ChargeError not caught

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-65-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8rc202405160048 (2024-05-16 00:48:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007e291ffe7640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007e2a1f41fb80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 460 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 460 in _prep_add
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 182 in hbond_add_hydrogens
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 176 in hbond_add_hydrogens
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 55 in run_for_dock_prep
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 48 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/tool.py", line 206 in add_h
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 52)
===== Log before crash start =====
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mobd-s/Documents/projects/Protup/receptor.pdb

Chain information for receptor.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select /A

2084 atoms, 2008 bonds, 219 residues, 1 model selected  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to receptor.pdb #1  
---  
warnings | Not adding hydrogens to /A TRP 42 CA because it is missing heavy-atom bond partners  
Not adding hydrogens to /A TRP 42 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 CB because it is missing heavy-atom bond
partners  
48 messages similar to the above omitted  
Skipped 14 atom(s) with bad connectivities; see log for details  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A GLU 176 N  
notes | No usable SEQRES records for receptor.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 38  
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 LYS 256  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A ALA 55 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ALA 55 O  
  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A LEU 119 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LEU 119 O  
  
9 messages similar to the above omitted  
119 hydrogen bonds  
/A LYS 256 is not terminus, removing H atom from 'C'  
1529 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non-
heavy atom /A GLU 39 1HN  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non-
heavy atom /A GLU 39 1HN  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
  
See log for complete Python traceback.  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 256: phi -100.0, psi none trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A GLU 176 N  

Applying LYS rotamer (chi angles: -68.5 176.2 69.4 177.3) to /A LYS 256  
Summary of feedback from adding hydrogens to receptor.pdb #1  
---  
warnings | Not adding hydrogens to /A TRP 42 CA because it is missing heavy-atom bond partners  
Not adding hydrogens to /A TRP 42 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 C because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A HIS 76 CB because it is missing heavy-atom bond
partners  
49 messages similar to the above omitted  
Skipped 14 atom(s) with bad connectivities; see log for details  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A GLU 176 N  
notes | No usable SEQRES records for receptor.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 38  
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 LYS 256  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A ALA 55 O  
Wrong number of grandchild atoms for phi/psi acceptor /A ALA 55 O  
  
Skipping possible acceptor with bad geometry: /A PHE 87 O  
Wrong number of grandchild atoms for phi/psi acceptor /A PHE 87 O  
  
Skipping possible acceptor with bad geometry: /A LEU 119 O  
Wrong number of grandchild atoms for phi/psi acceptor /A LEU 119 O  
  
9 messages similar to the above omitted  
118 hydrogen bonds  
/A LYS 256 is not terminus, removing H atom from 'C'  
11 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non-
heavy atom /A GLU 39 1HN  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 39 HN bonded to non-
heavy atom /A GLU 39 1HN  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 127, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to non-heavy atom %s" % (h, heavy))  
  
See log for complete Python traceback.  
  

> open /home/mobd-s/Documents/projects/Protup/temozolomide_docked.pdb

Chain information for temozolomide_docked.pdb #2  
---  
Chain | Description  
A | No description available  
  

> delete atoms sel

> delete bonds sel

> select ::name="UNL"

16 atoms, 17 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"

2102 atoms, 2007 bonds, 220 residues, 2 models selected  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  

receptor.pdb #1/A LYS 256 is missing heavy backbone atoms  

Filling out missing side chains  
temozolomide_docked.pdb #2/A LYS 256: phi -100.0, psi none trans  
Applying LYS rotamer (chi angles: 66.8 82.3 -83.6 -67.0) to
temozolomide_docked.pdb #2/A LYS 256  


===== Log before crash end =====

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 570.158.01
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: AS -4023S-TRT
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD EPYC 7252 8-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       7.4Gi       6.1Gi       411Mi        49Gi        54Gi
	Swap:          8.0Gi        11Mi       8.0Gi

Graphics:
	21:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1)	
	Subsystem: NVIDIA Corporation GA104GL [RTX A4000] [10de:14ad]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
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    certifi: 2024.2.2
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    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10