The following bug report has been submitted:
Platform: Linux-4.18.0-553.5.1.el8_10.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007f4b72cf8740 (most recent call first):
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91 in get_prop
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1255 in _changes_cb
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1069 in proxy_handler
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 54 in check_for_changes
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/contextlib.py", line 144 in __exit__
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 225 in delete
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 308 in _key_closed
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/color_key/model.py", line 105 in delete
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/models.py", line 1010 in close
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/models.py", line 676 in reset_state
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/session.py", line 552 in reset
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/std_commands/close.py", line 71 in close_session
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 806 in file_close_cb
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1156 in
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, psutil._psutil_linux, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._webp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
===== Log before crash start =====
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 /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/lip_rfn47_locSpiralMap.mrc
Opened lip_rfn47_locSpiralMap.mrc as #1, grid size 240,240,240, pixel 0.83,
shown at level 3.49, step 1, values float32
> volume #1 level 7
> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/fig1b_1hwk_align2lip.pdb
> /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/fig1b_apo_refined_expanded_align2lip.pdb
> /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/fig1b_lip_refined_expanded.pdb
Summary of feedback from opening /dls/industrial/cryoem/Staff/kmani/HMG-
CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/fig1b_1hwk_align2lip.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 463 LYS A 474 1 12
Start residue of secondary structure not found: HELIX 2 2 PRO A 477 LEU A 481
5 5
Start residue of secondary structure not found: HELIX 3 3 THR A 487 LEU A 503
1 17
Start residue of secondary structure not found: HELIX 4 4 SER A 507 LEU A 512
5 6
Start residue of secondary structure not found: HELIX 5 5 CYS A 561 LEU A 575
1 15
17 messages similar to the above omitted
End residue of secondary structure not found: HELIX 23 23 CYS B 561 LEU B 575
1 15
Start residue of secondary structure not found: HELIX 24 24 ARG B 598 THR B
611 1 14
Start residue of secondary structure not found: HELIX 25 25 THR B 611 SER B
624 1 14
Start residue of secondary structure not found: HELIX 26 26 GLY B 656 PHE B
675 1 20
Start residue of secondary structure not found: HELIX 27 27 ALA B 694 GLY B
701 1 8
Start residue of secondary structure not found: HELIX 28 28 PRO B 713 VAL B
720 1 8
2 messages similar to the above omitted
End residue of secondary structure not found: HELIX 31 31 HIS B 752 CYS B 764
1 13
Start residue of secondary structure not found: HELIX 32 32 ASP B 767 ALA B
769 5 3
Start residue of secondary structure not found: HELIX 33 33 GLN B 770 SER B
775 1 6
Start residue of secondary structure not found: HELIX 34 34 GLY B 806 ASN B
810 5 5
Start residue of secondary structure not found: HELIX 35 35 LEU B 811 LEU B
821 1 11
Start residue of secondary structure not found: HELIX 36 36 GLY B 832 GLY B
860 1 29
102 messages similar to the above omitted
fig1b_1hwk_align2lip.pdb title:
Complex of the catalytic portion of human HMG-coa reductase with atorvastatin
[more info...]
Chain information for fig1b_1hwk_align2lip.pdb #2
---
Chain | Description | UniProt
A B | HMG-coa reductase | HMDH_HUMAN 426-888
Non-standard residues in fig1b_1hwk_align2lip.pdb #2
---
117 — 7-[2-(4-fluoro-phenyl)-5-isopropyl-3-phenyl-4-phenylcarbamoyl-
pyrrol-1-yl]- 3,5-dihydroxy-heptanoicacid (atorvastatin)
Chain information for fig1b_apo_refined_expanded_align2lip.pdb #3
---
Chain | Description
A | No description available
C | No description available
Chain information for fig1b_lip_refined_expanded.pdb #4
---
Chain | Description
A | No description available
C | No description available
> volume zone #1 nearAtoms #4/117 range 4.5 newMap true
no atoms specified for zone
> volume zone #1 nearAtoms #4/2:117 range 4.5 newMap true
no atoms specified for zone
> volume zone #1 nearAtoms #4 /2:117 range 4.5 newMap true
no atoms specified for zone
> volume zone #1 nearAtoms #4/A:901 range 4.5 newMap true
Opened lip_rfn47_locSpiralMap.mrc zone as #5, grid size 240,240,240, pixel
0.83, shown at step 1, values float32
> volume zone #1 nearAtoms #4/A:901 range 2.5 newMap true
Opened lip_rfn47_locSpiralMap.mrc zone as #6, grid size 240,240,240, pixel
0.83, shown at step 1, values float32
> close #5
> close #6
> volume zone #1 nearAtoms #4/A:901 range 3 newMap true
Opened lip_rfn47_locSpiralMap.mrc zone as #5, grid size 240,240,240, pixel
0.83, shown at step 1, values float32
> volume #5 level 5
> volume #5 level 4.5
> volume #5 level 4
> ui tool show "Hide Dust"
> surface dust #5 size 3.46
> surface dust #5 size 4.53
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/lip_rfn47_locSpiralMap_chA_lip_only_densityLevel4.mrc
> models #5
> hide #!5 models
> show #!5 models
> volume #5 style mesh
> volume #5 subdivideSurface true subdivisionLevels 2
> volume #5 subdivideSurface true subdivisionLevels 1
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #4/A:901
41 atoms, 44 bonds, 1 residue, 1 model selected
> show #!4 models
> select add #4
199 atoms, 189 bonds, 12 pseudobonds, 21 residues, 2 models selected
> style sel ball
Changed 199 atom styles
> show sel atoms
> select subtract #4
Nothing selected
> style #!4 stick
Changed 199 atom styles
> color #!4 byhetero
> hide #!4 cartoons
> select clear
> hide sel pseudobonds
> select clear
> hide sel pseudobonds
> select clear
> hide sel pseudobonds
> select clear
> hide sel pseudobonds
> volume #5 level 3.5
> select add #4
199 atoms, 189 bonds, 12 pseudobonds, 21 residues, 2 models selected
> select subtract #4
Nothing selected
> select #4/A
105 atoms, 103 bonds, 4 pseudobonds, 9 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select down
1 bond, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
64 atoms, 59 bonds, 8 residues, 1 model selected
> select up
105 atoms, 103 bonds, 9 residues, 1 model selected
> select down
64 atoms, 59 bonds, 8 residues, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
94 atoms, 86 bonds, 12 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue
> color sel byhetero
> select clear
> hide #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select clear
> show #!5 models
> set bgColor white
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/Fig1b_chX_session.cxs
> select add #5
2 models selected
> color sel cornflower blue
> select subtract #5
Nothing selected
> hide #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> color sel brown
> color sel byhetero
> select clear
> show #!5 models
> hide #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> color sel byhetero
> select add #4
199 atoms, 189 bonds, 12 pseudobonds, 21 residues, 2 models selected
> show #!5 models
> select subtract #4
Nothing selected
> show #!3 models
> select add #3
158 atoms, 145 bonds, 12 pseudobonds, 20 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> select subtract #3
Nothing selected
> hide #!4 models
> hide #!5 models
> ~hbonds
> hide sel pseudobonds
> delete pseudobonds sel
> select clear
> delete pseudobonds sel
> show #!4 models
> select add #3
158 atoms, 145 bonds, 2 pseudobonds, 20 residues, 2 models selected
> select clear
> show #!2 models
> hide #!3 models
> hide #!4 models
> select add #2
199 atoms, 189 bonds, 12 pseudobonds, 21 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 199 atom styles
> select clear
> delete pseudobonds sel
> select clear
> delete pseudobonds sel
> select clear
> delete pseudobonds sel
> select add #2
199 atoms, 189 bonds, 21 residues, 1 model selected
