Opened 9 months ago
Last modified 9 months ago
#16727 assigned defect
ArtiaX: various errors
Reported by: | Owned by: | Utz Ermel | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: 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 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 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 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 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 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 pandas: 2.2.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pyarrow: 17.0.0 pycollada: 0.8 pydantic: 2.8.2 pydantic-core: 2.20.1 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 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 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 starfile: 0.5.8 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 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
Change History (1)
comment:1 by , 9 months ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ArtiaX: various errors |
Note:
See TracTickets
for help on using tickets.