Opened 5 years ago

Last modified 5 years ago

#4424 feedback defect

Missing bonds

Reported by: hello@… 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:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
The display of a molecule is missing links between c-c and c-o randomly.

With thanks

Vishal K Sahu

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 D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt

Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.1 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C_9 and O_15  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_10 and O_17  
  
157 messages similar to the above omitted  
  
Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds)  

> open D:/MDD/MDA5-SAB-2x23-w5/protein.pdbqt

Chain information for protein.pdbqt #2  
---  
Chain | Description  
A B E G | No description available  
  
Opened protein.pdbqt containing 1 structures (10016 atoms, 10187 bonds)  

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> hide #1.6 models

> hide #1.7 models

> hide #1.8 models

> hide #1.9 models

> close #1.2-9

> select #1.1

30 atoms, 31 bonds, 1 residue, 1 model selected  
No model chosen to save relative to  
No model chosen to save relative to  

> save D:/Desktop/lig.pdb models #1 relModel #1.1

> open D:/Desktop/lig.pdb

Summary of feedback from opening D:/Desktop/lig.pdb  
---  
warning | Ignored bad PDB record found on line 31  
END  
  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hbonds #2-3

987 hydrogen bonds found  

> close #1

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2

10016 atoms, 10187 bonds, 987 pseudobonds, 1081 residues, 2 models selected  

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #4

987 pseudobonds, 1 model selected  

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2

10016 atoms, 10187 bonds, 987 pseudobonds, 1081 residues, 2 models selected  

> ~select #4

10016 atoms, 10187 bonds, 1081 residues, 1 model selected  

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> hbonds sel

0 hydrogen bonds found  

> select #2

10016 atoms, 10187 bonds, 1081 residues, 1 model selected  

> ~select #2

Nothing selected  

> ~select #4

Nothing selected  

> close #4

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2

10016 atoms, 10187 bonds, 1081 residues, 1 model selected  

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2

10016 atoms, 10187 bonds, 1081 residues, 1 model selected  

> select #3

30 atoms, 31 bonds, 1 residue, 1 model selected  

> select #2

10016 atoms, 10187 bonds, 1081 residues, 1 model selected  

> select #3 #2

10046 atoms, 10218 bonds, 1082 residues, 2 models selected  

> hbonds sel

987 hydrogen bonds found  

> hide #3 models

> hide #2 models

> hide #1 models

> show #3 models

> show #2 models

> show #1 models

> ~select #2

30 atoms, 31 bonds, 1 residue, 1 model selected  

> close

> open D:/MDD/MDA5-SAB-2x23-w5/ligand.pdbqt

Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/ligand.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 2  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 3  
REMARK 1 A between atoms: C_9 and O_15  
  
Ignored bad PDB record found on line 4  
REMARK 2 A between atoms: C_10 and O_17  
  
Ignored bad PDB record found on line 5  
REMARK 3 A between atoms: C_13 and C_19  
  
12 messages similar to the above omitted  
  
Opened ligand.pdbqt containing 1 structures (30 atoms, 31 bonds)  

> close

> open D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt

Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.1 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C_9 and O_15  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_10 and O_17  
  
157 messages similar to the above omitted  
  
Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds)  

> close #1.2-9

> hbonds

0 hydrogen bonds found  

> interfaces ~solvent

0 buried areas:  

> style sphere

Changed 30 atom styles  
No Surface models open  

> show surfaces

> style stick

Changed 30 atom styles  

> style sphere

Changed 30 atom styles  

> style sphere

Changed 30 atom styles  

> style ball

Changed 30 atom styles  

> style ball

Changed 30 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style stick

Changed 30 atom styles  

> transparency 50

> select :0@C

25 atoms, 24 bonds, 1 residue, 1 model selected  

> select :0@C

25 atoms, 24 bonds, 1 residue, 1 model selected  

> select none

Expected an objects specifier or a keyword  

> select 0

Expected an objects specifier or a keyword  

> select all

30 atoms, 31 bonds, 1 residue, 2 models selected  

> select invert

Expected an objects specifier or a keyword  

> select off

Expected an objects specifier or a keyword  

> ~select #1

1 model selected  

> ~select

Nothing selected  

> select

30 atoms, 31 bonds, 1 residue, 2 models selected  

> ~select

Nothing selected  

> select

30 atoms, 31 bonds, 1 residue, 2 models selected  

> addh

Summary of feedback from adding hydrogens to out.pdbqt #1.1  
---  
warning | Unknown hybridization for atom (C) of residue type UNK; not adding
hydrogens to it  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
17 hydrogens added  
  

> close

> open D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt

Summary of feedback from opening D:/MDD/MDA5-SAB-2x23-w5/out.pdbqt  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK VINA RESULT: -9.1 0.000 0.000  
  
Ignored bad PDB record found on line 3  
REMARK 4 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C_9 and O_15  
  
Ignored bad PDB record found on line 6  
REMARK 2 A between atoms: C_10 and O_17  
  
157 messages similar to the above omitted  
  
Opened out.pdbqt containing 9 structures (270 atoms, 279 bonds)  

> hide #1.1-9 target m

> show #1.2 models

> show #1.1 models

> hide #1.2 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.3 models

> show #1.4 models

> hide #1.3 models

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Unknown hybridization for atom (C) of residue type UNK; not adding
hydrogens to it  
Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens
to it  
Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens
to it  
Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens
to it  
Unknown hybridization for atom (C) of residue type UNK; not adding hydrogens
to it  
4 messages similar to the above omitted  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
153 hydrogens added  
  




OpenGL version: 3.3.0 - Build 27.20.100.8681
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Desktop Pro G1 MT
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 4,147,757,056
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz"
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: 2.1.3
    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-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-Cytoscape: 0.1
    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: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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-RMF: 0.9
    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: 1.2.1
    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
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    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
    MolecularDynamicsViewer: 1.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1
File attachment: chimera-bug.pdf

chimera-bug.pdf​

Attachments (1)

chimera-bug.pdf​ (410.7 KB ) - added by hello@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by hello@…, 5 years ago

Attachment: chimera-bug.pdf​ 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 → Missing bonds

comment:2 by Eric Pettersen, 5 years ago

Status: accepted → feedback

Hi Vishal,

With the problematic structure open as model #1, and before adding any hydrogens, does the command "bond #1" add the missing bonds? If it does, then there is probably something wrong with your input structure file. You would have to send me a copy of the file for me to diagnose the problem further.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  4 comment:3 by hello@…, 5 years ago 

Hi Eric

Thank you for your time and email. While exploring the issue, I found that
other programs were showing the bond even when the dihedral angle was not
proper and structure was not energy minimised, which I think is a good
feature of ChimeraX.

Since the issue is with the structure of my file, I find Chimera to be
better than other programs which did not consider the inappropriate
dihedrals.

Again, many cordial thanks for the great program to the research community.

Sincerely


*Vishal Kumar Sahu*
CSIR-Junior Research Fellow
*Under the guidance of:*
Dr. Soumya Basu
Associate Professor
Cancer and Translational Research Laboratory
Dr. D. Y. Patil Biotechnology and Bioinformatics Institute
Pune, Maharashtra - 411033

On Mon, Mar 29, 2021 at 11:09 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by Eric Pettersen, 5 years ago

Hi Vishal,

You never provided the file, but I am guessing that it is one of the formats where bond information is explicitly provided (such as mmCIF or PDB). ChimeraX is honoring that bond information and the other programs are ignoring it and forming bonds based on inter-atomic distances. Both approaches have their advantages and disadvantages.
Glad I could help.

--Eric

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