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#3886 closed defect (fixed)

HELIX/SHEET records need to support Hybrid-36 chain IDs

Reported by:	Tristan Croll	Owned by:	pett
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
When a model with 2-character chain IDs is saved in Hybrid-36 format, the secondary structure information for the 2-character chains is lost on reopening.

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 working.cif

Summary of feedback from opening working.cif  
---  
warnings | Unknown polymer entity '1' near line 568  
Unknown polymer entity '2' near line 2939  
Unknown polymer entity '3' near line 6795  
Unknown polymer entity '4' near line 31849  
Unknown polymer entity '5' near line 32858  
6 messages similar to the above omitted  
Unable to fetch template for 'LMX': might have incorrect bonds  
Unknown polymer entity '12' near line 74342  
Unknown polymer entity '13' near line 80775  
Unknown polymer entity '14' near line 81837  
Unknown polymer entity '15' near line 92415  
Unknown polymer entity '16' near line 111955  
Atom H is not in the residue template for MET /AA:1  
Atom C1 is not in the residue template for GPC /AA:60  
Atom H is not in the residue template for MET /AB:1  
Atom C1 is not in the residue template for GPC /AB:60  
Atom C26 is not in the residue template for PEX /AB:62  
Atom H is not in the residue template for MET /AC:1  
Atom C1 is not in the residue template for GPC /AC:60  
Atom C26 is not in the residue template for PEX /AC:62  
Atom H is not in the residue template for MET /AD:1  
Atom C1 is not in the residue template for GPC /AD:60  
Atom H is not in the residue template for MET /AE:1  
Atom C1 is not in the residue template for GPC /AE:60  
Atom C26 is not in the residue template for PEX /AE:62  
Atom H is not in the residue template for MET /AF:1  
Atom C1 is not in the residue template for GPC /AF:60  
Atom C26 is not in the residue template for PEX /AF:62  
Atom H is not in the residue template for MET /AG:1  
Atom C1 is not in the residue template for GPC /AG:60  
Atom H is not in the residue template for MET /AH:1  
Atom C1 is not in the residue template for GPC /AH:60  
Atom C26 is not in the residue template for PEX /AH:62  
Atom H is not in the residue template for MET /AI:1  
Atom C1 is not in the residue template for GPC /AI:60  
Atom C26 is not in the residue template for PEX /AI:62  
Atom H is not in the residue template for MET /AJ:1  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom H is not in the residue template for MET /AK:1  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom H is not in the residue template for MET /AL:1  
Atom C1 is not in the residue template for GPC /AL:60  
Atom C26 is not in the residue template for PEX /AL:62  
Atom H is not in the residue template for MET /AM:1  
Atom C1 is not in the residue template for GPC /AM:60  
Atom H is not in the residue template for MET /AN:1  
Atom C1 is not in the residue template for GPC /AN:60  
Atom C26 is not in the residue template for PEX /AN:62  
Atom H is not in the residue template for MET /AO:1  
Atom C1 is not in the residue template for GPC /AO:60  
Atom C26 is not in the residue template for PEX /AO:62  
Atom H is not in the residue template for MET /AP:1  
Atom C1 is not in the residue template for GPC /AP:60  
Atom H is not in the residue template for MET /AQ:1  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom C26 is not in the residue template for PEX /AQ:62  
Atom H is not in the residue template for MET /AR:1  
Atom C1 is not in the residue template for GPC /AR:60  
Atom C26 is not in the residue template for PEX /AR:62  
Atom H is not in the residue template for MET /AS:1  
Atom C1 is not in the residue template for GPC /AS:60  
Atom H is not in the residue template for MET /AT:1  
Atom C1 is not in the residue template for GPC /AT:60  
Atom C26 is not in the residue template for PEX /AT:62  
Atom H is not in the residue template for MET /AU:1  
Atom C1 is not in the residue template for GPC /AU:60  
Atom C26 is not in the residue template for PEX /AU:62  
Atom H is not in the residue template for MET /AV:1  
Atom C1 is not in the residue template for GPC /AV:60  
Atom H is not in the residue template for MET /AW:1  
Atom C1 is not in the residue template for GPC /AW:60  
Atom C26 is not in the residue template for PEX /AW:62  
Atom H is not in the residue template for MET /AX:1  
Atom C1 is not in the residue template for GPC /AX:60  
Atom C26 is not in the residue template for PEX /AX:62  
Atom H is not in the residue template for GLY /BQ:5  
Atom H is not in the residue template for GLY /BR:5  
Atom H is not in the residue template for GLY /BS:5  
Atom H is not in the residue template for GLY /BT:5  
Atom H6 is not in the residue template for P5S /H1:1001  
Atom H11 is not in the residue template for BPH /L:606  
Atom H11 is not in the residue template for BPH /M:605  
Atom C1 is not in the residue template for RCC /M:701  
Atom HN2 is not in the residue template for ARG /ak:71  
Atom H is not in the residue template for GLY /C1:32  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
Atom C1 is not in the residue template for GPC /Be:60  
11 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
note | Fetching CCD PEX from http://ligand-expo.rcsb.org/reports/P/PEX/PEX.cif  
  
Chain information for working.cif #1  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
C2 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> show cartoons

