#4635 closed defect (fixed)
volume series slider: list index out of range
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202105130135 (2021-05-13 01:35:20 UTC)
Description
Cannot play a volume series (produced by cryoDRGN). Loaded volumes via Open dialog, then used command "vseries slider #1". Pushing the play button resulted in the error.
Log:
UCSF ChimeraX version: 1.3.dev202105130135 (2021-05-13)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_000.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_001.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_002.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_003.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_004.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_005.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_006.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_007.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_008.mrc
> /Users/priiteeklocal/Downloads/J272/00_vae128/analyze.10/pc1/vol_009.mrc
Opened vol_000.mrc as #1.1, grid size 128,128,128, pixel 2.58, shown at level
0.0294, step 1, values float32
Opened vol_001.mrc as #1.2, grid size 128,128,128, pixel 2.58, shown at level
0.029, step 1, values float32
Opened vol_002.mrc as #1.3, grid size 128,128,128, pixel 2.58, shown at level
0.0292, step 1, values float32
Opened vol_003.mrc as #1.4, grid size 128,128,128, pixel 2.58, shown at level
0.0288, step 1, values float32
Opened vol_004.mrc as #1.5, grid size 128,128,128, pixel 2.58, shown at level
0.0285, step 1, values float32
Opened vol_005.mrc as #1.6, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32
Opened vol_006.mrc as #1.7, grid size 128,128,128, pixel 2.58, shown at level
0.028, step 1, values float32
Opened vol_007.mrc as #1.8, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32
Opened vol_008.mrc as #1.9, grid size 128,128,128, pixel 2.58, shown at level
0.0279, step 1, values float32
Opened vol_009.mrc as #1.10, grid size 128,128,128, pixel 2.58, shown at level
0.0289, step 1, values float32
> vseries slider #1
Traceback (most recent call last):
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb
self.play()
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb
self.play()
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 142, in play_cb
self.play()
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
IndexError: list index out of range
IndexError: list index out of range
File
"/Applications/science_math/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_series/slider.py", line 148, in play
s0 = ser[0]
See log for complete Python traceback.
OpenGL version: 4.1 ATI-2.11.23
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: Intel Core i5
Processor Speed: 3.7 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 24 GB
Boot ROM Version: 1554.100.64.0.0
SMC Version (system): 2.46f12
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G9028)
Kernel Version: Darwin 18.7.0
Time since boot: 5 days 19:21
Graphics/Displays:
Radeon Pro 580X:
Chipset Model: Radeon Pro 580X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A1X-009
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.20
ChimeraX-AtomicLibrary: 3.2.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.3
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202105130135
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.9.3
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.23
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.3
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.5.1
numexpr: 2.7.3
numpy: 1.20.3
numpydoc: 1.1.0
openvr: 1.16.801
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.18
psutil: 5.8.0
ptyprocess: 0.7.0
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pydicom: 2.1.2
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PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
setuptools: 56.2.0
sfftk-rw: 0.6.7.dev1
six: 1.16.0
snowballstemmer: 2.1.0
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Sphinx: 4.0.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
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tables: 3.6.1
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wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
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Change History (8)
comment:1 by , 5 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem playing volume series: list index out of range |
comment:2 by , 5 years ago
follow-up: 3 comment:3 by , 5 years ago
Thanks for carifying this! The current documentation suggests that volume series can be opened using the GUI as well. Best regards, Priit
comment:4 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
| Summary: | Problem playing volume series: list index out of range → volume series slider: list index out of range |
Fixed.
The vseries slider command showed a slider even when no series is specified (for instance when just maps not in series are given). I've made it warn that no series were specified and not create the slider.
I don't see where in the documentation it suggests that volume series can be opened with the GUI unless it is a TIFF series of 5 or more maps or Chimera map format hdf5 file. For example here is an explanation of the rules from the documentation.
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#vseries
If you can show me the place in the documentation that suggests this I can get it fixed.
follow-up: 5 comment:5 by , 5 years ago
I googled for “chimerax volume series” and stumbled upon this page:
https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html
In the last paragraph: If a volume series is opened by choosing multiple files in the dialog from menu: File... Open, the sort order in the dialog may define the temporal order.
This suggests volume series can be opened that way. Opening volumes that way actually creates a group, which can be somewhat misleading to a user who hasn’t seen how a volume series should really look like in ChimeraX.
Thanks again for your help!
P.
On May 13, 2021, at 23:02, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#4635: volume series slider: list index out of range
----------------------------------+-------------------------
Reporter: priit.eek@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Volume Data | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Changes (by Tom Goddard):
* status: assigned => closed
* resolution: => fixed
Comment:
Fixed.
The vseries slider command showed a slider even when no series is
specified (for instance when just maps not in series are given). I've
made it warn that no series were specified and not create the slider.
I don't see where in the documentation it suggests that volume series can
be opened with the GUI unless it is a TIFF series of 5 or more maps or
Chimera map format hdf5 file. For example here is an explanation of the
rules from the documentation.
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fopen.html%23vseries&data=04%7C01%7Cpriit.eek%40psu.edu%7C2ebbac977aba41a6923f08d91684b35d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637565581481896707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9ES3l2075VIgdWFgxh1qXH5wBYudUX3N9jyKwYeCdA4%3D&reserved=0
If you can show me the place in the documentation that suggests this I can
get it fixed.
--
Ticket URL: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F4635%23comment%3A4&data=04%7C01%7Cpriit.eek%40psu.edu%7C2ebbac977aba41a6923f08d91684b35d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637565581481906707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=yzAM6t7Ameu9GjgwRR0YNGMMvzZKCiQ0xWzD8xDNIRE%3D&reserved=0>
ChimeraX <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=04%7C01%7Cpriit.eek%40psu.edu%7C2ebbac977aba41a6923f08d91684b35d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637565581481906707%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=x4%2F2HX0yYjXKPA8G7uU4tvAzASLvX9z%2B9UOv%2BCC%2Bzxc%3D&reserved=0>
ChimeraX Issue Tracker
comment:6 by , 5 years ago
| Cc: | added |
|---|
I see. I will ask our documentation person to clarify that. That will only work for TIFF stacks. The reasoning for it only applying to TIFF stacks is that that is the common format for 3D light microscopy time series. When using other formats like MRC it is much more likely the user is opening several electron microscopy maps that are not a series, so the default is to not treat them as a series. It would be possible to put an option in the Open panel to say to treat the files as a series. I guess with continuous EM conformations as obtained from cryoDRGN and other methods this may start to become more common.
comment:7 by , 5 years ago
Elaine, could you change "If a volume series is opened by choosing multiple files in the dialog from menu: File... Open, the sort order in the dialog may define the temporal order." in the volume series description on page https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html to indicate it only applies to TIFF files? Or I can do it if you like.
follow-up: 8 comment:8 by , 5 years ago
No problem for me to change it. I inserted the word "TIFF" but it you want it changed further, let me know. Preview version: <https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/trajectories.html>
This ChimeraX error is because your 10 open maps are not considered to be a series. Open them with this command so they are treated like a series
with the "vseries true" option at the end.
I will fix the code so it gives a clear error message instead of a traceback when the vseries command is used on maps that are not a series.