coordination number does not match sum of ligand denticity

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.11.0-37-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3.dev202109010710 (2021-09-01 07:10:41 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202109010710 (2021-09-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Structure Modification"

> open "/home/timofey/biochemdata/tdt/sasha/result /run1/t/mdnw/mdnw1.pdb"

Summary of feedback from opening /home/timofey/biochemdata/tdt/sasha/result
/run1/t/mdnw/mdnw1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
mdnw1.pdb title:  
Protein in water t= 0.00000 step= 0 [more info...]  
  
Chain information for mdnw1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in mdnw1.pdb #1  
---  
DTP — (DTP)  
MG — (MG)  
  

> open /home/timofey/biochemdata/tdt/sasha/mod-g.pdb

Chain information for mod-g.pdb #2  
---  
Chain | Description  
A | No description available  
C | No description available  
  

> select #2/A:602@MG

1 atom, 1 residue, 1 model selected  

> view clip false

> close #1

> show target m

> ui mousemode right zoom

> ui mousemode right "translate selected atoms"

> ui tool show "Coordination Complex Generator"

WARNING AaronTools.atoms.Atom._set_connectivity  
Connectivity not found for element: Mg  
  

WARNING AaronTools.atoms.Atom._set_saturation  
Saturation not found for element: Mg  
  

Traceback (most recent call last):  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/tools/coordination_complexes.py", line 215, in
create_complexes  
rescols, formula = ResidueCollection.get_coordination_complexes(  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 345, in get_coordination_complexes  
raise RuntimeError(  
RuntimeError: coordination number (6) does not match sum of ligand denticity
(0)  
  
RuntimeError: coordination number (6) does not match sum of ligand denticity
(0)  
  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 345, in get_coordination_complexes  
raise RuntimeError(  
  
See log for complete Python traceback.  
  

WARNING AaronTools.atoms.Atom._set_connectivity  
Connectivity not found for element: Ca  
  

WARNING AaronTools.atoms.Atom._set_saturation  
Saturation not found for element: Ca  
  

Traceback (most recent call last):  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/tools/coordination_complexes.py", line 215, in
create_complexes  
rescols, formula = ResidueCollection.get_coordination_complexes(  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 345, in get_coordination_complexes  
raise RuntimeError(  
RuntimeError: coordination number (6) does not match sum of ligand denticity
(0)  
  
RuntimeError: coordination number (6) does not match sum of ligand denticity
(0)  
  
File "/home/timofey/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 345, in get_coordination_complexes  
raise RuntimeError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ZET Gaming
Model: WARD H107
OS: Linux Mint 20.2 uma
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           31Gi        15Gi       4.6Gi       1.5Gi        11Gi        14Gi
	Swap:         2.0Gi       2.0Gi       0.0Ki

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Ti] [10de:2482] (rev a1)	
	Subsystem: Palit Microsystems Inc. Device [1569:2482]	
	Kernel driver in use: nvidia
Locale: ('ru_RU', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    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-ColorKey: 1.4.1
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109010710
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.1
    ChimeraX-ModelPanel: 1.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.0.1
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.2.1
    qtconsole: 5.1.0
    QtPy: 1.10.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    Send2Trash: 1.8.0
    SEQCROW: 1.2.2
    setuptools: 57.0.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
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    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

[Tony Schaefer]

The error indicates that a coordination geometry with a coordination number of 6 was selected (e.g. octahedral), but the sum of the denticity of all ligands specified was 0. This means no ligands were selected. We cannot build coordination complexes without knowing what ligands the user wants. I will clean this up with a more constructive error message in a future update.

To add ligands, click "add ligand" on the tool's table. This will allow you to select a monodentate or bidentate ligand from our library. Keep adding ligands to the table until the denticity is appropriate for the coordination number of the selected coordination geometry.

We have about 120 monodentate or bidentate ligands in the library that comes with SEQCROW, but users can add their own with the "Add to Personal Library" tool under Tools -> AaronTools.

On the table, you can also choose whether to treat bidentate ligands as C2-symmetric or not, so you will only get unique coordination complexes. The tool uses data from https://doi.org/10.1021/acs.inorgchem.8b01133 to only generate unique coordination complexes with any number of different monodentate or bidentate ligands.

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 21, 2021 1:13 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #5445: coordination number does not match sum of ligand denticity (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#5445: coordination number does not match sum of ligand denticity
--------------------------------------------+---------------------------
          Reporter:  chimerax-bug-report@…  |      Owner:  Tony Schaefer
              Type:  defect                 |     Status:  assigned
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tony Schaefer


--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5445#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Hi Tony,

Sorry to waste a bunch of your time, but this report was submitted anonymously. You can tell this because the "Reporter" field is chimerax-bug-report@… rather than some user email address. I thought the report could contain some useful information so I assigned it to you. If you would rather not get anonymous reports in the future, please let me know and I will just close them directly.

--Eric

[Tony Schaefer]

Eric,

Thanks, I had not noticed that. I think I would still like to receive all SEQCROW-related bug reports. I'm confident there are still bugs in my code - they're just hiding. There are also things like this where SEQCROW could catch the problematic input instead of AaronTools raising an exception. I think when some people see the ugly python traceback, they'll stop reading and just hit the bug report button. It can also serve as a reminder to write more/better documentation for certain tools. Everything I said in my reply should probably be on the wiki page for this tool or in a tutorial.

Thanks again,

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 21, 2021 8:57 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #5445: coordination number does not match sum of ligand denticity

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#5445: coordination number does not match sum of ligand denticity
--------------------------------------------+---------------------------
          Reporter:  chimerax-bug-report@…  |      Owner:  Tony Schaefer
              Type:  defect                 |     Status:  closed
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:  not a bug              |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  assigned => closed
 * resolution:   => not a bug


Comment:

 Hi Tony,
         Sorry to waste a bunch of your time, but this report was submitted
 anonymously.  You can tell this because the "Reporter" field is chimerax-
 bug-report@cgl.ucsf.edu rather than some user email address.  I thought
 the report could contain some useful information so I assigned it to you.
 If you would rather not get anonymous reports in the future, please let me
 know and I will just close them directly.

 --Eric

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5445#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

I admire your tenacity. :-)

--Eric