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#9457 closed defect (not a bug)
vseries unreliable coloring
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC)
Description
I haven't been able to figure out exactly what triggers it (seems more common with `movie record` and `perframe`, but there's some weirdness that happens when a vseries is coloured with `color zone`, where some frames will randomly drop their vertex colouring and revert to the original flat colour.
Log:
> isolde shorthand
Initialising ISOLDE-specific command aliases:
Alias Equivalent full command
-------------------------------------------------
st isolde step {arguments}
aw isolde add water {arguments}
awsf isolde add water {arguments} sim false
al isolde add ligand {arguments}
aa isolde add aa $1 sel {arguments}
ht isolde mod his sel {arguments}
so setattr sel atoms occupancy {arguments}
ab isolde adjust bfactors {arguments}
ss isolde sim start sel
rt isolde release torsions sel {arguments}
rd isolde release distances sel {arguments}
ra rd; rt
pf isolde pepflip sel
cf isolde cisflip sel
cbb color bfactor {arguments}
cbo color byattr occupancy {arguments}
cbc color {arguments} bychain; color {arguments} byhet
cs clipper set contourSensitivity {arguments}
UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc
> 01_cryosparc_P3_J103_006_volume_map_A_state.mrc
> 02_cryosparc_P3_J104_007_volume_map_A_state.mrc
> 03_cryosparc_P3_J105_006_volume_map_A_state.mrc
> 04_cryosparc_P3_J107_007_volume_map_A_state.mrc
> 05_cryosparc_P3_J108_006_volume_map_A_state.mrc
> 06_cryosparc_P3_J111_006_volume_map_A_state.mrc
> 07_cryosparc_P3_J112_006_volume_map_A_state.mrc vseries true
No such file/path: 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc
> cd "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/2023_07_21_cryosparc_pooled_classification"
Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\anti-
isrib\2023_07_21_cryosparc_pooled_classification
> open 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc
> 01_cryosparc_P3_J103_006_volume_map_A_state.mrc
> 02_cryosparc_P3_J104_007_volume_map_A_state.mrc
> 03_cryosparc_P3_J105_006_volume_map_A_state.mrc
> 04_cryosparc_P3_J107_007_volume_map_A_state.mrc
> 05_cryosparc_P3_J108_006_volume_map_A_state.mrc
> 06_cryosparc_P3_J111_006_volume_map_A_state.mrc
> 07_cryosparc_P3_J112_006_volume_map_A_state.mrc vseries true
Opened map series 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc as #1, 8
images, grid size 400,400,400, pixel 1.14, shown at level 0.0481, step 2,
values float32
> volume #1.1 level 0.1348
> volume #1.1 step 1
> volume #1.1 level 0.2162
> close #1.2-8#1#1.1
> open 01_cryosparc_P3_J103_006_volume_map_A_state.mrc
> 02_cryosparc_P3_J104_007_volume_map_A_state.mrc
> 03_cryosparc_P3_J105_006_volume_map_A_state.mrc
> 04_cryosparc_P3_J107_007_volume_map_A_state.mrc
> 05_cryosparc_P3_J108_006_volume_map_A_state.mrc
> 06_cryosparc_P3_J111_006_volume_map_A_state.mrc
> 07_cryosparc_P3_J112_006_volume_map_A_state.mrc
> 08_cryosparc_P3_J109_006_volume_map_mixed_A_I.mrc vseries true
Opened map series 01_cryosparc_P3_J103_006_volume_map_A_state.mrc as #1, 8
images, grid size 400,400,400, pixel 1.14, shown at level 0.06, step 2, values
float32
> volume #1.1 step 1
> volume #1.1 level 0.1727
> volume #1.1 level 0.2496
> open "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/pooled_datasets/cryosparc_P3_J50_009_model.cif"
Summary of feedback from opening C:/Users/Tristan
Croll/Documents/Structures/anti-
isrib/pooled_datasets/cryosparc_P3_J50_009_model.cif
---
warnings | Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /F:167
Chain information for cryosparc_P3_J50_009_model.cif #2
---
Chain | Description
A B | No description available
C D | No description available
E F | No description available
G H | No description available
I J | No description available
> select #2
60871 atoms, 60644 bonds, 2 pseudobonds, 4489 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.43214,0.88781,-0.15825,-44.307,-0.90163,0.42185,-0.095436,364.03,-0.017971,0.18393,0.98278,-34.149
> view matrix models
> #2,0.23012,0.95571,-0.18348,-7.5021,-0.95835,0.25532,0.12798,364.58,0.16916,0.14639,0.97466,-67.01
> fitmap #2 inMap #1.1
Fit molecule cryosparc_P3_J50_009_model.cif (#2) to map
01_cryosparc_P3_J103_006_volume_map_A_state.mrc (#1.1) using 60871 atoms
average map value = 0.2433, steps = 140
shifted from previous position = 7.5
rotated from previous position = 13 degrees
atoms outside contour = 35652, contour level = 0.24957
Position of cryosparc_P3_J50_009_model.cif (#2) relative to
01_cryosparc_P3_J103_006_volume_map_A_state.mrc (#1.1) coordinates:
Matrix rotation and translation
0.21805953 0.97593385 0.00177771 -44.97743871
-0.97593187 0.21805342 0.00311197 401.54659465
0.00264944 -0.00241352 0.99999358 0.38708014
Axis -0.00283086 -0.00044661 -0.99999589
Axis point 228.09400564 228.84196039 0.00000000
Rotation angle (degrees) 77.40528249
Shift along axis -0.43908879
> hide #2&~:UNL
> select clear
> open "C:/Users/Tristan
> Croll/Documents/Structures/isrib_workup/6o85_rebuild.pdb"
Chain information for 6o85_rebuild.pdb #3
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E F | No description available
G | No description available
H | No description available
I J | No description available
L | No description available
S | No description available
d | No description available
> matchmaker #3/E to #2/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker cryosparc_P3_J50_009_model.cif, chain E (#2) with 6o85_rebuild.pdb,
chain E (#3), sequence alignment score = 1776.3
RMSD between 354 pruned atom pairs is 0.431 angstroms; (across all 356 pairs:
0.468)
> hide #!2 models
> hide #3&~:C7B
> hide HC
> color :C7B orange
> color byhetero
> setattr :C7B bonds radius 0.4
Assigning radius attribute to 56 items
> select #1.1
2 models selected
> lighting soft
> select clear
> cofr centerOfView showPivot true
> lighting soft
> cofr showPivot false
> volume #1.1 level 0.3059
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> usage vseries
Subcommands are:
* vseries align
* vseries measure
* vseries play
* vseries save
* vseries slider
