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Opened 10 months ago
Closed 10 months ago
#16742 closed defect (duplicate)
ArtiaX session save: Unknown class name 'MarkerSetPlus'
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| 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: Linux-5.4.0-150-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> artiax start
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened KHG_ORANGE_3_tilt_series_44_alimc_rec_topaz_denoised_corrected.mrc as
#1.1.1, grid size 1024,1024,148, pixel 7.86,7.86,7.86, shown at level 0.237,
step 1, values float32
> artiax tomo #1.1.1 sliceDirection 0,0,1
> artiax view xy
> open /home/neherlab/Downloads/tilt44_filament1.axm format geomodel
Summary of feedback from opening /home/neherlab/Downloads/tilt44_filament1.axm
---
note | Created a Curved line through 5 particles.
Opened tilt44_filament1.axm, a CurvedLine Geometric Model.
> artiax tomo #1.1.1 slice 0
> artiax tomo #1.1.1 slice 55
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
> hide #!1.2.2 models
> hide #!1.2.1 models
> artiax particles #1.2.3 radius 4.0
> artiax particles #1.2.3 radius 64.01787
set axis size 13.88621
13.88621
['.arrow', '0', '0', '0', '13.88621', '0', '0', '0.9257473333333334',
'3.7029893333333335']
set axis size 18.89937
18.89937
['.arrow', '0', '0', '0', '18.89937', '0', '0', '1.2599580000000001',
'5.0398320000000005']
set axis size 23.28589
23.28589
['.arrow', '0', '0', '0', '23.28589', '0', '0', '1.5523926666666665',
'6.209570666666666']
set axis size 26.41912
26.41912
['.arrow', '0', '0', '0', '26.41912', '0', '0', '1.7612746666666665',
'7.045098666666666']
set axis size 36.44545
36.44545
['.arrow', '0', '0', '0', '36.44545', '0', '0', '2.4296966666666666',
'9.718786666666666']
set axis size 38.32539
38.32539
['.arrow', '0', '0', '0', '38.32539', '0', '0', '2.555026', '10.220104']
set axis size 39.57868
39.57868
['.arrow', '0', '0', '0', '39.57868', '0', '0', '2.6385786666666666',
'10.554314666666667']
set axis size 43.33856
43.33856
['.arrow', '0', '0', '0', '43.33856', '0', '0', '2.8892373333333334',
'11.556949333333334']
set axis size 55.87147
55.87147
['.arrow', '0', '0', '0', '55.87147', '0', '0', '3.7247646666666667',
'14.899058666666667']
set axis size 71.53762
71.53762
['.arrow', '0', '0', '0', '71.53762', '0', '0', '4.769174666666667',
'19.07669866666667']
set axis size 77.17743
77.17743
['.arrow', '0', '0', '0', '77.17743', '0', '0', '5.145162', '20.580648']
set axis size 79.05737
79.05737
['.arrow', '0', '0', '0', '79.05737', '0', '0', '5.270491333333334',
'21.081965333333336']
set axis size 81.56395
81.56395
['.arrow', '0', '0', '0', '81.56395', '0', '0', '5.437596666666667',
'21.750386666666667']
set axis size 84.07053
84.07053
['.arrow', '0', '0', '0', '84.07053', '0', '0', '5.6047020000000005',
'22.418808000000002']
set axis size 90.33699
90.33699
['.arrow', '0', '0', '0', '90.33699', '0', '0', '6.022466', '24.089864']
set axis size 95.35016
95.35016
['.arrow', '0', '0', '0', '95.35016', '0', '0', '6.356677333333334',
'25.426709333333335']
set axis size 97.23009
97.23009
['.arrow', '0', '0', '0', '97.23009', '0', '0', '6.482006', '25.928024']
set axis size 97.23009
97.23009
['.arrow', '0', '0', '0', '97.23009', '0', '0', '6.482006', '25.928024']
> artiax particles #1.2.3 axesSize 97.23009
> artiax particles #1.2.3 radius 54.61818
Opened egelman-helix-alone-110box.mrc as #2, grid size 110,110,110, pixel
0.876, shown at level 0.299, step 1, values float32
> artiax attach #2 toParticleList #1.2.3
Opened egelman-helix-alone-110box.mrc as #1.2.3.1.1, grid size 110,110,110,
pixel 0.876, shown at level 0.299, step 1, values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax hide markers
[Repeated 2 time(s)]
> hide #!1.2.3 models
> show #!1.2.3 models
> artiax hide markers
> hide #!1.3.1 models
> artiax hide axes
> artiax show surfaces
Opened egelman-helix-box228-lowpass40-resampled.mrc as #2, grid size 64,64,64,
