id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3936 Hybrid36 issues chris.moth@… Eric Pettersen "{{{ 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 Saving PDB files with residue #s > 9999 creates identical files for both hybrid36 and AMBER formats. Hybrid36 format does not agree with UCSF Sali Lab Modbase format. Open the Modbase hybrid36 file I left for you at: https://structbio.vanderbilt.edu/~mothcw/modbase_pdb36_example/ Note that residue numbers are correct on mouse hover. (Good work!). Save the file as pdb format. The residue numbers from modbase were: $ tail ENSP00000343764.6_133.pdb ATOM 934 CA ASN AABKW -12.167 2.530 23.510 1.00112.26 C ATOM 935 CB ASN AABKW -10.699 2.563 23.977 1.00112.26 C ATOM 936 CG ASN AABKW -10.226 1.147 24.273 1.00112.26 C ATOM 937 OD1 ASN AABKW -10.240 0.278 23.402 1.00112.26 O ATOM 938 ND2 ASN AABKW -9.778 0.909 25.535 1.00112.26 N ATOM 939 C ASN AABKW -13.008 2.001 24.665 1.00112.26 C ATOM 940 O ASN AABKW -13.741 0.999 24.451 1.00112.26 O ATOM 941 OXT ASN AABKW -12.929 2.591 25.776 1.00112.26 O TER 942 ASN AABKW but are now 5 decimal digits. (base) [mothcw@localhost tmp]$ tail ENSP00000343764.6_133_chimeraX.pdb ATOM 933 N ASN A25008 -12.660 3.834 23.192 1.00112.26 N ATOM 934 CA ASN A25008 -12.167 2.530 23.510 1.00112.26 C ATOM 935 CB ASN A25008 -10.699 2.563 23.977 1.00112.26 C ATOM 936 CG ASN A25008 -10.226 1.147 24.273 1.00112.26 C ATOM 937 OD1 ASN A25008 -10.240 0.278 23.402 1.00112.26 O ATOM 938 ND2 ASN A25008 -9.778 0.909 25.535 1.00112.26 N ATOM 939 C ASN A25008 -13.008 2.001 24.665 1.00112.26 C ATOM 940 O ASN A25008 -13.741 0.999 24.451 1.00112.26 O ATOM 941 OXT ASN A25008 -12.929 2.591 25.776 1.00112.26 O Also #1: Your helix/sheel entries may be in correct notation: HELIX 1 1 VAL A ABJ6 TRP A ABJ8 1 3 SHEET 1 1 1 GLU AABI5 SER AABI7 0 SHEET 2 2 1 MET AABIE THR AABIH 0 SHEET 3 3 1 ILE AABIT ASP AABJ2 0 SHEET 4 4 1 ASN AABJC THR AABJF 0 SHEET 5 5 1 ARG AABJK VAL AABJN 0 SHEET 6 6 1 SER AABJV ASN AABK4 0 SHEET 7 7 1 SER AABKF PHE AABKH 0 Also #2: Whether I chose hybrid36 or AMBER format, the output is unchanged. It might be easier to just convince our modbase friends to output in .cif, and to fix the chimeraX cif saver to include secondary structure annotaitons :) But, I wanted you to know abou thte bug. Attached find the file I get when I save the model from chimeraX with the hybrid36 option checked. Log: 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 /tmp/ENSP00000343764.6_133.pdb Summary of feedback from opening /tmp/ENSP00000343764.6_133.pdb --- warning | Ignored bad PDB record found on line 974 END ENSP00000343764.6_133.pdb title: Model of SubName: Full=Uncharacterized protein; [more info...] Chain information for ENSP00000343764.6_133.pdb #1 --- Chain | Description A | No description available > save /tmp/ENSP00000343764.6_133_chimeraX.pdb relModel #1 > save /tmp/ENSP00000343764.6_133_amber.pdb relModel #1 serialNumbering amber OpenGL version: 3.3.0 NVIDIA 440.82 OpenGL renderer: GeForce GTX 750 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T1700 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 4 Intel(R) Xeon(R) CPU E3-1220 v3 @ 3.10GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 31G 10G 10G 583M 10G 20G Swap: 15G 0B 15G Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2) Subsystem: Gigabyte Technology Co., Ltd Device [1458:3667] 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: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 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-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: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 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-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 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 openvr: 1.12.501 packaging: 20.4 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 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 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 File attachment: ENSP00000343764.6_133_chimeraX.pdb }}} [attachment:""ENSP00000343764.6_133_chimeraX.pdb""] " defect closed normal Input/Output fixed all ChimeraX