ArtiaX: various errors

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.0-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/warp_extract/minFL1300_rot_d4000_pix8_bo160_refine6_s-500_relion/Refine3D/Job005_fromJob3_mask3/run_data.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/warp_extract/minFL1300_rot_d4000_pix8_bo160_refine6_s-500_relion/Refine3D/Job005_fromJob3_mask3/run_data.star  
---  
notes | Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black  
    lighting depthCue false  
    camera ortho

  
Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list run_data.star with 333 particles.  

> save /Users/b.colcombetcazenav/Downloads/test.star partlist #1.2.1

Drag select of axes, 46 of 333 instances, 46 atoms  

> save /Users/b.colcombetcazenav/Downloads/test.star partlist sel

Invalid "partlist" argument: Must specify 1 model, got 2  

> save /Users/b.colcombetcazenav/Downloads/test.star partlist sel

Invalid "partlist" argument: Must specify 1 model, got 2  

> select clear

Drag select of axes, 2 of 333 instances, 1 atoms  
Drag select of axes, 5 of 333 instances, 5 atoms  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

>

Incomplete command: artiax fit curved  

> artiax fit line straight

Expected fewer arguments  

> artiax fit line curved

Expected fewer arguments  

> artiax fit line linear

Expected fewer arguments  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> select clear

> select add /M:213@M

1 atom, 1 residue, 1 model selected  

> select add /M:240@M

2 atoms, 2 residues, 1 model selected  

> select add /M:268@M

3 atoms, 3 residues, 1 model selected  

> select add /M:272@M

4 atoms, 4 residues, 1 model selected  

> select add /M:282@M

5 atoms, 5 residues, 1 model selected  

> select add /M:281@M

6 atoms, 6 residues, 1 model selected  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

> select clear

> open help:user/artiax_index.html

Opened help:user/artiax_index.html  

> artiax clip off

add_particlelist is being run  

> select clear

> select #1.2.1.3/M:241@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.1.3/M:255@M

2 atoms, 2 residues, 1 model selected  

> select add #1.2.1.3/M:219@M

3 atoms, 3 residues, 1 model selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

> select add #1.2.1.3/M:300@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.1.3/M:305@M

2 atoms, 2 residues, 1 model selected  

> select add #1.2.1.3/M:307@M

3 atoms, 3 residues, 1 model selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Drag select of axes, 5 of 333 instances, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Drag select of axes, 2 of 333 instances, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

Drag select of axes, 3 of 333 instances, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

[Repeated 1 time(s)]Drag select of axes, 2 of 333 instances, line, 6580 of
12000 triangles, 2 atoms  

> select #1.2.1.3/M:157@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.1.3/M:159@M

2 atoms, 2 residues, 1 model selected  

> select clear

Drag select of axes, 3 of 333 instances, line, 3 atoms  

> select clear

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/picks/t1_f1M.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/picks/t1_f1M.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list t1_f1M.star with 1 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/picks/t1_f1C.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/picks/t1_f1C.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list t1_f1C.star with 3 particles.  

> artiax particles #1.2.2 originScaleFactor 5.0

> artiax view xy

> artiax particles #1.2.1 originScaleFactor 8.0

> artiax view xy

Drag select of axes, axes, 4 atoms  

> artiax fit line

Created a Curved line through 4 particles.  

> artiax clip off

> select clear

> select #1.2.2.2

1 model selected  

> select clear

Drag select of axes, 2 of 3 instances, curved line, 4830 of 10080 triangles, 2
atoms  

> select clear

[Repeated 1 time(s)]

> artiax clip off

add_particlelist is being run  

> select clear

> artiax flip x

[Repeated 3 time(s)]

> artiax flip y

[Repeated 1 time(s)]

> artiax flip z

[Repeated 1 time(s)]Drag select of axes, 11 of 227 instances, curved line, 500
of 10080 triangles, direction_markers, 11 of 227 instances, 12 atoms  

> artiax flip x

[Repeated 3 time(s)]

> artiax flip y

[Repeated 5 time(s)]

> artiax flip z

[Repeated 3 time(s)]

> artiax flip x

[Repeated 5 time(s)]

> artiax flip y

[Repeated 7 time(s)]

