The following bug report has been submitted:
Platform: Linux-6.8.0-52-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/esen/Bioinformatics/bcHSD17B1.pdb
Chain information for bcHSD17B1.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> select ::name="EST"::name="NAP"::name="SO4"::name="UNL"
95 atoms, 101 bonds, 4 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> 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 ARG 37: phi -63.5, psi -41.9 trans
/A THR 190: phi 103.8, psi none trans
Swapping /A ALA 191 to ALA
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 53, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 215, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 164, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 96, in prep
swap_aa(session, targets, "same", rot_lib=style)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 60, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 442, in template_swap_res
add_bond(a, res_bonder)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
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 ARG 37: phi -63.5, psi -41.9 trans
/A THR 190: phi 103.8, psi none trans
Swapping /A ALA 191 to ALA
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 53, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 215, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 164, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 96, in prep
swap_aa(session, targets, "same", rot_lib=style)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 60, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 442, in template_swap_res
add_bond(a, res_bonder)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
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 ARG 37: phi -63.5, psi -41.9 trans
/A THR 190: phi 103.8, psi none trans
Swapping /A ALA 191 to ALA
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 53, in swap_aa
rots = get_rotamers(session, res, res_type=r_type, rot_lib=rot_lib, log=log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 215, in get_rotamers
raise NoResidueRotamersError("No rotamers for %s" % res_type)
chimerax.rotamers.rot_lib.NoResidueRotamersError: No rotamers for ALA
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 164, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 96, in prep
swap_aa(session, targets, "same", rot_lib=style)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 60, in swap_aa
template_swap_res(res, r_type, bfactor=bfactor)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/swap_res/swap_res.py", line 442, in template_swap_res
add_bond(a, res_bonder)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
AttributeError: 'chimerax.atomic.cytmpl.TmplAtom' object has no attribute
'num_bonds'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond
if a1.num_bonds > 0:
^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 570.86.10
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 81Q4
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 3.7Gi 1.2Gi 148Mi 11Gi 11Gi
Swap: 4.0Gi 256Ki 4.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU116M [GeForce GTX 1660 Ti Mobile] [10de:2191] (rev a1)
Subsystem: Lenovo TU116M [GeForce GTX 1660 Ti Mobile] [17aa:3ffc]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Though I can't reproduce the problem, I believe this fixes it: https://github.com/RBVI/ChimeraX/commit/d4581f0b1fe2df4244ec08d95b0199299738c2d2