pixel 7.86, shown at level 0.0367, step 1, values float32
> artiax attach #2 toParticleList #1.2.3
Opened egelman-helix-box228-lowpass40-resampled.mrc as #1.2.3.1.1, grid size
64,64,64, pixel 7.86, shown at level 0.0367, step 1, values float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 color 37,95,95,100
> artiax particles #1.2.3 color 0,46,86,100
> artiax particles #1.2.3 color 60,0,0,100
> artiax particles #1.2.3 color 30,0,36,100
> artiax particles #1.2.3 color 45,4,100,100
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil1-100A.em partlist #1.2.3
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-115px-box.mrc as #2, grid size 512,512,115, pixel
0.876,0.876,0.876, shown at level 0.11, step 2, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-115px-box.mrc as #1.2.1.1.1, grid size
512,512,115, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> hide #!1.2.3 models
> artiax particles #1.2.1 color 30,0,36,100
> artiax particles #1.2.1 color 45,4,100,100
> artiax geomodel color #1.3.1 100,66,73,100
> artiax particles #1.2.1 color 94,64,100,100
> artiax particles #1.2.1 color 56,49,0,100
> artiax particles #1.2.1 color 0,20,50,100
> artiax particles #1.2.1 color 0,36,19,100
> artiax particles #1.2.1 color 100,0,6,100
> artiax particles #1.2.1 color 88,100,40,100
> artiax particles #1.2.1 color 76,0,53,100
> artiax particles #1.2.1 color 17,81,28,100
> artiax particles #1.2.1 color 45,4,100,100
> artiax particles #1.2.1 color 60,25,0,100
> artiax particles #1.2.1 color 45,4,100,100
> artiax particles #1.2.1 color 100,31,2,100
> artiax particles #1.2.1 color 45,4,100,100
> artiax particles #1.2.1 color 45,4,100,76
> artiax particles #1.2.1 color 45,4,100,100
> show #!1.2.3 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.3 models
> artiax hide axes
> artiax hide markers
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil1-100A-croppedhelix1.em partlist #1.2.3
> artiax particles #1.2.1 surfaceLevel 0.13602
> lighting flat
> lighting simple
> lighting soft
> graphics silhouettes false
> open /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament2.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament3.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament4.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament5.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament6.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament7.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament8.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament9.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament10.axm
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament2.axm
---
note | Created a Curved line through 19 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament3.axm
---
note | Created a Curved line through 5 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament4.axm
---
note | Created a Curved line through 4 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament5.axm
---
note | Created a Curved line through 5 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament6.axm
---
note | Created a Curved line through 3 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament7.axm
---
note | Created a Curved line through 8 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament8.axm
---
note | Created a Curved line through 13 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament9.axm
---
note | Created a Curved line through 4 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament10.axm
---
note | Created a Curved line through 9 particles.
Opened tilt44_filament2.axm, a CurvedLine Geometric Model.
Opened tilt44_filament3.axm, a CurvedLine Geometric Model.
Opened tilt44_filament4.axm, a CurvedLine Geometric Model.
Opened tilt44_filament5.axm, a CurvedLine Geometric Model.
Opened tilt44_filament6.axm, a CurvedLine Geometric Model.
Opened tilt44_filament7.axm, a CurvedLine Geometric Model.
