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Opened 3 years ago
Closed 3 years ago
#8501 closed defect (not a bug)
swapna
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Tried to mutate a tRNA anticodon base with swapna (per ChimeraX documentation) but it says "unknown command"
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/md/Downloads/EF-Tu.cxs format session
Log from Fri Feb 3 16:11:03 2023UCSF 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/md/Downloads/1ob2.cif
Summary of feedback from opening /Users/md/Downloads/1ob2.cif
---
notes | Fetching CCD YG from http://ligand-expo.rcsb.org/reports/Y/YG/YG.cif
Fetching CCD PHA from http://ligand-expo.rcsb.org/reports/P/PHA/PHA.cif
Fetching CCD GLC from http://ligand-expo.rcsb.org/reports/G/GLC/GLC.cif
Fetching CCD FRU from http://ligand-expo.rcsb.org/reports/F/FRU/FRU.cif
Fetching CCD KIR from http://ligand-expo.rcsb.org/reports/K/KIR/KIR.cif
1ob2.cif title:
E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a
GTP analog, and Phe-tRNA [more info...]
Chain information for 1ob2.cif #1
---
Chain | Description | UniProt
A | ELONGATION FACTOR TU | EFTU2_ECOLI
B | TRANSFER-RNA, PHE |
Non-standard residues in 1ob2.cif #1
---
FRU — beta-D-fructofuranose
GLC — alpha-D-glucopyranose
GNP — phosphoaminophosphonic acid-guanylate ester
KIR — kirromycin (mocimycin; delvomycin; myc-8003)
MG — magnesium ion
> select /A:67,216,219,229,274
32 atoms, 27 bonds, 5 residues, 1 model selected
> name frozen EF-Sep_library sel
Drag select of 2 atoms, 19 residues, 1 bonds, 2 shapes
> select /A:67,216,219,229,274
32 atoms, 27 bonds, 5 residues, 1 model selected
> show sel atoms
> select up
153 atoms, 152 bonds, 20 residues, 1 model selected
> select up
3035 atoms, 3091 bonds, 393 residues, 1 model selected
> select /A
3125 atoms, 3184 bonds, 6 pseudobonds, 396 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select down
153 atoms, 152 bonds, 6 pseudobonds, 20 residues, 3 models selected
> select down
32 atoms, 27 bonds, 6 pseudobonds, 5 residues, 3 models selected
> select down
32 atoms, 27 bonds, 6 pseudobonds, 5 residues, 3 models selected
> select down
32 atoms, 27 bonds, 6 pseudobonds, 5 residues, 3 models selected
> select clear
> select /A
3125 atoms, 3184 bonds, 6 pseudobonds, 396 residues, 2 models selected
> hide sel atoms
> select /B
1662 atoms, 1856 bonds, 73 pseudobonds, 77 residues, 2 models selected
> select /B:75-77
53 atoms, 58 bonds, 3 residues, 1 model selected
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 53 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 53 atom styles
> select /B:75,76,77
53 atoms, 58 bonds, 3 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 53 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 53 atom styles
> select /B:76
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /A:67,216,219,229,274
32 atoms, 27 bonds, 5 residues, 1 model selected
> show sel atoms
> select /A:67,216,219,229,274
32 atoms, 27 bonds, 5 residues, 1 model selected
> select /A:1-393
3035 atoms, 3091 bonds, 393 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:365-371
48 atoms, 48 bonds, 7 residues, 1 model selected
> select /A:360-371
88 atoms, 89 bonds, 12 residues, 1 model selected
> select
> /A:23-39,45-50,52-59,84-97,112-125,136-140,142-161,173-198,282-286,312-316
941 atoms, 943 bonds, 120 residues, 1 model selected
> select
> /A:11-17,65-70,75-80,101-106,130-135,169-171,211-213,216-219,225-230,241-245,251-254,273-276,291-293,300-309,329-332,335-340,355-367,373-378,381-391
884 atoms, 884 bonds, 113 residues, 1 model selected
> select /A:66
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:66-67
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:67,216,219,229,274
32 atoms, 27 bonds, 5 residues, 1 model selected
> select /A
3125 atoms, 3184 bonds, 6 pseudobonds, 396 residues, 2 models selected
> hide sel atoms
> select /A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Model Panel"
> select /A:67,274,216,229,217,219
39 atoms, 34 bonds, 6 residues, 1 model selected
> show sel atoms
> undo
> select /A:68,275,217,230,218,22-
Expected an objects specifier or a keyword
> select /A:68,275,217,230,218,220
50 atoms, 46 bonds, 6 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]Drag select of 1ob2.cif_A SES surface, 38 of 331590
triangles, 1 bonds
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
1662 atoms, 1856 bonds, 77 residues, 1 model selected
> undo
> select sel :< 5
127 atoms, 127 bonds, 13 residues, 1 model selected
> show sel atoms
Drag select of 1ob2.cif_A SES surface, 608 of 331590 triangles, 1 atoms, 3
residues, 1 bonds
> select /A:66,215,218,228,273
45 atoms, 42 bonds, 5 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> name frozen EF-Sep_var sel
[Repeated 1 time(s)]
> name delete EF-Sep_library
> select clear
> select /A
3125 atoms, 3184 bonds, 6 pseudobonds, 396 residues, 2 models selected
> color (#!1 & sel) hot pink
> transparency (#!1 & sel) 80
> select /B
1662 atoms, 1856 bonds, 73 pseudobonds, 77 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1662 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 1662 atom styles
> sequence chain #1/B
Alignment identifier is 1/B
> select /B:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:74-77
73 atoms, 80 bonds, 4 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 73 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 73 atom styles
> select /B:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 11 atom styles
> select clear
> save /Users/md/Downloads/EF-Tu.cxs
——— End of log from Fri Feb 3 16:11:03 2023 ———
opened ChimeraX session
> select /B:34
24 atoms, 26 bonds, 1 residue, 1 model selected
> swapna /B:33 T
Unknown command: swapna /B:33 T
> swapna /B:33 G
Unknown command: swapna /B:33 G
> swapna /B:33 A
Unknown command: swapna /B:33 A
> swapna /B:33 C
Unknown command: swapna /B:33 C
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: Z15H00105LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2 (22D49)
Kernel Version: Darwin 22.3.0
Time since boot: 18 days, 2 hours, 38 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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
HP 27er:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
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
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 (2)
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 → swapna |
comment:2 by , 3 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | accepted → closed |
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Hi Sarah,
--Eric