> artiax flip x

[Repeated 3 time(s)]

> select clear

> select #1.2.2.3/M:2@M

1 atom, 1 residue, 1 model selected  

> artiax flip x

[Repeated 3 time(s)]

> artiax flip y

[Repeated 5 time(s)]

> artiax flip x

[Repeated 3 time(s)]

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/warp_extract/minFL1300_rot_d4000_pix8_bo160_refine6_s500_relion/Refine3D/job004/run_class001.mrc

Opened run_class001.mrc as #2, grid size 160,160,160, pixel 8, shown at level
1.07, step 1, values float32  

> artiax attach #2 toParticleList #1.2.2

Opened run_class001.mrc as #1.2.2.1.1, grid size 160,160,160, pixel 8, shown
at level 1.07, step 1, values float32  

> volume #1.2.2.1.1 capFaces false

> artiax flip y

[Repeated 3 time(s)]

> artiax flip x

[Repeated 1 time(s)]

> artiax flip y

[Repeated 1 time(s)]

> artiax flip x

[Repeated 1 time(s)]

> select #1.2.2.2

1 model selected  
Drag select of axes, 5 of 227 instances, curved line, 260 of 10080 triangles,
direction_markers, 5 of 227 instances, 6 atoms  

> select clear

Drag select of axes, 7 of 227 instances, curved line, 173 of 10080 triangles,
direction_markers, 4 of 227 instances, 4 atoms  

> select clear

> artiax particles #1.2.2 radius 91.96580882

> artiax particles #1.2.2 axesSize 200.0

> select #1.2.2.3/M:0@M

1 atom, 1 residue, 1 model selected  

> artiax flip x

[Repeated 4 time(s)]

> artiax flip y

[Repeated 6 time(s)]

> artiax flip x

[Repeated 1 time(s)]

> artiax flip y

> select clear

> artiax particles #1.2.2 surfaceLevel -1.00172448

> select clear

> select #1.2.2.3/M:0@M

1 atom, 1 residue, 1 model selected  

> artiax flip x

> select clear

[Repeated 1 time(s)]Drag select of axes, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Drag select of axes, 190 of 240 triangles, 1 atoms  

> select add #1.2.2.3/M:2@M

2 atoms, 2 residues, 2 models selected  

> artiax fit line

Created a Curved line through 2 particles.  

> artiax clip off

> select add #1.2.2.3/M:1@M

3 atoms, 3 residues, 3 models selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

> select #1.2.2.3/M:1@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.2.3/M:2@M

2 atoms, 2 residues, 1 model selected  

> artiax fit line

Created a Curved line through 2 particles.  

> artiax clip off

> select clear

Drag select of axes, 1 atoms  

> select add #1.2.2.3/M:1@M

2 atoms, 2 residues, 2 models selected  

> artiax fit line

Created a Curved line through 2 particles.  

> artiax clip off

Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 481, in
_axes_size_changed  
self.line.change_axes_size(self.axes_size_slider.value)  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/PopulatedModel.py", line 63, in
change_axes_size  
v, n, t, vc = self.get_direction_marker_surface()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/PopulatedModel.py", line 70, in
get_direction_marker_surface  
b.arrow_command(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bild/bild.py", line 172, in arrow_command  
raise ValueError("degenerate arrow")  
ValueError: degenerate arrow  
  
ValueError: degenerate arrow  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bild/bild.py", line 172, in arrow_command  
raise ValueError("degenerate arrow")  
  
See log for complete Python traceback.  
  

> artiax flip x

[Repeated 1 time(s)]

> select clear

> artiax clip off

add_particlelist is being run  

> select clear

> save /Users/b.colcombetcazenav/Downloads/test1.star partlist #1.2.3

Drag select of axes, 1 of 51 instances, line, 260 of 12000 triangles,
direction_markers, 2 of 51 instances, 1 atoms  

> select clear

[Repeated 1 time(s)]

> hide #!1.2.2 models

> hide #!1.2.1 models

> select clear

Drag select of axes, 1 of 51 instances, line, 340 of 12000 triangles,
direction_markers, 2 of 51 instances, 2 atoms  

> artiax flip x

[Repeated 1 time(s)]

> select clear

> select #1.2.3.3/M:21@M

1 atom, 1 residue, 1 model selected  

> select up

51 atoms, 51 residues, 1 model selected  

> artiax flip x

> save /Users/b.colcombetcazenav/Downloads/test2.star partlist #1.2.3

> open /Users/b.colcombetcazenav/Downloads/test2.star

Summary of feedback from opening
/Users/b.colcombetcazenav/Downloads/test2.star  
---  
notes | Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list test2.star with 1 particles.  

