Minimization failure: KeyError: 'N'

[etienne.reboul@…]

The following bug report has been submitted:
Platform:        macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Nitrogen atoms "N" doesn't seems to be recognized by mininimidzyion protocol. The file was generated using colabfold notebook : https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ereboul/projects/NFP-ab-initio-modelling/NFP6-3.cif

Summary of feedback from opening /Users/ereboul/projects/NFP-ab-initio-
modelling/NFP6-3.cif  
---  
warnings | Unknown polymer entity '1' on line 107  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for NFP6-3.cif #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Minimize Structure"

> minimize #1 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A HIS 590: phi -44.8, psi none trans  
Applying HIS rotamer (chi angles: -63.7 -72.9) to /A HIS 590  
Summary of feedback from adding hydrogens to NFP6-3.cif #1  
---  
notes | No usable SEQRES records for NFP6-3.cif (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
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: /A HIS 590  
528 hydrogen bonds  
/A HIS 590 is not terminus, removing H atom from 'C'  
5 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 107, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 173, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
Exception: Could not find typename 'N' for atom '<Atom 9244 (N) of chain 0
residue 589 (A-HIS-590)>' in list of known atom types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
Exception: Could not find typename 'N' for atom '' in list of known atom
types.  
Known atom types are: dict_keys(['tip3pfb_standard-Li+', 'tip3pfb_standard-
Na+', 'tip3pfb_standard-K+', 'tip3pfb_standard-Rb+', 'tip3pfb_standard-Cs+',
'tip3pfb_standard-F-', 'tip3pfb_standard-Cl-', 'tip3pfb_standard-Br-',
'tip3pfb_standard-I-', 'tip3pfb_standard-Be2+', 'tip3pfb_standard-Cu2+',
'tip3pfb_standard-Ni2+', 'tip3pfb_standard-Pt2+', 'tip3pfb_standard-Zn2+',
'tip3pfb_standard-Co2+', 'tip3pfb_standard-Pd2+', 'tip3pfb_standard-Ag2+',
'tip3pfb_standard-Cr2+', 'tip3pfb_standard-Fe2+', 'tip3pfb_standard-Mg2+',
'tip3pfb_standard-V2+', 'tip3pfb_standard-Mn2+', 'tip3pfb_standard-Hg2+',
'tip3pfb_standard-Cd2+', 'tip3pfb_standard-Yb2+', 'tip3pfb_standard-Ca2+',
'tip3pfb_standard-Sn2+', 'tip3pfb_standard-Pb2+', 'tip3pfb_standard-Eu2+',
'tip3pfb_standard-Sr2+', 'tip3pfb_standard-Sm2+', 'tip3pfb_standard-Ba2+',
'tip3pfb_standard-Ra2+', 'tip3pfb_standard-Al3+', 'tip3pfb_standard-Fe3+',
'tip3pfb_standard-Cr3+', 'tip3pfb_standard-In3+', 'tip3pfb_standard-Tl3+',
'tip3pfb_standard-Y3+', 'tip3pfb_standard-La3+', 'tip3pfb_standard-Ce3+',
'tip3pfb_standard-Pr3+', 'tip3pfb_standard-Nd3+', 'tip3pfb_standard-Sm3+',
'tip3pfb_standard-Eu3+', 'tip3pfb_standard-Gd3+', 'tip3pfb_standard-Tb3+',
'tip3pfb_standard-Dy3+', 'tip3pfb_standard-Er3+', 'tip3pfb_standard-Tm3+',
