id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4161	CIF vs. PDB deposition	coutandin@…	Greg Couch	"{{{
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:
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    appdirs: 1.4.4
    appnope: 0.1.2
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    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
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    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
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    ChimeraX-Positions: 1.0
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    ChimeraX-ResidueFit: 1.0
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    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
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    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
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    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
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    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
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File attachment: 2-C_LOBE-1_fixed2.pdb

}}}

[attachment:""2-C_LOBE-1_fixed2.pdb""]
"	defect	closed	normal		Input/Output		nonchimerax		Eric Pettersen				all	ChimeraX