> artiax particles #1.2.4 radius 72.85772059

> select clear

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> show #!1.2.2 models

> select clear

> select add #1.2.2.3/M:2@M

1 atom, 1 residue, 1 model selected  

> select clear

> artiax clip off

add_particlelist is being run  

> select clear

[Repeated 1 time(s)]

Select exactly one particle as a starting point.  

> select #1.2.1.3/M:0@M

1 atom, 1 residue, 1 model selected  

Select exactly one particle as a starting point.  

> select clear

Select exactly one particle as a starting point.  

[Repeated 1 time(s)]Drag select of axes, axes, line, direction_markers, 4
atoms  

> select clear

Drag select of axes, axes, line, direction_markers, 4 atoms  

> artiax fit line

Created a Curved line through 4 particles.  

> artiax clip off

> select clear

Select at least one chain of particles with a start.  

Select exactly one particle as a starting point.  

> select #1.2.2.3/M:0@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> hide #!1.2.2 models

> hide #!1.2.1 models

> show #!1.2.2 models

> hide #!1.2.2 models

> select clear

Drag select of axes, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> select clear

[Repeated 2 time(s)]Drag select of axes, axes, 4 atoms  

> artiax fit line

Created a Curved line through 4 particles.  

> artiax clip off

> select clear

[Repeated 1 time(s)]

> artiax clip off

add_particlelist is being run  

> select clear

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.3 models

> hide #!1.2.1 models

> select #1.2.5.3/M:1@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.5 models

> hide #!1.2.4 models

> show #!1.2.4 models

> select #1.2.4.3/M:1@M

1 atom, 1 residue, 1 model selected  

> select clear

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> hide #!1.2.4 models

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 5.0

> artiax view xy

Drag select of axes, 9 of 303 instances, 9 atoms  

> select clear

Drag select of axes, 1 of 303 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

Drag select of axes, 9 of 303 instances, axes, 9 of 303 instances, 18 atoms  

> artiax fit line

Created a Curved line through 18 particles.  

> artiax clip off

> select clear

Drag select of axes, 1 of 303 instances, axes, 1 of 303 instances, 2 atoms  

> select clear

[Repeated 1 time(s)]Drag select of axes, 1 of 303 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> show #!1.2.1 models

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> select clear

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> select clear

Drag select of axes, 1 of 303 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> select clear

Drag select of axes, 1 of 303 instances, curved line, 190 of 8240 triangles, 1
atoms  

> select clear

Drag select of axes, 1 of 303 instances, 1 atoms  

> show #!1.2.1 models

Drag select of axes, 1 of 303 instances, 1 atoms  

> select /M:52@M

1 atom, 1 residue, 1 model selected  

> select add /M:268@M

2 atoms, 2 residues, 1 model selected  

> select add /M:58@M

3 atoms, 3 residues, 1 model selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select subtract /M:268@M

2 atoms, 2 residues, 1 model selected  

> select add /M:93@M

3 atoms, 3 residues, 1 model selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

> select add /M:52@M

1 atom, 1 residue, 1 model selected  

> select add /M:268@M

2 atoms, 2 residues, 1 model selected  

> select add /M:57@M

3 atoms, 3 residues, 1 model selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Select at least one chain of particles with a start.  

> select #1.3.2

3 models selected  

Select at least one chain of particles with a start.  

[Repeated 1 time(s)]

> artiax fit line

Select at least two points  

> select clear

> select add /M:268@M

1 atom, 1 residue, 1 model selected  

> select add #1.3.2

1 atom, 1 residue, 4 models selected  

> select clear

> select /M:57@M

1 atom, 1 residue, 1 model selected  

> select add #1.2.1.2

1 atom, 1 residue, 2 models selected  

> select add /M:268@M

2 atoms, 2 residues, 2 models selected  

> select add /M:52@M

3 atoms, 3 residues, 2 models selected  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Drag select of axes, 5 of 303 instances, 5 atoms  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> ui mousemode right select

> select clear

Drag select of axes, 3 of 303 instances, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select clear

Drag select of axes, 4 of 303 instances, 4 atoms  

> artiax fit line

Created a Curved line through 4 particles.  

