Disconnected ribbon

[Qinglong.You@…]

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
DNA carton does not continue at oxoG (chain /I 8OG -49)

Log:
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/Qinglong.You/NCP_damage_cls3/RealSpaceRefine_3/fitting1_real_space_refined_real_space_refined-
> coot-6_real_space_refined_003.pdb

Chain information for fitting1_real_space_refined_real_space_refined-
coot-6_real_space_refined_003.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C G | No description available  
D H | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> style stick

Changed 12564 atom styles  

> show cartoons

> hide atoms

> set bgColor white




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel 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: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 428.60.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 12.2 (21D49)
      Kernel Version: Darwin 21.3.0
      Time since boot: 90 days 4:12

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    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
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    ChimeraX-AddH: 2.1.11
    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
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    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
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    ChimeraX-CellPack: 1.0
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    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
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    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
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    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
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    ChimeraX-Map: 1.1
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    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
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    ChimeraX-MLP: 1.1
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    ChimeraX-MMTF: 2.1
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    ChimeraX-ModelPanel: 1.3.2
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    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
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    ChimeraX-Neuron: 1.0
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    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
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    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
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    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: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
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    ChimeraX-VIPERdb: 1.0
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    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
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    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
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    h5py: 3.7.0
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    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
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    ipython: 7.31.1
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    Jinja2: 3.0.3
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    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
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    Pygments: 2.11.2
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    PyOpenGL-accelerate: 3.1.5
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    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
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    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: fitting1_real_space_refined_real_space_refined-coot-6_real_space_refined_003.pdb

fitting1_real_space_refined_real_space_refined-coot-6_real_space_refined_003.pdb​

[Qinglong.You@…]

Added by email2trac

[Eric Pettersen]

Hi Qinglong,

The 8OG residue seems to have a spurious OP3 atom that is only .483 angstroms away from the O3' atom of the next residue. If you delete that OP3 atom from your PDB file then everything works.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Qinglong.You@…]

Hi Eric,

Thanks a bunch for your quick response! Your suggestion just works just perfect to connect the ribbon at 8OG!

Have a good weekend!

Qinglong



From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, July 15, 2022 at 1:06 PM
To:
Cc: You, Qinglong <Qinglong.You@vai.org>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #7283: Disconnected ribbon
#7283: Disconnected ribbon
-------------------------------------+--------------------
          Reporter:  Qinglong.You@…  |      Owner:  pett
              Type:  defect          |     Status:  closed
          Priority:  normal          |  Milestone:
         Component:  Depiction       |    Version:
        Resolution:  not a bug       |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+--------------------
Changes (by pett):

 * status:  accepted => closed
 * resolution:   => not a bug


Comment:

 Hi Qinglong,
         The 8OG residue seems to have a spurious OP3 atom that is only
 .483 angstroms away from the O3' atom of the next residue.  If you delete
 that OP3 atom from your PDB file then everything works.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7283#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email was sent from outside of the organization (SRS0+H86in86j=XU=cgl.ucsf.edu=ChimeraX-bugs-admin@cgl.ucsf.edu). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk@vai.org <mailto:servicedesk@vai.org>.

[Eric Pettersen]

Great! You have a good weekend too.

--Eric

[Qinglong.You@…]

Hi Eric,

Thanks a bunch for your quick response! Your suggestion just works just perfect to connect the ribbon at 8OG!

Have a good weekend!

Qinglong

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, July 15, 2022 at 1:04 PM
To:
Cc: You, Qinglong <Qinglong.You@vai.org>, pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #7283: Disconnected ribbon (was: ChimeraX bug report submission)
#7283: Disconnected ribbon
-------------------------------------+----------------------
          Reporter:  Qinglong.You@…  |      Owner:  pett
              Type:  defect          |     Status:  accepted
          Priority:  normal          |  Milestone:
         Component:  Depiction       |    Version:
        Resolution:                  |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+----------------------
Changes (by pett):

 * status:  new => accepted
 * component:  Unassigned => Depiction
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => pett


--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7283#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
CAUTION: This email was sent from outside of the organization (SRS0+H86in86j=XU=cgl.ucsf.edu=ChimeraX-bugs-admin@cgl.ucsf.edu). Do not click links or open attachments unless you recognize the sender and know the content is safe. If you have any questions, please contact ServiceDesk@vai.org <mailto:servicedesk@vai.org>.