Opened 4 years ago

Closed 4 years ago

#6310 closed defect (duplicate)

Unknown problem

Reported by: stdegiet@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/stdegiet/Documents/Work/Alpo4/Paper/Draft5_20211213/Figures/J389/cryosparc_P16_J326_class_00_final_volume-2.mrc
> format mrc

Opened cryosparc_P16_J326_class_00_final_volume-2.mrc as #1, grid size
256,256,256, pixel 1.33, shown at level 0.195, step 1, values float32  

> set bgColor white

> lighting soft

> volume #1 color #d6d6d6

> graphics silhouettes true

> volume #1 level 0.3081

> open /Users/stdegiet/Downloads/cryosparc_P16_J399_map_locres.mrc

Opened cryosparc_P16_J399_map_locres.mrc as #2, grid size 448,448,448, pixel
0.76, shown at level 8.09, step 2, values float32  

> save
> /Users/stdegiet/Documents/Work/Alpo4/Paper/Draft5_20211213/Figures/J389/Class_0.png
> width 2000 height 1939 supersample 3 transparentBackground true

> open
> /Users/stdegiet/Documents/Work/Alpo4/Paper/Draft5_20211213/Figures/J389/cryosparc_P16_J326_class_01_final_volume.mrc

Opened cryosparc_P16_J326_class_01_final_volume.mrc as #3, grid size
256,256,256, pixel 1.33, shown at level 0.136, step 1, values float32  

> set bgColor white

> lighting soft

> volume #1 color #d6d6d6

> graphics silhouettes true

> volume #1 level 0.3081

> volume #3 color #d6d6d6

> volume #3 level 0.2828

> open /Users/stdegiet/Downloads/cryosparc_P16_J231_class_00_final_volume.mrc

Opened cryosparc_P16_J231_class_00_final_volume.mrc as #4, grid size
128,128,128, pixel 1.9, shown at level 0.411, step 1, values float32  

> volume #4 color #d6d6d6

> volume #4 level 0.2973

> open /Users/stdegiet/Downloads/cryosparc_P16_J231_class_01_final_volume.mrc

Opened cryosparc_P16_J231_class_01_final_volume.mrc as #5, grid size
128,128,128, pixel 1.9, shown at level 0.369, step 1, values float32  

> volume #5 color #d6d6d6

> ui tool show "Surface Color"

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key rainbow :0.00 :0.25 :0.50 :0.75 :1.00 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 0, mean 4.789, maximum 9.924  

> volume #1 level 0.4217

> volume #1 level 0.4653

> color single #1.1

> hide #6 models

> open /Users/stdegiet/Downloads/cryosparc_P16_J389_map_sharp-1.mrc

Opened cryosparc_P16_J389_map_sharp-1.mrc as #7, grid size 448,448,448, pixel
0.76, shown at level 0.0881, step 2, values float32  

> color #7 #d6d6d6 models transparency 0

> ui mousemode right "rotate selected models"

> ui mousemode right pivot

> ui mousemode right "rotate selected models"

> ui mousemode right pivot

[Repeated 1 time(s)]

> ui mousemode right "translate selected models"

> ui mousemode right select

> select #7

2 models selected  

> ui mousemode right select

> select clear

> ui tool show "Surface Color"

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> ui mousemode right select

> color sample #7.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 0, mean 4.869, maximum 11.06  

> volume #7 level 0.23

> volume #7 step 1

> volume #7 level 0.3557

> color sample #7.1 map #2 palette
> 0,#0000ff:2.765,#00ffff:5.53,#00ff00:8.295,#ffff00:11.06,#ff0000

Map values for surface "surface": minimum 3.221, mean 3.659, maximum 5.787  

> color sample #7.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 3.221, mean 3.659, maximum 5.787  

> save
> /Users/stdegiet/Documents/Work/Alpo4/Paper/Draft5_20211213/Figures/J389/J389.cxs

> key rainbow :3.22 :3.86 :4.50 :5.14 :5.79 showTool true

> ui mousemode right "color key"

> save
> /Users/stdegiet/Documents/Work/Alpo4/Paper/Draft5_20211213/Figures/J389/J389.cxs

> ui mousemode right select

> close #1

> close

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J604_class_00_final_volume-1.mrc