Opened tilt44_filament8.axm, a CurvedLine Geometric Model.
Opened tilt44_filament9.axm, a CurvedLine Geometric Model.
Opened tilt44_filament10.axm, a CurvedLine Geometric Model.
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
> hide #!1.3.2 models
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/filament2-100A.em partlist #1.2.1
> show #!1.3.1 models
Opened egelman-helix-512-512-43px-box.mrc as #2, grid size 512,512,43, pixel
0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-43px-box.mrc as #1.2.1.1.1, grid size 512,512,43,
pixel 0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
Opened egelman-helix-512-512-115px-box.mrc as #2, grid size 512,512,115, pixel
0.876,0.876,0.876, shown at level 0.11, step 2, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-115px-box.mrc as #1.2.1.1.1, grid size
512,512,115, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 0.12534
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-43px-box.mrc as #2, grid size 512,512,43, pixel
0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened egelman-helix-512-512-43px-box.mrc as #1.2.2.1.1, grid size 512,512,43,
pixel 0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> hide #!1.2.1 models
> artiax particles #1.2.2 color 45,4,100,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.1 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-43px-box.mrc as #2, grid size 512,512,43, pixel
0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened egelman-helix-512-512-43px-box.mrc as #1.2.2.1.1, grid size 512,512,43,
pixel 0.876,0.876,0.876, shown at level 0.111, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 color 30,0,36,100
> artiax particles #1.2.2 color 45,4,100,100
> artiax particles #1.2.2 surfaceLevel 0.17596
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.2.1 models
> hide #!1.2.1 models
> show #!1.3.2 models
> hide #!1.3.2 models
> show #!1.3.1 models
> show #!1.2.1 models
Opened egelman-helix-512-512-115px-box.mrc as #2, grid size 512,512,115, pixel
0.876,0.876,0.876, shown at level 0.11, step 2, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-115px-box.mrc as #1.2.1.1.1, grid size
512,512,115, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax hide markers
> artiax hide axes
> hide #!1.3.1 models
Opened egelman-helix-512-512-137px-box.mrc as #2, grid size 512,512,137, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-137px-box.mrc as #1.2.1.1.1, grid size
512,512,137, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 0.12
> open /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil2-100A.em format motl
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/44-fil2-100A.em
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list 44-fil2-100A.em with 4 particles.
Opened 44-fil1-100A-croppedhelix1.em as #2, grid size 20,4,1, pixel 8.08e+05,
shown at step 1, values float32
> artiax attach #2 toParticleList #1.2.2
Opened 44-fil1-100A-croppedhelix1.em as #1.2.2.1.1, grid size 20,4,1, pixel
8.08e+05, shown at level 3.1e+03, step 1, values float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
Opened egelman-helix-512-512-137px-box.mrc as #2, grid size 512,512,137, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.2
Opened egelman-helix-512-512-137px-box.mrc as #1.2.2.1.1, grid size
512,512,137, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> hide #!1.2.2 models
> show #!1.3.2 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-137px-box.mrc as #2, grid size 512,512,137, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.2
Opened egelman-helix-512-512-137px-box.mrc as #1.2.2.1.1, grid size
512,512,137, pixel 0.876,0.876,0.876, shown at level 0.11, step 1, values
float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 color 45,4,100,100
> artiax particles #1.2.2 surfaceLevel 0.14937
28 atoms, 28 residues, atom cross_correlation range 0 to 0
[Repeated 1 time(s)]
> artiax colormap #1.2.2.3 cross_correlation palette redgreen minValue 0.0
> maxValue 0.0 transparency 0.0
> artiax particles #1.2.2 color 45,4,100,100
> artiax hide markers
> artiax hide axes
> artiax particles #1.2.2 surfaceLevel 0.14403
> hide #!1.3.2 models
> artiax particles #1.2.2 surfaceLevel 0.13602
> artiax particles #1.2.2 color 45,4,100,100
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.2
Opened egelman-helix-512-512-149px-box.mrc as #1.2.2.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.2.1.1 capFaces false
> artiax show #1.2.2 surfaces
> artiax particles #1.2.2 surfaceLevel 0.1467
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil1-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil2-100A.em partlist #1.2.1