> hide protein

> hide H

> ~cartoon

> style sphere

Changed 113333 atom styles  

> style stick

Changed 113333 atom styles  

> show

> cofr centerOfView showPivot true

> hide H

> close #1

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_noh.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working_noh.cif  
---  
warnings | Unknown polymer entity '1' near line 568  
Unknown polymer entity '2' near line 1714  
Unknown polymer entity '3' near line 3562  
Unknown polymer entity '4' near line 15540  
Unknown polymer entity '5' near line 16034  
6 messages similar to the above omitted  
Unable to fetch template for 'LMX': might have incorrect bonds  
Unknown polymer entity '12' near line 36483  
Unknown polymer entity '13' near line 39665  
Unknown polymer entity '14' near line 40186  
Unknown polymer entity '15' near line 45290  
Unknown polymer entity '16' near line 55049  
Atom C1 is not in the residue template for GPC /AA:60  
Atom C1 is not in the residue template for GPC /AB:60  
Atom C26 is not in the residue template for PEX /AB:62  
Atom C1 is not in the residue template for GPC /AC:60  
Atom C26 is not in the residue template for PEX /AC:62  
Atom C1 is not in the residue template for GPC /AD:60  
Atom C1 is not in the residue template for GPC /AE:60  
Atom C26 is not in the residue template for PEX /AE:62  
Atom C1 is not in the residue template for GPC /AF:60  
Atom C26 is not in the residue template for PEX /AF:62  
Atom C1 is not in the residue template for GPC /AG:60  
Atom C1 is not in the residue template for GPC /AH:60  
Atom C26 is not in the residue template for PEX /AH:62  
Atom C1 is not in the residue template for GPC /AI:60  
Atom C26 is not in the residue template for PEX /AI:62  
Atom C1 is not in the residue template for GPC /AJ:60  
Atom C1 is not in the residue template for GPC /AK:60  
Atom C26 is not in the residue template for PEX /AK:62  
Atom C1 is not in the residue template for GPC /AL:60  
Atom C26 is not in the residue template for PEX /AL:62  
Atom C1 is not in the residue template for GPC /AM:60  
Atom C1 is not in the residue template for GPC /AN:60  
Atom C26 is not in the residue template for PEX /AN:62  
Atom C1 is not in the residue template for GPC /AO:60  
Atom C26 is not in the residue template for PEX /AO:62  
Atom C1 is not in the residue template for GPC /AP:60  
Atom C1 is not in the residue template for GPC /AQ:60  
Atom C26 is not in the residue template for PEX /AQ:62  
Atom C1 is not in the residue template for GPC /AR:60  
Atom C26 is not in the residue template for PEX /AR:62  
Atom C1 is not in the residue template for GPC /AS:60  
Atom C1 is not in the residue template for GPC /AT:60  
Atom C26 is not in the residue template for PEX /AT:62  
Atom C1 is not in the residue template for GPC /AU:60  
Atom C26 is not in the residue template for PEX /AU:62  
Atom C1 is not in the residue template for GPC /AV:60  
Atom C1 is not in the residue template for GPC /AW:60  
Atom C26 is not in the residue template for PEX /AW:62  
Atom C1 is not in the residue template for GPC /AX:60  
Atom C26 is not in the residue template for PEX /AX:62  
Atom C1 is not in the residue template for RCC /M:701  
Atom C1 is not in the residue template for GPC /Ba:60  
Atom C1 is not in the residue template for GPC /Bb:60  
Atom C1 is not in the residue template for GPC /Bc:60  
Atom C1 is not in the residue template for GPC /Bd:60  
12 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for working_noh.cif #1  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | ?  
AC AD | ?  
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | ?  
BB BD BE BI BQ BR BS BT BV BW bn | ?  
C | ?  
C1 | ?  
C2 | ?  
H1 | ?  
H2 | ?  
L | ?  
M | ?  
aa | ?  
ab ad ae af ag ah ai aj al am an ao ap | ?  
ac | ?  
ak | ?  
  

> style stick

Changed 55382 atom styles  

> close #1

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/collaboration/pu_qian/2020_10_new_maps/model1b/working.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2
TRP A 5 1 4  
Start residue of secondary structure not found: HELIX 2 2 PRO A 10 GLN A 35 1
26  
Start residue of secondary structure not found: HELIX 3 3 ALA A 40 LYS A 45 1
6  
Start residue of secondary structure not found: HELIX 4 4 ARG A 3 TRP A 5 1 3  
Start residue of secondary structure not found: HELIX 5 5 PRO A 10 PHE A 36 1
27  
208 messages similar to the above omitted  
Cannot find LINK/SSBOND residue MAN (1 )  
Cannot find LINK/SSBOND residue MAN (1 )  
Cannot find LINK/SSBOND residue MAN (1 )  
Cannot find LINK/SSBOND residue GCU (2 )  
Cannot find LINK/SSBOND residue MAN (1 )  
3 messages similar to the above omitted  
  
Chain information for working.pdb #1  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available  
AC AD | No description available  
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | No description available  
BB BD BE BI BQ BR BS BT BV BW bn | No description available  
C | No description available  
C1 | No description available  
C2 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ad ae af ag ah ai aj al am an ao ap | No description available  
ac | No description available  
ak | No description available  
  

> style stick

Changed 113333 atom styles  

> save test.cif #1

Not saving entity_poly_seq for non-authoritative sequences  

> show cartoons

> hide atoms




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         14G         36G        220M         11G         47G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	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-Async: 0.1
    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-Clipper: 0.15.0
    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-ISOLDE: 1.0.2
    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-Phenix: 0.1
    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
    graphviz: 0.14.1
    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
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    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
    Send2Trash: 1.5.0
    SEQCROW: 0.17
    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
    versioneer: 0.18
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by pett, 5 years ago

Component:	Unassigned → Input/Output
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → HELIX/SHEET records need to support Hybrid-36 chain IDs

comment:2 by pett, 5 years ago

Resolution:	→ fixed
Status:	accepted → closed

Available in tomorrow's build.

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