id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6524 Loss of occupancy/bfactor mhunkeler@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.14.6-x86_64-i386-64bit ChimeraX Version: 1.4.dev202202040724 (2022-02-04 07:24:35 UTC) Description Hi, Thanks for actively developing this great piece of software! I encountered what I think is a bug. When saving a pdb file chimeraX sets accupancy & B-factors of all atoms to 0! I can't imagine that this is the intended behavior, since it represents a loss of information and leads to a lot of problems in downstream applications in other software. In addition, also the space group information ('P 1' on the CRYST1 line) is lost after saving. here snippets from two pdb files, before and after saving in chimeraX (literaly just opened the pdb and then saved it immediately): BEFORE: ""HELIX 1 1 HIS A 32 MET A 35 1 4 CRYST1 396.000 396.000 396.000 90.00 90.00 90.00 P 1 ATOM 1 N ASN A 31 207.656 273.296 178.276 1.00 30.00 N ATOM 2 CA ASN A 31 209.106 273.230 178.470 1.00 30.00 C ATOM 3 C ASN A 31 209.615 271.997 177.753 1.00 30.00 C ATOM 4 O ASN A 31 210.628 272.124 177.095 1.00 30.00 O ATOM 5 CB ASN A 31 209.476 273.204 179.954 1.00 30.00 C ATOM 6 CG ASN A 31 209.279 274.547 180.628 1.00 30.00 C ATOM 7 OD1 ASN A 31 209.276 275.589 179.973 1.00 30.00 O ATOM 8 ND2 ASN A 31 209.113 274.529 181.946 1.00 30.00 N"" AFTER SAVING: ""SEQRES 1 A 9 ASN HIS ASP ASN MET CYS LYS VAL LYS HELIX 1 1 HIS A 32 MET A 35 1 4 CRYST1 396.000 396.000 396.000 90.00 90.00 90.00 ATOM 1 N ASN A 31 207.656 273.296 178.276 0.00 0.00 N ATOM 2 CA ASN A 31 209.106 273.230 178.470 0.00 0.00 C ATOM 3 C ASN A 31 209.615 271.997 177.753 0.00 0.00 C ATOM 4 O ASN A 31 210.628 272.124 177.095 0.00 0.00 O ATOM 5 CB ASN A 31 209.476 273.204 179.954 0.00 0.00 C ATOM 6 CG ASN A 31 209.279 274.547 180.628 0.00 0.00 C ATOM 7 OD1 ASN A 31 209.276 275.589 179.973 0.00 0.00 O ATOM 8 ND2 ASN A 31 209.113 274.529 181.946 0.00 0.00 N"" Best, Moritz OpenGL version: 4.1 INTEL-12.10.31 OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200 OpenGL vendor: Intel Inc. Locale: UTF-8 Qt version: PyQt5 5.15.2, Qt 5.15.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac16,2 Processor Name: Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Memory: 16 GB Boot ROM Version: 427.140.8.0.0 SMC Version (system): 2.32f20 Software: System Software Overview: System Version: macOS 10.14.6 (18G9323) Kernel Version: Darwin 18.7.0 Time since boot: 46 days 1:57 Graphics/Displays: Intel Iris Pro Graphics 6200: Chipset Model: Intel Iris Pro Graphics 6200 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1622 Revision ID: 0x000a Metal: Supported, feature set macOS GPUFamily1 v4 Displays: DELL P2217H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 668VC77B81AB Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort HP E190i: Resolution: 1280 x 1024 (SXGA - Super eXtended Graphics Array) UI Looks like: 1280 x 1024 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CN47280B9M Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No iMac: Display Type: Built-In Retina LCD Resolution: 4096 x 2304 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 678221B832F23 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.5.2 charset-normalizer: 2.0.11 ChimeraX-AddCharge: 1.2.3 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: 1.35.1 ChimeraX-AtomicLibrary: 5.0 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 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: 1.5.1 ChimeraX-CommandLine: 1.2 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202202040724 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-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: 1.1.5 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: 2.6 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.1 ChimeraX-ModelPanel: 1.3.1 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: 1.8 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: 1.1 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: 1.7.6 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 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1 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: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.29.1 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.26 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: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.0.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 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: 9.0.0 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.26 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: 3.0.7 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: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 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: 1.26.8 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output duplicate all ChimeraX