Version misreported

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Super-minor thing, but I have both ChimeraX 1.1 and a recent daily build installed in the same Linux system. When I'm running 1.1, the version is misreported as 1.2.dev... in the Linux menu bar (see attached screenshot).

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

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

> open 7bv2.pdb

7bv2.pdb title:  
The NSP12-NSP7-NSP8 complex bound to the template-primer RNA and triphosphate
form of remdesivir(RTP) [more info...]  
  
Chain information for 7bv2.pdb #1  
---  
Chain | Description  
A | sars-cov-2 NSP12  
B | sars-cov-2 NSP8  
C | sars-cov-2 NSP7  
P | primer  
T | templete  
  
Non-standard residues in 7bv2.pdb #1  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-F][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> open working.cif

Summary of feedback from opening working.cif  
---  
warnings | Unknown polymer entity '1' near line 155  
Unknown polymer entity '2' near line 13550  
Unknown polymer entity '3' near line 15303  
Unknown polymer entity '4' near line 16298  
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "RMP" near line 16648  
Unknown polymer entity '5' near line 16684  
Atom O2 is not in the residue template for RMP /P:101  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
note | Fetching CCD RMP from http://ligand-expo.rcsb.org/reports/R/RMP/RMP.cif  
  
Chain information for working.cif #2  
---  
Chain | Description  
A | ?  
B | ?  
C | ?  
P | ?  
T | ?  
  

> open EMD-30210.mrc

Opened EMD-30210.mrc, grid size 192,192,192, pixel 1.01, shown at level
0.0278, step 1, values float32  

> clipper associate #3 toModel #1

7bv2.pdb title:  
The NSP12-NSP7-NSP8 complex bound to the template-primer RNA and triphosphate
form of remdesivir(RTP) [more info...]  
  
Chain information for 7bv2.pdb  
---  
Chain | Description  
1.2/A | sars-cov-2 NSP12  
1.2/B | sars-cov-2 NSP8  
1.2/C | sars-cov-2 NSP7  
1.2/P | primer  
1.2/T | templete  
  
Non-standard residues in 7bv2.pdb #1.2  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-F][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> clipper spotlight #2

Chain information for working.cif  
---  
Chain | Description  
2.2/A | ?  
2.2/B | ?  
2.2/C | ?  
2.2/P | ?  
2.2/T | ?  
  