> artiax clip off

> select clear

Drag select of axes, 7 of 303 instances, 7 atoms  

> artiax fit line

Created a Curved line through 7 particles.  

> artiax clip off

> select clear

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> select clear

Drag select of axes, 5 of 303 instances, 5 atoms  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> select clear

> select /M:293@M

1 atom, 1 residue, 1 model selected  

> select /M:154@M

1 atom, 1 residue, 1 model selected  

> select clear

> hide #!1.3.3 models

> show #!1.3.3 models

> hide #!1.3.4 models

> show #!1.3.4 models

> hide #!1.3.5 models

> show #!1.3.5 models

> hide #!1.3.2 models

> show #!1.3.2 models

> select clear

Drag select of axes, 3 of 301 instances, 3 atoms  

> artiax fit line

Created a Curved line through 3 particles.  

> artiax clip off

> select /M:152@M

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of axes, 5 of 301 instances, 5 atoms  

Select exactly one particle as a starting point.  

> select clear

> select /M:232@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

Drag select of axes, 5 of 301 instances, 5 atoms  

> show #!1.2.1 models

> hide #!1.2.1 models

Drag select of axes, 1 of 5 instances, 1 atoms  

> artiax lock #1.2.2 translation

Locked translation of models: particles #1.2.2  

> select clear

Drag select of axes, 1 of 5 instances, 1 atoms  

> artiax unlock #1.2.2 translation

Unlocked translation of models: particles #1.2.2  

> artiax clip off

add_particlelist is being run  

> select clear

Drag select of axes, 5 atoms  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> select clear

> hide #!1.3.8 models

> show #!1.3.8 models

> artiax clip off

add_particlelist is being run  

> hide #!1.2.3 models

> show #!1.2.3 models

> select clear

> show #!1.2.1 models

Drag select of axes, 6 of 301 instances, 6 atoms  

Select exactly one particle as a starting point.  

> select clear

[Repeated 2 time(s)]

> select #1.2.1.3/M:278@M

1 atom, 1 residue, 1 model selected  

Select exactly one particle as a starting point.  

> hide #!1.2.3 models

> select clear

> hide #!1.2.1 models

> show #!1.2.3 models

> show #!1.2.1 models

> select clear

Drag select of axes, 9 of 301 instances, 9 atoms  

Select at least one chain of particles with a start.  

> select clear

[Repeated 1 time(s)]

> select /M:278@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select #1.2.1.3/M:232@M

1 atom, 1 residue, 1 model selected  

Select exactly one particle as a starting point.  

> select #1.2.1.3/M:0@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select #1.2.1.3/M:35@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> select #1.2.1.3/M:292@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

> hide #!1.2.2 models

> show #!1.2.2 models

> show #!1.2.1 models

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 5.0

> artiax view xy

> name #1.2.1 id #1.2.100

"id #1.2.100": invalid atom specifier  

> rename #1.2.1 id #1.2.100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 1.0

> artiax view xy

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

Drag select of axes, 8 of 303 instances, 8 atoms  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

Drag select of axes, 9 of 303 instances, 9 atoms  

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.1 models

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

Drag select of axes, 6 of 303 instances, 9 atoms  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> select clear

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> show #!1.2.2 models

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.1 models

> show #!1.2.1 models

> select clear

Drag select of axes, 1 of 9 instances, 1 atoms  

> select clear

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.1 models

> hide #!1.2.2 models

> select clear

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.3 models

> show #!1.2.2 models

> hide #!1.2.4 models

> show #!1.2.4 models

> artiax particles #1.2.4 color 100,0,6,100

[Repeated 1 time(s)]

> artiax particles #1.2.4 color 60,25,0,100

> artiax particles #1.2.4 axesSize 0.1

> select clear

> artiax particles #1.2.4 color 100,0,6,100

[Repeated 1 time(s)]