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.1
Opened egelman-helix-512-512-149px-box.mrc as #1.2.1.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.1.1.1 capFaces false
> artiax show #1.2.1 surfaces
> artiax particles #1.2.1 surfaceLevel 0.13602
> artiax particles #1.2.1 surfaceLevel 0.14403
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.3
Opened egelman-helix-512-512-149px-box.mrc as #1.2.3.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.3.1.1 capFaces false
> artiax show #1.2.3 surfaces
> artiax particles #1.2.3 surfaceLevel 0.14136
> artiax hide markers
> artiax hide axes
> artiax particles #1.2.3 color 30,0,36,100
> artiax particles #1.2.3 color 45,4,100,100
> hide #!1.3.3 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.4
Opened egelman-helix-512-512-149px-box.mrc as #1.2.4.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.4.1.1 capFaces false
> artiax show #1.2.4 surfaces
> artiax particles #1.2.4 color 45,4,100,100
> artiax particles #1.2.4 surfaceLevel 0.15471
> hide #!1.3.4 models
> artiax hide markers
> artiax hide axes
[Repeated 1 time(s)]
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil3-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil4-100A.em partlist #1.2.1
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.5
Opened egelman-helix-512-512-149px-box.mrc as #1.2.5.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.5.1.1 capFaces false
> artiax show #1.2.5 surfaces
> artiax particles #1.2.5 surfaceLevel 0.1467
> hide #!1.3.5 models
> show #!1.3.5 models
> hide #!1.3.5 models
> show #!1.3.5 models
> hide #!1.3.5 models
> show #!1.3.5 models
> hide #!1.2.5 models
> show #!1.2.5 models
> artiax hide markers
> artiax hide axes
> hide #!1.3.5 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.6
Opened egelman-helix-512-512-149px-box.mrc as #1.2.6.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.6.1.1 capFaces false
> artiax show #1.2.6 surfaces
> artiax particles #1.2.6 color 45,4,100,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.6 models
> artiax particles #1.2.6 surfaceLevel 0.13869
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.7
Opened egelman-helix-512-512-149px-box.mrc as #1.2.7.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.7.1.1 capFaces false
> artiax show #1.2.7 surfaces
> artiax particles #1.2.7 color 45,4,100,100
> artiax particles #1.2.7 surfaceLevel 0.19744
> hide #!1.3.7 models
> hide #!1.3.8 models
> artiax hide markers
> artiax hide axes
> show #!1.3.8 models
> hide #!1.3.8 models
> show #!1.3.8 models
> hide #!1.3.8 models
> show #!1.3.8 models
> show #!1.3.7 models
> hide #!1.3.7 models
> show #!1.3.7 models
> hide #!1.3.7 models
> show #!1.3.7 models
> hide #!1.3.7 models
> show #!1.3.7 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.7
Opened egelman-helix-512-512-149px-box.mrc as #1.2.7.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.7.1.1 capFaces false
> artiax show #1.2.7 surfaces
> artiax particles #1.2.7 color 45,4,100,100
> artiax particles #1.2.7 surfaceLevel 0.15204
> artiax hide markers
> artiax hide axes
> hide #!1.3.7 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.8
Opened egelman-helix-512-512-149px-box.mrc as #1.2.8.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.8.1.1 capFaces false
> artiax show #1.2.8 surfaces
> artiax particles #1.2.8 color 45,4,100,100
> artiax particles #1.2.8 surfaceLevel 0.1467
> hide #!1.3.8 models
> artiax hide markers
> artiax hide axes
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.9
Opened egelman-helix-512-512-149px-box.mrc as #1.2.9.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.9.1.1 capFaces false
> artiax show #1.2.9 surfaces
> artiax particles #1.2.9 color 45,4,100,100
> artiax particles #1.2.9 surfaceLevel 0.14937
> artiax hide markers
> artiax hide axes
> hide #!1.3.9 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.10
Opened egelman-helix-512-512-149px-box.mrc as #1.2.10.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.10.1.1 capFaces false
> artiax show #1.2.10 surfaces
> artiax particles #1.2.10 color 62,80,0,100
> artiax particles #1.2.10 surfaceLevel 0.15204
> open /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament11.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament12.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament13.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament14.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament15.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament16.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament17.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament18.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament19.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament20.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament21.axm
