id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18396 Ribbon does not include non-standard residues e24soep0001@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Hello, I was working on PROTAC structure complex (PDB ID: 8EBK), this is where i see that the leucine (residue id 3) doesnot appear to bind with residue id 2, 3V3 in ChimeraX. when I compared the same in Chimera program, there is no issue and the bond is also visible linking to residues. portion is highlighted in the attached image for both ChimeraX and Chimera. i would highly appreciate the resolution of this matter Log: > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8ebk format mmcif fromDatabase pdb 8ebk title: Crystal Structure Analysis of xHDMX in complex with the stapled peptide PROTAC analog [more info...] Chain information for 8ebk #1 --- Chain | Description A | HDMX B | ACE-LEU-THR-PHE-0EH-GLU-TYR-TRP-ALA-GLN-LEU-MK8-SER-ALA-ALA Non-standard residues in 8ebk #1 --- 0EH — (2R)-2-amino-2-methylnonanoic acid 3V3 — 1-amino-3,6,9,12-tetraoxapentadecan-15-oic acid WG0 — [(6S,10P)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetic acid 29 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select /B 196 atoms, 172 bonds, 48 residues, 1 model selected > show sel atoms > sequence chain #1/B Alignment identifier is 1/B > select /B:3 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:3 8 atoms, 7 bonds, 1 residue, 1 model selected > select ::name=""HOH"" 119 atoms, 119 residues, 1 model selected > delete atoms sel > delete bonds sel > dockprep Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Summary of feedback from adding hydrogens to 8ebk #1 --- notes | Termini for 8ebk (#1) chain A determined from SEQRES records Termini for 8ebk (#1) chain B determined from SEQRES records Chain-initial residues that are actual N termini: /B WG0 1 Chain-initial residues that are not actual N termini: /A GLY 21 Chain-final residues that are actual C termini: /B ALA 16 Chain-final residues that are not actual C termini: /A LEU 106 88 hydrogen bonds Adding 'H' to /A GLY 21 /A LEU 106 is not terminus, removing H atom from 'C' 870 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue WG0+3V3 (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.10/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TUSHA_~1\AppData\Local\Temp\tmpoen7gylx\ante.in.mol2 -fi mol2 -o C:\Users\TUSHA_~1\AppData\Local\Temp\tmpoen7gylx\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (WG0+3V3) `` (WG0+3V3) `Welcome to antechamber 20.0: molecular input file processor.` (WG0+3V3) `` (WG0+3V3) `Info: Finished reading file (C:\Users\TUSHA_~1\AppData\Local\Temp\tmpoen7gylx\ante.in.mol2); atoms read (86), bonds read (89).` (WG0+3V3) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (WG0+3V3) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (WG0+3V3) `bash.exe: warning: could not find /tmp, please create!` (WG0+3V3) `` (WG0+3V3) `` (WG0+3V3) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (WG0+3V3) `bash.exe: warning: could not find /tmp, please create!` (WG0+3V3) `Info: Total number of electrons: 350; net charge: 0` (WG0+3V3) `` (WG0+3V3) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (WG0+3V3) `bash.exe: warning: could not find /tmp, please create!` (WG0+3V3) `` (WG0+3V3) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/am1bcc"" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p ""C:/Program Files/ChimeraX 1.10/bin/amber20/dat/antechamber/BCCPARM.DAT"" -s 2 -j 1` (WG0+3V3) `bash.exe: warning: could not find /tmp, please create!` (WG0+3V3) `` (WG0+3V3) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (WG0+3V3) `bash.exe: warning: could not find /tmp, please create!` (WG0+3V3) `` Charges for residue WG0+3V3 determined Assigning partial charges to residue 0EH+MK8 (net charge +0) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX 1.10/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TUSHA_~1\AppData\Local\Temp\tmpmmt4n9h3\ante.in.mol2 -fi mol2 -o C:\Users\TUSHA_~1\AppData\Local\Temp\tmpmmt4n9h3\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (0EH+MK8) `` (0EH+MK8) `Welcome to antechamber 20.0: molecular input file processor.` (0EH+MK8) `` (0EH+MK8) `Info: Finished reading file (C:\Users\TUSHA_~1\AppData\Local\Temp\tmpmmt4n9h3\ante.in.mol2); atoms read (73), bonds read (72).` (0EH+MK8) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (0EH+MK8) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/bondtype"" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (0EH+MK8) `bash.exe: warning: could not find /tmp, please create!` (0EH+MK8) `` (0EH+MK8) `` (0EH+MK8) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/atomtype"" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (0EH+MK8) `bash.exe: warning: could not find /tmp, please create!` (0EH+MK8) `Info: Total number of electrons: 240; net charge: 0` (0EH+MK8) `` (0EH+MK8) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/sqm"" -O -i sqm.in -o sqm.out` (0EH+MK8) `bash.exe: warning: could not find /tmp, please create!` (0EH+MK8) `` (0EH+MK8) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/am1bcc"" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p ""C:/Program Files/ChimeraX 1.10/bin/amber20/dat/antechamber/BCCPARM.DAT"" -s 2 -j 1` (0EH+MK8) `bash.exe: warning: could not find /tmp, please create!` (0EH+MK8) `` (0EH+MK8) `Running: ""C:/Program Files/ChimeraX 1.10/bin/amber20/bin/atomtype"" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (0EH+MK8) `bash.exe: warning: could not find /tmp, please create!` (0EH+MK8) `` Charges for residue 0EH+MK8 determined 1 structure has non-integral total charge. Details in log. Here are the structures will non-integral total charge along with the particular residues from those structures with non-integral total charge: 8ebk #1: /B WG0 1: 0.0119995, /B 3V3 2: -0.0189995, /B 0EH 6: 0.00934653, and /B MK8 13: -0.0123465 Dock prep finished Drag select of 1 residues > help help:contact.html > select /B 320 atoms, 328 bonds, 16 residues, 1 model selected > select /B:3 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:3 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:3 19 atoms, 18 bonds, 1 residue, 1 model selected > select /B:3 19 atoms, 18 bonds, 1 residue, 1 model selected OpenGL version: 3.3.0 NVIDIA 572.83 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_IN.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: HP Model: OMEN by HP 45L Gaming Desktop GT22-1xxx OS: Microsoft Windows 11 Home Single Language (Build 26100) Memory: 68,388,151,296 MaxProcessMemory: 137,438,953,344 CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2025.6.15 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: 14.1.18 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-clix: 0.2.3 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 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-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: 1.1.2 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: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 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: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 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-cuda-cupti-cu12: 12.9.79 nvidia-cuda-nvcc-cu12: 12.9.86 nvidia-cuda-nvrtc-cu12: 12.9.86 nvidia-cuda-runtime-cu12: 12.9.79 nvidia-cufft-cu12: 11.4.1.4 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 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 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 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 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: 4.14.0 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: Screenshot 2025-08-08 121834.png }}} [attachment:""Screenshot 2025-08-08 121834.png""] " defect closed normal Depiction not a bug Greg Couch Eric Pettersen all ChimeraX