> select clear
> select add #2
199 atoms, 189 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select down
199 atoms, 188 bonds, 21 residues, 1 model selected
> select add #2
199 atoms, 189 bonds, 21 residues, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> color sel purple
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
94 atoms, 86 bonds, 12 residues, 1 model selected
> color sel pink
> color sel byhetero
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
64 atoms, 59 bonds, 8 residues, 1 model selected
> color sel pink
> color sel byhetero
> select clear
> show #!4 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
94 atoms, 86 bonds, 12 residues, 1 model selected
> select up
158 atoms, 145 bonds, 20 residues, 1 model selected
> color sel dark orchid
> color sel byhetero
> select clear
> show #!4 models
> hide #!4 models
> select add #3
158 atoms, 145 bonds, 2 pseudobonds, 20 residues, 2 models selected
> color sel coral
> color sel byhetero
> select subtract #3
Nothing selected
> show #!4 models
> select add #3
158 atoms, 145 bonds, 2 pseudobonds, 20 residues, 2 models selected
> color sel black
> color sel byhetero
> color sel green
> color sel byhetero
> select subtract #3
Nothing selected
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
64 atoms, 59 bonds, 8 residues, 1 model selected
> select up
66 atoms, 60 bonds, 9 residues, 1 model selected
> select up
72 atoms, 66 bonds, 9 residues, 1 model selected
> select up
158 atoms, 145 bonds, 20 residues, 1 model selected
> select down
72 atoms, 66 bonds, 9 residues, 1 model selected
> select up
158 atoms, 145 bonds, 20 residues, 1 model selected
> select up
199 atoms, 189 bonds, 21 residues, 1 model selected
> select up
556 atoms, 523 bonds, 62 residues, 7 models selected
> select up
556 atoms, 523 bonds, 62 residues, 7 models selected
> select up
556 atoms, 523 bonds, 62 residues, 7 models selected
> select down
199 atoms, 189 bonds, 21 residues, 1 model selected
> select down
158 atoms, 145 bonds, 20 residues, 1 model selected
> select up
199 atoms, 189 bonds, 21 residues, 1 model selected
> select down
158 atoms, 145 bonds, 20 residues, 1 model selected
> select clear
> hide #4/A:580-860
> hide #4/C:580-860
> hide #4/A,C:560-860
> hide #4/A,C:550-860
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> ui tool show "Side View"
> show #!5 models
> lighting full
> lighting depthCue false
> show #!2 models
> hide #2/A,B:550-860
> save fig1b_EMlip_Xlip_in_EMdensity.tiff format tiff width 1000 height 750
> supersample 6
> hide #!5 models
> show #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> show #2/A,B:550-860
> hide #2/A,B:550-860
> select add #4
199 atoms, 189 bonds, 12 pseudobonds, 21 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!2 models
> hide #!4 models
> show #4/A,C:550-860
> show #!4 models
> show #4/A,C:550-860
> hide #4/A:901
> transparency #4/A,C:550-860 50 target s
> transparency #4/A,C:550-860 80 target s
> transparency #4/A,C:550-860 80 target ab
> transparency #4/A,C:550-860 60 target ab
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> transparency #4/A,C:550-860 40 target ab
> hide #!3 models
> show #!3 models
> save fig1b_EM_apo_lip_interacting_residues.tiff format tiff width 1000
> height 750 supersample 6
> show #!2 models
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
41 atoms, 44 bonds, 1 residue, 1 model selected
> select clear
> hide #2/A:2
> show #2/A,B:550-860
> save fig1b_EMlip_Xlip_interacting_residues.tiff format tiff width 1000
> height 750 supersample 6
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/Fig1b_chX_session.cxs
> show #4/A:901
> hide #2/A:2
> show #2/A:2
> save fig1b_EMlip_Xlip_interacting_residues_withLipitor.tiff format tiff
> width 1000 height 750 supersample 6
> show #!3 models
> hide #!2 models
> save fig1b_EM_apo_lip_interacting_residues_withLipitor.tiff format tiff
> width 1000 height 750 supersample 6
> show #!5 models
> ui tool show "Map Statistics"
> measure mapstats #!5
Map lip_rfn47_locSpiralMap_chA_lip_only_densityLevel4.mrc #5, minimum 0,
maximum 18.81, mean 0.0003017, SD 0.05015, RMS 0.05015
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig1/Fig1b_chX_session.cxs
> hide #!5 models
> show #!2 models
> hide #!3 models
> close session
> open /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig2/lip_refined_expanded.pdb