> artiax particles #1.2.4 color 50,50,50,100

> artiax particles #1.2.4 color 17,81,28,100

[Repeated 3 time(s)]

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

Drag select of axes, 9 of 303 instances, 9 atoms  

> select clear

> hide #!1.2.1 models

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> show #!1.2.1 models

> artiax particles #1.2.2 radius 5.0

> artiax particles #1.2.2 radius 7.0

> artiax particles #1.2.2 radius 25.0875

> artiax particles #1.2.2 radius 25.0

> artiax particles #1.2 color 17,81,28,100

> artiax particles #1.2 radius 25.0

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> view

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax particles #1.2 color 17,81,28,100

> artiax particles #1.2 radius 25.0

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 color 17,81,28,100

> artiax particles #1.2 radius 50.0

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2.2 axesSize 0.1

[Repeated 1 time(s)]

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0 axesSize 0.1

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

> artiax particles axesSize 0.1

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

Drag select of axes, 9 of 303 instances, 9 atoms  

> select clear

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.1 models

> show #!1.2.1 models

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

Drag select of axes, 9 of 303 instances, 9 atoms  

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> hide #!1.2.1 models

Drag select of axes, 9 of 303 instances, 9 atoms  

> select clear

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> show #!1.2.1 models

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.1 models

> hide #!1.2.2 models

> hide #!1.2.3 models

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> show #!1.2.3 models

> hide #!1.2.3 models

> show #!1.2.3 models

> show #!1.2.2 models

Drag select of axes, 5 of 303 instances, 5 atoms  

> select clear

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.2 models

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.3 models

> show #!1.2.3 models

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> select down

303 atoms, 303 residues, 2 models selected  

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.3 models

> show #!1.2.3 models

> hide #!1.2.3 models

> select clear

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> show #!1.2.3 models

> show #!1.2.2 models

> show #!1.2.1 models

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.1 models

> hide #!1.2.2 models

> hide #!1.2.3 models

> hide #!1.2.4 models

> select clear

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> show #!1.2.4 models

> show #!1.2.3 models

> show #!1.2.2 models

> show #!1.2.1 models

Drag select of axes, 6 of 303 instances, 6 atoms  

> hide #!1.2.5 models

> hide #!1.2.4 models

> hide #!1.2.3 models

> hide #!1.2.2 models

> hide #!1.2.1 models

> select clear

> show #!1.2.1 models

> show #!1.2.2 models

> show #!1.2.3 models

> show #!1.2.4 models

> show #!1.2.5 models

> select clear

> hide #!1.2.5 models

> hide #!1.2.4 models

> hide #!1.2.3 models

> hide #!1.2.2 models

> hide #!1.2.6 models

Drag select of axes, 1 of 9 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> show #!1.2.2 models

> hide #!1.2.1 models

> select clear

Drag select of axes, 1 of 9 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> hide #!1.2.2 models

> show #!1.2.3 models

> select clear

Drag select of axes, 1 of 6 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> hide #!1.2.3 models

> show #!1.2.4 models

> select clear

Drag select of axes, 1 of 6 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.4 models

> show #!1.2.5 models

> select clear

[Repeated 1 time(s)]

Select exactly one particle as a starting point.  

Drag select of axes, 1 of 6 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> show #!1.2.6 models

> hide #!1.2.5 models

> select clear

Drag select of axes, 1 of 6 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.6 models

Drag select of axes, 9 atoms  

> ui mousemode right select

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

Drag select of axes, 9 atoms  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

Drag select of axes, 6 atoms  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

Drag select of axes, 6 atoms  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

Drag select of axes, 6 atoms  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

Drag select of axes, 4 of 6 instances, 5 atoms  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> select clear

[Repeated 1 time(s)]Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 464, in
_spacing_toggled  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
Error in sys.excepthook:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 188, in
_edit_changed  
self._emit_value_changed()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 205, in
_emit_value_changed  
self.valueChanged.emit(self._value)  
SystemError: <method 'emit' of 'PyQt6.QtCore.pyqtBoundSignal' objects>
returned a result with an exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QExposeEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook  
self.session.ui.thread_safe(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception  
self.bug(err_msg.replace("\n", "<br>"), is_html=True)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug  
self._log(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log  
if log.log(*args):  
^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log  
self.session.ui.thread_safe(f)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in <lambda>  
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message  
ed.showMessage(msg)  
SystemError: <built-in method showMessage of BiggerErrorDialog object at
0x289c16b00> returned a result with an exception set  
  