> set bgColor white

> isolde start

> set selectionWidth 4

Done loading forcefield  

> volume gaussian #1 bfactor 50

> clipper associate #3 toModel #1

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 7bv2.pdb #1.2/A LYS 98 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to 7bv2.pdb #1.2/A ASP 100 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 7bv2.pdb #1.2/A ASP 218 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 7bv2.pdb #1.2/A ARG 365 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 7bv2.pdb #1.2/A ASP 824 CB because it is missing
heavy-atom bond partners  
19 messages similar to the above omitted  
notes | Termini for 7bv2.pdb (#1.2) chain A determined from SEQRES records  
Termini for 7bv2.pdb (#1.2) chain B determined from SEQRES records  
Termini for 7bv2.pdb (#1.2) chain C determined from SEQRES records  
Termini for 7bv2.pdb (#1.2) chain P determined from SEQRES records  
Termini for 7bv2.pdb (#1.2) chain T determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 7bv2.pdb #1.2/A VAL 31,
7bv2.pdb #1.2/A GLU 84, 7bv2.pdb #1.2/A ARG 118, 7bv2.pdb #1.2/A MET 906,
7bv2.pdb #1.2/B ASP 78, 7bv2.pdb #1.2/C LYS 2, 7bv2.pdb #1.2/P G 10, 7bv2.pdb
#1.2/T U 8  
Chain-final residues that are actual C termini: 7bv2.pdb #1.2/P U 20  
Chain-final residues that are not actual C termini: 7bv2.pdb #1.2/A LYS 50,
7bv2.pdb #1.2/A ASP 100, 7bv2.pdb #1.2/A LEU 895, 7bv2.pdb #1.2/A GLU 919,
7bv2.pdb #1.2/B ALA 191, 7bv2.pdb #1.2/C GLY 64, 7bv2.pdb #1.2/T C 21  
858 hydrogen bonds  
Adding 'H' to 7bv2.pdb #1.2/A VAL 31  
Adding 'H' to 7bv2.pdb #1.2/A GLU 84  
Adding 'H' to 7bv2.pdb #1.2/A ARG 118  
Adding 'H' to 7bv2.pdb #1.2/A MET 906  
Adding 'H' to 7bv2.pdb #1.2/B ASP 78  
1 messages similar to the above omitted  
7bv2.pdb #1.2/A GLU 919 is not terminus, removing H atom from 'C'  
7bv2.pdb #1.2/B ALA 191 is not terminus, removing H atom from 'C'  
7bv2.pdb #1.2/C GLY 64 is not terminus, removing H atom from 'C'  
No usable SEQRES records for working.cif (#2.2) chain A; guessing termini
instead  
No usable SEQRES records for working.cif (#2.2) chain B; guessing termini
instead  
No usable SEQRES records for working.cif (#2.2) chain C; guessing termini
instead  
No usable SEQRES records for working.cif (#2.2) chain P; guessing termini
instead  
No usable SEQRES records for working.cif (#2.2) chain T; guessing termini
instead  
Chain-initial residues that are actual N termini: working.cif #2.2/A VAL 31,
working.cif #2.2/B ASP 78, working.cif #2.2/C LYS 2, working.cif #2.2/P G 10,
working.cif #2.2/T U 8  
Chain-initial residues that are not actual N termini: working.cif #2.2/A GLU
84, working.cif #2.2/A ARG 118, working.cif #2.2/A ASN 911  
Chain-final residues that are actual C termini: working.cif #2.2/P RMP 101,
working.cif #2.2/T C 21  
Chain-final residues that are not actual C termini: working.cif #2.2/A THR
929, working.cif #2.2/A LYS 50, working.cif #2.2/A ASP 100, working.cif #2.2/A
LEU 895, working.cif #2.2/B ALA 191, working.cif #2.2/C GLY 64  
1149 hydrogen bonds  
working.cif #2.2/A THR 929 is not terminus, removing H atom from 'C'  
working.cif #2.2/B ALA 191 is not terminus, removing H atom from 'C'  
working.cif #2.2/C GLY 64 is not terminus, removing H atom from 'C'  
8099 hydrogens added  
  

> hide #!2 models

> view /A:505

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select clear

> hide #!1.1.1.2 models

> graphics silhouettes true

> save b183_transpro.jpg

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!1.2 models

> select clear

> cofr showPivot false

> hide #!2 models

> show #!1.1.1.2 models

> hide #!1.1.1.2 models

> show #!1.2 models

> select clear

> save b183_transpro.jpg

> hide #!1.2 models

> show #!2 models

> save b183_cisspro.jpg

> view /A:505

> hide #!2 models

> show #!1.2 models

> view /B:505

No objects specified.  

> view /B:183

> hide #!1.2 models

> show #!2 models

> windowsize size

Expected an integer >= 1 or a keyword  

> windowsize

window size 1339 868  

> save b183_cispro.png supersample 3 width 2678 height 1736

> show #!1.2 models

> hide #!2 models

> save b183_transpro.png supersample 3 width 2678 height 1736




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.4G         47G        156M         11G         57G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
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-Async: 0.1
    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-Clipper: 0.15.0
    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-ISOLDE: 1.1.0
    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-Phenix: 0.1
    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
    graphviz: 0.14.1
    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
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    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
    Send2Trash: 1.5.0
    SEQCROW: 0.24.3
    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
    versioneer: 0.18
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
File attachment: chimerax_wrong_version_display.png

chimerax_wrong_version_display.png​

[Tristan Croll]

Added by email2trac

[Greg Couch]

I can reproduce this. This is due to the StartupWMClass in the .desktop file being the same for each version. And the last one installed wins.