id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8077 coulombic → ribbon → coulombic: structure gone kristen.browne@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.6.dev202211220200 (2022-11-22 02:00:46 UTC) Description open 2JSJ go to coulombic -> OK go to a ribbon -> OK go back to coulombic -> structure is gone Log: UCSF ChimeraX version: 1.6.dev202211220200 (2022-11-22) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 2JSJ 2jsj title: Obestatin in water solution [more info...] Chain information for 2jsj --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A | Appetite-regulating hormone, Obestatin | GHRL_MOUSE > close #1.2-29 > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 352 atom radii, 356 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2jsj #1.1 --- notes | Termini for 2jsj (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: /A PHE 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A NH2 224 Chain-final residues that are not actual C termini: 1 hydrogen bonds 4 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for Surface #1.1 #1.1.1: minimum, -7.55, mean 2.85, maximum 15.98 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 surface #1.1 enclose #1.1 grid 0.5 sharp true color white coulombic surfaces #* > preset nih3d ""ribbon by chain"" Using preset: NIH3D / Ribbon by Chain Changed 356 atom radii, 360 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. 114 atoms, 92 bonds, 23 residues, 1 model selected Nothing selected Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent delete H preset 'initial styles' cartoon nucleotides ladder radius 1.2 color white target abc color helix marine color strand firebrick color coil goldenrod color nucleic-acid forest color :A:C:G:U grape color byatom select (C & ligand) | (C & ligand :< 5 & ~nucleic-acid) | (C & protein) | (C & disulfide) color sel carbon_grey atoms color ligand | protein & sideonly byhet atoms ~select rainbow #1.1@ca,c4' chains palette marine:marine target rs > preset nih3d ""surface coulombic"" Using preset: NIH3D / Surface Coulombic Changed 179 atom radii, 183 bond radii, 0 pseudobond radii Changed 0 pseudobond dashes Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff Color 'forest' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 Color 'tangerine' is opaque: rgb(95.3%, 51.8%, 0%) hex: #f38400 Color 'grape' is opaque: rgb(64.3%, 0%, 86.7%) hex: #a400dd Color 'nih_blue' is opaque: rgb(12.5%, 33.3%, 54.1%) hex: #20558a Color 'jmol_carbon' is opaque: gray(56.5%) hex: #909090 Color 'bond_purple' is opaque: rgb(57.6%, 43.9%, 85.9%) hex: #9370db Color 'struts_grey' is opaque: gray(48%) hex: #7a7a7a Color 'carbon_grey' is opaque: gray(22.2%) hex: #393939 Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. Summary of feedback from adding hydrogens to 2jsj #1.1 --- notes | Termini for 2jsj (#1.1) chain A determined from SEQRES records Chain-initial residues that are actual N termini: /A PHE 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A NH2 224 Chain-final residues that are not actual C termini: 2 hydrogen bonds 176 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for Surface #1.1 #1.1.1: minimum, -11.42, mean 1.56, maximum 11.28 Preset expands to these ChimeraX commands: ~struts ~hbonds size atomRadius default stickRadius 0.2 pseudobondRadius 0.2 style dashes 7 graphics bgcolor white color name marine 0,50,100 color name forest 13.3,54.5,13.3 color name tangerine 95.3,51.8,0 color name grape 64.3,0,86.7 color name nih_blue 12.5,33.3,54.1 color name jmol_carbon 56.5,56.5,56.5 color name bond_purple 57.6,43.9,85.9 color name struts_grey 48,48,48 color name carbon_grey 22.2,22.2,22.2 surface close preset 'initial styles' 'original look' delete solvent hide H|ligand|~(protein|nucleic-acid) ~nuc ~ribbon ~display addh #1.1 surface #1.1 enclose #1.1 grid 0.5 sharp true color white coulombic surfaces #* OpenGL version: 3.3.0 NVIDIA 466.47 OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP Z4 G4 Workstation OS: Microsoft Windows 10 Enterprise (Build 19044) Memory: 137,220,087,808 MaxProcessMemory: 137,438,953,344 CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.5.5 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.4 ChimeraX-AtomicLibrary: 8.0.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202211220200 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.9 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.7 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.3 ChimeraX-PDB: 2.6.9 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.2 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.6 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.0.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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 stack-data: 0.6.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.10.0 }}} " defect closed normal Depiction can't reproduce all ChimeraX