Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-513.11.1.el8_9.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f8c18ff9700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c197fa700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c19ffb700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/selectors.py", line 415 in select
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c1a7fc700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c1affd700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c1b7fe700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007f8c1bfff700 (most recent call first):
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 975 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f8cdbfc1740 (most recent call first):
  Garbage-collecting
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/dls_sw/apps/EM/chimerax_industry/1.7/chimerax-1.7/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._webp, chimerax.segment._segment, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgcoalip_map_model/hmgcoalip_rfn47_run_half1_class001_unfil.mrc

Opened hmgcoalip_rfn47_run_half1_class001_unfil.mrc as #1, grid size
240,240,240, pixel 0.83, shown at level 0.00568, step 1, values float32  

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/Refine3D/job055/run_half1_class001_unfil.mrc

Opened run_half1_class001_unfil.mrc as #2, grid size 240,240,240, pixel 0.925,
shown at level 0.00389, step 1, values float32  

> volume #2 level 0.007841

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-8.3861,0,1,0,-10.477,0,0,1,-1.116

> view matrix models #2,1,0,0,-6.8312,0,1,0,-11.613,0,0,1,-10.072

> select subtract #2

Nothing selected  

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit map run_half1_class001_unfil.mrc in map
hmgcoalip_rfn47_run_half1_class001_unfil.mrc using 74868 points  
correlation = 0.6718, correlation about mean = 0.06966, overlap = 4.934  
steps = 72, shift = 4.76, angle = 0.0102 degrees  
  
Position of run_half1_class001_unfil.mrc (#2) relative to
hmgcoalip_rfn47_run_half1_class001_unfil.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00003540 -0.00017335 -11.37662539  
0.00003540 1.00000000 -0.00001251 -11.39287853  
0.00017335 0.00001250 0.99999998 -11.42058916  
Axis 0.07049711 -0.97733716 0.19960518  
Axis point 75149.22013822 0.00000000 -68910.73081768  
Rotation angle (degrees) 0.01016242  
Shift along axis 8.05305562  
  

> volume flip #2 axis z

Opened run_half1_class001_unfil.mrc z flip as #3, grid size 240,240,240, pixel
0.925, shown at step 1, values float32  

> fitmap #3 inMap #1

Fit map run_half1_class001_unfil.mrc z flip in map
hmgcoalip_rfn47_run_half1_class001_unfil.mrc using 74868 points  
correlation = 0.9816, correlation about mean = 0.8155, overlap = 12.32  
steps = 40, shift = 0.933, angle = 0.0138 degrees  
  
Position of run_half1_class001_unfil.mrc z flip (#3) relative to
hmgcoalip_rfn47_run_half1_class001_unfil.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00002451 0.00006673 -11.40286000  
0.00002451 1.00000000 0.00000615 -11.40394000  
-0.00006673 -0.00000614 1.00000000 -10.45849686  
Axis -0.08612096 0.93518230 0.34353637  
Axis point -88390.16657885 0.00000000 188011.38208901  
Rotation angle (degrees) 0.00408833  
Shift along axis -13.27561165  
  

> volume #1 style mesh

> volume #1 level 0.006852

> volume #1 level 0.006

> volume #3 level 0.006

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgcoalip_map_model/hmgcoalip_deposited_chA.pdb

hmgcoalip_deposited_chA.pdb title:  
\--- [more info...]  
  
Chain information for hmgcoalip_deposited_chA.pdb #4  
---  
Chain | Description  
B | No description available  
  
Non-standard residues in hmgcoalip_deposited_chA.pdb #4  
---  
117 — (117)  
  

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgcoalip_map_model/hmgcoalip_j38_mask.mrc

Opened hmgcoalip_j38_mask.mrc as #5, grid size 240,240,240, pixel 0.83, shown
at level 1, step 1, values float32  

> volume #5 style mesh

> volume #5 level 0.8853

> volume #1 style surface

> close

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/rfn40_run_half1_class001_unfil_flipZ.mrc

Opened rfn40_run_half1_class001_unfil_flipZ.mrc as #1, grid size 240,240,240,
pixel 0.925, shown at level 0.00389, step 1, values float32  

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgrApo_rfn40_locspiralSharpen_flipZ.pdb

hmgrApo_rfn40_locspiralSharpen_flipZ.pdb title:  
\--- [more info...]  
  