Original exception was:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
Error in sys.excepthook:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 188, in
_edit_changed  
self._emit_value_changed()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 205, in
_emit_value_changed  
self.valueChanged.emit(self._value)  
SystemError: <method 'emit' of 'PyQt6.QtCore.pyqtBoundSignal' objects>
returned a result with an exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QExposeEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook  
self.session.ui.thread_safe(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception  
self.bug(err_msg.replace("\n", "<br>"), is_html=True)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug  
self._log(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log  
if log.log(*args):  
^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log  
self.session.ui.thread_safe(f)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in <lambda>  
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message  
ed.showMessage(msg)  
SystemError: <built-in method showMessage of BiggerErrorDialog object at
0x289c16b00> returned a result with an exception set  
  
Original exception was:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

> artiax particles #1.2 color 17,81,28,100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2 originScaleFactor 5.0

> artiax particles #1.2 axesSize 0.1

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> artiax particles #1.2.2 originScaleFactor 8.0

> artiax view xy

> select clear

Drag select of axes, 6 of 303 instances, axes, 1 of 29 instances, 7 atoms  
Drag select of axes, axes, 7 atoms  

> select clear

Drag select of axes, 1 atoms  

> select clear

Drag select of axes, 1 atoms  

> select clear

Drag select of axes, axes, 7 atoms  

> artiax fit line

Created a Curved line through 7 particles.  

> artiax clip off

> select clear

[Repeated 1 time(s)]Drag select of axes, 1 of 6 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

Drag select of axes, axes, 7 atoms  

> artiax fit line

Created a Curved line through 7 particles.  

> artiax clip off

> select clear

> artiax clip off

add_particlelist is being run  

> hide #!1.2.3 models

> hide #!1.2.2 models

> select clear

Drag select of curved line, 30 of 12000 triangles, 1 atoms  

> select clear

> select #1.2.4.3/M:1@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.4 models

Drag select of axes, curved line, direction_markers, 301 atoms  

> select clear

Drag select of axes, curved line, direction_markers, 301 atoms  

> select clear

Drag select of axes, curved line, direction_markers, 301 atoms  

> select clear

[Repeated 2 time(s)]

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.500

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.501

> artiax particles #1.2.500 originScaleFactor 5.0

> artiax particles #1.2.501 originScaleFactor 8.0

> select clear

Drag select of axes, 5 of 303 instances, axes, 1 of 29 instances, 6 atoms  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  

> select clear

> rename #1.2.1 id #1.2.501

> select clear

> select #1.2.500.3/M:28@M

1 atom, 1 residue, 1 model selected  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.500 models

Drag select of axes, axes, 6 atoms  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

[Repeated 1 time(s)]add_particlelist is being run  

> select clear

> hide #!1.2.501 models

> hide #!1.2.1 models

> show #!1.2.500 models

> show #!1.2.501 models

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.500

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.501

> artiax particles #1.2.500 originScaleFactor 5.0

> artiax particles #1.2.501 originScaleFactor 8.0

Drag select of axes, 7 of 303 instances, axes, 1 of 29 instances, 8 atoms  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  

> select clear

Drag select of axes, 1 of 7 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> hide #!1.2.500 models

> select clear

Drag select of axes, axes, 8 atoms  

> select up

8 atoms, 8 residues, 4 models selected  

> select up

8 atoms, 8 residues, 6 models selected  

> select up

8 atoms, 8 residues, 8 models selected  

> select up

8 atoms, 8 residues, 9 models selected  

> select down

8 atoms, 8 residues, 8 models selected  

> select down

8 atoms, 8 residues, 6 models selected  

> select down

8 atoms, 8 residues, 4 models selected  

> select down

8 atoms, 8 residues, 2 models selected  

> select down

8 atoms, 8 residues, 2 models selected  

> select down

8 atoms, 8 residues, 2 models selected  

> select clear

Drag select of axes, axes, 8 atoms  

> artiax fit line

Created a Curved line through 8 particles.  

