![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#8474 closed defect (fixed)
SEQCROW: crash forming tsbond
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tony Schaefer | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Opened 4 files and I wanted to add a TS bond in only one of the structures
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"SIRI_UNDERSTANDING_ASR_ASSISTANT" : "63d9be3e2cb48e1296b07524",
"SIRI_UNDERSTANDING_MORPHUN" : "62ec7220c682040ba94e6a20"
},
"deploymentId" : 240000612
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
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 /Users/andrea/Downloads/pk(i).gjf
Summary of feedback from opening /Users/andrea/Downloads/pk(i).gjf
---
errors | could not open pk(i).gjf
LookupError('Could not find atom: [] on\npk(i).gjf\n')
SEQCROW failed to open pk(i).gjf
> open /Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_R.log
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_R.log
---
notes | ts_attacco_R.log has 1 imaginary harmonic vibrational mode
233.89i
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 142 items
> setattr a radius 0.9
Assigning radius attribute to 135 items
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 142 items
> setattr a radius 0.9
Assigning radius attribute to 135 items
Opened ts_attacco_R.log as a Gaussian output file
> open /Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_S.log
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_S.log
---
notes | ts_attacco_S.log has 1 imaginary harmonic vibrational mode
100.41i
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 284 items
> setattr a radius 0.9
Assigning radius attribute to 270 items
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 284 items
> setattr a radius 0.9
Assigning radius attribute to 270 items
Opened ts_attacco_S.log as a Gaussian output file
> close
> open /Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_R_b3lyp_SP.log
> /Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_S_b3lyp_SP.log
> /Users/andrea/Desktop/epoxy_lattanzi/ts_chiusura_RR_b3lyp_SP.log
> /Users/andrea/Desktop/epoxy_lattanzi/ts_chiusura_SS_b3lyp_SP.log
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_R_b3lyp_SP.log
---
warning | AttributeError("'super' object has no attribute 'close'")
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_attacco_S_b3lyp_SP.log
---
warning | AttributeError("'super' object has no attribute 'close'")
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_chiusura_RR_b3lyp_SP.log
---
warning | AttributeError("'super' object has no attribute 'close'")
Summary of feedback from opening
/Users/andrea/Desktop/epoxy_lattanzi/ts_chiusura_SS_b3lyp_SP.log
---
warning | AttributeError("'super' object has no attribute 'close'")
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 568 items
> setattr a radius 0.9
Assigning radius attribute to 540 items
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 568 items
> setattr a radius 0.9
Assigning radius attribute to 540 items
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 568 items
> setattr a radius 0.9
Assigning radius attribute to 540 items
> color C grey
> setattr b radius 0.1
Assigning radius attribute to 568 items
> setattr a radius 0.9
Assigning radius attribute to 540 items
Opened ts_attacco_R_b3lyp_SP.log as a Gaussian output file
Opened ts_attacco_S_b3lyp_SP.log as a Gaussian output file
Opened ts_chiusura_RR_b3lyp_SP.log as a Gaussian output file
Opened ts_chiusura_SS_b3lyp_SP.log as a Gaussian output file
> hide #2 models
> hide #3 models
> hide #4 models
> ui mousemode right tsbond
> tsbond #1/a:1@O4 #1/a:1@C28 radius 0.100
===== Log before crash end =====
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
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
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: MacBookPro18,3
Model Number: MKGP3T/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 6 days, 12 hours, 34 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
22N1:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
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
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
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
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.5.14
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (5)
comment:1 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: crash forming tsbond |
follow-up: 2 comment:2 by , 3 years ago
Thanks for reporting this. It looks like there's a few other errors showing up in the log as well. Unfortunately, I don't understand why tsbond is causing a crash. Does this always happen with this structure? Can you add TS bonds to other structures? Tony On Mon, Feb 13, 2023 at 11:32 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
follow-up: 3 comment:3 by , 3 years ago
Andrea said this error is inconsistent. It sounds like this issues has come
up before, but might not happen for the same structure every time. I use TS
bonds quite a bit on Windows and haven't had any issues lately. Could this
be an OS-dependent issue?
The crash happens while/after running the tsbond command. This command
essentially just creates a pseudobond group, deletes a bond if it exists,
and adds a new pseudobond. Here's the entire function with a few comments
added:
```py
def tsbond(session, selection, transparency=50, color=[170, 255, 255, 255],
radius=0.16):
# selection - ObjectsArg
# transparency - FloatArg
# color - ColorArg
# radius - FloatArg
if not isinstance(color, list):
color = color.uint8x4()
color = [c for c in color][:-1]
color.append(int( 255 * ( transparency / 100.)))
if transparency >= 100 or transparency <= 0:
session.logger.error("transparency must be between 0 and 100")
return
# check if atoms are in the selection
# Andrea's command specified two atoms
ts_bond = None
atoms = selection.atoms
if len(atoms) != 2 and len(atoms) > 0:
session.logger.error("2 atoms must be selected")
elif len(atoms) == 2:
if atoms[0].structure is not atoms[1].structure:
session.logger.error("atoms must be on the same structure")
else:
# draw a bond between this pair of atoms if it does not exist,
or grab
# the bond object if it does exist
structure = atoms[0].structure
for bond in structure.bonds:
if all(atom in bond.atoms for atom in atoms):
ts_bond = bond
if ts_bond is None:
ts_bond = structure.new_bond(*atoms)
# go through all bonds in the spec and the new bond we just added/found
# replace them all with pseudobonds
bonds = [bond for bond in selection.bonds]
if ts_bond is not None and ts_bond not in bonds:
bonds.append(ts_bond)
for bond in bonds:
atom1, atom2 = bond.atoms
pbg = bond.structure.pseudobond_group("TS bonds", create_type=1)
if not any(all(atom in pb.atoms for atom in bond.atoms) for pb in
pbg.pseudobonds):
pbg.new_pseudobond(*bond.atoms)
pbg.dashes = 0
pbg.halfbond = False
pbg.radius = radius
pbg.color = color
if pbg not in bond.structure.child_models():
bond.structure.add([pbg])
bond.delete()
```
I'm sure there are some inefficiencies here, but I'm not sure what could
cause a crash. I'd welcome any advice for how to make this command more
robust.
Thanks,
Tony
On Mon, Feb 13, 2023 at 11:32 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
comment:4 by , 3 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
Do not do this:
if pbg not in bond.structure.child_models():
bond.structure.add([pbg])
That automatically happens as part of:
pbg = bond.structure.pseudobond_group("TS bonds", create_type=1)
Nonetheless, that doesn't seem to be the actual issue here. The issue is that:
pbg = bond.structure.pseudobond_group("TS bonds", create_type=1)
creates the group in the C++ layer, which in turn has to call the Python constructor (in order to return the instance). Somehow, before the Python constructor finishes, something is requesting the group instance, which causes another call to the Python constructor, etc. I'm reassigning to myself to try to figure out how this is happening/possible.
comment:5 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
The PseudobondGroup constructor for structure-associated groups adds the group to the structure submodels, which in turn fires the ADD_MODELS trigger (if the structure is open). So, depending on what the handlers for that trigger are doing, this could result in a loop of the C++ layer trying to create Python instances. Now, the ADD_MODELS trigger is suppressed until the C++ call finishes. I'm not 1000% convinced that this was the problem here, but am nonetheless closing this ticket until the problem is reported again -- which is hopefully never. :-)
Fix: https://github.com/RBVI/ChimeraX/commit/83420b0902619bed5fb0efd96c2c7ca4e8672960
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Reported by Andrea Pellegrini