Mercury radius

[mhvg1994@…]

The following bug report has been submitted:
Platform:        macOS-15.0.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Whenever I view the output of a calculation containing a Hg atom, the Hg atom appears to be very small—smaller than a hydrogen atom. I am not sure why this is the case. Is it possible that ChimeraX does not actually recognise Hg as an element, and is treating it like a dummy atom?

I have attached a screenshot of an example, where a mercury atom is loosely bound to a CO molecule.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/matthewgraneri/Documents/Postdoc/calculations/complexes/hg.co/1co/triplet/casscf/opt-
> freq/hg.co-opt-freq-casscf-tz.out format out

Summary of feedback from opening
/Users/matthewgraneri/Documents/Postdoc/calculations/complexes/hg.co/1co/triplet/casscf/opt-
freq/hg.co-opt-freq-casscf-tz.out  
---  
note | hg.co-opt-freq-casscf-tz.out has 0 imaginary harmonic vibrational modes  
  

> style ball

Changed 3 atom styles  

> size stickRadius 0.09

Changed 1 bond radii  

> size ballScale 0.25

Changed 1 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

Opened hg.co-opt-freq-casscf-tz.out as an ORCA output file  

> open
> /Users/matthewgraneri/Documents/Postdoc/calculations/complexes/hg.co/1co/triplet/casscf/nevpt2/opt-
> freq/hg.co-opt-freq-nevpt2-tz.out

Summary of feedback from opening
/Users/matthewgraneri/Documents/Postdoc/calculations/complexes/hg.co/1co/triplet/casscf/nevpt2/opt-
freq/hg.co-opt-freq-nevpt2-tz.out  
---  
warning | error or warning in hg.co-opt-freq-nevpt2-tz.out:  
! !  
! * Positive correlation energy contribution. !  
! !  
! Approximated reference wave function and densities might cause false
intruder states. !  
  

> style ball

Changed 6 atom styles  

> size stickRadius 0.09

Changed 2 bond radii  

> size ballScale 0.25

Changed 2 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

> style ball

Changed 6 atom styles  

> size stickRadius 0.09

Changed 2 bond radii  

> size ballScale 0.25

Changed 2 ball scales  

> color byelement

> lighting depthCue false

> lighting intensity 0.5

Opened hg.co-opt-freq-nevpt2-tz.out as an ORCA output file  

> close #1

> ui tool show "Orbital Viewer"

> ui tool show Distances

Exactly two atoms must be selected!  

> ui tool show "Z-Matrix Builder"

> ui mousemode right distance

> distance /a:1@C1 /a:1@Hg1

Distance between /a UNK 1 C1 and Hg1: 2.721Å  

> ui tool show Angles/Torsions

> ui mousemode right select

> select /a:1@O1

1 atom, 1 residue, 1 model selected  

> select /a:1@C1

1 atom, 1 residue, 1 model selected  

> select /a:1@Hg1

1 atom, 1 residue, 1 model selected  
Either three or four atoms must be selected!  

> select /a:1@O1

1 atom, 1 residue, 1 model selected  

> select /a:1@C1

1 atom, 1 residue, 1 model selected  

> select /a:1@Hg1

1 atom, 1 residue, 1 model selected  

> select add /a:1@C1

2 atoms, 1 residue, 1 model selected  

> select add /a:1@O1

3 atoms, 1 residue, 1 model selected  

> close #1

> select clear




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000EVX/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 11881.1.1

Software:

    System Software Overview:

      System Version: macOS 15.0.1 (24A348)
      Kernel Version: Darwin 24.0.0
      Time since boot: 5 hours, 16 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    appnope: 0.1.4
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    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
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    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
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    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
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    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-ChangeChains: 1.1
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    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-IUPAC: 1.0
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    ChimeraX-ListInfo: 1.2.2
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    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
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    ChimeraX-Mask: 1.0.2
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    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
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    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-OpenCommands: 1.2
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RemoteControl: 1.0
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    ChimeraX-Shape: 1.0.1
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    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
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    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
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    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
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    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
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File attachment: Screenshot 2024-10-25 at 2.49.39 pm.png

Screenshot 2024-10-25 at 2.49.39 pm.png​

[mhvg1994@…]

Added by email2trac

[Eric Pettersen]

Hi Matthew,

For metal cations, ChimeraX uses ionic radii values from the Handbook of Chemistry and Physics. The radius for mercury depends on the number of covalent and coordination bond partners it has, as follows:

0-2: 0.69
3-4: 0.96
5-7: 1.02
8+: 1.14

You can always increase the radius yourself to your liking with the setattr command, e.g. "setattr Hg a radius 1.2"

--Eric

Eric Pettersen
UCSF Computer Graphics Lab