* vseries stop
> perframe "movie duplicate 15"
> vseries play #1
> wait 8
> perframe stop
> movie stop
> pwd
Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\anti-
isrib\2023_07_21_cryosparc_pooled_classification
> movie encode pooled_maps_playthrough_isrib_site.mp4
Movie saved to pooled_maps_playthrough_isrib_site.mp4
> show #1.1 models
> hide #!1 models
> movie record
> show #!1 models
> movie stop
> movie reset
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie encode pooled_maps_playthrough_isrib_site.mp4
Movie saved to pooled_maps_playthrough_isrib_site.mp4
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie reset
> movie record size 1920,1080
> movie stop
> movie reset
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie encode overview.mp4
Movie saved to overview.mp4
> color zone #1 near #2
> color #2 bychain
> color zone #1 near #2
> volume #1.1 level 0.2726
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie encode fulcrum_and_t_helix.mp4
Movie saved to fulcrum_and_t_helix.mp4
> color zone #1 near #2
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie reset
> color zone #1.1-1.8 near #2
color zone: No surfaces specified.
> color zone #1 near #2
> movie reset
No movie being recorded.
> movie record size 1920,1080
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file
or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_b4pn
--0001.ppm'
> perframe stop
> movie reset
> color zone #1 near #2
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie reset
> color zone #1 near #2
> hide #!1 models
> movie record size 1920,1080
> show #!1 models
> perframe "color zone #1 near #2; movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie reset
> color zone #1 near #2
> hide #!1 models
> movie record
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie encode isrib_site.mp4
Movie saved to isrib_site.mp4
> color zone #1 near #2
> movie record
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file
or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_QpdU
--0001.ppm'
> perframe stop
> movie stop
> movie reset
> color zone #1 near #2
> movie record
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file
or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_FoR2
--0001.ppm'
> perframe stop
> movie reset
> movie record
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file
or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_M9Dz
--0001.ppm'
> perframe stop
> movie stop
> movie reset
> color zone #1 near #2
> hide #!1 models
> movie record
> show #!1 models
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
> perframe stop
> movie stop
> movie encode overview.mp4
Movie saved to overview.mp4
> color zone #1 near #2
> hide #!1 models
> show #!1 models
> movie record
> movie stop
> movie reset
> movie record
> perframe "movie duplicate 15"
> vseries play #1
> wait 9
Error executing per-frame command 'movie duplicate 15': [Errno 2] No such file
or directory: 'C:\\\Users\\\TRISTA~1\\\AppData\\\Local\\\Temp\\\chimovie_GKYs
--0001.ppm'
> perframe stop
> movie stop
> movie reset
> hide #!1 models
> show #!1 models
> color zone #1 near #2
> show #2
> style #!3 stick
Changed 70792 atom styles
> show #!2 models
> hide #!3 models
> color byhetero
> select #2
60871 atoms, 60644 bonds, 2 pseudobonds, 4489 residues, 2 models selected
> style sel stick
Changed 60871 atom styles
> select #1.1
2 models selected
> hide HC
> cartoon
> hide #!1 models
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #1.4 level 0.2625
> show #!2 models
> hide #!2 models
OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46
ChimeraX-AtomicLibrary: 10.0.7
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: 2.10.3
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307112022
ChimeraX-CoreFormats: 1.1
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: 1.1.2
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
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: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
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: 2.2.1
ChimeraX-TapeMeasure: 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: 1.30.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
comtypes: 1.1.14
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.8.1
prompt-toolkit: 3.0.39
psutil: 5.9.4
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
pyparsing: 3.1.0
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pywin32: 305
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
WMI: 1.5.1
Change History (5)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → vseries unreliable coloring |
comment:2 by , 2 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
comment:3 by , 2 years ago
By the way, the vseries gui slider keeps all the surfaces, so you won't notice the loss of coloring just using the slider.
comment:4 by , 2 years ago
Also, this exact loss of coloring problem is described in the documentation under the vseries play "loop" option.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html
comment:5 by , 2 years ago
Thanks - that all makes a lot of sense. On Tue, Jul 25, 2023 at 6:54 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > >
Note:
See TracTickets
for help on using tickets.
When a volume series is played with "vseries play #1" it deletes all each surface except the one currently being displayed and then recreates the surface the next time it is shown. This avoid running out of memory for series with hundreds of maps. When a surface is deleted its per-vertex coloring is lost. The way to avoid this is to have vseries play not delete the surfaces. You do that using the cacheFrames option. For example if you have 10 maps in your series then
will avoid deleting any of the surfaces so per-vertex colors will be preserved.
Probably a better default would be that vseries play keeps all the surfaces and if you wanted the more memory efficient behavior you could specify an option to delete undisplayed surfaces. But the code was originally developed for 3D light microscopy series that often had 500 volumes each of large size so the current default behavior made more sense.