Chain information for hmgrApo_rfn40_locspiralSharpen_flipZ.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  

> volume #1 style mesh

> close #2

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgrApo_rfn40_locspiralSharpen_flipZ_chA.pdb

Chain information for hmgrApo_rfn40_locspiralSharpen_flipZ_chA.pdb #2  
---  
Chain | Description  
A | No description available  
  

> close #2

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgcoalip_map_model/hmgcoalip_rfn47_run_half1_class001_unfil.mrc

Opened hmgcoalip_rfn47_run_half1_class001_unfil.mrc as #2, grid size
240,240,240, pixel 0.83, shown at level 0.00568, step 1, values float32  

> ui tool show "Map Coordinates"

> hide #!2 models

> hide #!1 models

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/hmgcoalip_map_model/hmgcoalip_deposited.pdb

hmgcoalip_deposited.pdb title:  
\--- [more info...]  
  
Chain information for hmgcoalip_deposited.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  
Non-standard residues in hmgcoalip_deposited.pdb #3  
---  
117 — (117)  
  

> windowsize 700 500

> camera ortho

> preset pub

Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)  

> preset pub 1

No preset name matches 'pub 1'  

> preset pub1

No preset name matches 'pub1'  

> preset pub

Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)  

> preset pub:1

No preset name matches 'pub:1'  

> preset pub : 1

No preset name matches 'pub : 1'  

> preset licorice

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> show atoms

> delete solvent

> style ligand sphere

Changed 164 atom styles  

> color bfactor palette blue:red:yellow range 0,40 key true

> key blue:0 red:20 yellow:40 showTool true

> ui mousemode right "color key"

12768 atoms, 1696 residues, atom bfactor range 46.7 to 432  

> color bfactor palette blue:red:yellow range 0,140 key true

> key blue:0 red:70 yellow:140 showTool true

12768 atoms, 1696 residues, atom bfactor range 46.7 to 432  

> color bfactor palette blue:red:yellow range 0,100 key true

> key blue:0 red:50 yellow:100 showTool true

12768 atoms, 1696 residues, atom bfactor range 46.7 to 432  

> hide atoms

> preset pub

Multiple preset names match 'pub': publication 1 (silhouettes); publication 2
(depth-cued)  

> preset pub silhouettes

No preset name matches 'pub silhouettes'  

> preset silhouettes

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> key pos 0.85,0.2 size 0.04,0.6 justification left labelOffset 5

> 2dlabels text B-factor size 30 xpos .8 ypos .05

> key pos 0.882753,0.727273 size 0,0

> undo

> key yellow:100 red:50 blue:0

> key blue:0 red:50 yellow:100

> key labelSide right/bottom

> key labelSide left/top

> key pos 0.85,0.2 size 0.04,0.6 justification left labelOffset 5

> ui mousemode right "translate selected models"

> ui mousemode left 'color key'

> ui mousemode left rotate

> ui mousemode right 'color key'

> key justification right

> key justification left

> key justification right

> hide atoms

> show ligand atoms

> hide #!5 models

> hide #4 models

> hide #3 models

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/rfn40_locSpiralMap_flipZ.mrc

Opened rfn40_locSpiralMap_flipZ.mrc as #6, grid size 240,240,240, pixel 0.925,
shown at level 2.59, step 1, values float32  

> volume #6 level 7.739

> ui tool show "Surface Color"

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/LocalRes/job057/relion_locres_filtered_flipZ.mrc

Opened relion_locres_filtered_flipZ.mrc as #7, grid size 240,240,240, pixel
0.925, shown at level 0.00622, step 1, values float32  

> color sample #7.1 map #6 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 0, mean 2.288, maximum 12.16  

> hide #!7 models

> color sample #7.1 map #6 palette 0,#ff0000:6.081,#ffffff:12.16,#0000ff

Map values for surface "surface": minimum 0, mean 2.288, maximum 12.16  

> color sample #6.1 map #7 palette 0,#ff0000:6.081,#ffffff:12.16,#0000ff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#ffffff:12.16,#ff0000

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#7f7fff:12.16,#ffffff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#7f7fff:12.16,#ffffff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#7f7fff:12.16,#ffffff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color single #6.1

