ISOLDE: 5 CB neighbors in SER MD template

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The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
When choosing MD template for unparametrized Ser residues before starting Isolde simulation, there is an error:
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (SER).

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jane/Downloads/cryosparc_P36_J200_007_volume_map_sharp.mrc

Opened cryosparc_P36_J200_007_volume_map_sharp.mrc as #1, grid size
324,324,324, pixel 1.09, shown at level 0.641, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.7888

> surface dust #1 size 10.9

> volume #1 level 0.8875

> volume #1 level 0.8134

> volume #1 level 0.9121

> volume #1 level 0.7147

> open /Users/jane/Documents/PhD-
> files/Project_BAL/cryoEM_NLRP3-decamer_BAL1558_BAL1516/20231031_Cond1_Krios_1558/cryosparc_P64_J125_map_sharp.mrc

Opened cryosparc_P64_J125_map_sharp.mrc as #2, grid size 324,324,324, pixel
1.12, shown at level 0.0876, step 2, values float32  

> open /Users/jane/Documents/PhD-
> files/Project_BAL/cryoEM_NLRP3-decamer_BAL1558_BAL1516/20231031_Cond1_Krios_1558/cryosparc_P64_J126_map_sharp.mrc

Opened cryosparc_P64_J126_map_sharp.mrc as #3, grid size 324,324,324, pixel
1.12, shown at level 0.00858, step 2, values float32  

> open /Users/jane/Documents/PhD-
> files/Project_BAL/cryoEM_NLRP3-decamer_BAL1558_BAL1516/20231031_Cond1_Krios_1558/cryosparc_P64_J68_006_volume_map_sharp.mrc

Opened cryosparc_P64_J68_006_volume_map_sharp.mrc as #4, grid size
324,324,324, pixel 1.12, shown at level 0.663, step 2, values float32  

> volume #3 step 1

> volume #2 step 1

> volume #4 step 1

> volume #4 level 1.435

> volume #4 level 1.821

> surface dust #4 size 11.2

> volume #4 level 1.307

[Repeated 1 time(s)]

> volume #3 level 0.09266

> volume #3 level 0.09997

> surface dust #3 size 11.2

> volume #3 level 0.1182

> volume #2 level 0.1478

> volume #2 level 0.1797

> volume #4 level 1.628

> volume #3 level 0.04879

> open
> /Users/jane/Downloads/cryosparc_P36_J193_series_000/J193_series_000_frame_000.mrc

Opened J193_series_000_frame_000.mrc as #5, grid size 300,300,300, pixel 1.09,
shown at level 0.0232, step 2, values float32  

> open
> /Users/jane/Downloads/cryosparc_P36_J193_series_000/J193_series_000_frame_040.mrc

Opened J193_series_000_frame_040.mrc as #6, grid size 300,300,300, pixel 1.09,
shown at level 0.0238, step 2, values float32  

> open
> /Users/jane/Downloads/cryosparc_P36_J193_series_000/J193_series_000_frame_030.mrc

Opened J193_series_000_frame_030.mrc as #7, grid size 300,300,300, pixel 1.09,
shown at level 0.0233, step 2, values float32  

> open
> /Users/jane/Downloads/cryosparc_P36_J193_series_000/J193_series_000_frame_020.mrc

Opened J193_series_000_frame_020.mrc as #8, grid size 300,300,300, pixel 1.09,
shown at level 0.023, step 2, values float32  

> open
> /Users/jane/Downloads/cryosparc_P36_J193_series_000/J193_series_000_frame_010.mrc

Opened J193_series_000_frame_010.mrc as #9, grid size 300,300,300, pixel 1.09,
shown at level 0.023, step 2, values float32  

> volume #3 level 0.03783

> volume #9 level 0.02147

> volume #8 level 0.02151

> volume #7 level 0.01954

> volume #6 level 0.02032

> volume #5 level 0.02117

> open /Users/jane/Downloads/cryosparc_P36_J208_006_volume_map_sharp.mrc

Opened cryosparc_P36_J208_006_volume_map_sharp.mrc as #10, grid size
324,324,324, pixel 1.09, shown at level 0.581, step 2, values float32  

> volume #10 step 1

> volume #10 level 0.7385

> volume #10 level 0.7911

> surface dust #10 size 10.9

> volume #10 level 0.9139

> volume #10 level 0.8437

> volume #10 level 0.9665

> volume #10 level 0.8788

> volume #10 level 0.7911

> volume #10 level 0.984

> open "/Users/jane/Documents/PhD-files/Project
> mouseNLRP3/20240229_Krios_duodecamer/20240328_trimer-addLoop.pdb"

Chain information for 20240328_trimer-addLoop.pdb #11  
---  
Chain | Description  
A B | No description available  
E F G | No description available  
  

> show atoms

> show cartoons

> style stick

Changed 39179 atom styles  

> style stick

Changed 39179 atom styles  

> hide atoms

> ui mousemode right select

> select /E:224

10 atoms, 9 bonds, 1 residue, 1 model selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #11,1,0,0,11.507,0,1,0,-16.17,0,0,1,1.1576

> view matrix models #11,1,0,0,-0.97685,0,1,0,-27.675,0,0,1,-0.039692

> view matrix models #11,1,0,0,-12.348,0,1,0,-28.216,0,0,1,-59.66

> view matrix models #11,1,0,0,-27.461,0,1,0,-37.599,0,0,1,-88.266

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.82537,-0.53602,0.17732,349.21,0.16191,-0.5256,-0.83518,293.87,0.54087,-0.66063,0.5206,-9.8129

> view matrix models
> #11,-0.99784,-0.053532,0.038158,338.6,0.00019083,0.57807,0.81599,-124.78,-0.06574,0.81423,-0.57681,92.31

> view matrix models
> #11,-0.96365,0.24296,0.11114,278.13,0.2618,0.77561,0.57436,-156.91,0.053347,0.58257,-0.81103,144.54

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.96365,0.24296,0.11114,296.42,0.2618,0.77561,0.57436,-177.44,0.053347,0.58257,-0.81103,183.65

> view matrix models
> #11,-0.96365,0.24296,0.11114,297.85,0.2618,0.77561,0.57436,-126.47,0.053347,0.58257,-0.81103,201.76

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.96365,0.24296,0.11114,298.97,0.2618,0.77561,0.57436,-118.57,0.053347,0.58257,-0.81103,209.47

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.96964,-0.12752,0.20865,334.11,-0.008073,0.86948,0.4939,-67.872,-0.2444,0.47722,-0.84411,284.48

> view matrix models
> #11,-0.96901,-0.11487,0.21869,330.44,0.007409,0.87139,0.49054,-70.368,-0.24691,0.47696,-0.84353,284.87

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.99713,0.025261,-0.071346,367.93,-0.016614,0.84661,0.53195,-69.929,0.07384,0.53161,-0.84376,218.65

> view matrix models
> #11,-0.9877,-0.042758,-0.15039,389.77,-0.089321,0.94378,0.31829,-31.962,0.12833,0.32781,-0.93599,253.46

> view matrix models
> #11,-0.98518,-0.06028,-0.1606,393.57,-0.10729,0.94702,0.30273,-26.346,0.13384,0.31548,-0.93945,254.78

> fitmap #11 inMap #10

Fit molecule 20240328_trimer-addLoop.pdb (#11) to map
cryosparc_P36_J208_006_volume_map_sharp.mrc (#10) using 39179 atoms  
average map value = 0.9246, steps = 172  
shifted from previous position = 6.9  
rotated from previous position = 13 degrees  
atoms outside contour = 24061, contour level = 0.98402  
  
Position of 20240328_trimer-addLoop.pdb (#11) relative to
cryosparc_P36_J208_006_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.99870011 0.03839245 0.03352770 343.68288196  
0.04811435 0.92719972 0.37146425 -65.52123394  
-0.01682545 0.37259455 -0.92784169 270.82518710  
Axis 0.02203508 0.98162817 0.18952729  
Axis point 174.35284648 0.00000000 139.49176385  
Rotation angle (degrees) 178.53032991  
Shift along axis -5.41564370  
  

> ui mousemode right select

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 18 residues in model #11 to IUPAC-IUB
standards.  
Chain information for 20240328_trimer-addLoop.pdb  
---  
Chain | Description  
11.2/A 11.2/B | No description available  
11.2/E 11.2/F 11.2/G | No description available  
  

> clipper associate #10 toModel #11

Opened cryosparc_P36_J208_006_volume_map_sharp.mrc as #11.1.1.1, grid size
324,324,324, pixel 1.09, shown at step 1, values float32  

> isolde sim start /G,E-F,A-B

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['HB3', 'HB2'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
[Repeated 1 time(s)]Failed to add atoms ['HB2', 'HB3'] to atom C because this
will lead to having 5 atoms attached, which is more than its assigned geometry
can support. This is probably due to an error in the MD template (SER). If
this template is built into ISOLDE, please report this using Help/Report a bug  
[Repeated 2 time(s)]




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14W0004VD/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 8 days, 6 hours, 16 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      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: No
          Connection Type: Internal
        DELL U2719D:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
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    backcall: 0.2.0
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    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
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    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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
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    ChimeraX-ISOLDE: 1.7.1
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    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
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    ChimeraX-Maestro: 1.9.1
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    ChimeraX-MapData: 2.0
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    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
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    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
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    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
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    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
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    ChimeraX-RotamerLibsDunbrack: 2.0
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    ChimeraX-SaveCommand: 1.5.1
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    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
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    ChimeraX-SideView: 1.0.1
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    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
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    ChimeraX-TapeMeasure: 1.0
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    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
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    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
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    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
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    contourpy: 1.2.0
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    platformdirs: 4.1.0
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[pett]

Reported by Jane Torp

[Tristan Croll]

This seems to be down to a bit of weirdness around the way ISOLDE matches partial residues to templates for rebuilding, and only really affects serine residues... problem is I haven't figured out how to replicate it for myself. Anyway, the easiest way to work around it is to just use the "swapaa" right mouse mode to mutate the residue away from and back to serine, which will fill in the sidechain for you.