Opened 3 years ago

Closed 3 years ago

#7401 closed defect (not a bug)

Maps not aligned

Reported by: michelle.moritz@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I opened (sequentially) two related cryoEM maps that have the same voxel and box size, but they did not align upon opening.  I did not move the first map that I opened before opening the second map.  See attached files for images.  These maps were generated in Relion4.  Thanks for your help.  

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  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/startup_volume_1_1_2109_104_3p34.mrc"

Opened startup_volume_1_1_2109_104_3p34.mrc as #1, grid size 104,104,104,
pixel 3.34, shown at level 6, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/initial_model026.mrc"

Opened initial_model026.mrc as #2, grid size 104,104,104, pixel 3.34, shown at
level 0.0515, step 1, values float32  

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/initial_model026.mrc"

Opened initial_model026.mrc as #1, grid size 104,104,104, pixel 3.34, shown at
level 0.0515, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run026_it100_class001.mrc"

Opened run026_it100_class001.mrc as #2, grid size 104,104,104, pixel 3.34,
shown at level 0.0515, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/initial_model027.mrc"

Opened initial_model027.mrc as #3, grid size 104,104,104, pixel 3.34, shown at
level 0.0525, step 1, values float32  

> tile columns 3 spacingFactor 1

3 models tiled  

> tile columns 3 spacingFactor 1.4

3 models tiled  

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.53632,-0.7197,-0.4409,0.65409,0.3571,0.66681,-0.6541,204.82,0.76475,0.19336,0.61463,379.21

> view matrix models
> #3,-0.47269,-0.87377,-0.11439,136.89,-0.21868,0.24205,-0.9453,425.28,0.85366,-0.42182,-0.3055,633.6

> view matrix models
> #3,-0.73331,-0.41925,0.53525,-12.624,-0.67802,0.39252,-0.62146,418.93,0.050457,-0.81863,-0.5721,883.36

> view matrix models
> #3,-0.67039,-0.56718,0.47842,11.52,-0.74103,0.47852,-0.47106,387.94,0.038238,-0.67032,-0.74109,891.8

> view matrix models
> #3,0.87614,-0.35742,-0.32346,-137.93,0.28575,0.92549,-0.24863,100.2,0.38823,0.12541,0.91299,399.56

> select subtract #3

Nothing selected  

> select add #3

2 models selected  

> view matrix models
> #3,-0.14672,-0.52712,0.83703,-148.98,-0.80388,0.55663,0.20963,261.44,-0.57641,-0.64212,-0.5054,947.95

> view matrix models
> #3,-0.13533,-0.41428,0.90003,-181.01,-0.86313,0.49534,0.098222,301.89,-0.48651,-0.76355,-0.42461,938.05

> view matrix models
> #3,-0.60085,-0.78241,0.16375,92.709,-0.70515,0.42231,-0.56958,409.13,0.37649,-0.4577,-0.80546,811.35

> view matrix models
> #3,-0.063619,-0.74937,-0.65909,146.69,-0.02716,0.66148,-0.74947,288,0.9976,-0.02978,-0.062435,500.26

> view matrix models
> #3,0.67904,-0.46177,-0.57068,-42.312,0.4019,0.88438,-0.23739,85.314,0.61431,-0.068163,0.78611,416.46

> select subtract #3

Nothing selected  

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run026_it100_class001.mrc"

Opened run026_it100_class001.mrc as #1, grid size 104,104,104, pixel 3.34,
shown at level 0.0515, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run027_it100_class001.mrc"

Opened run027_it100_class001.mrc as #2, grid size 104,104,104, pixel 3.34,
shown at level 0.0525, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run028_it100_class001.mrc"

Opened run028_it100_class001.mrc as #3, grid size 104,104,104, pixel 3.34,
shown at level 0.0487, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run028_it100_class002.mrc"

Opened run028_it100_class002.mrc as #4, grid size 104,104,104, pixel 3.34,
shown at level 0.0529, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run029_it100_class001.mrc"

Opened run029_it100_class001.mrc as #5, grid size 104,104,104, pixel 3.34,
shown at level 0.103, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/InitialModel/jobs026-029/run029_it100_class002.mrc"

Opened run029_it100_class002.mrc as #6, grid size 104,104,104, pixel 3.34,
shown at level 0.0495, step 1, values float32  