> /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/tilt44-filaments/tilt44_filament22.axm
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament11.axm
---
note | Created a Curved line through 2 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament12.axm
---
note | Created a Curved line through 10 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament13.axm
---
note | Created a Curved line through 8 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament14.axm
---
note | Created a Curved line through 9 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament15.axm
---
note | Created a Curved line through 4 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament16.axm
---
note | Created a Curved line through 8 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament17.axm
---
note | Created a Curved line through 5 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament18.axm
---
note | Created a Curved line through 7 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament19.axm
---
note | Created a Curved line through 10 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament20.axm
---
note | Created a Curved line through 5 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament21.axm
---
note | Created a Curved line through 8 particles.
Summary of feedback from opening
/mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
Modeling/tilt44-filaments/tilt44_filament22.axm
---
note | Created a Curved line through 9 particles.
Opened tilt44_filament11.axm, a CurvedLine Geometric Model.
Opened tilt44_filament12.axm, a CurvedLine Geometric Model.
Opened tilt44_filament13.axm, a CurvedLine Geometric Model.
Opened tilt44_filament14.axm, a CurvedLine Geometric Model.
Opened tilt44_filament15.axm, a CurvedLine Geometric Model.
Opened tilt44_filament16.axm, a CurvedLine Geometric Model.
Opened tilt44_filament17.axm, a CurvedLine Geometric Model.
Opened tilt44_filament18.axm, a CurvedLine Geometric Model.
Opened tilt44_filament19.axm, a CurvedLine Geometric Model.
Opened tilt44_filament20.axm, a CurvedLine Geometric Model.
Opened tilt44_filament21.axm, a CurvedLine Geometric Model.
Opened tilt44_filament22.axm, a CurvedLine Geometric Model.
> hide #!1.3.10 models
> show #!1.3.10 models
> hide #!1.2.10 models
> hide #!1.3.10 models
> show #!1.2.10 models
Traceback (most recent call last):
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 236, in
_spacing_toggled
self.line.create_spheres()
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 153, in
create_spheres
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi
ValueError: math domain error
ValueError: math domain error
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 153, in
create_spheres
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi
See log for complete Python traceback.
> hide #!1.3.11 models
> show #!1.3.11 models
> hide #!1.3.11 models
> show #!1.3.11 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.11
Opened egelman-helix-512-512-149px-box.mrc as #1.2.11.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.11.1.1 capFaces false
> artiax show #1.2.11 surfaces
> artiax particles #1.2.11 color 45,4,100,100
> artiax particles #1.2.11 surfaceLevel 0.14403
> artiax hide markers
> artiax hide axes
> hide #!1.3.11 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.12
Opened egelman-helix-512-512-149px-box.mrc as #1.2.12.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.12.1.1 capFaces false
> artiax show #1.2.12 surfaces
> artiax particles #1.2.12 color 45,4,100,100
> artiax particles #1.2.12 surfaceLevel 0.14136
> artiax hide markers
> artiax hide axes
> hide #!1.3.12 models
> show #!1.3.12 models
> hide #!1.3.12 models
> show #!1.3.12 models
> hide #!1.3.12 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.13
Opened egelman-helix-512-512-149px-box.mrc as #1.2.13.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.13.1.1 capFaces false
> artiax show #1.2.13 surfaces
> artiax particles #1.2.13 surfaceLevel 0.15738
> artiax particles #1.2.13 color 45,4,100,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.13 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.14
Opened egelman-helix-512-512-149px-box.mrc as #1.2.14.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.14.1.1 capFaces false
> artiax show #1.2.14 surfaces
> artiax particles #1.2.14 color 100,64,2,100
> artiax particles #1.2.14 surfaceLevel 0.15471
> hide #!1.3.14 models
