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Opened 3 years ago
Closed 3 years ago
#7661 closed defect (not a bug)
Crash deleting atoms
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-11.6.1-arm64-arm-64bit
ChimeraX Version: 1.5.dev202209200803 (2022-09-20 08:03:20 UTC)
Description
When I used the "delete atoms" command, the session crashed. However, when I opened the session again, it did do the job and saved (deleted the atoms of interest).
Log:
UCSF ChimeraX version: 1.5.dev202209200803 (2022-09-20)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922 v3.cxs" format session
Log from Thu Sep 22 15:15:12 2022UCSF ChimeraX version: 1.5.dev202209200803
(2022-09-20)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saEM/Sau ES-AU 2022_0812.cxs"
Log from Wed Sep 21 11:27:17 2022UCSF ChimeraX version: 1.5.dev202209200803
(2022-09-20)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Fri Sep 16 00:36:57 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM/Sau ES-AU v1.cxs"
> format session
Log from Fri Aug 12 16:35:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saES.pdb"
Summary of feedback from opening /Volumes/GoogleDrive/Shared drives/Harris Lab
Shared Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saES.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
2596 messages similar to the above omitted
Chain information for saES.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A:1-115
945 atoms, 958 bonds, 115 residues, 1 model selected
> select /C:900-977
1656 atoms, 1850 bonds, 78 residues, 1 model selected
> color sel forest green
> select /B:0-390
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> color (#!1 & sel) medium blue
> color (#!1 & sel) cornflower blue
> cd "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM"
Current working directory is: /Volumes/GoogleDrive/Shared drives/Harris Lab
Shared Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM
> save "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM/Sau ES-AU v1.cxs"
——— End of log from Fri Aug 12 16:35:20 2022 ———
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /C
Alignment identifier is 1/C
> select /C:977
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:900-977
1656 atoms, 1850 bonds, 78 residues, 1 model selected
> select /A:112-115
35 atoms, 34 bonds, 4 residues, 1 model selected
> select /A:1-115
945 atoms, 958 bonds, 115 residues, 1 model selected
> name frozen rnpA sel
[Repeated 1 time(s)]
> select /B:0
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /B:0-390
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> name frozen rnpB sel
[Repeated 1 time(s)]
> select /C:977
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:900-977
1656 atoms, 1850 bonds, 78 residues, 1 model selected
> name frozen ptRNA sel
[Repeated 1 time(s)]
> select /C:900
20 atoms, 22 bonds, 1 residue, 1 model selected
> select /C:900-904
102 atoms, 113 bonds, 5 residues, 1 model selected
> select /A:114-115
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:1-115
945 atoms, 958 bonds, 115 residues, 1 model selected
> surface sel
> surface style mesh
> ui tool show "Color Actions"
> color sel goldenrod
> color sel gold
> color sel burly wood
> color sel olive
> color sel chocolate
> color sel saddle brown
> color sel orange
> color sel dark orange
> transparency (#!1 & sel) 50
> select ~sel
10753 atoms, 11884 bonds, 5 pseudobonds, 444 residues, 2 models selected
> select clear
> select /B:390
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:35-390
8272 atoms, 9121 bonds, 4 pseudobonds, 331 residues, 2 models selected
> select /B:357-390
891 atoms, 979 bonds, 34 residues, 1 model selected
> select /B:0-390
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> select /B:357-390
891 atoms, 979 bonds, 34 residues, 1 model selected
> select /B:0-390
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel steel blue
> color sel royal blue
> color sel dodger blue target a
> color sel coral target a
> color sel chartreuse target c
> color sel salmon target l
> color sel royal blue target c
> color sel cornflower blue target acspfl
> color sel royal blue target c
> select /C:905
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /C:900-905
125 atoms, 139 bonds, 6 residues, 1 model selected
> select /C:900
20 atoms, 22 bonds, 1 residue, 1 model selected
> select /C:900-904
102 atoms, 113 bonds, 5 residues, 1 model selected
> color sel red
> save "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM/Sau ES-AU
> 2022_0812.cxs"
> select /B:0-390
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> select /B:386
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /B:386-390
136 atoms, 147 bonds, 5 residues, 1 model selected
> select /B:329
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
[Repeated 3 time(s)]
> select /B:167
31 atoms, 32 bonds, 1 residue, 1 model selected
> select clear
> select /B:199
30 atoms, 31 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> save "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/cryoEM/Sau ES-AU
> 2022_0812.cxs"
——— End of log from Fri Sep 16 00:36:57 2022 ———
opened ChimeraX session
> select /B:39
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /B:73
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:72-115
352 atoms, 355 bonds, 44 residues, 1 model selected
> select /A
945 atoms, 958 bonds, 115 residues, 1 model selected
> color (#!1 & sel) orange
> color (#!1 & sel) orange red
> color (#!1 & sel) orange
> transparency (#!1 & sel) 70
> transparency (#!1 & sel) 30
> save "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saEM/Sau ES-AU 2022_0812.cxs"
> select /B:166
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /B:166
33 atoms, 35 bonds, 1 residue, 1 model selected
> select /C:961
20 atoms, 21 bonds, 1 residue, 1 model selected
> save "/Volumes/GoogleDrive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saEM/Sau ES-AU 2022_0812.cxs"
——— End of log from Wed Sep 21 11:27:17 2022 ———
opened ChimeraX session
> set bgColor white
> select clear
> save "/Users/lochuynh/Google Drive/Shared drives/Harris Lab Shared
