id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7401 Maps not aligned michelle.moritz@… Tom Goddard "{{{ 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 File attachment: Screen Shot 2022-08-05 at 9.25.29 AM.png }}} [attachment:""Screen Shot 2022-08-05 at 9.25.29 AM.png""] " defect closed normal Volume Data not a bug all ChimeraX