Opened 3 years ago

Closed 3 years ago

#8077 closed defect (can't reproduce)

coulombic → ribbon → coulombic: structure gone

Reported by: kristen.browne@… Owned by: pett
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
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
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    webcolors: 1.12
    wheel: 0.37.1
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    WMI: 1.5.1
    zipp: 3.10.0

Change History (5)

in reply to:  1 ; comment:1 by kristen.browne@…, 3 years ago 

Same thing happens with 2A93 (note - I deleted all but the first representation for each before using the presets)


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Wednesday, November 23, 2022 2:19 PM
To: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>
Subject: [EXTERNAL] [ChimeraX] #8077: ChimeraX bug report submission

#8077: ChimeraX bug report submission
------------------------------+-----------------------------
 Reporter:  kristen.browne@...  |                Type:  defect
   Status:  new               |            Priority:  normal
Component:  Unassigned        |          Blocked By:
 Blocking:                    |  Notify when closed:
------------------------------+-----------------------------
 {{{
 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)  (c) 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

 }}}

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comment:2 by pett, 3 years ago

Component: Unassigned → Depiction
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → coulombic → ribbon → coulombic: structure gone

comment:3 by pett, 3 years ago

Status: accepted → feedback

Hi Kristen,

I cannot reproduce this. I will need you to try again with _tomorrow's_ daily build. Unfortunately, today's daily build has a bug in it (that should not be in the build you're using AFAICT) because I enhanced the coulombic command to allow computing electrostatic volumes as well as surfaces, and the bug is that the volume computation became the default. Clearly, you probably won't try this again tomorrow per se :-), but hopefully in the next few days.

--Eric

in reply to:  4 ; comment:4 by kristen.browne@…, 3 years ago 

No problem.  We’re going to be rerunning all the entries in 3DPX again in a week or so with all the new fixes.  This was just the last of the weirdness I found in failures from the last round.  Hopefully everything just gets through a-ok when we try again!

Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, November 23, 2022 7:24:31 PM
Cc: Browne, Kristen (NIH/NIAID) [C] <kristen.browne@nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8077: coulombic → ribbon → coulombic: structure gone

#8077: coulombic → ribbon → coulombic: structure gone
---------------------------------------+----------------------
          Reporter:  kristen.browne@…  |      Owner:  pett
              Type:  defect            |     Status:  feedback
          Priority:  normal            |  Milestone:
         Component:  Depiction         |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+----------------------
Changes (by pett):

 * status:  accepted => feedback


Comment:

 Hi Kristen,
         I cannot reproduce this.  I will need you to try again with
 _tomorrow's_ daily build.  Unfortunately, today's daily build has a bug in
 it (that should not be in the build you're using AFAICT) because I
 enhanced the coulombic command to allow computing electrostatic volumes as
 well as surfaces, and the bug is that the volume computation became the
 default.  Clearly, you probably won't try this again tomorrow per se :-),
 but hopefully in the next few days.

 --Eric

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comment:5 by pett, 3 years ago

Resolution: → can't reproduce
Status: feedback → closed

I assume that you will just file a new ticket if this happens again when you rerun the pipeline, so I am closing this ticket.

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