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Opened 3 years ago
Closed 3 years ago
#7822 closed defect (fixed)
SEQCROW: memory reporting: unsupported operand type(s) for *: 'function' and 'float'
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202209100708 (2022-09-10 07:08:19 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5.dev202209100708 (2022-09-10)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/andrea/Desktop/scratch/m.xyz format xyz
Opened m.xyz as an XYZ file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> close
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> close
> open /Users/andrea/Desktop/scratch/m.xyz format xyz
Opened m.xyz as an XYZ file
> open /Users/andrea/Desktop/scratch/cstr_optf_631.out
Opened cstr_optf_631.out as an ORCA output file
> close
> close #
Expected a models specifier or a keyword
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right distance
> distance /a:1@H10 /a:1@N4
Distance between /a UNK 1 H10 and N4: 2.151Å
> distance /a:1@C28 /a:1@N5
Distance between /a UNK 1 C28 and N5: 3.457Å
> ui mousemode right "bond rotation"
> torsion /a:1@C35,C30,C28,C27 66.93
> ui mousemode right minimize
Missing atoms or parameterization needed by force field.
All heavy atoms and hydrogens with standard names are required.
Error with ignoreExternalBonds=False was
No template found for residue 1 (UNK). This might mean your input topology is
missing some atoms or bonds, or possibly that you are using the wrong force
field.
Error with ignoreExternalBonds=True was
No template found for residue 1 (UNK). This might mean your input topology is
missing some atoms or bonds, or possibly that you are using the wrong force
field.
[Repeated 4 time(s)]
> close
> ui mousemode right select
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right distance
> distance /a:1@C28 /a:1@N5
Distance between /a UNK 1 C28 and N5: 3.480Å
> distance /a:1@H10 /a:1@N4
Distance between /a UNK 1 H10 and N4: 2.151Å
> close
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right "translate selected models"
> ui mousemode right distance
> distance /a:1@C28 /a:1@N5
Distance between /a UNK 1 C28 and N5: 3.402Å
> close
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> ui mousemode right tsbond
> tsbond /a:1@H10 /a:1@N4 radius 0.200
> tsbond /a:1@N2 /a:1@C27 radius 0.200
> tsbond /a:1@C27 /a:1@C28 radius 0.200
> tsbond /a:1@C28 /a:1@N5 radius 0.200
> tsbond /a:1@N5 /a:1@N4 radius 0.200
> close
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right "change element"
no element selected; shift-click to set element
> ui mousemode right "structure eraser"
> close
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right distance
> distance /a:1@H10 /a:1@N4
Distance between /a UNK 1 H10 and N4: 2.124Å
> distance /a:1@C28 /a:1@N5
Distance between /a UNK 1 C28 and N5: 3.699Å
> ui mousemode right swapaa
swapaa cannot align to residues /a UNK 1 which has fewer than 3 backbone atoms
(N, C, CA)
[Repeated 2 time(s)]
> ui mousemode right "play coordinates"
> ui mousemode right windowing
> mlp
mlp: no amino acids specified
> coulombic
Coulombic values for cstr_berny_a SES surface #1.1: minimum, -6.13, mean
-0.24, maximum 3.82
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
mlp: no amino acids specified
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
Coulombic values for cstr_berny_a SES surface #1.1: minimum, -6.13, mean
-0.24, maximum 3.82
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
mlp: no amino acids specified
> color bynucleotide
> hbonds reveal true
244 hydrogen bonds found in 51 coordsets
> style ball
Changed 124 atom styles
> style ball
Changed 124 atom styles
> style sphere
Changed 124 atom styles
> style ball
Changed 124 atom styles
> style stick
Changed 124 atom styles
> style sphere
Changed 124 atom styles
> close
> ui tool show "Selection Inspector"
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui mousemode right distance
> distance /a:1@C28 /a:1@N5
Distance between /a UNK 1 C28 and N5: 3.735Å
> open /Users/andrea/Desktop/scratch format dicom
> close
> open /Users/andrea/Desktop/scratch format dicom
[Repeated 2 time(s)]
> open /Users/andrea/Desktop/scratch/cstr_berny.out format out
Opened cstr_berny.out as an ORCA output file
> ui mousemode right swapaa
> ui mousemode right "play coordinates"
> open /Users/andrea/Desktop/scratch/cstr_optf_631.out format out