> artiax hide markers
> artiax hide axes
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.15
Opened egelman-helix-512-512-149px-box.mrc as #1.2.15.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.15.1.1 capFaces false
> artiax show #1.2.15 surfaces
> artiax particles #1.2.15 color 100,0,6,100
> artiax particles #1.2.15 color 60,0,0,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.15 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.16
Opened egelman-helix-512-512-149px-box.mrc as #1.2.16.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.16.1.1 capFaces false
> artiax show #1.2.16 surfaces
> artiax particles #1.2.16 color 37,95,95,100
> artiax particles #1.2.16 surfaceLevel 0.14403
> artiax hide markers
> artiax hide axes
> hide #!1.3.16 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.17
Opened egelman-helix-512-512-149px-box.mrc as #1.2.17.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.17.1.1 capFaces false
> artiax show #1.2.17 surfaces
> artiax particles #1.2.17 color 17,81,28,100
> artiax particles #1.2.17 color 94,64,100,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.17 models
> artiax particles #1.2.17 surfaceLevel 0.15471
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.18
Opened egelman-helix-512-512-149px-box.mrc as #1.2.18.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.18.1.1 capFaces false
> artiax show #1.2.18 surfaces
> artiax particles #1.2.18 color 0,20,50,100
> artiax particles #1.2.18 surfaceLevel 0.16272
> artiax hide markers
> artiax hide axes
> hide #!1.3.18 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.19
Opened egelman-helix-512-512-149px-box.mrc as #1.2.19.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.19.1.1 capFaces false
> artiax show #1.2.19 surfaces
> artiax particles #1.2.19 color 58,100,71,100
> artiax particles #1.2.19 surfaceLevel 0.14403
> artiax hide markers
> artiax hide axes
> hide #!1.3.19 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.20
Opened egelman-helix-512-512-149px-box.mrc as #1.2.20.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.20.1.1 capFaces false
> artiax show #1.2.20 surfaces
> artiax particles #1.2.20 color 100,0,6,100
> artiax hide markers
> artiax hide axes
> hide #!1.3.20 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.21
Opened egelman-helix-512-512-149px-box.mrc as #1.2.21.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.21.1.1 capFaces false
> artiax show #1.2.21 surfaces
> artiax particles #1.2.21 color 37,95,95,100
> artiax particles #1.2.21 surfaceLevel 0.12267
> artiax particles #1.2.21 surfaceLevel 0.16272
> artiax hide markers
> artiax hide axes
[Repeated 1 time(s)]
> hide #!1.3.21 models
15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened egelman-helix-512-512-149px-box.mrc as #2, grid size 512,512,149, pixel
0.876,0.876,0.876, shown at level 0.109, step 2, values float32
> artiax attach #2 toParticleList #1.2.22
Opened egelman-helix-512-512-149px-box.mrc as #1.2.22.1.1, grid size
512,512,149, pixel 0.876,0.876,0.876, shown at level 0.109, step 1, values
float32
> volume #1.2.22.1.1 capFaces false
> artiax show #1.2.22 surfaces
> artiax particles #1.2.22 color 100,31,2,100
> artiax particles #1.2.22 color 100,100,50,100
> artiax particles #1.2.22 surfaceLevel 0.13869
> artiax particles #1.2.15 surfaceLevel 0.17073
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/20250129-tilt44.cxs includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 295, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 294, in convert
return add_obj(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 268, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 470, in get_class
return f(class_name)
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x7f433f7dcee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f42f9c0a700> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 295, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 294, in convert
return add_obj(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 268, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 470, in get_class
return f(class_name)
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x7f433f7dcee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f42f9c0a700> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> delete #1.2.5.2 particle 1/4
Expected a keyword
> show #!1.3.5 models
> artiax show markers
> ui mousemode right select
fine
> select clear
> ui mousemode right translate