> Drive/Research/Manuscripts/MOLEC_Type B cryoEM/saEM/Sau ES-AU 2022_0812.cxs"
> save "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> select /C:959
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:959-964
127 atoms, 141 bonds, 6 residues, 1 model selected
> select clear
> save "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922.cxs"
> save "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922 v2.cxs"
> select /B:322-390
1180 atoms, 1295 bonds, 1 pseudobond, 45 residues, 2 models selected
> select /B
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> surface (#!1 & sel)
> color sel bynucleotide
> undo
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> ui favorite true Toolbar
> ui tool show Toolbar
[Repeated 1 time(s)]
> ui favorite false Toolbar
> ui dockable false Toolbar
> select /B:322-390
1180 atoms, 1295 bonds, 1 pseudobond, 45 residues, 2 models selected
> select /B
9097 atoms, 10034 bonds, 5 pseudobonds, 366 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel blue
> color sel cornflower blue
> color sel medium blue
> color sel cornflower blue
> color sel dodger blue
> color sel cornflower blue
> color sel steel blue
> select /C:977
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C
1656 atoms, 1850 bonds, 78 residues, 1 model selected
No visible Surface models selected
> surface sel
> color sel pale green
> color sel forest green
> select /C:919-920
43 atoms, 47 bonds, 2 residues, 1 model selected
> select /C:919-947
616 atoms, 688 bonds, 29 residues, 1 model selected
> select /C:910
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:910-913
85 atoms, 94 bonds, 4 residues, 1 model selected
> select /C:905
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /C:905-911
151 atoms, 168 bonds, 7 residues, 1 model selected
> select /C:912
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /C:912-953
895 atoms, 1000 bonds, 42 residues, 1 model selected
> select clear
> save "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922 v2.cxs"
> save "/Users/lochuynh/OneDrive - University of Florida/LAB RESEARCH/123
> TALKs/2022_09 CBI-Pharmacy/Sau ES-AU 2022_0922 v3.cxs"
——— End of log from Thu Sep 22 15:15:12 2022 ———
opened ChimeraX session
> help help:credits.html
OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini9,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7429.41.5
OS Loader Version: 6723.140.2
Software:
System Software Overview:
System Version: macOS 11.6.1 (20G224)
Kernel Version: Darwin 20.6.0
Time since boot: 22:19
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
LG HDR 4K:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
LG HDR 4K:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.8
Babel: 2.10.3
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
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: 1.41.3
ChimeraX-AtomicLibrary: 7.0.3
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
ChimeraX-CheckWaters: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.2
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.dev202209200803
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: 1.8.1
ChimeraX-Map: 1.1.1
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: 2.0.7
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.1
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
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: 2.6.7
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: 1.24.1
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
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: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.0.0
filelock: 3.7.1
fonttools: 4.37.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 4.12.0
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: 4.11.1
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: 1.5.5
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
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
prompt-toolkit: 3.0.31
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: 6.3.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.1
python-dateutil: 2.8.2
pytz: 2022.2.1
pyzmq: 24.0.0
qtconsole: 5.3.1
QtPy: 2.2.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
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: 0.5.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.8.1
Change History (6)
comment:1 by , 3 years ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash deleting atoms |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
| Status: | accepted → feedback |
|---|
follow-up: 4 comment:4 by , 3 years ago
Hi Eric,
Thanks for getting back to me. It would still crash for "delete atoms" for opening a fresh session. I just learned that I should have used "delete sel" instead as I selected and wanted to delete a few residues.
Hope it helps and thank you for working so hard to make Chimera X better each day.
Loc
On 9/22/22, 3:37 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
[External Email]
#7661: Crash deleting atoms
----------------------------------------+----------------------
Reporter: lochuynh@… | Owner: pett
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Comment (by pett):
Hi Loc,
Thanks for reporting this problem. If you just open your
structure and immediately delete the atoms, does it crash?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
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ChimeraX Issue Tracker
comment:5 by , 3 years ago
Glad you found something that works. ChimeraX should not crash with plain "delete atoms", but I would need the structure/session you're using to reproduce the problem. I can imagine that it's possible that you wouldn't want to share it, and that's fine too.
--Eric
comment:6 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | feedback → closed |
Hi Loc,
Thanks for sending the session. If you type "delete atoms" without the "sel", it will delete all atoms, which in turns closes all models and shows the "Rapid Access" gallery of recently opened files again. So the behavior you see is actually intentional and not a bug per se.
--Eric
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Hi Loc,
--Eric