Opened 3 years ago

Closed 3 years ago

#7475 closed defect (duplicate)

No symmetries for 2bbv

Reported by: john.obrien@… Owned by: pett
Priority: normal Milestone:
Component: Higher-Order Structure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
When following the Quick Start Guide, Example Atomic Structure Commands, the "sym #1" command does not appear to produce the table of symmetries, as shown in the guide. Could you please help me with this? Thanks

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  

> ui windowfill toggle

[Repeated 1 time(s)]

> open "C:\Users\johno\OneDrive\Documents\PhD\S3\Structural immunology journal
> club\PDB structures\2bbv.pdb" format pdb

2bbv.pdb title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv.pdb #1  
---  
Chain | Description | UniProt  
A B | black beetle virus capsid protein | COAT_BBV  
C | black beetle virus capsid protein | COAT_BBV  
D E F | black beetle virus capsid protein | COAT_BBV  
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3') |  
  
Non-standard residues in 2bbv.pdb #1  
---  
CA — calcium ion  
  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> color bychain

> style /b stick

Changed 2382 atom styles  

> color /n teal

> hide /c

> ribbon /c

> select /N:4@C5'

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel gold

> select clear

> color sel gold

> select clear

> surface #1

> color /n fromatoms

> style solvent sphere

Changed 208 atom styles  

> color solvent red

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1 assembly 3 newModel false copies false

Assembly "3" not found, have  

> view

> sym #1 assembly 3 newModel false copies false

Assembly "3" not found, have  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> sym

Missing or invalid "structures" argument: empty atom specifier  

> sym 1

Missing or invalid "structures" argument: invalid atomic structures specifier  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> symmetry #1

Unknown command: symmetry #1  

> symmetry #4

Unknown command: symmetry #4  

> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> log metadata #1

Metadata for 2bbv.pdb #1  
---  
Title | The refined three-dimensional structure of an insect virus At 2.8
angstroms resolution  
Citation | The refined three-dimensional structure of an insect virusat 2.8 A
resolution. PMID: 8289282  
Non-standard residue | CA — calcium ion  
Gene source | Black beetle virus  
Experimental method | X-ray diffraction  
Resolution | 2.80Å  
  
> sym #1

2bbv.pdb mmCIF Assemblies  
---  
  

> save "C:/Users/johno/Documents/2bbv practice.cxs"




OpenGL version: 3.3.13559 Core Profile Forward-Compatible Context 26.20.12071.1002
OpenGL renderer: AMD Radeon(TM) Vega 9 Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Laptop 3
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 6,416,310,272
MaxProcessMemory: 137,438,953,344
CPU: 8 AMD Ryzen 5 Microsoft Surface (R) Edition
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    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
    ChimeraX-AxesPlanes: 2.1
    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
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    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
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    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
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    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
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
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    imagecodecs: 2021.11.20
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    Jinja2: 3.0.3
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    line-profiler: 3.4.0
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File attachment: 2bbv practice.cxs

2bbv practice.cxs​

Attachments (1)

2bbv practice.cxs​ (26.8 MB ) - added by john.obrien@… 3 years ago.
Added by email2trac

Change History (3)

by john.obrien@…, 3 years ago

Attachment: 2bbv practice.cxs​ added

Added by email2trac

comment:1 by pett, 3 years ago

Component: Unassigned → Higher-Order Structure
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → No symmetries for 2bbv

comment:2 by pett, 3 years ago

Resolution: → duplicate
Status: accepted → closed

Asked and answered on the chimerax-users list.

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