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil5-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil6-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil7-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil8-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil9-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil10-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil11-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil12-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil13-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil14-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil15-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil16-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil17-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil18-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil19-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil20-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil21-100A.em partlist #1.2.1
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/44-fil22-100A.em partlist #1.2.1
> artiax particles #1.2.22 color 100,64,2,100
> hide #!1.2.22 models
> artiax particles #1.2.21 color 0,60,56,100
> hide #!1.2.21 models
> show #!1.2.21 models
> artiax particles #1.2.21 color 0,46,86,100
> artiax particles #1.2.21 color 100,64,2,100
> artiax particles #1.2.21 color 26,40,0,100
> artiax particles #1.2.21 color 56,49,0,100
> artiax particles #1.2.21 color 100,100,50,100
> artiax particles #1.2.21 color 62,80,0,100
> artiax particles #1.2.18 color 37,95,95,100
> artiax particles #1.2.18 color 76,0,53,100
> hide #!1.2.17 models
> artiax particles #1.2.20 color 100,0,6,100
> artiax particles #1.2.20 color 88,100,40,100
> artiax particles #1.2.20 color 76,0,53,100
> hide #!1.2.16 models
> show #!1.2.16 models
> artiax particles #1.2.13 color 0,46,86,100
> artiax particles #1.2.12 color 50,50,50,100
> artiax particles #1.2.12 color 30,0,36,100
> artiax particles #1.2.11 color 100,64,2,100
> hide #!1.2.10 models
> artiax particles #1.2.9 color 94,64,100,100
> artiax particles #1.2.8 color 100,66,73,100
> artiax particles #1.2.7 color 100,31,2,100
> artiax particles #1.2.6 color 100,64,2,100
> artiax particles #1.2.6 color 0,20,50,100
> artiax particles #1.2.8 color 0,60,56,100
> artiax particles #1.2.4 color 62,80,0,100
> artiax particles #1.2.3 color 0,36,19,100
> artiax particles #1.2.3 color 37,95,95,100
> artiax particles #1.2.1 color 100,66,73,100
> hide #!1.2.3 models
> show #!1.2.3 models
> ui mousemode right select
fine
> hide #!1.3.5 models
> hide #!1.3.22 models
> hide #!1.2.19 models
> show #!1.2.19 models
> save /mnt/disks/data-1/20231211_relion_subtomogram_LPL_20220907/ArtiaX-
> Modeling/20250130.cxs includeMaps true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 295, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 294, in convert
return add_obj(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 268, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 470, in get_class
return f(class_name)
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x7f433f7dcee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f42f9c0a700> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 295, in process
return copy_state(data, convert=convert)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 294, in convert
return add_obj(obj, parents)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 268, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 470, in get_class
return f(class_name)
File "/home/neherlab/.local/share/ChimeraX/1.3/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class
raise ValueError("Unknown class name '%s'" % class_name)
ValueError: Unknown class name 'MarkerSetPlus'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x7f433f7dcee0> ->
<chimerax.atomic.molobject.Atom object at 0x7f42f9c0a700> 'M': Unknown class
name 'MarkerSetPlus'
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: X570 AORUS ULTRA
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 AMD Ryzen 9 3900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62G 13G 1.1G 198M 48G 48G
Swap: 2.0G 101M 1.9G
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP108 [GeForce GT 1030] [10de:1d01] (rev a1)
Subsystem: Micro-Star International Co., Ltd. [MSI] GP108 [GeForce GT 1030] [1462:8c98]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
geomdl: 5.3.1
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
pandas: 2.0.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
starfile: 0.4.12
suds-jurko: 0.6
superqt: 0.4.1
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX session save: Unknown class name 'MarkerSetPlus' |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Fixed as of ArtiaX 0.4.1 (this ticket has 0.3)