changechains JIg H

Chain IDs of 196 residues changed  

> changechains JIi I

Chain IDs of 196 residues changed  

> changechains JIj J

Chain IDs of 196 residues changed  

> changechains JIk K

Chain IDs of 196 residues changed  

> changechains JIl L

Chain IDs of 196 residues changed  

> changechains JIn M

Chain IDs of 196 residues changed  

> changechains JIq N

Chain IDs of 196 residues changed  

> changechains JIs O

Chain IDs of 196 residues changed  

> changechains JIu P

Chain IDs of 196 residues changed  

> changechains JIv Q

Chain IDs of 196 residues changed  

> changechains JIz R

Chain IDs of 195 residues changed  

> save "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/Fionn_TailTube_3rings_TEST4.pdb" relModel #1

> open "C:/Users/kgf4/Dropbox/CryoEM_Modelling/Fionnbharth/Tail
> tube/Fionn_TailTube_3rings_TEST4.pdb"

Chain information for Fionn_TailTube_3rings_TEST4.pdb #2  
---  
Chain | Description  
A B R | No description available  
C | No description available  
D | No description available  
E F G H I J K L M N O P Q | No description available  
  

> hide atoms

> show cartoons

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models




OpenGL version: 3.3.0 NVIDIA 573.24
OpenGL renderer: NVIDIA GeForce RTX 5090 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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: LENOVO
Model: 83F5
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 68,112,736,256
MaxProcessMemory: 137,438,953,344
CPU: 24 Intel(R) Core(TM) Ultra 9 275HX
OSLanguage: en-US

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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-Clipper: 0.25.2
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.10
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
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    matplotlib-inline: 0.1.7
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    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    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: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
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    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
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    six: 1.16.0
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    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1
File attachment: J126_MA.cif

J126_MA.cif​

Attachments (1)

J126_MA.cif​ (5.8 MB ) - added by kgf4@… 6 days ago.
Added by email2trac

Change History (3)

by kgf4@…, 6 days ago

Attachment: J126_MA.cif​ added

Added by email2trac

comment:1 by Eric Pettersen, 6 days ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Chain integrity in PDB format

comment:2 by Eric Pettersen, 5 days ago

Resolution: → fixed
Status: accepted → closed

Hi Krista,

Thanks for reporting this problem. Please try the ChimeraX 1.11 release candidate. I can reproduce your problem in the 1.10.1 production release but not in the 1.11 release candidate.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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