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#7f7fff:12.16,#ffffff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette 0,#0000ff:6.081,#7f7fff:12.16,#ffffff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> color sample #6.1 map #7 palette
> -0.04112,#ff0000:-0.002064,#ff7f7f:0.03699,#ffffff:0.07605,#7f7fff:0.1151,#0000ff

Map values for surface "surface": minimum -0.04112, mean 0.02535, maximum
0.1151  

> volume #6 level 7.97

> volume #6 level 9.06

> color sample #6.1 map #7 palette
> 0,#ff0000:-0.002064,#ff7f7f:0.03699,#ffffff:0.07605,#7f7fff:0.1151,#0000ff

Map values for surface "surface": minimum -0.02483, mean 0.0307, maximum
0.1297  

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/LocalRes/job057/relion_locres_flipZ.mrc

Opened relion_locres_flipZ.mrc as #8, grid size 240,240,240, pixel 0.925,
shown at level 15.9, step 1, values float32  

> color sample #6.1 map #8 palette
> 0,#ff0000:-0.002064,#ff7f7f:0.03699,#ffffff:0.07605,#7f7fff:0.1151,#0000ff

Map values for surface "surface": minimum 2.004, mean 2.121, maximum 2.827  

> color sample #6.1 map #8 palette #ff0000:#ff7f7f:#ffffff:#7f7fff:#0000ff

Map values for surface "surface": minimum 2.004, mean 2.121, maximum 2.827  

> color sample #6.1 map #8 palette
> 2.004,#0000ff:2.21,#7f7fff:2.415,#ffffff:2.621,#ff7f7f:2.827,#ff0000

Map values for surface "surface": minimum 2.004, mean 2.121, maximum 2.827  

> volume #6 level 7.144

> volume #6 level 7.243

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_apo/vol_colored_by_localRes.tiff format tiff width
> 1000 height 750 supersample 6

> ui mousemode right "translate selected models"

> color single #6.1

> close #8

> close #7

> ui tool show "Segment Map"

Segmenting rfn40_locSpiralMap_flipZ.mrc, density threshold 7.243081  
Only showing 60 of 105 regions.  
Showing 60 of 105 region surfaces  
2979 watershed regions, grouped to 105 regions  
Showing rfn40_locSpiralMap_flipZ.seg - 105 regions, 60 surfaces  
Ungrouped to 151 regions, but did not show all surfaces, see Options  
Ungrouped to 318 regions, but did not show all surfaces, see Options  
Ungrouped to 1070 regions, but did not show all surfaces, see Options  
Ungrouped to 2640 regions, but did not show all surfaces, see Options  
Ungrouped to 0 regions, but did not show their surfaces, see Options  
Segmenting rfn40_locSpiralMap_flipZ.mrc, density threshold 7.243081  
Only showing 4 of 105 regions.  
Showing 4 of 105 region surfaces  
2979 watershed regions, grouped to 105 regions  
Showing rfn40_locSpiralMap_flipZ.seg - 105 regions, 4 surfaces  
Ungrouped to 151 regions, but did not show all surfaces, see Options  
Ungrouped to 318 regions, but did not show all surfaces, see Options  
Ungrouped to 1070 regions, but did not show all surfaces, see Options  
Ungrouped to 2640 regions, but did not show all surfaces, see Options  
Ungrouped to 0 regions, but did not show their surfaces, see Options  

> show #3 models

> close #7

> select add #3

12768 atoms, 12968 bonds, 1696 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,12.656,0,1,0,11.213,0,0,1,6.3608

> view matrix models #3,1,0,0,13.126,0,1,0,11.403,0,0,1,10.515

> view matrix models #3,1,0,0,11.995,0,1,0,11.408,0,0,1,10.617

> select subtract #3

Nothing selected  

> hide #3 models

> ui tool show "Surface Zone"

> surface zone #6 nearAtoms #3 distance 5.5

> ui tool show "Surface Color"

> show #3 models

> ui tool show "Segment Map"