> tile columns 2 spacingFactor 1.4

6 models tiled  

> tile columns 2 spacingFactor 1

6 models tiled  

> volume level 0.0515

> volume #5 level 0.0515

> volume #5 level 0.1132

> volume level 0.113

> volume level 0.06

> volume level 0.05

> volume #5 level 0.105

> volume level 0.105

> volume #5 level 0.1008

> volume #1 level 0.03442

> volume #2 level 0.02922

> volume #3 level 0.0347

> volume #4 level 0.02293

> volume #6 level 0.02968

> volume #1 level 0.07139

> volume #2 level 0.0629

> volume #3 level 0.06608

> volume #4 level 0.03742

> volume #4 level 0.03849

> volume #3 level 0.0486

> volume #1 level 0.04162

> volume #3 level 0.03311

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run022_it025_class001.mrc"

Opened run022_it025_class001.mrc as #1, grid size 104,104,104, pixel 3.34,
shown at level 0.0474, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run023_it025_class001.mrc"

Opened run023_it025_class001.mrc as #2, grid size 104,104,104, pixel 3.34,
shown at level 0.0477, step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run022_it025_class001.mrc"

Opened run022_it025_class001.mrc as #1, grid size 104,104,104, pixel 3.34,
shown at level 0.0474, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run023_it025_class001.mrc"

Opened run023_it025_class001.mrc as #2, grid size 104,104,104, pixel 3.34,
shown at level 0.0477, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run024_it025_class001.mrc"

Opened run024_it025_class001.mrc as #3, grid size 104,104,104, pixel 3.34,
shown at level 0.0512, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run024_it025_class002.mrc"

Opened run024_it025_class002.mrc as #4, grid size 104,104,104, pixel 3.34,
shown at level 0.0472, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run025_it025_class001.mrc"

Opened run025_it025_class001.mrc as #5, grid size 104,104,104, pixel 3.34,
shown at level 0.055, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run025_it025_class002.mrc"

Opened run025_it025_class002.mrc as #6, grid size 104,104,104, pixel 3.34,
shown at level 0.0437, step 1, values float32  

> tile columns 2 spacingFactor 1

6 models tiled  

> volume level 0.0474

> volume #5 level 0.04343

> volume #5 level 0.0474

> volume #1 level 0.04297

> volume #5 level 0.03483

> volume #3 level 0.04955

> volume #6 level 0.0315

> volume #1 level 0.04677

> volume #2 level 0.03738

> volume #2 level 0.04005

> volume #1 level 0.03792

> volume #5 level 0.03748

> volume #2 level 0.03804

> volume #1 level 0.02907

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Refine3D/job030/run030_class001.mrc"

Opened run030_class001.mrc as #1, grid size 104,104,104, pixel 3.34, shown at
level 0.0496, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run022_it025_class001.mrc"

Opened run022_it025_class001.mrc as #2, grid size 104,104,104, pixel 3.34,
shown at level 0.0474, step 1, values float32  

> close session

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Class3D/jobs022-025/run022_it025_class001.mrc"

Opened run022_it025_class001.mrc as #1, grid size 104,104,104, pixel 3.34,
shown at level 0.0474, step 1, values float32  

> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/220720BRCA_BARD_SPN_PP1a_Krios1/Refine3D/job030/run030_class001.mrc"

Opened run030_class001.mrc as #2, grid size 104,104,104, pixel 3.34, shown at
level 0.0496, step 1, values float32  

> ui tool show "Map Coordinates"

> volume #2 level 0.0474




OpenGL version: 4.1 ATI-2.11.26
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,2
      Processor Name: Intel Core i5
      Processor Speed: 3.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 429.140.8.0.0
      SMC Version (system): 2.40f0

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 142 days 23:20

Graphics/Displays:

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AA-921
      VBIOS Version: 113-C9810A1X-017
      EFI Driver Version: 01.00.921
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
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Screen Shot 2022-08-05 at 9.25.29 AM.png​

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Change History (9)

by michelle.moritz@…, 3 years ago

Attachment: Screen Shot 2022-08-05 at 9.25.29 AM.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Maps not aligned

comment:2 by Tom Goddard, 3 years ago

I see both maps are 104 by 104 by 104 grid points with the same voxel size 3.34 Angstroms. There are two possibilities for why the maps do not align. One is that the two maps use a different origin. When you used Tools / Volume Data / Map Coordinates did it show the same "Origin Index" for both of the maps? Another way you can see if the two volumes are in register is to show a white outline box around them using command

volume #1,​2 showOutline true

and see if the two outlines are exactly on top of each other or shifted relative to one another. If the origins are the same then the problem is Relion did not center the maps in the same way.