Opened cstr_optf_631.out as an ORCA output file
> style ball
Changed 248 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 248 items
> setattr a radius 1
Assigning radius attribute to 248 items
> hide #1 models
> ui tool show "Visualize Normal Modes"
> ui mousemode right tsbond
> tsbond #2/a:1@H10 #2/a:1@N4 radius 0.150
> tsbond #2/a:1@C28 #2/a:1@N5 radius 0.150
> close
> close #
Expected a models specifier or a keyword
> open /Users/andrea/Desktop/scratch format dicom
[Repeated 3 time(s)]
> open /Users/andrea/Desktop/scratch/sp.out
Opened sp.out as an ORCA output file
> style ball
Changed 124 atom styles
> color C grey
> setattr b radius 0.15
Assigning radius attribute to 124 items
> setattr a radius 1
Assigning radius attribute to 124 items
> ui tool show "Orbital Viewer"
Traceback (most recent call last):
File "/Users/andrea/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/mo_viewer.py", line 750, in show_orbit
"the available memory (%.1fGB).\n" % (available_memory * 1e-9) +
TypeError: unsupported operand type(s) for *: 'function' and 'float'
TypeError: unsupported operand type(s) for *: 'function' and 'float'
File "/Users/andrea/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/mo_viewer.py", line 750, in show_orbit
"the available memory (%.1fGB).\n" % (available_memory * 1e-9) +
See log for complete Python traceback.
Traceback (most recent call last):
File "/Users/andrea/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/mo_viewer.py", line 750, in show_orbit
"the available memory (%.1fGB).\n" % (available_memory * 1e-9) +
TypeError: unsupported operand type(s) for *: 'function' and 'float'
TypeError: unsupported operand type(s) for *: 'function' and 'float'
File "/Users/andrea/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/tools/mo_viewer.py", line 750, in show_orbit
"the available memory (%.1fGB).\n" % (available_memory * 1e-9) +
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.3
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: 6.3.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.6 (21G115)
Kernel Version: Darwin 21.6.0
Time since boot: 4 days 17:55
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
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
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: 1.6.1
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: 1.41.2
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.dev202209100708
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: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
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: 1.9
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
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: 4.37.1
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 4.12.0
ipykernel: 6.15.1
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: 23.2.1
qtconsole: 5.3.1
QtPy: 2.2.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
Send2Trash: 1.8.0
SEQCROW: 1.5.4
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 (3)
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: memory reporting: unsupported operand type(s) for *: 'function' and 'float' |
follow-up: 2 comment:2 by , 3 years ago
comment:3 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
fixed in SEQCROW 1.5.5 ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Wednesday, October 19, 2022 2:04 PM Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu> Subject: Re: [ChimeraX] #7822: SEQCROW: memory reporting: unsupported operand type(s) for *: 'function' and 'float' (was: ChimeraX bug report submission) [EXTERNAL SENDER - PROCEED CAUTIOUSLY] #7822: SEQCROW: memory reporting: unsupported operand type(s) for *: 'function' and 'float' --------------------------------------------+--------------------------- Reporter: chimerax-bug-report@… | Owner: Tony Schaefer Type: defect | Status: assigned Priority: normal | Milestone: Component: Third Party | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | --------------------------------------------+--------------------------- Changes (by pett): * status: new => assigned * component: Unassigned => Third Party * project: => ChimeraX * platform: => all * owner: (none) => Tony Schaefer -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7822#comment:1> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker