GTP N3

[owen.donohoe@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)I atted chaeges

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\\\Dropbox\\\Marie Curie Project\\\Marie Cure Project V2.0\\\saRNA
> Vaccine\\\p#3 Series\\\p#3-NSP-MC-V2\\\p#3-NSP-MC-
> Repair_V2\\\VEEV_NSP124_Model_Prediction\\\swissmodel\\\VEEV_NSP124_Model_Prediction\\\models\\\01\\\model.pdb"

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) VEEV NSP1-2-4 Model
Prediction [more info...]  
  
Chain information for model.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
G H L | No description available  
I | No description available  
J | No description available  
K | No description available  
M | No description available  
N | No description available  
  
Non-standard residues in model.pdb #1  
---  
GTP — (GTP)  
ZN — (ZN)  
  

> select :GTP

352 atoms, 374 bonds, 11 residues, 1 model selected  

> ui mousemode right select

> select clear

> interfaces ~solvent

34 buried areas: A L 3896, E F 3859, C D 3799, F G 3791, K J 3734, B C 3724, A
B 3703, I J 3690, G H 3670, H I 3609, D E 3566, L K 3438, M N 896, M K 855, M
L 674, M I 589, M J 482, M E 460, M H 459, J _ 436, C _ 432, K _ 414, D _ 414,
G _ 409, M A 408, F _ 404, I _ 403, M F 393, A _ 391, E _ 390, L _ 389, H _
382, M D 379, M B 329  

> undo

[Repeated 1 time(s)]

> select :ZN

12 atoms, 12 residues, 1 model selected  

> select :GTP

352 atoms, 374 bonds, 11 residues, 1 model selected  

> addh

Summary of feedback from adding hydrogens to model.pdb #1  
---  
notes | No usable SEQRES records for model.pdb (#1) chain A; guessing termini
instead  
No usable SEQRES records for model.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for model.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for model.pdb (#1) chain D; guessing termini instead  
No usable SEQRES records for model.pdb (#1) chain E; guessing termini instead  
9 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 2, /B GLU 2, /C GLU
2, /D GLU 2, /E GLU 2, /F GLU 2, /G LYS 3, /H LYS 3, /I GLU 2, /J LYS 3, /K
LYS 3, /L LYS 3, /M TYR 1, /N GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 476, /B LYS 476, /C LYS
476, /D LYS 476, /E LYS 476, /F LYS 476, /G LYS 476, /H LYS 476, /I LEU 472,
/J GLU 473, /K GLU 474, /L LYS 476, /M GLY 607, /N ASP 465  
Chain-final residues that are not actual C termini:  
6106 hydrogen bonds  
53928 hydrogens added  
  

> addcharge

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 134, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
KeyError: ('GTP', 'n3')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 136, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen //chain_id='_' GTP 4 H3
bonded to atom that should not have hydrogens (//chain_id='_' GTP 4 N3)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen //chain_id='_' GTP 4 H3
bonded to atom that should not have hydrogens (//chain_id='_' GTP 4 N3)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 136, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 561.19
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_IE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: HP
Model: HP ENVY x360 Convertible 
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 16,959,295,488
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
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    executing: 1.2.0
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    h5py: 3.7.0
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    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
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    Jinja2: 3.1.2
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    matplotlib-inline: 0.1.6
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    nest-asyncio: 1.5.6
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    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
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    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

[pett]

Hi Owen,

Thanks for reporting this problem. It seems that ChimeraX is mistakenly adding a hydrogen to the GTP N3 atom, which means it didn't determine the N3's hybridization correctly, probably due to inaccurate bond lengths and angles in the GTP. My suggested workaround would be to inform ChimeraX what the correct atom type for the N3 is before adding hydrogens to the structure. You can do that with the command "setattr :gtp@n3 a idatm_type N2".

--Eric

Eric Pettersen
UCSF Computer Graphics Lab