No segmentation chosen  
Segmenting rfn40_locSpiralMap_flipZ.mrc, density threshold 7.243081  
Only showing 4 of 105 regions.  
Showing 4 of 105 region surfaces  
2979 watershed regions, grouped to 105 regions  
Showing rfn40_locSpiralMap_flipZ.seg - 105 regions, 4 surfaces  
Segmenting rfn40_locSpiralMap_flipZ.mrc, density threshold 7.243081  
Only showing 60 of 105 regions.  
Showing 60 of 105 region surfaces  
2979 watershed regions, grouped to 105 regions  
Showing rfn40_locSpiralMap_flipZ.seg - 105 regions, 60 surfaces  

> hide #!7 models

> color #6 by chain

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #6 bychain

> hide #!6 models

> show #!6 models

> color zone #6 near #3 distance 12

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/RefmacServalcat/Full_model_in_rfn40_half_maps/refined.pdb

Chain information for refined.pdb #8  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!6 models

> show #!6 models

> hide #3 models

> undo color

Expected fewer arguments  

> undo color #6

Expected fewer arguments  

> volume #6 color #d3d7cf

> hide #!6 models

> show #!6 models

> color #8 bychain

> color zone #6 near #8 distance 12

> hide #8 models

> lighting full

> show #8 models

> color zone #6 near #8 distance 12

> transparency #6 50

> transparency #6 75

> transparency #6 25

> transparency #6 60

> transparency #6 40

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> lighting soft

> view

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/model_refinement/RefmacServalcat/Full_model_in_rfn40_half_maps/refined.pdb
> format pdb

Chain information for refined.pdb #9  
---  
Chain | Description  
A B C D | No description available  
  

> hide #9 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_apo/vol_colored_by_bychain_withpdb.tiff format tiff
> width 1000 height 750 supersample 6

> hide #8 models

> lighting full

> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_apo/vol_colored_by_bychain.tiff format tiff width
> 1000 height 750 supersample 6

> open
> /dls/m08/data/2024/cm37220-6/processing/kmani_proc_inR5_hmgcoaApo/Refine3D/job040/run_class001.mrc

Opened run_class001.mrc as #10, grid size 240,240,240, pixel 0.925, shown at
level 0.0039, step 1, values float32  

> hide #!6 models

> volume #10 level 0.002144

> volume #10 level 0.02

> volume #10 level 0.005

> hide #!10 models

> volume #1 level 0.004

> close

> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_apo/hmgrapo_refined.pdb

Chain information for hmgrapo_refined.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_lipitor/refined_new.pdb

refined_new.pdb title:  
\--- [more info...]  
  
Chain information for refined_new.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  
Non-standard residues in refined_new.pdb #2  
---  
117 — (117)  
  

> matchmaker #2 to #1 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker hmgrapo_refined.pdb, chain B (#1) with refined_new.pdb, chain B
(#2), sequence alignment score = 2188.3  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: hmgrapo_refined.pdb #1/B,
refined_new.pdb #2/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 423 pruned atom pairs is 0.049 angstroms; (across all 423 pairs:
0.049)  
  

> ui tool show "Render by Attribute"

> color byattribute r:seq_rmsd #1 target absc palette
> 0.005,blue:0.08,white:0.15,red

12604 atoms, 1692 residues, atom seq_rmsd range 0.00771 to 0.116  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> ui tool show Matchmaker

> matchmaker #1/D to #2/D pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker refined_new.pdb, chain D (#2) with hmgrapo_refined.pdb, chain D
(#1), sequence alignment score = 2177.5  
RMSD between 423 pruned atom pairs is 0.049 angstroms; (across all 423 pairs:
0.049)  
  

> ui tool show "Render by Attribute"

> color byattribute r:seq_rmsd #1 target absc palette
> 0.00770925,blue:0.0621005,white:0.116492,red

12604 atoms, 1692 residues, atom seq_rmsd range 0.00771 to 0.116  

> hide #2 models

> close #1

> close

> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_apo/hmgrapo_refined.pdb

Chain information for hmgrapo_refined.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/hmgr_lipitor/refined_new.pdb

refined_new.pdb title:  
\--- [more info...]  
  
Chain information for refined_new.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  
Non-standard residues in refined_new.pdb #2  
---  
117 — (117)  
  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-custom-session
XDG_SESSION_DESKTOP=gnome-custom-session
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Red Hat Enterprise Linux 8.9 Ootpa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       7.9Gi        44Gi       158Mi       9.9Gi        53Gi
	Swap:         8.0Gi          0B       8.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:119e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9