> artiax clip off

> select clear

> artiax clip off

add_particlelist is being run  

> hide #!1.2.501 models

> hide #!1.2.1 models

> show #!1.2.1 models

> hide #!1.2.1 models

> hide #!1.2.2 models

> show #!1.2.2 models

> hide #!1.2.2 models

> show #!1.2.2 models

> select clear

> close #1.2.500

> close #1.2.501

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.500

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.501

> artiax particles #1.2.500 originScaleFactor 5.0

> artiax particles #1.2.501 originScaleFactor 8.0

> close #1.2.500

> close #1.2.501

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.500

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.501

> artiax particles #1.2.500 originScaleFactor 5.0

> artiax particles #1.2.501 originScaleFactor 8.0

> close #1.2.100

> close #1.2.101

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.101

> artiax particles #1.2.100 originScaleFactor 5.0

> artiax particles #1.2.101 originScaleFactor 8.0

> close #1.2.100

> close #1.2.101

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> rename #1.2.1 id #1.2.100

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> rename #1.2.1 id #1.2.101

> artiax particles #1.2.100 originScaleFactor 5.0

> artiax particles #1.2.101 originScaleFactor 8.0

Drag select of axes, 7 of 303 instances, axes, 1 of 29 instances, 9 atoms  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/options_window.py", line 1269, in _partlist_changed  
opl = artia.partlists.get(artia.options_partlist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 59, in get  
return func(identifier)  
^^^^^^^^^^^^^^^^  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
IndexError: list index out of range  
  
Error processing trigger "partlist changed":  
IndexError: list index out of range  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/util/ManagerModel.py", line 210, in _get_by_model_id  
return models[0]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  

> select clear

Drag select of axes, 1 of 8 instances, 1 atoms  

> select clear

> close #1.2.1

> close #1.2.2

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> artiax particles #1.2.1 originScaleFactor 5.0

> artiax particles #1.2.2 originScaleFactor 8.0

Drag select of axes, 3 of 303 instances, axes, 1 of 29 instances, 4 atoms  
Drag select of axes, 1 of 3 instances, 1 atoms  

Select exactly one particle as a starting point.  

> artiax clip off

add_particlelist is being run  

> select clear

> hide #!1.2.1 models

Drag select of axes, axes, 4 atoms  

> artiax fit line

Created a Curved line through 4 particles.  

> artiax clip off

> select clear

> select #1.2.2 #1.2.3

4 atoms, 4 residues, 8 models selected  

> select clear

> artiax clip off

add_particlelist is being run  

> select clear

> view

> artiax fit line polynome 1

Expected fewer arguments  

> artiax fit line 1

Expected fewer arguments  

> artiax fit line order

Expected fewer arguments  

> artiax fit line order 1

Expected fewer arguments  

> artiax fit line

Select at least two points  

> select clear

[Repeated 2 time(s)]

> close #1.2.1

> close #1.2.2

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> artiax particles #1.2.1 originScaleFactor 5.0

> artiax particles #1.2.2 originScaleFactor 8.0

> view

Drag select of axes, 7 of 303 instances, curved line, 25 of 12000 triangles, 7
atoms  

> select add #1.2.2.2

7 atoms, 7 residues, 3 models selected  
Drag select of curved line, 310 of 12000 triangles, 1 atoms  
Drag select of axes, 1 of 7 instances, 1 atoms  

> select clear

> close #1.2.1

> close #1.2.2

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.2 originScaleFactor 8.0

> artiax particles #1.2.1 originScaleFactor 5.0

> view

> artiax particles #1.2.1 originScaleFactor 8.0

> artiax particles #1.2.2 originScaleFactor 5.0

Drag select of axes, 1 of 29 instances, axes, 11 of 303 instances, 14 atoms  

> select clear

Drag select of axes, 2 of 13 instances, 1 atoms  
Drag select of axes, 1 of 11 instances, 1 atoms  
Drag select of axes, 1 of 10 instances, 1 atoms  
[Repeated 1 time(s)]Drag select of axes, 1 of 8 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select #1.2.1 #1.2.3

9 atoms, 9 residues, 8 models selected  

> artiax fit line

Created a Curved line through 9 particles.  

