id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
5185	Missing bond	roger.y.tam@…	Eric Pettersen	"The following bug report has been submitted:
 Platform:        macOS-10.14.5-x86_64-i386-64bit
 ChimeraX Version: 1.3.dev202109020559 (2021-09-02 05:59:02 UTC)
 Description
 Hi, we are currently trying to model ligand/protein interactions using
 glycan ligands with a protein. When we try to input a glycan structure, it
 is displaying the molecule with a cleavage near where the branching is
 occurring (please see attached ChimeraX screenshot and a cartoon
 representation of the structure. Green line/arrow shows where cleavage is
 occurring). We have tried several glycans and they all seem to be cleaving
 at the similar spot.
 We obtained the PDB file from the website https://dev.glycam.org/cb
 and the input value of :
 DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAca1-OH

 Any help you can provide is highly appreciated.
 Thanks!
 Roger

 OpenGL version: 4.1 INTEL-12.9.22
 OpenGL renderer: Intel Iris OpenGL Engine
 OpenGL vendor: Intel Inc.Hardware:

     Hardware Overview:

       Model Name: MacBook Pro
       Model Identifier: MacBookPro11,1
       Processor Name: Intel Core i5
       Processor Speed: 2.6 GHz
       Number of Processors: 1
       Total Number of Cores: 2
       L2 Cache (per Core): 256 KB
       L3 Cache: 3 MB
       Hyper-Threading Technology: Enabled
       Memory: 8 GB
       Boot ROM Version: 153.0.0.0.0
       SMC Version (system): 2.16f68

 Software:

     System Software Overview:

       System Version: macOS 10.14.5 (18F132)
       Kernel Version: Darwin 18.6.0
       Time since boot: 10 days 17:51

 Graphics/Displays:

     Intel Iris:

       Chipset Model: Intel Iris
       Type: GPU
       Bus: Built-In
       VRAM (Dynamic, Max): 1536 MB
       Vendor: Intel
       Device ID: 0x0a2e
       Revision ID: 0x0009
       Metal: Supported, feature set macOS GPUFamily1 v4
       Displays:
         Color LCD:
           Display Type: Built-In Retina LCD
           Resolution: 2560 x 1600 Retina
           Framebuffer Depth: 24-Bit Color (ARGB8888)
           Main Display: Yes
           Mirror: Off
           Online: Yes
           Rotation: Supported
           Automatically Adjust Brightness: No

 Locale: (None, 'UTF-8')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     appnope: 0.1.2
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.5.30
     cftime: 1.5.0
     chardet: 4.0.0
     charset-normalizer: 2.0.4
     ChimeraX-AddCharge: 1.1.4
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.2.2
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.29
     ChimeraX-AtomicLibrary: 4.1.4
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 2.0
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.5.3
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.1
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.4.1
     ChimeraX-CommandLine: 1.1.5
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3.dev202109020559
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2.1
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.4
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.1
     ChimeraX-Hbonds: 2.1.1
     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
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.4
     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: 2.0.1
     ChimeraX-MDcrds: 2.5
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.4
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.1
     ChimeraX-ModelPanel: 1.1
     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-Nucleotides: 2.0.2
     ChimeraX-OpenCommand: 1.7
     ChimeraX-PDB: 2.6.1
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.1
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.5
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.2
     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: 1.6
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.12
     ChimeraX-uniprot: 2.2
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     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: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     cxservices: 1.0.1
     cycler: 0.10.0
     Cython: 0.29.23
     decorator: 5.0.9
     distlib: 0.3.1
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.4.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.20
     imagecodecs: 2021.4.28
     imagesize: 1.2.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 2.11.3
     jupyter-client: 6.1.12
     jupyter-core: 4.7.1
     kiwisolver: 1.3.2
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 1.1.1
     matplotlib: 3.4.2
     matplotlib-inline: 0.1.2
     msgpack: 1.0.2
     netCDF4: 1.5.6
     networkx: 2.6.2
     numexpr: 2.7.3
     numpy: 1.21.0
     numpydoc: 1.1.0
     openvr: 1.16.801
     packaging: 21.0
     ParmEd: 3.2.0
     parso: 0.8.2
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 8.2.0
     pip: 21.1.1
     pkginfo: 1.7.0
     prompt-toolkit: 3.0.20
     psutil: 5.8.0
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.9.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pyzmq: 22.2.1
     qtconsole: 5.1.0
     QtPy: 1.10.0
     RandomWords: 0.3.0
     requests: 2.25.1
     scipy: 1.6.3
     setuptools: 57.0.0
     sfftk-rw: 0.7.1
     six: 1.16.0
     snowballstemmer: 2.1.0
     sortedcontainers: 2.4.0
     Sphinx: 4.0.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     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-jurko: 0.6
     tifffile: 2021.4.8
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.1.0
     urllib3: 1.26.6
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.2
     wheel-filename: 1.3.0
 File attachment: Glycan Cleave ChimeraX.jpg
"	defect	closed	moderate		Input/Output		not a bug						all	ChimeraX