Opened 4 years ago

Closed 4 years ago

#4603 closed defect (not a bug)

Using Chimera atom spec syntax

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-72-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open /home/diego/Documents/Proyectos/Coevolucion/CCR/seq/14g_14z_align.cxs

Log from Tue May 4 15:58:01 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/diego/Documents/Proyectos/Coevolucion/CCR/seq/3uzd_1qja_AL.pdb

Summary of feedback from opening
/home/diego/Documents/Proyectos/Coevolucion/CCR/seq/3uzd_1qja_AL.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 4
GLN A 16 1 13  
Start residue of secondary structure not found: HELIX 2 2 TYR A 20 LEU A 33 1
14  
Start residue of secondary structure not found: HELIX 3 3 ASN A 39 THR A 70 1
32  
Start residue of secondary structure not found: HELIX 4 4 LYS A 77 ASN A 111 1
35  
Start residue of secondary structure not found: HELIX 5 5 TYR A 117 VAL A 137
1 21  
11 messages similar to the above omitted  
  
Chain information for 3uzd_1qja_AL.pdb  
---  
Chain | Description  
1.1/A 1.1/B | No description available  
1.2/A | No description available  
1.2/B | No description available  
  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select #1.1/A

1884 atoms, 1912 bonds, 233 residues, 1 model selected  

> select #1.1/B

1884 atoms, 1912 bonds, 233 residues, 1 model selected  

> delete sel

> select #1.2/B

1837 atoms, 1862 bonds, 229 residues, 1 model selected  

> select #1.2/A

1843 atoms, 1868 bonds, 230 residues, 1 model selected  

> delete sel

> select :243.a

Expected an objects specifier or a keyword  

> select :243.A

Expected an objects specifier or a keyword  

> select :243:A

Nothing selected  

> select :234:A

8 atoms, 7 bonds, 1 residue, 1 model selected  
Alignment identifier is 1.1/A  

> select #1.2/B

1837 atoms, 1862 bonds, 229 residues, 1 model selected  
Alignment identifier is 1.2/B  

> select clear

> select :234:A

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select :229:A

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select clear

> select :229:A

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select :229.A

Expected an objects specifier or a keyword  

> select :229

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select :220

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select :220.chainA

Expected an objects specifier or a keyword  

> select :220.chain_A

Expected an objects specifier or a keyword  

> select :220.chain.a

Expected an objects specifier or a keyword  

> select :220.a

Expected an objects specifier or a keyword  

> select :220

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select :220.a

Expected an objects specifier or a keyword  

> select :22

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select :22.a

Expected an objects specifier or a keyword  

> select :22.b

Expected an objects specifier or a keyword  

> save /home/diego/Documents/Proyectos/Coevolucion/CCR/seq/14g_14z_align.cxs

> select :22,23

29 atoms, 27 bonds, 4 residues, 2 models selected  

> select
> :102,106,11,111,112,114,120,138,142,143,144,151,155,159,162,165,166,171,172,176,189,19,190,199,20,200,206,209,21,211,22,23,231,234,241,243,25,26,29,32,36,52,56,6,70,81,83,86,89,98

746 atoms, 683 bonds, 94 residues, 2 models selected  

> show sel atoms

> color sel red

> select #1.2/B

1837 atoms, 1862 bonds, 229 residues, 1 model selected  

> hide sel atoms

> color sel bychain

> select clear

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select
> :10,109,114,115,12,13,134,14,141,143,144,146,147,162,187,19,190,2,232,237,239,24,242,245,3,62,64,66,69,7,74,80,84,85,91

481 atoms, 438 bonds, 61 residues, 2 models selected  

> show sel atoms

> select clear

> save /home/diego/Documents/Proyectos/Coevolucion/CCR/seq/14g_14z_align.cxs

opened ChimeraX session  




OpenGL version: 4.6 (Core Profile) Mesa 20.0.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z390 GAMING X
OS: elementary OS 5.1.7 hera
Architecture: 64bit ELF
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        2.2G         10G        421M        2.6G         12G
	Swap:          2.0G          0B        2.0G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e92]	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:d000]	
	Kernel driver in use: i915
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by pett, 4 years ago

Component: Unassigned → Command Line
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Using Chimera atom spec syntax

comment:2 by pett, 4 years ago

Resolution: → not a bug
Status: accepted → closed
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