'tip3pfb_standard-Lu3+', 'tip3pfb_standard-Hf4+', 'tip3pfb_standard-Zr4+',
'tip3pfb_standard-Ce4+', 'tip3pfb_standard-U4+', 'tip3pfb_standard-Pu4+',
'tip3pfb_standard-Th4+', 'tip3p-fb-O', 'tip3p-fb-H', 'protein-C', 'protein-
CA', 'protein-CB', 'protein-CC', 'protein-CN', 'protein-CR', 'protein-CT',
'protein-CV', 'protein-CW', 'protein-C*', 'protein-CX', 'protein-H', 'protein-
HC', 'protein-H1', 'protein-HA', 'protein-H4', 'protein-H5', 'protein-HO',
'protein-HS', 'protein-HP', 'protein-N', 'protein-NA', 'protein-NB',
'protein-N2', 'protein-N3', 'protein-O', 'protein-O2', 'protein-OH',
'protein-S', 'protein-SH', 'protein-CO', 'protein-2C', 'protein-3C',
'protein-C8', 'DNA-C', 'DNA-CA', 'DNA-CB', 'DNA-CK', 'DNA-CM', 'DNA-CQ', 'DNA-
CT', 'DNA-H', 'DNA-HC', 'DNA-H1', 'DNA-H2', 'DNA-HA', 'DNA-H4', 'DNA-H5',
'DNA-HO', 'DNA-NA', 'DNA-NB', 'DNA-NC', 'DNA-N2', 'DNA-N*', 'DNA-O', 'DNA-O2',
'DNA-OH', 'DNA-OS', 'DNA-P', 'DNA-C7', 'DNA-C2', 'DNA-C1', 'DNA-CJ', 'RNA-C',
'RNA-CA', 'RNA-CB', 'RNA-CI', 'RNA-CP', 'RNA-CS', 'RNA-CQ', 'RNA-CT',
'RNA-C5', 'RNA-C4', 'RNA-H', 'RNA-H1', 'RNA-H2', 'RNA-HA', 'RNA-H4', 'RNA-H5',
'RNA-HO', 'RNA-NA', 'RNA-NB', 'RNA-NC', 'RNA-N2', 'RNA-N*', 'RNA-O', 'RNA-O2',
'RNA-OH', 'RNA-OS', 'RNA-P', 'cA', 'cB', 'cC', 'cD', 'hA', 'hB', 'hE', 'hL',
'hN', 'hO', 'hX', 'nA', 'oC', 'oH', 'oO', 'oP', 'oS', 'oT', 'pA', 'c', 'cs',
'c1', 'c2', 'c3', 'ca', 'cp', 'cq', 'cc', 'cd', 'ce', 'cf', 'cg', 'ch', 'cx',
'cy', 'c5', 'c6', 'cu', 'cv', 'cz', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc',
'hn', 'ho', 'hp', 'hs', 'hw', 'hx', 'f', 'cl', 'br', 'i', 'n', 'n1', 'n2',
'n3', 'n4', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'ns', 'nt', 'nx',
'ny', 'nz', 'n+', 'nu', 'nv', 'n7', 'n8', 'n9', 'ni', 'nj', 'nk', 'nl', 'nm',
'nn', 'np', 'nq', 'n5', 'n6', 'o', 'oh', 'op', 'oq', 'os', 'ow', 'p2', 'p3',
'p4', 'p5', 'pb', 'pc', 'pd', 'pe', 'pf', 'px', 'py', 's', 's2', 's4', 's6',
'sh', 'ss', 'sx', 'sy', 'sp', 'sq'])  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 1280, in createSystem  
raise Exception(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac16,9
      Model Number: Z1CD000KXFN/A
      Chip: Apple M4 Max
      Total Number of Cores: 14 (10 Performance and 4 Efficiency)
      Memory: 36 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3 (25D125)
      Kernel Version: Darwin 25.3.0
      Time since boot: 2 heures et 29 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        LS32D80xU:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    ChimeraX-MutationScores: 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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0
File attachment: ptm0.939_r3_default.pdb

ptm0.939_r3_default.pdb​

[etienne.reboul@…]

Added by email2trac

[Eric Pettersen]

Hi Etienne,

Thanks for reporting this problem and providing a file to reproduce it with. I will investigate it soon.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab