Opened 6 hours ago

Last modified 3 hours ago

#20542 assigned defect

ArtiaX: read RELION STAR file: Cannot interpret as a data type

Reported by: nathalie.lavoie@… 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:        macOS-15.7.1-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Attempt to open a .star generated by Relion 4.01 in ArtiaX but I receive this error::
open /Users/nathalielavoie/Library/CloudStorage/Box-Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/job038_particles.star format star
Summary of feedback from opening /Users/nathalielavoie/Library/CloudStorage/Box-Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/job038_particles.star
notes
Processed as relion
Processed as relion
Traceback (most recent call last):   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe     run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run     results = command.run(text, log=log, return_json=return_json)               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open     models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215, in provider_open     models, status = collated_open(session, None, [data], data_format, _add_models,                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526, in collated_open     return remember_data_format()            ^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497, in remember_data_format     models, status = func(*func_args, **func_kw)                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/formats.py", line 25, in open     return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True)            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/io.py", line 104, in open_particle_list     data = formats[format_name].particle_data(            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in __init__     super().__init__(   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__     self.read_file()   File "/Users/nathalielavoie/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in read_file     if np.issubdtype(df.dtypes[key], np.number):        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype     arg1 = dtype(arg1).type            ^^^^^^^^^^^ TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type TypeError: Cannot interpret '' as a data type

File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened TS_4.mrc as #2.1.1, grid size 1364,1364,332, pixel 10, shown at step 1,
values float32  
Opened Fig5_gb_zone12A.mrc as #2.2.1.1.1, grid size 120,120,120, pixel 6.08,
shown at level 0.0386, step 1, values float32  
Opened TS_4.mrc scaled as #1, grid size 1364,1364,332, pixel 10, shown at
level 0.6, step 4, values float32  
Opened TS_4_external_membrane.mrc as #3, grid size 1364,1364,332, pixel 10,
shown at level 0.834, step 4, values float32  
Opened TS_4.mrc scaled zone as #6, grid size 1364,1364,332, pixel 10, shown at
level 0.6, step 4, values float32  
Opened volume maximum gaussian as #7, grid size 1364,1364,332, pixel 10, shown
at level 0.996, step 1, values float32  
Opened TS_4_external_membrane.mrc as #10, grid size 1364,1364,332, pixel 10,
shown at level 0.834, step 2, values float32  
Opened TS_4_membrane_clean_round3.mrc as #5, grid size 1364,1364,332, pixel
10, shown at level 0.795, step 2, values float32  
Opened TS_4_all_PEV.mrc as #14, grid size 1364,1364,332, pixel 10, shown at
level 0.773, step 1, values float32  
Opened TS_4_membrane_clean_round3.mrc copy as #8, grid size 1364,1364,332,
pixel 10, shown at level 0.773, step 4, values float32  
Opened TS_4_membrane_clean_round3.mrc copy as #11, grid size 1364,1364,332,
pixel 10, shown at level 0.773, step 1, values float32  
Opened TS_4_all_spike.mrc as #12, grid size 1364,1364,332, pixel 10, shown at
level 0.993, step 2, values float32  
Opened TS_4_intermediate_filament_clean.mrc as #13, grid size 1364,1364,332,
pixel 10, shown at level 0.0061, step 4, values int8  
Opened volume difference as #15, grid size 1364,1364,332, pixel 10, shown at
level 0.795, step 1, values float32  
Log from Wed Jun 24 10:56:21 2026UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened TS_4.mrc as #2.1.1, grid size 1364,1364,332, pixel 10, shown at step 1,
values float32  
Opened TS_4.mrc scaled as #1, grid size 1364,1364,332, pixel 10, shown at
level 0.6, step 4, values float32  
Opened TS_4_external_membrane.mrc as #3, grid size 1364,1364,332, pixel 10,
shown at level 0.834, step 4, values float32  
Opened TS_4.mrc scaled zone as #6, grid size 1364,1364,332, pixel 10, shown at
level 0.6, step 4, values float32  
Opened volume maximum gaussian as #7, grid size 1364,1364,332, pixel 10, shown
at level 0.996, step 1, values float32  
Opened TS_4_external_membrane.mrc as #10, grid size 1364,1364,332, pixel 10,
shown at level 0.834, step 2, values float32  
Opened TS_4_membrane_clean_round3.mrc as #5, grid size 1364,1364,332, pixel
10, shown at level 0.795, step 2, values float32  
Opened TS_4_all_PEV.mrc as #14, grid size 1364,1364,332, pixel 10, shown at
level 0.773, step 1, values float32  
Opened TS_4_membrane_clean_round3.mrc copy as #8, grid size 1364,1364,332,
pixel 10, shown at level 0.773, step 4, values float32  
Opened TS_4_membrane_clean_round3.mrc copy as #11, grid size 1364,1364,332,
pixel 10, shown at level 0.773, step 1, values float32  
Opened TS_4_all_spike.mrc as #12, grid size 1364,1364,332, pixel 10, shown at
level 0.773, step 1, values float32  
Opened TS_4_intermediate_filament_clean.mrc as #13, grid size 1364,1364,332,
pixel 10, shown at level 0.0061, step 4, values int8  
Opened volume difference as #15, grid size 1364,1364,332, pixel 10, shown at
level 0.795, step 1, values float32  
Log from Tue Jun 23 15:35:14 2026UCSF ChimeraX version: 1.11.dev202506260705
(2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open TS_4.mrc

Opened TS_4.mrc as #1, grid size 1364,1364,332, pixel 9.12,9.12,9.12, shown at
step 1, values float32  

> ui tool show Toolbar

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> artiax add tomo #1

Opened TS_4.mrc as #2.1.1, grid size 1364,1364,332, pixel 9.12,9.12,9.12,
shown at level 0.156, step 1, values float32  

> artiax clip off

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #2.1.1 pixelSize 10.0

> artiax view xy

> artiax tomo #2.1.1 pixelSize 10.0

> artiax view xy

> vop scale #2.1.1 factor -1

Opened TS_4.mrc scaled as #1, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> volume #1

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_external_membrane.mrc

Opened TS_4_external_membrane.mrc as #3, grid size 1364,1364,332, pixel 10,
shown at step 1, values float32  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_external_membrane_holes.cmm

Opened 1 marker sets containing 991 markers  

> volume #3 region 0,0,0,1363,1363,331 step 4

[Repeated 1 time(s)]

> volume #3 change image level -7.593e-16,0 level 1,0.8 level 1.433,1

> volume #3 level 0.8343

> volume #1 level 0.6

> volume #1 change image level 0.1213,0 level 1.203,0.8 level 4.627,1

> vop zone #1 nearAtoms #4 range 75 newMap true

Opened TS_4.mrc scaled zone as #5, grid size 1364,1364,332, pixel 10, shown at
step 1, values float32  

> hide #4 models

> vop zone #1 nearAtoms #4 range 100 newMap true

Opened TS_4.mrc scaled zone as #6, grid size 1364,1364,332, pixel 10, shown at
step 1, values float32  

> close #5

> vop maximum #3 #6

Opened volume maximum as #5, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> set bgColor white

> graphics silhouettes true

> vop gaussian #5 sdev 3

Opened volume maximum gaussian as #7, grid size 1364,1364,332, pixel 10, shown
at step 1, values float32  

> vop gaussian #5 sdev 6

Opened volume maximum gaussian as #8, grid size 1364,1364,332, pixel 10, shown
at step 1, values float32  

> surface dust #3 size 100

> ui mousemode right "map eraser"

> volume erase #3 center 8049,4254.6,2326.3 radius 904.35

Opened TS_4_external_membrane.mrc copy as #10, grid size 1364,1364,332, pixel
10, shown at step 1, values float32  

> volume #10 step 4

> volume erase #10 center 8265.4,3956.8,2610.6 radius 900.24

> volume erase #10 center 6351.6,4423.1,2517.7 radius 900.24

> volume erase #10 center 7235.6,4349.5,2400.3 radius 900.24

> volume erase #10 center 7590.5,4543.9,3173.6 radius 900.24

> volume erase #10 center 8589.1,4935.4,3049.3 radius 900.24

> volume erase #10 center 9329.6,2707.8,1794.4 radius 900.24

> volume erase #10 center 5439.4,9626.6,1424.9 radius 900.24

> volume erase #10 center 7928.3,10101,1588.6 radius 900.24

> volume erase #10 center 8069.9,10333,1614.9 radius 900.24

> volume erase #10 center 9641.3,8578.5,474.54 radius 900.24

> volume erase #10 center 10900,12136,2671.8 radius 900.24

> volume erase #10 center 10434,11826,3148.4 radius 900.24

> volume erase #10 center 8450.5,629.95,3327.3 radius 900.24

> volume erase #10 center 6014.3,354.82,3064 radius 900.24

> volume erase #10 center 6331.7,3960.3,861.59 radius 900.24

> volume erase #10 center 7552.6,4486,691.15 radius 900.24

> volume erase #10 center 8250,4376.3,629.39 radius 900.24

> volume erase #10 center 8535,4564.9,680.6 radius 900.24

> volume erase #10 center 8453.8,4598,673.72 radius 900.24

> volume erase #10 center 8587.6,4873.6,67.017 radius 900.24

> volume erase #10 center 7693.1,2412.9,-224.03 radius 900.24

> volume erase #10 center 3385.1,2930,2538.6 radius 900.24

> volume erase #10 center 4801.2,1678.2,2592.5 radius 900.24

> volume erase #10 center 451.04,1515.2,901.79 radius 900.24

> volume erase #10 center -396.66,1239.2,1672.6 radius 900.24

[Repeated 1 time(s)]

> volume erase #10 center -262.77,1515.1,2191.7 radius 900.24

> volume erase #10 center 704.97,899.36,2520.3 radius 900.24

> volume erase #10 center 165.99,4257,2497.7 radius 900.24

> volume erase #10 center 688.94,7800.7,3291.2 radius 900.24

> volume erase #10 center 2300.1,9233.3,3194.4 radius 900.24

> artiax view xy

> volume erase #10 center 13188,8556.9,1228.3 radius 900.24

> volume erase #10 center 12258,7842.6,1382.6 radius 900.24

> volume erase #10 center 10735,12026,1133 radius 900.24

> volume erase #10 center 11282,11657,567.75 radius 900.24

> volume erase #10 center 13080,8837.2,1156.4 radius 900.24

> volume erase #10 center 12530,9662.5,975.57 radius 900.24

> volume erase #10 center 6387.9,8361.4,1528.3 radius 654.72

> volume erase #10 center 6772.7,8994.2,2570.8 radius 654.72

> volume erase #10 center 7329.3,8456.5,2291 radius 429.66

> volume erase #10 center 6157.8,10592,1597.3 radius 429.66

> volume erase #10 center 5997.7,9417.8,1763.6 radius 429.66

> volume erase #10 center 6014.4,9184.3,1823.1 radius 429.66

> volume erase #10 center 6030.4,8682.6,2181.1 radius 429.66

> volume erase #10 center 7274.1,7575.4,364.51 radius 429.66

> volume erase #10 center 4953.8,6504.9,1222.2 radius 429.66

> volume erase #10 center 5076.5,5747.7,1166.9 radius 429.66

> volume erase #10 center 5154.9,5636.4,701.5 radius 429.66

> volume erase #10 center 3607.3,7037.6,1395.3 radius 429.66

> volume erase #10 center 3552.3,6709.5,1574.1 radius 429.66

> volume erase #10 center 5919.4,5296.7,1608.8 radius 429.66

> volume erase #10 center 6700.3,5167.6,863.98 radius 429.66

> volume erase #10 center 3987.5,7241,1865.7 radius 429.66

> volume erase #10 center 4571.4,7036.2,1978.6 radius 429.66

> volume erase #10 center 3349.1,6078.8,2804.9 radius 429.66

> volume erase #10 center 3713.2,6096.8,2386.3 radius 429.66

> volume erase #10 center 3724,7381,1963.1 radius 429.66

> volume erase #10 center 5932.1,7651.8,2322.3 radius 429.66

> volume erase #10 center 5905.6,7820.2,2206.9 radius 429.66

> volume erase #10 center 6740,8487.2,953.4 radius 429.66

> volume erase #10 center 6880.8,8194.7,998.49 radius 429.66

> volume erase #10 center 7476.9,7118.4,2270 radius 429.66

> volume erase #10 center 6557.5,7776,1896 radius 429.66

> volume erase #10 center 4804.4,6454.3,1776.3 radius 429.66

> volume erase #10 center 5302.3,5276.7,2963.3 radius 429.66

> volume erase #10 center 5619.9,6311.2,218.67 radius 429.66

> volume erase #10 center 10289,1788.4,838.25 radius 429.66

> volume erase #10 center 10193,2381.1,912.24 radius 429.66

> volume erase #10 center 10075,3249.5,457.01 radius 429.66

> volume erase #10 center 7463.4,5306.3,1710.8 radius 429.66

> volume erase #10 center 8761.3,5713.4,1489.5 radius 429.66

> volume erase #10 center 8636.7,5783.5,1764.7 radius 429.66

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_external_membrane.mrc models #10

> volume erase #10 center 8836.2,5111.2,1688.3 radius 429.66

> volume erase #10 center 10521,8789.3,1119.3 radius 429.66

> volume erase #10 center 13094,10369,725.28 radius 429.66

> volume erase #10 center 11375,7007.9,1428.4 radius 163.68

> volume erase #10 center 11093,6997.8,1155.7 radius 163.68

> volume erase #10 center 10971,6850.1,1135.7 radius 163.68

> volume erase #10 center 11043,7628.8,725.15 radius 163.68

> volume erase #10 center 11695,8895.9,897.32 radius 163.68

> volume erase #10 center 11409,8619.8,675.99 radius 163.68

> volume erase #10 center 8927.2,11114,2125 radius 163.68

> volume erase #10 center 7509.9,9039.5,3061.8 radius 265.98

> volume erase #10 center 5125.4,7685.3,3246.1 radius 265.98

> volume erase #10 center 6170.9,9647.8,2248.8 radius 265.98

> volume erase #10 center 6107.1,9656.8,2048.9 radius 265.98

> volume erase #10 center 7261.9,10113,765.47 radius 265.98

> volume erase #10 center 4169.5,7441,961.8 radius 265.98

> volume erase #10 center 4093.5,7298.5,1012.4 radius 265.98

> volume erase #10 center 2733.6,4901.3,852.06 radius 265.98

> volume erase #10 center 4125.7,5200.7,2539.5 radius 265.98

> volume erase #10 center 4401.7,5132.3,2500.6 radius 265.98

> volume erase #10 center 3830.1,6029.5,1991.7 radius 265.98

> volume erase #10 center 2723.5,6838.5,2347 radius 265.98

> volume erase #10 center 2204.3,3857.9,775.96 radius 265.98

> volume erase #10 center 7228.9,3507,903.92 radius 265.98

> volume erase #10 center 7010.9,3166.2,964.66 radius 265.98

> volume erase #10 center 6206.9,2897.5,1004.6 radius 265.98

> volume erase #10 center 6899.8,3151.1,615.92 radius 265.98

> volume erase #10 center 5682.3,2812.6,2896.9 radius 265.98

> view

> close #5

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_membrane_clean_round3.mrc

Opened TS_4_membrane_clean_round3.mrc as #5, grid size 1364,1364,332, pixel
10, shown at step 1, values float32  

> volume #5 region 0,0,0,1363,1363,331 step 4

[Repeated 1 time(s)]

> volume #5 change image level -7.593e-16,0 level 1,0.8 level 1.662,1

> volume #5 level 0.6016

> volume #5 level 0.7729

> show #!2.1.1 models

> hide #!2.1.1 models

> volume erase #5 center 6604.8,3265.3,1472.2 radius 716.1 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #11, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike1.mrc models #11

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 257

> hide #!2.1.1 models

> volume erase #5 center 6232.5,4707.1,2583.4 radius 716.1 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #12, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike2.mrc models #12

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!12 models

> show #!5 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 237

> hide #!2.1.1 models

> volume erase #5 center 7752.4,5076.6,2501.7 radius 777.48 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #13, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike3.mrc models #13

> show #!5 models

> hide #!13 models

> show #!2.1.1 models

> show #!13 models

> show #!12 models

> show #!11 models

> hide #!5 models

> show #!5 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!2.1.1 models

> volume erase #5 center 4842.2,4877.5,2032.7 radius 777.48 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #14, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #14 center 3843.4,5207.1,2784 radius 777.48

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike4.mrc models #14

> hide #!14 models

> show #!5 models

> show #!2.1.1 models

> hide #!5 models

> show #!12 models

> hide #!12 models

> show #!11 models

> show #!12 models

> hide #!11 models

> hide #!12 models

> show #!13 models

> show #!14 models

> show #!12 models

> show #!11 models

> artiax tomo #2.1.1 slice 202

> artiax tomo #2.1.1 slice 212

> artiax tomo #2.1.1 slice 222

> artiax tomo #2.1.1 slice 232

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 262

> artiax tomo #2.1.1 slice 272

> artiax tomo #2.1.1 slice 282

> artiax tomo #2.1.1 slice 292

> artiax tomo #2.1.1 slice 302

> artiax tomo #2.1.1 slice 312

> artiax tomo #2.1.1 slice 322

> artiax tomo #2.1.1 slice 332

[Repeated 1 time(s)]

> artiax tomo #2.1.1 slice 322

> artiax tomo #2.1.1 slice 312

> artiax tomo #2.1.1 slice 302

> artiax tomo #2.1.1 slice 292

> artiax tomo #2.1.1 slice 282

> artiax tomo #2.1.1 slice 272

> artiax tomo #2.1.1 slice 262

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 232

> artiax tomo #2.1.1 slice 222

> artiax tomo #2.1.1 slice 212

> artiax tomo #2.1.1 slice 202

> artiax tomo #2.1.1 slice 192

> artiax tomo #2.1.1 slice 182

> artiax tomo #2.1.1 slice 172

> artiax tomo #2.1.1 slice 162

> artiax tomo #2.1.1 slice 152

> artiax tomo #2.1.1 slice 142

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!2.1.1 models

> volume erase #5 center 5434.8,5964.7,1034.2 radius 777.48 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #15, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike5.mrc models #15

> hide #!15 models

> show #!5 models

> show #!2.1.1 models

> show #!11 models

> hide #!5 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!5 models

> show #!10 models

> hide #!5 models

> show #!5 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!2.1.1 models

> volume erase #5 center 8212.3,3219.2,931.52 radius 1452.7 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #16, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #16 center 9612.6,2557.1,-198.49 radius 1452.7

> volume erase #16 center 10122,3958.8,1616 radius 1452.7

> volume erase #16 center 9583.9,4443.6,-295.92 radius 1452.7

> volume erase #16 center 6574.3,3918.7,-532.14 radius 1452.7

> volume erase #16 center 5949.3,3371,1106.8 radius 1452.7

> volume erase #16 center 7170.5,1658.9,1287.8 radius 634.26

> volume erase #16 center 8346.6,1836.3,166.81 radius 634.26

> volume erase #16 center 7516.1,3181.2,26.388 radius 634.26

> volume erase #16 center 6913.8,3500.3,541.63 radius 634.26

> volume erase #16 center 6887.2,3259.2,552.16 radius 634.26

> volume erase #16 center 6567.4,2579,605.59 radius 634.26

> volume erase #16 center 7940.1,2675.1,-264.26 radius 634.26

> volume erase #16 center 9253.4,3703.9,583.36 radius 634.26

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike6_joint.mrc models #16

> show #!5 models

> hide #!5 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> surface dust #11 size 100

> surface dust #12 size 100

> surface dust #13 size 100

> surface dust #14 size 100

> surface dust #15 size 100

> surface dust #16 size 100

> show #!2.1.1 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> show #!5 models

> hide #!2.1.1 models

> volume erase #5 center 6856.5,4852.9,1270.3 radius 757.02 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #17, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike7.mrc models #17

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 132

> artiax tomo #2.1.1 slice 122

> show #!5 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!2.1.1 models

> volume erase #5 center 8574.3,5693.5,1078 radius 757.02 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #18, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike8.mrc models #18

> show #!5 models

> hide #!5 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 112

> artiax tomo #2.1.1 slice 102

> artiax tomo #2.1.1 slice 92

> artiax tomo #2.1.1 slice 82

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> show #!5 models

> hide #!2.1.1 models

> volume erase #5 center 5568.7,4275.6,543.16 radius 838.86 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #19, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #19 center 4802.3,2955.5,652.33 radius 838.86

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_spike9.mrc models #19

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 72

> artiax tomo #2.1.1 slice 62

> artiax tomo #2.1.1 slice 52

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 32

> artiax tomo #2.1.1 slice 22

> artiax tomo #2.1.1 slice 12

> artiax tomo #2.1.1 slice 2

> artiax tomo #2.1.1 slice 12

> artiax tomo #2.1.1 slice 22

> artiax tomo #2.1.1 slice 32

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 52

> artiax tomo #2.1.1 slice 62

> artiax tomo #2.1.1 slice 52

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 32

> artiax tomo #2.1.1 slice 22

> hide #!2.1.1 models

> show #!5 models

> show #!2.1.1 models

> hide #!5 models

> show #!10 models

> view

> hide #!2.1.1 models

> show #!5 models

> hide #!5 models

> show #!2.1.1 models

> show #!5 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #!2.1.1 models

Can only have one displayed volume when erasing  

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> volume erase #5 center 8539.7,1583.6,69.868 radius 1043.5 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #20, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev1.mrc models #20

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 32

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 52

> artiax tomo #2.1.1 slice 62

> artiax tomo #2.1.1 slice 72

> artiax tomo #2.1.1 slice 82

> artiax tomo #2.1.1 slice 92

> artiax tomo #2.1.1 slice 102

> artiax tomo #2.1.1 slice 112

> artiax tomo #2.1.1 slice 122

> artiax tomo #2.1.1 slice 132

> artiax tomo #2.1.1 slice 142

> artiax tomo #2.1.1 slice 152

> artiax tomo #2.1.1 slice 162

> artiax tomo #2.1.1 slice 172

> artiax tomo #2.1.1 slice 182

> artiax tomo #2.1.1 slice 192

> artiax tomo #2.1.1 slice 202

> artiax tomo #2.1.1 slice 212

> artiax tomo #2.1.1 slice 222

> artiax tomo #2.1.1 slice 232

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 252

> hide #!2.1.1 models

> show #!5 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> volume erase #5 center 5211.2,7453.2,2624.9 radius 1084.4 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #21, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #21 center 6915.8,8477,2627.5 radius 1084.4

> volume erase #21 center 5132.2,5416.3,2959.1 radius 1084.4

> volume erase #21 center 5867,5511.7,2785.9 radius 1084.4

> volume erase #21 center 3676.6,6575.4,3567.7 radius 1084.4

> volume erase #21 center 3409.7,6983.4,3348.8 radius 1084.4

> volume erase #21 center 4129.8,7154.9,3216.4 radius 368.28

> volume erase #21 center 4052.4,7194.9,3060.9 radius 368.28

> volume erase #21 center 4202.1,6687,2912.8 radius 368.28

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev2.mrc models #21

Cannot save '/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/TS_4_pev2.mrc': [Errno 28] No space left on device  

> spine #21

Unknown command: measure spine #21  

> measure volume #21

Enclosed volume for surface (#21.1) = 3.293e+08  

> measure blob #21

Missing required "triangle_number" argument  

> ui mousemode right "pick blobs"

> measure blob #!21.1 triangleNumber 222129 color #0000ccff outline true

Surface TS_4_membrane_clean_round3.mrc copy #21.1 blob:  
volume = 3.2173e+08  
area = 1.2253e+07  
size = 1846.7 1913.4 1286.4  
  

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!20 models

> hide #!20 models

> show #!21 models

> show #!5 models

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> measure blob #!21.1 triangleNumber 59674 color #0000ccff outline true

Surface TS_4_membrane_clean_round3.mrc copy #21.1 blob:  
volume = 3.2173e+08  
area = 1.2253e+07  
size = 1846.7 1913.4 1286.4  
  

> view

> hide #2.3 models

> show #2.3 models

> hide #!21 models

> show #!20 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> close #21

> measure blob #!9 triangleNumber 799 color #0000ccff outline true

Surface eraser sphere #9 blob:  
volume = 3.6823e+09  
area = 1.1549e+07  
size = 1918.4 1916 1916.8  
  

> color #9 #ff9df3ff

> close #21

> ui mousemode right "map eraser"

> transparency #9#20.1 50

> show #!5 models

> hide #!2.1.1 models

Can only have one displayed volume when erasing  

[Repeated 1 time(s)]

> hide #!20 models

> volume erase #5 center 3582.4,5188,2724.3 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #21, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #21 center 3994.8,3144.7,2750.8 radius 1104.8

> volume erase #21 center 5357.6,4887.2,1751 radius 1104.8

> volume erase #21 center 4154.5,7060,2865.1 radius 1104.8

> volume erase #21 center 2679.7,6926.7,3252 radius 1104.8

> volume erase #21 center 1730.7,5049,1922.7 radius 1104.8

> volume erase #21 center 1761.6,5996.4,1989 radius 1104.8

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev2.mrc models #21

> hide #!21 models

> show #!5 models

> hide #!5 models

> show #!20 models

> show #!21 models

> hide #!21 models

> hide #!20 models

> show #!5 models

> volume erase #5 center 3698.7,6836.1,3137 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #22, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 331

> artiax tomo #2.1.1 slice 305

> artiax tomo #2.1.1 slice 190

> hide #!2.1.1 models

> volume erase #22 center 5506.1,7324.6,2647 radius 1104.8

> volume erase #22 center 5300.5,7572.5,2285.8 radius 1104.8

> volume erase #22 center 5368.6,7784.6,2713.5 radius 1104.8

> volume erase #22 center 3216.1,8855.7,2997.8 radius 1104.8

> volume erase #22 center 1571.7,6854.9,3245.5 radius 1104.8

> volume erase #22 center 4024.8,4860.3,2664 radius 1104.8

> volume erase #22 center 3700.1,4983.3,2230.7 radius 1104.8

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev3.mrc models #22

> show #!5 models

> show #!2.1.1 models

> show #!21 models

> color #22 #d5404dff models

> color #21 #d53f55ff models

> show #!20 models

> color #20 #d53a3980 models

> artiax tomo #2.1.1 slice 281

> hide #!2.1.1 models

Can only have one displayed volume when erasing  

> hide #!22 models

> hide #!21 models

> hide #!20 models

> volume erase #5 center 5271.4,7440.6,2514.4 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #23, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume #23 step 4

> volume erase #23 center 6710.6,6789.9,1246.6 radius 1104.8

> volume erase #23 center 7201,6765.9,2104.5 radius 1104.8

> volume erase #23 center 6950.2,8484.1,2555.6 radius 1104.8

> volume erase #23 center 6061.2,5520.2,2748.4 radius 1104.8

> volume erase #23 center 5202.4,5414,2850 radius 1104.8

> volume erase #23 center 3608,6718,3573.2 radius 1104.8

> volume erase #23 center 3439.4,7050.2,3506.8 radius 1104.8

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev4.mrc models #23

> show #!5 models

> color #23 #d54e49ff models

> show #!22 models

> show #!21 models

> show #!20 models

> hide #!22 models

> show #!22 models

> hide #!23 models

> show #!23 models

> hide #!5 models

> hide #!23 models

> show #!23 models

> show #!5 models

> show #!2.1.1 models

> hide #!2.1.1 models

> view

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!23 models

> volume erase #5 center 6845.6,8554,2755.5 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #24, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume #24 step 4

> volume erase #24 center 5010.4,9118.9,3309.3 radius 1104.8

> volume erase #24 center 5109.5,9626.1,3042.8 radius 1104.8

> volume erase #24 center 7020.4,10568,2738.8 radius 1104.8

> volume erase #24 center 8371.1,9465.8,1886 radius 1104.8

> volume erase #24 center 8649.4,8913.5,1934.1 radius 1104.8

> volume erase #24 center 8244.9,9868.5,2167.4 radius 1104.8

> volume erase #24 center 8596.5,9389,2283.3 radius 1104.8

> volume erase #24 center 7539.7,6598.7,2978.7 radius 1104.8

> volume erase #24 center 7461.2,6623.6,2244.7 radius 1104.8

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev5.mrc models #24

> color #24 #d55731ff models

> show #!5 models

> show #!20 models

> show #!21 models

> show #!22 models

> show #!23 models

> hide #!5 models

> show #!2.1.1 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> show #!5 models

> hide #!2.1.1 models

> volume erase #5 center 6228,10493,2677.4 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #25, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume #25 step 4

> volume erase #25 center 6786.9,11615,1351 radius 1104.8

> volume erase #25 center 4551.5,11443,1975.3 radius 1104.8

> volume erase #25 center 4457.3,11619,2734.1 radius 1104.8

> volume erase #25 center 4626.9,11619,3522.2 radius 1104.8

> volume erase #25 center 5251.5,12200,3404.8 radius 1104.8

> volume erase #25 center 5012.2,12150,2369.5 radius 1104.8

> volume erase #25 center 5055.4,8965.8,3160.6 radius 1104.8

> volume erase #25 center 4839.5,9019.9,2732.2 radius 1104.8

> volume erase #25 center 7249.4,9512.5,1325.3 radius 1104.8

> volume erase #25 center 8251.9,10834,2202.1 radius 1104.8

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_pev6.mrc models #25

Cannot save '/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/TS_4_pev6.mrc': [Errno 28] No space left on device  

> hide #!25 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> ui tool show Toolbar

> ui mousemode right "pick blobs"

> measure blob #!19.1 triangleNumber 1568

Surface TS_4_spike9.mrc #19.1 blob:  
volume = 1.8903e+08  
area = 6.3367e+06  
size = 1567 1481.1 1064.9  
  

> show #!25 models

> hide #!25 models

> show #!25 models

> hide #!25 models

> hide #!19 models

> hide #!18 models

> show #!18 models

> hide #!17 models

> hide #!18 models

> hide #!16 models

> hide #!15 models

> hide #!12 models

> hide #!14 models

> hide #!13 models

> ui tool show Toolbar

> ui mousemode right "pick blobs"

[Repeated 1 time(s)]

> measure blob #!11.1 triangleNumber 31853 color #18c99bff outline true

Surface TS_4_spike1.mrc #11.1 blob:  
volume = 2.1421e+08  
area = 6.5248e+06  
size = 1349.2 1190.6 1110.4  
  

> ui tool show Toolbar

> ui autostart true Toolbar

> hide #!11 models

> show #!12 models

> measure blob #!12.1 triangleNumber 36130 color #18c99bff outline true

Surface TS_4_spike2.mrc #12.1 blob:  
volume = 1.8335e+08  
area = 5.5957e+06  
size = 1189.2 1258.4 907.62  
  

> hide #!12 models

> show #!13 models

> measure blob #!13.1 triangleNumber 6079 color #18c99bff outline true

Surface TS_4_spike3.mrc #13.1 blob:  
volume = 2.1861e+08  
area = 6.7382e+06  
size = 1303.7 1224.9 1243.9  
  

> hide #!13 models

> show #!14 models

> measure blob #!14.1 triangleNumber 43661 color #18c99bff outline true

Surface TS_4_spike4.mrc #14.1 blob:  
volume = 2.0052e+08  
area = 6.2697e+06  
size = 1265.2 1229.5 1104.6  
  

> hide #!14 models

> show #!15 models

> measure blob #!15.1 triangleNumber 13310 color #18c99bff outline true

Surface TS_4_spike5.mrc #15.1 blob:  
volume = 2.0661e+08  
area = 6.2685e+06  
size = 1412.5 1409.6 1217.4  
  

> hide #!15 models

> show #!16 models

> measure blob #!16.1 triangleNumber 66868 color #18c99bff outline true

Surface TS_4_spike6_joint.mrc #16.1 blob:  
volume = 4.3572e+08  
area = 1.336e+07  
size = 2719.6 1300.6 1407.4  
  

> hide #!16 models

> show #!17 models

> measure blob #!17.1 triangleNumber 69646 color #18c99bff outline true

Surface TS_4_spike7.mrc #17.1 blob:  
volume = 2.2143e+08  
area = 6.9996e+06  
size = 1223 1373.2 1195.5  
  

> hide #!17 models

> show #!18 models

> measure blob #!18.1 triangleNumber 3404 color #18c99bff outline true

Surface TS_4_spike8.mrc #18.1 blob:  
volume = 1.622e+08  
area = 5.6625e+06  
size = 1306.2 1307.8 1083.2  
  

> hide #!18 models

> show #!19 models

> measure blob #!19.1 triangleNumber 35319 color #18c99bff outline true

Surface TS_4_spike9.mrc #19.1 blob:  
volume = 1.8903e+08  
area = 6.3367e+06  
size = 1567 1481.1 1064.9  
  

> hide #!19 models

> volume maximum #11 #12 #13 #14 #15 #16 #17 #18 #19

Opened volume maximum as #26, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> transparency #26.1 50

> show #!5 models

> hide #!5 models

> color #26 #d56744ff models

> volume #26 step 4

> volume #26 level 0.4257

> transparency #26.1 50

> show #!5 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 30

> artiax tomo #2.1.1 slice 50

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> artiax tomo #2.1.1 slice 28

> hide #!5 models

> show #!5 models

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> artiax tomo #2.1.1 slice 119

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_allPEV.mrc models #26

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all_spike_vesicles.mrc models #26

Cannot save '/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/TS_4_all_spike_vesicles.mrc': [Errno 28] No space
left on device  

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> close #11-19

> hide #!26 models

> hide #!2.1.1 models

> hide #!5 models

> show #!25 models

> hide #!25 models

> show #!25 models

> show #!24 models

> hide #!24 models

> show #!24 models

> show #!23 models

> show #!22 models

> show #!21 models

> show #!20 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 293

> measure blob #!9 triangleNumber 137 color #18c99bff outline true

Surface eraser sphere #9 blob:  
volume = 5.5847e+09  
area = 1.5245e+07  
size = 2204.2 2201.4 2202.2  
  

> close #11

> hide #9 models

> show #9 models

> color #9 #d5a3bbff

> transparency #9#20.1#21.1#22.1#23.1#24.1#25.1 0

> measure blob #!9 triangleNumber 201

Surface eraser sphere #9 blob:  
volume = 5.5847e+09  
area = 1.5245e+07  
size = 2204.2 2201.4 2202.2  
  

> ui mousemode right "map eraser"

> transparency #9#20.1#21.1#22.1#23.1#24.1#25.1 50

> show #!5 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> hide #!20 models

> hide #!2.1.1 models

> volume erase #5 center 5190.3,9158.7,2894.8 radius 1104.8 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #11, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume #11 step 4

> volume erase #11 center 5294,7300.9,2590.4 radius 1104.8

> volume erase #11 center 7042.2,8655.3,2498 radius 1104.8

> volume erase #11 center 6896.4,8189.2,2514.3 radius 1104.8

> volume erase #11 center 6285.8,10690,2619.4 radius 1104.8

> volume erase #11 center 6785.1,10403,2795.7 radius 1104.8

> volume erase #11 center 3954.7,10696,2722.1 radius 1104.8

> volume erase #11 center 3414.1,10020,2849.5 radius 1104.8

> volume erase #11 center 3340.3,8931.5,2306.8 radius 1104.8

> volume erase #11 center 3214.7,8669.8,2753.9 radius 1104.8

> volume erase #11 center 3900.7,9398.3,1592.8 radius 1104.8

> volume erase #11 center 3685.4,9587.3,1979.7 radius 1104.8

> volume erase #11 center 3154.4,9143.7,3087.9 radius 1104.8

> show #!20 models

> show #!21 models

> show #!22 models

> show #!23 models

> show #!24 models

> show #!25 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 212

> artiax tomo #2.1.1 slice 10

> volume #!11,20-25#!2.1.1 hide

> show #!5 models

> volume erase #5 center 10413,4105.6,311.75 radius 1186.7 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #12, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #12 center 11075,4643.3,2075.4 radius 1186.7

> volume #12 step 4

> volume erase #12 center 11291,3769.3,2154.8 radius 1186.7

> volume erase #12 center 12033,2808.9,1032.3 radius 1186.7

> ui favorite true Toolbar

> volume erase #12 center 12147,2698.6,399.14 radius 1186.7

> volume erase #12 center 12089,2851.7,440 radius 1186.7

> volume erase #12 center 12181,3195.3,623.33 radius 1186.7

> volume erase #12 center 12310,3619,158.45 radius 1186.7

> ui autostart true ArtiaX

> volume erase #12 center 12025,3526.5,1325.7 radius 1186.7

> volume erase #12 center 11957,3599.1,1349.5 radius 1186.7

> volume erase #12 center 9884.3,4421.7,1964.2 radius 1186.7

> ui mousemode right "pick blobs"

> measure blob #!12.1 triangleNumber 10454

Surface TS_4_membrane_clean_round3.mrc copy #12.1 blob:  
volume = 4.3179e+07  
area = 1.8777e+06  
size = 1403.4 773.41 291.29  
  

> measure blob #!12.1 triangleNumber 9301 color #18c99bff outline true

Surface TS_4_membrane_clean_round3.mrc copy #12.1 blob:  
volume = 2.6422e+07  
area = 1.3275e+06  
size = 1348.5 735.08 248.11  
  

> measure blob #!12.1 triangleNumber 8259 color #18c99bff outline true

Surface TS_4_membrane_clean_round3.mrc copy #12.1 blob:  
volume = 4.3179e+07  
area = 1.8777e+06  
size = 1403.4 773.41 291.29  
  

> show #!26 models

> close #26

> show #!25 models

> show #!24 models

> show #!23 models

> show #!22 models

> show #!21 models

> show #!20 models

> show #!11 models

> measure blob #!20.1 triangleNumber 219881 color #18c99bff outline true

Surface TS_4_pev1.mrc #20.1 blob:  
volume = 2.0389e+08  
area = 8.4575e+06  
size = 1891.9 1908.2 813.22  
  

> measure blob #!24.1 triangleNumber 18711 color #18c99bff outline true

Surface TS_4_pev5.mrc #24.1 blob:  
volume = 2.5845e+08  
area = 9.884e+06  
size = 1954.5 1936.7 1078.4  
  

> measure blob #!11.1 triangleNumber 7051 color #18c99bff outline true

Surface TS_4_membrane_clean_round3.mrc copy #11.1 blob:  
volume = 6.2686e+07  
area = 2.4011e+06  
size = 1578.1 789.77 550.96  
  

> measure blob #!25.1 triangleNumber 21797 color #18c99bff outline true

Surface TS_4_membrane_clean_round3.mrc copy #25.1 blob:  
volume = 3.2376e+08  
area = 1.1176e+07  
size = 1920.4 1851 1071.1  
  

> measure blob #!23.1 triangleNumber 21072 color #18c99bff outline true

Surface TS_4_pev4.mrc #23.1 blob:  
volume = 2.503e+08  
area = 1.0175e+07  
size = 1828.6 1968.6 1244.6  
  

> measure blob #!22.1 triangleNumber 110423 color #18c99bff outline true

Surface TS_4_pev3.mrc #22.1 blob:  
volume = 1.4488e+08  
area = 6.4122e+06  
size = 1853.2 1861.6 910.01  
  

> measure blob #!21.1 triangleNumber 237770 color #18c99bff outline true

Surface TS_4_pev2.mrc #21.1 blob:  
volume = 8.7938e+07  
area = 3.5639e+06  
size = 1875 905.34 853.59  
  

> measure blob #!21.1 triangleNumber 248459 color #18c99bff outline true

Surface TS_4_pev2.mrc #21.1 blob:  
volume = 8.4332e+07  
area = 3.8001e+06  
size = 1908.4 985.4 966.36  
  

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> hide #!20 models

> show #!2.1.1 models

> hide #!21 models

> hide #!12 models

> hide #!11 models

> show #!12 models

> ui mousemode right "mark plane"

> marker #4 position 9888,3254,95 color yellow radius 10

> marker change #4:1057 radius 50

> show #4 models

> ui mousemode right "delete markers"

[Repeated 1 time(s)]

> hide #4 models

> select add #4

992 atoms, 992 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #13 models

> show #13 models

> ui mousemode right "mark plane"

> marker #13 position 9988,3193,95 color yellow radius 50

> marker #13 position 9904,3243,95 color yellow radius 50

> marker #13 position 9817,3279,95 color yellow radius 50

> marker #13 position 9741,3335,95 color yellow radius 50

> marker #13 position 9676,3404,95 color yellow radius 50

> marker #13 position 1.015e+04,3150,95 color yellow radius 50

> marker #13 position 1.006e+04,3171,95 color yellow radius 50

> marker #13 position 9622,3457,95 color yellow radius 50

> marker #13 position 1.088e+04,4801,95 color yellow radius 50

> marker #13 position 1.078e+04,4844,95 color yellow radius 50

> marker #13 position 1.068e+04,4893,95 color yellow radius 50

> marker #13 position 1.113e+04,3685,95 color yellow radius 50

> marker #13 position 1.109e+04,3620,95 color yellow radius 50

> marker #13 position 1.104e+04,3507,95 color yellow radius 50

> marker #13 position 1.106e+04,3567,95 color yellow radius 50

> marker #13 position 1.093e+04,3373,95 color yellow radius 50

> marker #13 position 1.087e+04,3327,95 color yellow radius 50

> marker #13 position 1.081e+04,3290,95 color yellow radius 50

> marker #13 position 1.074e+04,3236,95 color yellow radius 50

> marker #13 position 1.067e+04,3206,95 color yellow radius 50

> marker #13 position 1.06e+04,3175,95 color yellow radius 50

> artiax tomo #2.1.1 slice 11

> artiax tomo #2.1.1 slice 12

> artiax tomo #2.1.1 slice 13

> artiax tomo #2.1.1 slice 14

> artiax tomo #2.1.1 slice 15

> show #!25 models

> hide #!25 models

> marker #13 position 1.101e+04,4658,145 color yellow radius 50

> marker #13 position 1.095e+04,4717,145 color yellow radius 50

> marker #13 position 1.09e+04,4773,145 color yellow radius 50

> marker #13 position 1.002e+04,3179,145 color yellow radius 50

> marker #13 position 9951,3240,145 color yellow radius 50

> marker #13 position 9885,3254,145 color yellow radius 50

> marker #13 position 9821,3313,145 color yellow radius 50

> marker #13 position 9759,3368,145 color yellow radius 50

> marker #13 position 9675,3440,145 color yellow radius 50

> marker #13 position 9607,3490,145 color yellow radius 50

> marker #13 position 9550,3572,145 color yellow radius 50

> marker #13 position 9526,3644,145 color yellow radius 50

> marker #13 position 9516,3695,145 color yellow radius 50

> marker #13 position 1.088e+04,3344,145 color yellow radius 50

> marker #13 position 1.084e+04,3306,145 color yellow radius 50

> marker #13 position 1.079e+04,3259,145 color yellow radius 50

> marker #13 position 1.072e+04,3228,145 color yellow radius 50

> marker #13 position 1.064e+04,3179,145 color yellow radius 50

> marker #13 position 1.093e+04,3409,145 color yellow radius 50

> marker #13 position 1.102e+04,3501,145 color yellow radius 50

> marker #13 position 1.106e+04,3583,145 color yellow radius 50

> artiax tomo #2.1.1 slice 16

> artiax tomo #2.1.1 slice 17

> artiax tomo #2.1.1 slice 18

> artiax tomo #2.1.1 slice 19

> artiax tomo #2.1.1 slice 20

> artiax tomo #2.1.1 slice 21

> marker #13 position 1.092e+04,3398,205 color yellow radius 50

> marker #13 position 1.087e+04,3360,205 color yellow radius 50

> marker #13 position 1.083e+04,3342,205 color yellow radius 50

> marker #13 position 1.073e+04,3267,205 color yellow radius 50

> marker #13 position 1.067e+04,3214,205 color yellow radius 50

> marker #13 position 1.06e+04,3176,205 color yellow radius 50

> marker #13 position 9500,3706,205 color yellow radius 50

> marker #13 position 9472,3777,205 color yellow radius 50

> marker #13 position 9443,3841,205 color yellow radius 50

> marker #13 position 9659,3448,205 color yellow radius 50

> marker #13 position 9610,3511,205 color yellow radius 50

> marker #13 position 9562,3577,205 color yellow radius 50

> marker #13 position 9535,3648,205 color yellow radius 50

> marker #13 position 1.02e+04,3152,205 color yellow radius 50

> marker #13 position 1.014e+04,3154,205 color yellow radius 50

> marker #13 position 1.006e+04,3184,205 color yellow radius 50

> marker #13 position 1e+04,3227,205 color yellow radius 50

> marker #13 position 9933,3248,205 color yellow radius 50

> marker #13 position 9848,3301,205 color yellow radius 50

> marker #13 position 9803,3353,205 color yellow radius 50

> marker #13 position 9722,3405,205 color yellow radius 50

> marker #13 position 1.099e+04,3487,205 color yellow radius 50

> marker #13 position 1.102e+04,3562,205 color yellow radius 50

> marker #13 position 9394,3917,205 color yellow radius 50

> artiax tomo #2.1.1 slice 22

> artiax tomo #2.1.1 slice 23

> artiax tomo #2.1.1 slice 24

> artiax tomo #2.1.1 slice 25

> marker #13 position 1.095e+04,3446,245 color yellow radius 50

> marker #13 position 1.105e+04,3618,245 color yellow radius 50

> marker #13 position 9460,3651,245 color yellow radius 50

> marker #13 position 9370,3857,245 color yellow radius 50

> marker #13 position 9359,3951,245 color yellow radius 50

> marker #13 position 9396,4034,245 color yellow radius 50

> marker #13 position 9391,4104,245 color yellow radius 50

> artiax tomo #2.1.1 slice 26

> artiax tomo #2.1.1 slice 27

> artiax tomo #2.1.1 slice 28

> artiax tomo #2.1.1 slice 29

> artiax tomo #2.1.1 slice 30

> marker #13 position 1.094e+04,3451,295 color yellow radius 50

> marker #13 position 1.09e+04,3415,295 color yellow radius 50

> marker #13 position 1.083e+04,3366,295 color yellow radius 50

> marker #13 position 1.076e+04,3334,295 color yellow radius 50

> marker #13 position 1.069e+04,3286,295 color yellow radius 50

> marker #13 position 1.1e+04,4647,295 color yellow radius 50

> marker #13 position 1.093e+04,4713,295 color yellow radius 50

> marker #13 position 1.082e+04,4765,295 color yellow radius 50

> marker #13 position 9704,3404,295 color yellow radius 50

> marker #13 position 9494,3831,295 color yellow radius 50

> marker #13 position 9964,3224,295 color yellow radius 50

> marker #13 position 9903,3253,295 color yellow radius 50

> marker #13 position 9869,3272,295 color yellow radius 50

> marker #13 position 9811,3316,295 color yellow radius 50

> marker #13 position 9766,3341,295 color yellow radius 50

> marker #13 position 1.063e+04,3208,295 color yellow radius 50

> marker #13 position 1.108e+04,4436,295 color yellow radius 50

> marker #13 position 1.103e+04,4513,295 color yellow radius 50

> artiax tomo #2.1.1 slice 31

> artiax tomo #2.1.1 slice 32

> artiax tomo #2.1.1 slice 33

> artiax tomo #2.1.1 slice 34

> marker #13 position 9707,3367,335 color yellow radius 50

> marker #13 position 1e+04,3180,335 color yellow radius 50

> marker #13 position 1.11e+04,4366,335 color yellow radius 50

> marker #13 position 1.111e+04,4292,335 color yellow radius 50

> marker #13 position 1.099e+04,4522,335 color yellow radius 50

> marker #13 position 1.088e+04,4686,335 color yellow radius 50

> marker #13 position 9690,3471,335 color yellow radius 50

> marker #13 position 9638,3562,335 color yellow radius 50

> marker #13 position 9593,3645,335 color yellow radius 50

> marker #13 position 9526,3718,335 color yellow radius 50

> marker #13 position 9546,3854,335 color yellow radius 50

> artiax tomo #2.1.1 slice 35

> artiax tomo #2.1.1 slice 36

> artiax tomo #2.1.1 slice 37

> marker #13 position 1.094e+04,4586,365 color yellow radius 50

> marker #13 position 1.091e+04,4627,365 color yellow radius 50

> marker #13 position 1.085e+04,4721,365 color yellow radius 50

> marker #13 position 1.08e+04,4783,365 color yellow radius 50

> artiax tomo #2.1.1 slice 38

> artiax tomo #2.1.1 slice 39

> artiax tomo #2.1.1 slice 40

> marker #13 position 9575,3611,395 color yellow radius 50

> marker #13 position 9577,3670,395 color yellow radius 50

> marker #13 position 9552,3724,395 color yellow radius 50

> marker #13 position 9643,3555,395 color yellow radius 50

> marker #13 position 9693,3490,395 color yellow radius 50

> marker #13 position 9722,3458,395 color yellow radius 50

> artiax tomo #2.1.1 slice 41

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 43

> marker #13 position 9485,4001,425 color yellow radius 50

> marker #13 position 9502,3940,425 color yellow radius 50

> marker #13 position 9493,3856,425 color yellow radius 50

> marker #13 position 9520,3781,425 color yellow radius 50

> marker #13 position 9811,3398,425 color yellow radius 50

> marker #13 position 9877,3368,425 color yellow radius 50

> marker #13 position 9938,3298,425 color yellow radius 50

> artiax tomo #2.1.1 slice 44

> artiax tomo #2.1.1 slice 45

> artiax tomo #2.1.1 slice 46

> marker #13 position 9773,3434,455 color yellow radius 50

> marker #13 position 9742,3487,455 color yellow radius 50

> marker #13 position 9715,3534,455 color yellow radius 50

> marker #13 position 9637,3605,455 color yellow radius 50

> marker #13 position 9594,3649,455 color yellow radius 50

> marker #13 position 9566,3683,455 color yellow radius 50

> marker #13 position 9538,3731,455 color yellow radius 50

> marker #13 position 9512,4078,455 color yellow radius 50

> artiax tomo #2.1.1 slice 47

> artiax tomo #2.1.1 slice 48

> artiax tomo #2.1.1 slice 49

> marker #13 position 9522,3819,485 color yellow radius 50

> marker #13 position 9495,3901,485 color yellow radius 50

> marker #13 position 9474,3935,485 color yellow radius 50

> marker #13 position 9666,3561,485 color yellow radius 50

> marker #13 position 9476,4012,485 color yellow radius 50

> hide #!2.1.1 models

> show #!2.1.1 models

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> hide #!2.1.1 models

> show #!25 models

> show #!24 models

> show #!23 models

> show #!22 models

> show #!21 models

> show #!20 models

> view

> show #!2.1.1 models

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> hide #!2.1.1 models

> show #!12 models

> show #!11 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> hide #!20 models

> hide #!12 models

> hide #!11 models

> show #!5 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 305

> ui mousemode right "rotate slab"

> volume #2.1.1 tiltedSlabAxis -0.07808,0.1091,0.991 tiltedSlabOffset 3305

> volume #2.1.1 tiltedSlabAxis -0.09171,0.09254,0.9915 tiltedSlabOffset 3172

> ui mousemode right "mark plane"

> marker #14 position 4228,4676,3154 color yellow radius 50

> marker #14 position 4172,4618,3154 color yellow radius 50

> marker #14 position 4141,4559,3157 color yellow radius 50

> marker #14 position 4078,4518,3155 color yellow radius 50

> marker #14 position 3926,4385,3153 color yellow radius 50

> marker #14 position 3867,4355,3150 color yellow radius 50

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> artiax tomo #2.1.1 slice 400

clip back plane is in front of front plane  

> artiax tomo #2.1.1 slice 383

> marker #14 position 3940,4312,2588 color yellow radius 50

> marker #14 position 3864,4270,2585 color yellow radius 50

> close #13-14

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> hide #!2.1.1 models

> show #!22 models

> show #!23 models

> show #!24 models

> show #!25 models

> show #!20 models

> show #!12 models

> show #!11 models

> hide #!5 models

> vop maximum #11 #12 #20 #21 #22

Opened volume maximum as #13, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> vop maximum #13 #23 #24 #25

Opened volume maximum as #14, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> hide #!14 models

> show #!14 models

> close #13

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all_PEV.mrc mdoel #14

Expected a models specifier or a keyword  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all_PEV.mrc models #14

> close #20-25

> close #11-12

> surface dust #14 size 100

[Repeated 1 time(s)]

> surface dust #14 size 200

> surface dust #14 size 240

> show #!10 models

> surface dust #10 size 300

> show #!3 models

> hide #!3 models

> show #!8 models

> hide #!8 models

> close #8

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all_spike_vesicles.mrc

File size 446520064 too small for grid size (1364,1364,332)  

> show #!5 models

> hide #!5 models

> transparency #9#10.1#14.1 0

> transparency #9#10.1#14.1 50

> show #!5 models

> ui mousemode right "map eraser"

Can only have one displayed volume when erasing  

> hide #9 models

> show #9 models

> hide #!10 models

> hide #!14 models

> volume erase #5 center 7710.6,3775.1,1501.9 radius 3982.9 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #8, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume #8 step 4

> volume erase #8 center 7234.8,10144,2064.1 radius 3982.9

> surface dust #8 size 300

> volume erase #8 center 3436.9,5052.9,3140.8 radius 1145.8

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> hide #!2.1.1 models

> volume erase #8 center 10196,5893.8,3743.4 radius 1145.8

> view orient

> volume erase #8 center 10996,4784.5,2046.3 radius 1145.8

> volume erase #8 center 10197,3307.2,3293.7 radius 1145.8

> volume erase #8 center 10840,1556.7,2846.1 radius 1145.8

> volume erase #8 center 10573,424.58,400.09 radius 1145.8

> volume erase #8 center 10404,1075.6,982.86 radius 1145.8

[Repeated 1 time(s)]

> volume erase #8 center 10403,789.32,639.31 radius 1145.8

> volume erase #8 center 10113,180.62,625.09 radius 1145.8

> view orient

> volume erase #8 center 11458,3244.8,1129.3 radius 1145.8

> volume erase #8 center 10816,3604,2115.1 radius 1145.8

> volume erase #8 center 10363,4665.2,2222 radius 1145.8

> volume erase #8 center 10375,5935.7,1935.7 radius 1145.8

> volume erase #8 center 9781.1,4245.1,1856.5 radius 1145.8

> volume erase #8 center 5300.7,6336.1,3376.2 radius 1145.8

> volume erase #8 center 6688.9,6449.2,2484.1 radius 1145.8

> volume erase #8 center 10152,7192.2,499.27 radius 1145.8

> volume erase #8 center 10096,6554.7,218.5 radius 1145.8

> volume erase #8 center 10372,5512.8,153.06 radius 1145.8

> volume erase #8 center 11016,3983.4,-29.219 radius 1145.8

> volume erase #8 center 9764.2,3376.3,335.68 radius 1145.8

> volume erase #8 center 10040,3907.6,347.05 radius 1145.8

> volume erase #8 center 10128,2520,2090.2 radius 1145.8

> volume erase #8 center 5327.9,1421.9,324.17 radius 1145.8

> volume erase #8 center 4509.8,1868.4,900.68 radius 1145.8

> volume erase #8 center 3827.7,2441,797.79 radius 1145.8

> volume erase #8 center 3890.6,2428.8,1211.7 radius 1145.8

> volume erase #8 center 4016.1,2614.1,1188.1 radius 1145.8

> volume erase #8 center 3588.5,2943.1,736.47 radius 1145.8

> volume erase #8 center 4004.6,2671.1,752.7 radius 1145.8

> volume erase #8 center 4496.8,2356.9,823.69 radius 1145.8

> volume erase #8 center 5926.8,1173.6,2093.1 radius 1145.8

> volume erase #8 center 7475.2,357.35,2133.3 radius 1145.8

> volume erase #8 center 8076.3,202.91,2107.4 radius 1145.8

> view

> volume erase #8 center 4251.4,5108.3,333.25 radius 531.96

> volume erase #8 center 4020,4366.4,433.24 radius 531.96

> volume erase #8 center 4271,3834.2,664.59 radius 531.96

> volume erase #8 center 4251.9,4549.9,-120.97 radius 531.96

> volume erase #8 center 4023.9,4444.9,661.37 radius 531.96

> volume erase #8 center 4480.5,3435.5,1460.6 radius 531.96

> volume erase #8 center 4838.8,3348.5,1177.7 radius 531.96

> volume erase #8 center 3781.3,3651.3,1546.4 radius 531.96

> volume erase #8 center 4238.5,4114.1,565.47 radius 531.96

> volume erase #8 center 4802.7,3783.6,411.24 radius 531.96

> show #!14 models

> color #14 #d5756880 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 168

> hide #!2.1.1 models

Can only have one displayed volume when erasing  

> hide #!14 models

> volume erase #8 center 5716,2255.6,1721.5 radius 531.96

> volume erase #8 center 5318.9,2744.1,1666.2 radius 531.96

> volume erase #8 center 5494.6,2759.9,2052.5 radius 531.96

> volume erase #8 center 6131.2,2223.4,1070.6 radius 531.96

> volume erase #8 center 5523,2637.7,1279.8 radius 531.96

> volume erase #8 center 5373.3,3034.6,1290.6 radius 531.96

> volume erase #8 center 5201.1,3062.7,673.16 radius 531.96

> volume erase #8 center 3680.7,4785.6,1161.3 radius 531.96

> volume erase #8 center 3911,4163.7,1435 radius 531.96

> view

> volume erase #8 center 4297.8,3815.8,1279.3 radius 531.96

> volume erase #8 center 5227.2,3288.4,1927.6 radius 531.96

> volume erase #8 center 3848.2,4263,2331.1 radius 531.96

> volume erase #8 center 4016,4472.7,2731.7 radius 531.96

> volume erase #8 center 4928.7,3687.8,2054.9 radius 388.74

> volume erase #8 center 4416.1,3945.5,2061.8 radius 388.74

> volume erase #8 center 9652.8,6077.7,1171.9 radius 388.74

> volume erase #8 center 9282.5,6374.6,1682 radius 388.74

> volume erase #8 center 9116.1,6420.1,2197.9 radius 388.74

> volume erase #8 center 9421.9,6361.6,1337.1 radius 388.74

> volume erase #8 center 9424,6510.2,938.79 radius 388.74

> volume erase #8 center 9123.2,6681.3,946.49 radius 388.74

> volume erase #8 center 8847.1,6627,138.02 radius 388.74

> volume erase #8 center 8201.9,6720.3,228.69 radius 388.74

> volume erase #8 center 7681.7,6552.3,348.94 radius 388.74

> volume erase #8 center 7395.1,6287,448.68 radius 388.74

> volume erase #8 center 7102,6025.3,548.79 radius 388.74

> volume erase #8 center 6757.1,6156.1,581.58 radius 388.74

> volume erase #8 center 6549.4,6425.8,564.33 radius 388.74

> volume erase #8 center 6143.2,6720.7,427.17 radius 388.74

> volume erase #8 center 6645.4,6267.4,1026 radius 388.74

> volume erase #8 center 6836.3,6030.7,1042.6 radius 388.74

> volume erase #8 center 7120.8,5996.8,992.61 radius 388.74

> volume erase #8 center 7115.3,5901.6,1016 radius 388.74

> volume erase #8 center 7390.3,6040.7,927.45 radius 388.74

> volume erase #8 center 7621.7,6390,798.56 radius 388.74

> volume erase #8 center 8006.1,6610.7,668.63 radius 388.74

> volume erase #8 center 8474.5,6695.4,553.45 radius 388.74

> volume erase #8 center 7480,6203.2,1212 radius 388.74

> volume erase #8 center 6285.6,2255.1,2280.9 radius 388.74

> volume erase #8 center 6593.3,1852.1,1884.1 radius 388.74

> volume erase #8 center 6877,2154.5,1675 radius 388.74

> volume erase #8 center 7450.3,1849.6,1806 radius 388.74

> volume erase #8 center 7712.9,1628.9,1674.9 radius 388.74

> volume erase #8 center 7597.9,1522.5,1276.9 radius 388.74

> volume erase #8 center 7233,1889.7,1221.4 radius 388.74

> volume erase #8 center 7024.6,2166.7,826.24 radius 388.74

> volume erase #8 center 6992.5,2724.5,583.22 radius 388.74

> volume erase #8 center 8780.4,3012.6,244.76 radius 388.74

> volume erase #8 center 7393.2,1784.2,805.14 radius 388.74

> volume erase #8 center 7582.1,2291.5,489.83 radius 286.44

> volume erase #8 center 4343.7,5782.6,544.76 radius 286.44

> volume erase #8 center 4359.5,5489.9,2621.2 radius 286.44

> show #!2.1.1 models

> hide #!8 models

> show #!5 models

> hide #!2.1.1 models

> volume erase #5 center 5576,4345,507.28 radius 818.4 outside true

Opened TS_4_membrane_clean_round3.mrc copy as #11, grid size 1364,1364,332,
pixel 10, shown at step 1, values float32  

> volume erase #11 center 5576,4345,507.28 radius 818.4 outside true

[Repeated 1 time(s)]

> show #!8 models

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 418

> hide #!11 models

> hide #!8 models

> show #!8 models

> artiax tomo #2.1.1 slice 417

> artiax tomo #2.1.1 slice 416

> artiax tomo #2.1.1 slice 415

> artiax tomo #2.1.1 slice 414

> artiax tomo #2.1.1 slice 413

> artiax tomo #2.1.1 slice 412

> artiax tomo #2.1.1 slice 411

> artiax tomo #2.1.1 slice 410

> artiax tomo #2.1.1 slice 409

> artiax tomo #2.1.1 slice 408

> artiax tomo #2.1.1 slice 407

> artiax tomo #2.1.1 slice 406

> artiax tomo #2.1.1 slice 405

> artiax tomo #2.1.1 slice 404

> artiax tomo #2.1.1 slice 403

> artiax tomo #2.1.1 slice 402

> artiax tomo #2.1.1 slice 401

> artiax tomo #2.1.1 slice 400

> artiax tomo #2.1.1 slice 399

> artiax tomo #2.1.1 slice 398

> artiax tomo #2.1.1 slice 397

> artiax tomo #2.1.1 slice 396

> hide #!8 models

> show #!8 models

> hide #!2.1.1 models

> volume erase #8 center 4406.5,3583.7,2922.9 radius 818.4

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 348

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> artiax tomo #2.1.1 slice 96

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> mousemode rightMode "move planes"

> artiax tomo #2.1.1 slice 116

> artiax tomo #2.1.1 slice 28

> hide #!2.1.1 models

> volume #8 region 0,0,0,1363,1363,331

[Repeated 1 time(s)]

> ui mousemode right "map eraser"

> show #!11 models

> hide #!11 models

> volume erase #8 center 8921.6,1337.1,235.13 radius 818.4

> volume erase #8 center 8237.4,970.76,232.7 radius 818.4

> volume erase #8 center 8241,1488.4,95.633 radius 818.4

> volume erase #8 center 9255.3,1930.5,113.1 radius 818.4

> volume erase #8 center 8605.3,1841.9,93.284 radius 818.4

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 48

> hide #!8 models

> show #!8 models

> hide #!8 models

> artiax tomo #2.1.1 slice 17

> hide #!2.1.1 models

> show #!8 models

> volume erase #8 center 6915.1,3867.2,229.2 radius 675.18

> volume erase #8 center 7006.5,3457.9,70.889 radius 675.18

> show #!2.1.1 models

> hide #!2.1.1 models

> show #!11 models

> vop maximum #8 #11 onGrid #2.1.1

Opened volume maximum as #12, grid size 1364,1364,332, pixel 10, shown at step
1, values float32  

> surface dust #12 size 100

> show #!14 models

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all_spike.mrc models #12

> surface dust #12 size 300

> surface dust #12 size 450

> surface dust #12 size 5000

> surface dust #12 size 500

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!10 models

> color #10 #a9fe8880 models

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_intermediate_filament_clean.mrc

Opened TS_4_intermediate_filament_clean.mrc as #13, grid size 1364,1364,332,
pixel 10, shown at step 1, values int8  

> volume #13 region 0,0,0,1363,1363,331 step 4

[Repeated 1 time(s)]

> volume #13 step 2

> volume #13 step 4

> surface dust #13 size 500

> show #!5 models

> volume #5 step 2

> volume #5 level 0.7947

> hide #!5 models

> vop subtract #5 #10

Opened volume difference as #15, grid size 1364,1364,332, pixel 10, shown at
step 1, values float32  

> show #!10 models

> surface dust #10 size 100

> surface dust #14 size 100

> surface dust #12 size 100

> surface dust #13 size 100

> surface dust #15 size 100

> volume #10 step 2

> surface dust #10 size 250

> surface dust #14 size 250

> surface dust #12 size 250

> surface dust #13 size 250

> surface dust #15 size 250

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

——— End of log from Tue Jun 23 15:35:14 2026 ———

> view name session-start

opened ChimeraX session  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles.star format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles.star  
---  
notes | Processed as relion5  
Using sizes: X: 1364, Y: 1364, Z: 332  
Using pixelsize: 9.12  
  

> artiax clip off

Opened Particle list TS_4_corrected_particles.star with 3141 particles.  

> artiax particles #2.2.1 originScaleFactor 10.0

> artiax view xy

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!10 models

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

> ui mousemode right "delete picked particle"

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star model #2.2.1

Expected a keyword  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star models #2.2.1

Expected a keyword  

> artiax save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star #2.2.1

Expected fewer arguments  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star #2.2.1

Expected a keyword  

> artiax save list #2.2.1 /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star

Expected fewer arguments  

> artiax save #2.2.1

Expected fewer arguments  

> artiax save

Saving particle lists and geomodels is based on ChimeraX save command,
therefore necessary command is 'save' without artiax prefix! For further
informations type 'help artiax save'.  

> help artiax save

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star partlist
> #2.2.1 format relion

> view

> ui tool show "Side View"

> view

> show #!2.1.1 models

> artiax tomo #2.1.1 slice 4

> artiax tomo #2.1.1 slice 5

> artiax tomo #2.1.1 slice 6

> artiax tomo #2.1.1 slice 7

> artiax tomo #2.1.1 slice 8

> artiax tomo #2.1.1 slice 9

> artiax tomo #2.1.1 slice 10

> artiax tomo #2.1.1 slice 11

> artiax tomo #2.1.1 slice 12

> artiax tomo #2.1.1 slice 13

> artiax tomo #2.1.1 slice 14

> artiax tomo #2.1.1 slice 15

> artiax tomo #2.1.1 slice 16

> artiax tomo #2.1.1 slice 17

> artiax tomo #2.1.1 slice 18

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> artiax tomo #2.1.1 slice 19

> artiax tomo #2.1.1 slice 20

> artiax tomo #2.1.1 slice 21

> artiax tomo #2.1.1 slice 22

> artiax tomo #2.1.1 slice 23

> artiax tomo #2.1.1 slice 24

> artiax tomo #2.1.1 slice 25

> artiax tomo #2.1.1 slice 26

> artiax tomo #2.1.1 slice 27

> artiax tomo #2.1.1 slice 28

> artiax tomo #2.1.1 slice 29

> artiax tomo #2.1.1 slice 39

> artiax tomo #2.1.1 slice 40

> artiax tomo #2.1.1 slice 41

> artiax tomo #2.1.1 slice 42

> artiax tomo #2.1.1 slice 43

> artiax tomo #2.1.1 slice 44

> artiax tomo #2.1.1 slice 45

> artiax tomo #2.1.1 slice 46

> artiax tomo #2.1.1 slice 47

> artiax tomo #2.1.1 slice 48

> artiax tomo #2.1.1 slice 49

> artiax tomo #2.1.1 slice 50

> artiax tomo #2.1.1 slice 51

> artiax tomo #2.1.1 slice 52

> artiax tomo #2.1.1 slice 53

> artiax tomo #2.1.1 slice 63

> artiax tomo #2.1.1 slice 64

> artiax tomo #2.1.1 slice 65

> artiax tomo #2.1.1 slice 66

> artiax tomo #2.1.1 slice 67

> artiax tomo #2.1.1 slice 77

> artiax tomo #2.1.1 slice 87

> artiax tomo #2.1.1 slice 97

> artiax tomo #2.1.1 slice 107

> artiax tomo #2.1.1 slice 106

> artiax tomo #2.1.1 slice 105

> artiax tomo #2.1.1 slice 104

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> ui mousemode right "delete picked particle"

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> artiax tomo #2.1.1 slice 103

> artiax tomo #2.1.1 slice 102

> artiax tomo #2.1.1 slice 101

> artiax tomo #2.1.1 slice 111

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> hide #!2.1.1 models

> view

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_corrected_particles_clean.star partlist
> #2.2.1 format relion

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/MANUSCRIPT_FIGURES_FINAL/Fig5_gb_zone12A.mrc

Opened Fig5_gb_zone12A.mrc as #9, grid size 120,120,120, pixel 6.08, shown at
level 4.73e-07, step 1, values float32  

> artiax attach #9 toParticleList #2.2.1

Opened Fig5_gb_zone12A.mrc as #2.2.1.1.1, grid size 120,120,120, pixel 6.08,
shown at level 4.73e-07, step 1, values float32  

> volume #2.2.1.1.1 capFaces false

> artiax show #2.2.1 surfaces

> artiax particles #2.2.1 radius 0.1

> artiax particles #2.2.1 axesSize 0.1

> artiax particles #2.2.1 surfaceLevel 0.03855256

> volume #12 level 0.9932

> volume #12 level 1.042

> volume #12 step 2

> volume #12 level 0.9931

> volume #13 change image level 0,0 level 6.1,0.8 level 61,1

> show #!15 models

> hide #!15 models

> show #!2.1.1 models

> artiax clip toggle

Clipping thickness set to 300 A around slabs of #2.1.1.  

> save /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/TS_4_all.cxs

——— End of log from Wed Jun 24 10:56:21 2026 ———

> view name session-start

opened ChimeraX session  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/tomonet_manual_assemble_particles.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/tomonet_manual_assemble_particles.star  
---  
notes | Processed as relion  
  

> artiax clip off

Opened Particle list tomonet_manual_assemble_particles.star with 4127
particles.  

> artiax particles #2.2.2 originScaleFactor 3.041

> artiax view xy

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/vesicles_job039_particles.star
> format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/vesicles_job039_particles.star  
---  
notes | Processed as relion  
Processed as relion  
  
Traceback (most recent call last):  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/formats.py",
line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/io.py", line
104, in open_particle_list  
data = formats[format_name].particle_data(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__  
super().__init__(  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__  
self.read_file()  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file  
if np.issubdtype(df.dtypes[key], np.number):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype  
arg1 = dtype(arg1).type  
^^^^^^^^^^^  
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type  
  
TypeError: Cannot interpret '' as a data type  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype  
arg1 = dtype(arg1).type  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/nathalielavoie/Library/CloudStorage/Box-
> Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/job038_particles.star format star

Summary of feedback from opening
/Users/nathalielavoie/Library/CloudStorage/Box-
Box/Aim_2/A2NL146_pytom_gB/NEC_placeback/job038_particles.star  
---  
notes | Processed as relion  
Processed as relion  
  
Traceback (most recent call last):  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/formats.py",
line 25, in open  
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/io.py", line
104, in open_particle_list  
data = formats[format_name].particle_data(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__  
super().__init__(  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__  
self.read_file()  
File "/Users/nathalielavoie/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file  
if np.issubdtype(df.dtypes[key], np.number):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype  
arg1 = dtype(arg1).type  
^^^^^^^^^^^  
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type  
  
TypeError: Cannot interpret '' as a data type  
  
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype  
arg1 = dtype(arg1).type  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-7.0.24
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2092.0.0.0.0 (iBridge: 23.16.10350.0.0,0)
      OS Loader Version: 583~2317

Software:

    System Software Overview:

      System Version: macOS 15.7.1 (24G231)
      Kernel Version: Darwin 24.6.0
      Time since boot: 1 day, 9 hours, 47 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
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    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
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    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.25.2
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crosslinks: 1.0
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    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
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    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.10.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
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    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
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    ChimeraX-MapFit: 2.0
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    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
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    ChimeraX-ModelArchive: 1.0
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    ChimeraX-VIPERdb: 1.0
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    ChimeraX-vrml: 1.0
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    ChimeraX-WavefrontOBJ: 1.0
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    pip: 25.0.1
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    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing-inspection: 0.4.2
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    tzdata: 2025.2
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    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
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    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 3 hours ago

Component: Unassigned → Third Party
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX: read RELION STAR file: Cannot interpret as a data type

comment:2 by Eric Pettersen, 3 hours ago

Hi Nathalie,

Thanks for reporting this problem. It may be fixed with the 0.7.0 release of ArtiaX, so please try that.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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