Opened cryosparc_P30_J604_class_00_final_volume-1.mrc as #1, grid size
128,128,128, pixel 2.09, shown at level 0.525, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_01_final_volume.mrc

Opened cryosparc_P30_J604_class_01_final_volume.mrc as #2, grid size
128,128,128, pixel 2.09, shown at level 0.529, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_02_final_volume.mrc

Opened cryosparc_P30_J604_class_02_final_volume.mrc as #3, grid size
128,128,128, pixel 2.09, shown at level 0.533, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_03_final_volume.mrc

Opened cryosparc_P30_J604_class_03_final_volume.mrc as #4, grid size
128,128,128, pixel 2.09, shown at level 0.529, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_04_final_volume.mrc

Opened cryosparc_P30_J604_class_04_final_volume.mrc as #5, grid size
128,128,128, pixel 2.09, shown at level 0.521, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_05_final_volume.mrc

Opened cryosparc_P30_J604_class_05_final_volume.mrc as #6, grid size
128,128,128, pixel 2.09, shown at level 0.52, step 1, values float32  

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_06_final_volume.mrc

Opened cryosparc_P30_J604_class_06_final_volume.mrc as #7, grid size
128,128,128, pixel 2.09, shown at level 0.479, step 1, values float32  

> volume #2 color #d6d6d6

> volume #3 color #d6d6d6

> volume #4 color #d6d6d6

> volume #5 color #d6d6d6

> volume #6 color #d6d6d6

> volume #7 color #d6d6d6

> volume #1 color #d6d6d6

> open /Users/stdegiet/Downloads/cryosparc_P30_J604_class_07_final_volume.mrc

Opened cryosparc_P30_J604_class_07_final_volume.mrc as #8, grid size
128,128,128, pixel 2.09, shown at level 0.536, step 1, values float32  

> hide #!3 models

> volume #8 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_00_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_00_00202_volume_sharp.mrc as #9, grid size
128,128,128, pixel 2.09, shown at level 0.63, step 1, values float32  

> volume #9 color #d6d6d6

> volume #9 level 0.6679

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_01_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_01_00202_volume_sharp.mrc as #10, grid size
128,128,128, pixel 2.09, shown at level 0.667, step 1, values float32  

> volume #10 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_02_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_02_00202_volume_sharp.mrc as #11, grid size
128,128,128, pixel 2.09, shown at level 0.646, step 1, values float32  

> volume #11 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_04_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_04_00202_volume_sharp.mrc as #12, grid size
128,128,128, pixel 2.09, shown at level 0.641, step 1, values float32  

> volume #12 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_05_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_05_00202_volume_sharp.mrc as #13, grid size
128,128,128, pixel 2.09, shown at level 0.618, step 1, values float32  

> volume #13 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_06_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_06_00202_volume_sharp.mrc as #14, grid size
128,128,128, pixel 2.09, shown at level 0.605, step 1, values float32  

> volume #14 color #d6d6d6

> hide #!14 models

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J605_class_07_00202_volume_sharp.mrc

Opened cryosparc_P30_J605_class_07_00202_volume_sharp.mrc as #15, grid size
128,128,128, pixel 2.09, shown at level 0.652, step 1, values float32  

> volume #15 color #d6d6d6

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J607_class_03_00182_volume_sharp.mrc

Opened cryosparc_P30_J607_class_03_00182_volume_sharp.mrc as #16, grid size
128,128,128, pixel 2.09, shown at level 0.672, step 1, values float32  

> volume #16 color #d6d6d6

> volume #16 level 0.7056

> open
> /Users/stdegiet/Downloads/cryosparc_P30_J607_class_07_00182_volume_sharp.mrc

Opened cryosparc_P30_J607_class_07_00182_volume_sharp.mrc as #17, grid size
128,128,128, pixel 2.09, shown at level 0.549, step 1, values float32  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 13 days 16:29

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Unknown problem

comment:2 by Eric Pettersen, 4 years ago

Status: accepted → feedback

Hi Steven,

I don't see an error in the information you sent. What is the problem you're reporting?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: feedback → closed

Steven was just providing machine info for the faulty silhouette edge bug #6301.

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