CIF vs. PDB deposition

[coutandin@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202101220441 (2021-01-22 04:41:35 UTC)
Description
I open a pdb and save it as cif. Validating both the pdb and the cif at
https://validate-rcsb-2.wwpdb.org/ gives no issues for the pdb file but several issues for the cif file (see below). 
I am providing the pdb file so you can reproduce the problem.
As the protein data bank prefers cif over pdb it would be great to have that problem solved.

The following planarity outliers were identified
Plane outliers
Model/Chain/Number/Residue
Region not planar
1/A/177/ARG
SIDE CHAIN

The following bond angles were found to be significantly different from the expected bond angle.
Bond angle outliers
Model/chain
Number/Residue/Atom
Number/Residue/Atom
Number/Residue/Atom
Expected bond angle (°)
Measured bond angle (°)
1/A
168/ARG/NE
168/ARG/CZ
168/ARG/NH1
120.3 ± 0.5
123.5
1/A
338/ARG/NE
338/ARG/CZ
338/ARG/NH1
120.3 ± 0.5
124.4
1/A
338/ARG/NE
338/ARG/CZ
338/ARG/NH2
120.3 ± 0.5
117.2
1/A
358/ARG/NE
358/ARG/CZ
358/ARG/NH1
120.3 ± 0.5
123.9
1/A
449/ARG/NE
449/ARG/CZ
449/ARG/NH1
120.3 ± 0.5
124.5
1/A
504/ARG/NE
504/ARG/CZ
504/ARG/NH1
120.3 ± 0.5
123.6
1/B
168/ARG/NE
168/ARG/CZ
168/ARG/NH1
120.3 ± 0.5
123.3
1/B
177/ARG/NE
177/ARG/CZ
177/ARG/NH2
120.3 ± 0.5
123.9
1/B
197/ARG/NE
197/ARG/CZ
197/ARG/NH1
120.3 ± 0.5
124.5
1/B
359/ARG/NE
359/ARG/CZ
359/ARG/NH1
120.3 ± 0.5
123.7
1/B
449/ARG/NE
449/ARG/CZ
449/ARG/NH1
120.3 ± 0.5
124.7
1/B
506/ARG/NE
506/ARG/CZ
506/ARG/NH1
120.3 ± 0.5
123.4
1/B
583/ARG/NE
583/ARG/CZ
583/ARG/NH1
120.3 ± 0.5
124.5
1/B
583/ARG/NE
583/ARG/CZ
583/ARG/NH2
120.3 ± 0.5
117.3
1/C
32/ARG/NE
32/ARG/CZ
32/ARG/NH1
120.3 ± 0.5
125.3
1/C
32/ARG/NE
32/ARG/CZ
32/ARG/NH2
120.3 ± 0.5
116.1
1/C
36/ARG/NE
36/ARG/CZ
36/ARG/NH1
120.3 ± 0.5
124.5
1/K
518/ARG/NE
518/ARG/CZ
518/ARG/NH1
120.3 ± 0.5
123.5

The following atoms were found to be less than 2.2 Å apart and are considered too close unless they are covalently bonded.
Clashes
Model/Chain/Number/Residue
Atom
Model/Chain/Number/Residue
Atom
Distance between the atoms
1/B/418/GLU
OE1
1/C/127/SER
HG
1.55
1/B/61/ASP
OD1
1/B/63/SER
HG
1.59
1/B/34/SER
HG
1/B/393/GLU
OE1
1.60



Log:
UCSF ChimeraX version: 1.2.dev202101220441 (2021-01-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/daniel/Box/emdb_pdb_deposition/fixed/2-C_LOBE-1_fixed2.pdb

Chain information for 2-C_LOBE-1_fixed2.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
K | No description available  
  

> save /Users/daniel/Box/emdb_pdb_deposition/fixed/2-C_LOBE-1_fixed2.cif

Not saving entity_poly_seq for non-authoritative sequences  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i9
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.60.15.0.0 (iBridge: 18.16.13030.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H114)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1 day 20:47

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501U-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Pro Display XDR:
          Display Type: LCD
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 59 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02ZT03LML9V
          Display Firmware Version: 4.2.37
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, 'UTF-8')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.3.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.10.5
    ChimeraX-AtomicLibrary: 1.1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202101220441
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.1
    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: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 2.2
    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: 1.5
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    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: 1.0
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.4.1
    ChimeraX-uniprot: 2.1
    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: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    flake8: 3.8.3
    flake8-polyfill: 1.0.2
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.0
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    mccabe: 0.6.1
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.2
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.8
    ParmEd: 3.2.0
    parso: 0.7.1
    pep8: 1.7.1
    pep8-naming: 0.10.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.3.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.11
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycodestyle: 2.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    pyflakes: 2.2.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PySide2: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 21.0.1
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    shiboken2: 5.15.2
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0
File attachment: 2-C_LOBE-1_fixed2.pdb

2-C_LOBE-1_fixed2.pdb​

[coutandin@…]

Added by email2trac

[Greg Couch]

tl;dr -- mostly a PDB validator bug.

There are lots of issues here.

I hope you filed a bug with the PDB's validator. The mmCIF coordinates are exactly the same as the PDB ones. So if the angles are bad in one, then they should be bad in the other.

ChimeraX's mmCIF output is not complete. For example, sheet information is lost because ChimeraX does not preserve that information from PDB files nor mmCIF files. The PDB comments are not translated. If you want to convert a PDB file into a mmCIF one, you should use the PDB's MAXIT software suite. Not sure how well it works for PDB files that aren't deposition ready.

And ideally your PDB file would have SEQRES records with the actual sequence. That is critical information needed to write mmCIF files so that different mmCIF readers will generate the same connectivity. This is what Phenix's mmtbx.prepare_pdb_deposition tool does. You can fake it by saving the mmCIF file with "save filename.cif bestGuess true". If there were no gaps in your chains and no sheets, then it would be okay. But you have both.