> artiax clip off

> select clear

> close #1.2.1

> close #1.2.2

> close #1.2.3

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 8.0

> artiax particles #1.2.2 originScaleFactor 5.0

> view

Drag select of axes, 1 of 29 instances, axes, 4 of 303 instances, 5 atoms  
Drag select of axes, 1 of 4 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select #1.2.1 #1.2.3

5 atoms, 5 residues, 8 models selected  

> artiax fit line

Created a Curved line through 5 particles.  

> artiax clip off

> select clear

> close #1.2.1

> close #1.2.2

> close #1.2.3

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 8.0

> artiax particles #1.2.2 originScaleFactor 5.0

> view

Drag select of axes, 1 of 29 instances, axes, 5 of 303 instances, 6 atoms  
Drag select of axes, 1 of 5 instances, 1 atoms  

> artiax clip off

add_particlelist is being run  

> select #1.2.1 #1.2.3

6 atoms, 6 residues, 8 models selected  

> artiax fit line

Created a Curved line through 6 particles.  

> artiax clip off

> select clear

> close #1.2.1

> close #1.2.2

> close #1.2.3

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Mstar_topick/M2_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list M2_run_data_t18.mrc.star with 29 particles.  

> open
> /Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star

Summary of feedback from opening
/Volumes/beegfs/home/b.colcombetcazenav/Dzone/Dzone_mouRig/new/unified_filaments/Cstar_topick/C_run_data_t18.mrc.star  
---  
notes | Processed as relion  
Processed as relion  
  

> artiax clip off

add_particlelist is being run  
Opened Particle list C_run_data_t18.mrc.star with 303 particles.  

> artiax particles #1.2.1 originScaleFactor 8.0

> artiax particles #1.2.2 originScaleFactor 5.0

> view

> artiax clip off

add_particlelist is being run  

> artiax clip off

add_particlelist is being run  

> artiax clip off

add_particlelist is being run  

> artiax clip off

add_particlelist is being run  

> artiax clip off

add_particlelist is being run  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 464, in
_spacing_toggled  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
Error in sys.excepthook:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 188, in
_edit_changed  
self._emit_value_changed()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/LabelEditRangeSlider.py", line 205, in
_emit_value_changed  
self.valueChanged.emit(self._value)  
SystemError: <method 'emit' of 'PyQt6.QtCore.pyqtBoundSignal' objects>
returned a result with an exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QPaintEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
SystemError: <class 'PyQt6.QtGui.QExposeEvent'> returned a result with an
exception set  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 334, in ehook  
self.session.ui.thread_safe(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 516, in report_exception  
self.bug(err_msg.replace("\n", "<br>"), is_html=True)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 394, in bug  
self._log(  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 572, in _log  
if log.log(*args):  
^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 342, in log  
self.session.ui.thread_safe(f)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 423, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 341, in <lambda>  
f = lambda self=self, msg=dlg_msg: self.show_error_message(msg, bug=bug)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 262, in show_error_message  
ed.showMessage(msg)  
SystemError: <built-in method showMessage of BiggerErrorDialog object at
0x289c16b00> returned a result with an exception set  
  
Original exception was:  
Traceback (most recent call last):  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/widgets/CurvedLineOptions.py", line 486, in
spacing_value_changed  
self.line.create_spheres()  
File "/Users/b.colcombetcazenav/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/artiax/geometricmodel/CurvedLine.py", line 203, in
create_spheres  
theta = math.acos(np.dot(n, x_axes)) * 180 / math.pi  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
ValueError: math domain error  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,13
      Model Number: Z17Z000J8D/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 60 days, 2 hours, 54 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        EV2795:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        EV2795:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        S2202W:
          Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus)
          UI Looks like: 1680 x 1050 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    annotated-types: 0.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.5.0
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
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    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
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    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    glfw: 2.7.0
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    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
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    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
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    openvr: 1.26.701
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    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pyarrow: 17.0.0
    pycollada: 0.8
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    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
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    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
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    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
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    sphinxcontrib-jsmath: 1.0.1
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    tifffile: 2024.1.30
    tinyarray: 1.2.4
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    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11