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RBVI / ChimeraX

Source code for molecular graphics program UCSF ChimeraX
https://www.rbvi.ucsf.edu/chimerax/
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Random `shift` and `rot` initializations in `fitmap` global search are not random in some cases but random in some other cases #40

Closed RodenLuo closed 3 months ago

RodenLuo commented 4 months ago

Hi,

The following lines returned deterministic values in one case for my settings. I suppose they should be random and this should not happen by design.

https://github.com/RBVI/ChimeraX/blob/4d2ef439300bfa2587e272a0b0de85382e2b5993/src/bundles/map_fit/src/search.py#L71-L74

To reproduce

On Windows 11, ChimeraX version 1.7.1 (2024-01-23)

  1. Modify fit_search def as fit_search.txt. No change in the logic, only added debugging log output.
  2. Place the first 46 lines of this fit_in_chimerax.py script on disk.
  3. Download PDB-8JGF and EMD-36232
  4. Run a similar command as: runscript "PATH to fit_in_chimerax.py" "PATH to 8jgf.cif" "PATH to any valid folder for a log output, such as the Downloads folder" "PATH to emd_36232.map" 0.20 2.7 3
  5. Extract the log from the ChimeraX log window. And then repeat Step 4 and 5. One may change the last argument (which represents N initial placements) in Step 4 to, for example, 5.

Out of 3 runs, I got the following log. The random variables are the same. This is reproducible on different days (I first thought there might be a seed using the date). This is not happening for any other cases I have performed so far. 

0, e_tf_shift: [287.46300308 111.67675212 73.33363845], e_tf_qwxyz: [ 0.0416866 -0.43709143 0.40134146 0.80382731], e_shift_end: [262.96216839 102.11161093 132.88168751], e_qwxyz_end: [ 0.18288082 -0.56415443 0.38728483 0.70590003], Hit-correlation: 0.2540
1, e_tf_shift: [114.31578033 257.75091402 132.25534664], e_tf_qwxyz: [ 0.23761378 -0.57421587 0.55043732 -0.55752541], e_shift_end: [199.24023548 188.39057584 174.30266798], e_qwxyz_end: [ 0.00149964 0.30405883 -0.80032784 0.51674106], Hit-correlation: 0.3565
2, e_tf_shift: [ 99.91321453 168.7359389 -4.11126584], e_tf_qwxyz: [ 0.59228646 0.37187973 -0.36361838 -0.61537297], e_shift_end: [ 82.40818325 193.39436196 8.66309773], e_qwxyz_end: [ 0.65995154 0.48166497 -0.22395551 -0.53132546], Hit-correlation: 0.2598

0, e_tf_shift: [287.46300308 111.67675212 73.33363845], e_tf_qwxyz: [ 0.0416866 -0.43709143 0.40134146 0.80382731], e_shift_end: [262.96216839 102.11161093 132.88168751], e_qwxyz_end: [ 0.18288082 -0.56415443 0.38728483 0.70590003], Hit-correlation: 0.2540
1, e_tf_shift: [114.31578033 257.75091402 132.25534664], e_tf_qwxyz: [ 0.23761378 -0.57421587 0.55043732 -0.55752541], e_shift_end: [199.24023548 188.39057584 174.30266798], e_qwxyz_end: [ 0.00149964 0.30405883 -0.80032784 0.51674106], Hit-correlation: 0.3565
2, e_tf_shift: [ 99.91321453 168.7359389 -4.11126584], e_tf_qwxyz: [ 0.59228646 0.37187973 -0.36361838 -0.61537297], e_shift_end: [ 82.40818325 193.39436196 8.66309773], e_qwxyz_end: [ 0.65995154 0.48166497 -0.22395551 -0.53132546], Hit-correlation: 0.2598

0, e_tf_shift: [287.46300308 111.67675212 73.33363845], e_tf_qwxyz: [ 0.0416866 -0.43709143 0.40134146 0.80382731], e_shift_end: [262.96216839 102.11161093 132.88168751], e_qwxyz_end: [ 0.18288082 -0.56415443 0.38728483 0.70590003], Hit-correlation: 0.2540
1, e_tf_shift: [114.31578033 257.75091402 132.25534664], e_tf_qwxyz: [ 0.23761378 -0.57421587 0.55043732 -0.55752541], e_shift_end: [199.24023548 188.39057584 174.30266798], e_qwxyz_end: [ 0.00149964 0.30405883 -0.80032784 0.51674106], Hit-correlation: 0.3565
2, e_tf_shift: [ 99.91321453 168.7359389 -4.11126584], e_tf_qwxyz: [ 0.59228646 0.37187973 -0.36361838 -0.61537297], e_shift_end: [ 82.40818325 193.39436196 8.66309773], e_qwxyz_end: [ 0.65995154 0.48166497 -0.22395551 -0.53132546], Hit-correlation: 0.2598
3, e_tf_shift: [144.74647325 276.2729621 118.30345416], e_tf_qwxyz: [ 0.21782782 0.87900245 -0.1815385 -0.38333993], e_shift_end: [112.7460626 250.76642775 155.91959524], e_qwxyz_end: [ 0.13023495 0.91244972 -0.06673891 -0.38212601], Hit-correlation: 0.2328
4, e_tf_shift: [-53.09864822 45.02704452 143.33846239], e_tf_qwxyz: [ 0.95366473 -0.21739301 0.17571088 -0.11130833], e_shift_end: [ 75.78299516 -20.34512099 72.29272581], e_qwxyz_end: [ 0.95245981 -0.14655562 -0.0861452 0.25282555], Hit-correlation: 0.1864

I tried to open this at Trac (totally new to me), but seemed not possible for me to do so. So, I'm still posting here...

Thanks, Roden

tomgoddard commented 4 months ago

Fit search is supposed to be reproducible. As with any scientific computation, even ones involving random choices, it is important to be able to exactly reproduce results. So I think the behavior you see is correct. You may want to have an option to set the random seed to get different results.

Best to report issues such as this using ChimeraX menu Help / Report a Bug so it goes to our Trac database.

RodenLuo commented 4 months ago

(Encountered "Error while submitting feedback." Reported via Email.)

The other non-random case is with PDB-8GAM and EMD-29900.

If one tries the same thing with PDB-8TNP and EMD-41423, then the inits seem to be random and not reproducible.

Important parts of the log are attached at the end. I have another random example, but the input data is a bit hard to describe (can send them to you if needed). My general feeling is when the target volume's box size is small, the inits are random. When the box is large, the inits are reproducible.

I expected the default to be fully random at all times unless the user specifies a random seed. Even with a random seed, I expected the inits to be different with different N (searching times). But this is more of a personal preference. To be consistent should be by design I guess.

Click to see the Logs
``` # ======= 8GAM # Opened emd_29900_3.46A.map as #1, grid size 280,280,280, pixel 1.41, shown at level 0.0873, step 2, values float32 # Run 1 0, e_tf_shift: [414.79088565 306.10153552 296.49909686], e_tf_qwxyz: [ 0.41116268 0.62607635 -0.65311036 -0.11144735], e_shift_end: [432.61247919 276.75578706 293.15928755], e_qwxyz_end: [ 0.41723871 0.58785037 -0.68513064 -0.10459352], Hit-correlation: -0.0025 1, e_tf_shift: [ 374.79719173 -201.64467725 66.71918982], e_tf_qwxyz: [ 0.6807122 -0.39271611 -0.59110882 0.18164614], e_shift_end: [ 334.62174399 -221.40256068 41.77450189], e_qwxyz_end: [ 0.67503504 -0.41335282 -0.60017385 0.11514551], Hit-correlation: -0.0162 2, e_tf_shift: [ -20.17495283 396.86143567 -180.79641642], e_tf_qwxyz: [ 0.65912475 0.71955783 -0.21440603 0.04267491], e_shift_end: [ -27.80067453 383.92908074 -185.55773179], e_qwxyz_end: [ 0.67459632 0.70965728 -0.1933026 0.06277295], Hit-correlation: 0.0175 # Run 2 0, e_tf_shift: [414.79088565 306.10153552 296.49909686], e_tf_qwxyz: [ 0.41116268 0.62607635 -0.65311036 -0.11144735], e_shift_end: [432.61247919 276.75578706 293.15928755], e_qwxyz_end: [ 0.41723871 0.58785037 -0.68513064 -0.10459352], Hit-correlation: -0.0025 1, e_tf_shift: [ 374.79719173 -201.64467725 66.71918982], e_tf_qwxyz: [ 0.6807122 -0.39271611 -0.59110882 0.18164614], e_shift_end: [ 334.62174399 -221.40256068 41.77450189], e_qwxyz_end: [ 0.67503504 -0.41335282 -0.60017385 0.11514551], Hit-correlation: -0.0162 2, e_tf_shift: [ -20.17495283 396.86143567 -180.79641642], e_tf_qwxyz: [ 0.65912475 0.71955783 -0.21440603 0.04267491], e_shift_end: [ -27.80067453 383.92908074 -185.55773179], e_qwxyz_end: [ 0.67459632 0.70965728 -0.1933026 0.06277295], Hit-correlation: 0.0175 # Run 3 0, e_tf_shift: [414.79088565 306.10153552 296.49909686], e_tf_qwxyz: [ 0.41116268 0.62607635 -0.65311036 -0.11144735], e_shift_end: [432.61247919 276.75578706 293.15928755], e_qwxyz_end: [ 0.41723871 0.58785037 -0.68513064 -0.10459352], Hit-correlation: -0.0025 1, e_tf_shift: [ 374.79719173 -201.64467725 66.71918982], e_tf_qwxyz: [ 0.6807122 -0.39271611 -0.59110882 0.18164614], e_shift_end: [ 334.62174399 -221.40256068 41.77450189], e_qwxyz_end: [ 0.67503504 -0.41335282 -0.60017385 0.11514551], Hit-correlation: -0.0162 2, e_tf_shift: [ -20.17495283 396.86143567 -180.79641642], e_tf_qwxyz: [ 0.65912475 0.71955783 -0.21440603 0.04267491], e_shift_end: [ -27.80067453 383.92908074 -185.55773179], e_qwxyz_end: [ 0.67459632 0.70965728 -0.1933026 0.06277295], Hit-correlation: 0.0175 3, e_tf_shift: [428.11330072 273.36196777 617.96122554], e_tf_qwxyz: [ 0.03299178 0.33735783 0.79694895 -0.49997362], e_shift_end: [418.01970286 240.5873258 643.33543291], e_qwxyz_end: [ 0.05229818 0.38024948 0.80183887 -0.45796251], Hit-correlation: -0.0012 4, e_tf_shift: [321.29927869 408.56171186 -10.81192404], e_tf_qwxyz: [ 0.24801752 0.10325985 0.20936904 -0.94020706], e_shift_end: [303.90966423 401.96121943 -0.98952467], e_qwxyz_end: [ 0.27348209 0.12795639 0.24370304 -0.92165261], Hit-correlation: -0.0015 # ======= 8TNP # Opened emd_41423_3.3A.map as #1, grid size 224,224,224, pixel 1.28, shown at level 0.229, step 1, values float32 # Run 1 0, e_tf_shift: [426.67526703 96.06725818 124.98850645], e_tf_qwxyz: [ 0.76022408 -0.12241001 -0.28548568 0.5705901 ], e_shift_end: [460.59739811 156.3874586 139.39369557], e_qwxyz_end: [ 0.65552719 -0.10479698 -0.32162736 0.67517223], Hit-correlation: 0.0167 1, e_tf_shift: [154.29225983 36.86684229 61.72219143], e_tf_qwxyz: [0.26018446 0.45421799 0.67391289 0.52137461], e_shift_end: [141.95236534 36.40737167 68.55006143], e_qwxyz_end: [0.3198268 0.46249411 0.66365414 0.49332869], Hit-correlation: 0.0213 2, e_tf_shift: [-112.43158484 392.66208624 257.02302263], e_tf_qwxyz: [ 0.53295278 -0.25304428 0.47020972 -0.65637851], e_shift_end: [-102.1864177 394.99177435 267.86306402], e_qwxyz_end: [ 0.5112743 -0.26562598 0.49221569 -0.65250681], Hit-correlation: 0.0109 # Run 2 0, e_tf_shift: [392.33433689 -32.27491197 101.53439117], e_tf_qwxyz: [ 0.60704259 -0.10575183 0.23322934 0.75227649], e_shift_end: [382.81482509 -39.81276184 104.15482391], e_qwxyz_end: [ 0.6067602 -0.09863529 0.26827199 0.74171644], Hit-correlation: 0.0135 1, e_tf_shift: [ 80.80217081 308.03797396 168.08926384], e_tf_qwxyz: [ 0.48935608 -0.01706829 0.37248327 -0.78834987], e_shift_end: [ 87.78161696 311.88173416 177.87287329], e_qwxyz_end: [ 0.47127471 -0.00591225 0.38825081 -0.79191319], Hit-correlation: 0.0082 2, e_tf_shift: [299.30385955 365.14872063 274.09380408], e_tf_qwxyz: [ 0.04090856 0.41086038 -0.82175336 0.39273612], e_shift_end: [304.267189 358.74287181 270.64625865], e_qwxyz_end: [ 0.0557654 0.37564093 -0.81917548 0.42980885], Hit-correlation: 0.0230 ```
Click to see the Gathered Information and etc.
``` Windows-10-10.0.22631 1.7.1 (2024-01-23 01:58:08 UTC) OpenGL version: 3.3.0 NVIDIA 528.24 OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Supermicro Model: AS -5014A-TT OS: Microsoft Windows 11 Pro for Workstations (Build 22631) Memory: 274,724,102,144 MaxProcessMemory: 137,438,953,344 CPU: 128 AMD Ryzen Threadripper PRO 3995WX 64-Cores OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1 ```
tomgoddard commented 4 months ago

I will investigate in April. The behavior should not vary based on the data and reproducible or random should be bith possible based on a seed parameter.

tomgoddard commented 3 months ago

I've made a ticket in our ChimeraX Trac database for this since that is where ChimeraX bug reports are handled.

https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14863

Sorry you got "Error while submitting feedback" when trying to report the problem in ChimeraX. That happens when our UCSF web server that receives the reports is down.