Opened 5 years ago

Closed 5 years ago

#3936 closed defect (fixed)

Hybrid36 issues

Reported by: chris.moth@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

ENSP00000343764.6_133_chimeraX.pdb​

Attachments (1)

ENSP00000343764.6_133_chimeraX.pdb​ (75.0 KB ) - added by chris.moth@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by chris.moth@…, 5 years ago

Attachment: ENSP00000343764.6_133_chimeraX.pdb​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Hybrid36 issues

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Hi Chris,

Thanks for reporting this problem. Before Hybrid-36 was supported, large residue numbers would "steal" the insertion-code column if needed for an extra digit. Disabling that hack fixes this. Using Hybrid-36 is better than the hack since it coordinates with HELIX/SHEET records and other records that require large residue numbers.
Amber and Hybrid-36 formats are identical unless there are atom serial numbers > 99,999, in which case Amber format steals a blank column from "ATOM " for an extra digit.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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