If Relion did not center them the same way you can move one map to align the density with the other with the command

fitmap #2 in #1

in reply to:  4 comment:3 by Michelle.Moritz@…, 3 years ago 

Hello,
Thanks for the suggestions.  I tried these and found that the origin index is 0 for each map, but when I display the outline boxes, they are indeed shifted with respect to one another.  So I guess Relion is not centering the maps in the same way.
Michelle

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, August 5, 2022 at 10:42 AM
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu>
Subject: Re: [ChimeraX] #7401: Maps not aligned
#7401: Maps not aligned
----------------------------------------+-------------------------
          Reporter:  michelle.moritz@…  |      Owner:  Tom Goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------

Comment (by Tom Goddard):

 I see both maps are 104 by 104 by 104 grid points with the same voxel size
 3.34 Angstroms.  There are two possibilities for why the maps do not
 align.  One is that the two maps use a different origin.  When you used
 Tools / Volume Data / Map Coordinates did it show the same "Origin Index"
 for both of the maps?  Another way you can see if the two volumes are in
 register is to show a white outline box around them using command

     volume #1,2 showOutline true

 and see if the two outlines are exactly on top of each other or shifted
 relative to one another.  If the origins are the same then the problem is
 Relion did not center the maps in the same way.

 If Relion did not center them the same way you can move one map to align
 the density with the other with the command

     fitmap #2 in #1

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7401#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by Tom Goddard, 3 years ago

If the outline boxes are shifted but the origin is the same then that means one of the maps has been moved in ChimeraX relative to the other. It does not indicate that Relion centered the particle differently within the map.

in reply to:  6 comment:5 by Michelle.Moritz@…, 3 years ago 

I have now discovered that if I completely shut down ChimeraX, restart it, and then reopen the two maps they are aligning properly.  If I display their boxes, they are also aligned.  So apparently it is not sufficient to just close the maps and reopen them.  I have to shut down ChimerX as well.
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, August 5, 2022 at 1:31 PM
To:
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>, Moritz, Michelle <Michelle.Moritz@ucsf.edu>
Subject: Re: [ChimeraX] #7401: Maps not aligned
#7401: Maps not aligned
----------------------------------------+-------------------------
          Reporter:  michelle.moritz@…  |      Owner:  Tom Goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------

Comment (by Tom Goddard):

 If the outline boxes are shifted but the origin is the same then that
 means one of the maps has been moved in ChimeraX relative to the other.
 It does not indicate that Relion centered the particle differently within
 the map.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7401#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  7 ; comment:6 by goddard@…, 3 years ago 

Do you use the "tile" command?  It changes the mouse rotation to rotate each data set about its own center.  Even though your two maps are aligned, the center of the contour surfaces may be different so they can go out of alignment if you have previously used "tile" in the same ChimeraX session.  Using command "tile off" returns to normal rotation where all models are rotated about a common center point.  There is a bug report to make the independent center of rotation turn off if you close all the models to avoid it messing up the alignment if you forget to use "tile off".  https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405>

in reply to:  8 ; comment:7 by Michelle.Moritz@…, 3 years ago 

Yes, I use ‘tile’ a lot.  Thanks for the tip---I will try to remember to turn it off from now on.

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Friday, August 5, 2022 at 1:55 PM
To: Moritz, Michelle <Michelle.Moritz@ucsf.edu>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7401: Maps not aligned
#7401: Maps not aligned
----------------------------------------+-------------------------
          Reporter:  michelle.moritz@…  |      Owner:  Tom Goddard
              Type:  defect             |     Status:  assigned
          Priority:  normal             |  Milestone:
         Component:  Volume Data        |    Version:
        Resolution:                     |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------

Comment (by goddard@…):

 {{{
 Do you use the "tile" command?  It changes the mouse rotation to rotate
 each data set about its own center.  Even though your two maps are
 aligned, the center of the contour surfaces may be different so they can
 go out of alignment if you have previously used "tile" in the same
 ChimeraX session.  Using command "tile off" returns to normal rotation
 where all models are rotated about a common center point.  There is a bug
 report to make the independent center of rotation turn off if you close
 all the models to avoid it messing up the alignment if you forget to use
 "tile off".  https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405
 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7405>
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7401#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:8 by Tom Goddard, 3 years ago

Resolution: → not a bug
Status: assigned → closed

Ok. I hope to put in a fix soon (next week?) that will automatically turn off the rotating about individual centers if you close models, bug #7405. I'll add your email to that ticket so you get notified when the daily build has that improvement.

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