> /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig2/apo_refined_expanded_align2lip.pdb
Chain information for lip_refined_expanded.pdb #1
---
Chain | Description
A B C D | No description available
Chain information for apo_refined_expanded_align2lip.pdb #2
---
Chain | Description
A B C D | No description available
> 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 lip_refined_expanded.pdb, chain A (#1) with
apo_refined_expanded_align2lip.pdb, chain A (#2), sequence alignment score =
2157.1
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: lip_refined_expanded.pdb #1/A,
apo_refined_expanded_align2lip.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 422 pruned atom pairs is 0.229 angstroms; (across all 423 pairs:
0.295)
> ui tool show "Render/Select by Attribute"
> key blue-white-red :0.016 :0.161 :0.400 showTool true
> ui mousemode right "color key"
> key blue-white-red :0.01 :0.20 :0.40 showTool true
> color byattribute r:seq_rmsd #1-2 target scab palette
> 0.01,blue:0.2,white:0.4,red noValueColor #4e9a06
25372 atoms, 3388 residues, atom seq_rmsd range 0.0161 to 3.82
> key delete
> ui mousemode right translate
> select #1/A:861 #2/A:861
20 atoms, 20 bonds, 2 residues, 2 models selected
> hide #1 models
> show #1 models
> hide #2 models
> select add #2
12614 atoms, 12802 bonds, 1693 residues, 2 models selected
> select add #1
25372 atoms, 25760 bonds, 3388 residues, 2 models selected
> select subtract #2
12768 atoms, 12968 bonds, 1696 residues, 1 model selected
> select subtract #1
Nothing selected
> matchmaker #2/A,B,C,D to #1/A,B,C,D 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 lip_refined_expanded.pdb, chain A (#1) with
apo_refined_expanded_align2lip.pdb, chain A (#2), sequence alignment score =
2157.1
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: lip_refined_expanded.pdb #1/A,
apo_refined_expanded_align2lip.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 422 pruned atom pairs is 0.229 angstroms; (across all 423 pairs:
0.295)
> matchmaker #2/A,B,C,D to #1/A,B,C,D pairing ss showAlignment true
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 lip_refined_expanded.pdb, chain A (#1) with
apo_refined_expanded_align2lip.pdb, chain A (#2), sequence alignment score =
2157.1
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: lip_refined_expanded.pdb #1/A,
apo_refined_expanded_align2lip.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Matchmaker lip_refined_expanded.pdb, chain B (#1) with
apo_refined_expanded_align2lip.pdb, chain B (#2), sequence alignment score =
2157.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: lip_refined_expanded.pdb #1/B,
apo_refined_expanded_align2lip.pdb #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
Matchmaker lip_refined_expanded.pdb, chain C (#1) with
apo_refined_expanded_align2lip.pdb, chain C (#2), sequence alignment score =
2155.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: lip_refined_expanded.pdb #1/C,
apo_refined_expanded_align2lip.pdb #2/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
Matchmaker lip_refined_expanded.pdb, chain D (#1) with
apo_refined_expanded_align2lip.pdb, chain D (#2), sequence alignment score =
2155.9
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: lip_refined_expanded.pdb #1/D,
apo_refined_expanded_align2lip.pdb #2/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 1688 pruned atom pairs is 0.266 angstroms; (across all 1692
pairs: 0.329)
> ui tool show "Render/Select by Attribute"
> key blue-white-red :0.01 :0.20 :0.40 showTool true
> ui mousemode right "color key"
> color byattribute r:seq_rmsd #1 target scab palette
> 0.01,blue:0.2,white:0.4,red noValueColor grey
12768 atoms, 1696 residues, atom seq_rmsd range 0.0102 to 3.97
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> key size 0.24000,0.05000
> key size 0.23000,0.05000
> key size 0.24000,0.05000
> key size 0.25000,0.05000
> key size 0.25000,0.04000
> key size 0.25000,0.03000
> key size 0.25000,0.02000
> key size 0.25000,0.01000
> key size 0.25000,0.02000
> key pos 0.69000,0.08000
> key pos 0.70000,0.08000
> key pos 0.70000,0.07000
> key pos 0.70000,0.06000
> key pos 0.70000,0.05000
> key bold true
> key italic true
> key italic false
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig2/Fig2a_chimerax_session.cxs
> hide #1 atoms
> save ../Fig2/fig2a_apo2lip_colorlip_Calpha_show_withoutlip.tiff format tiff
> width 1000 height 750 supersample 6
> key size 0.25000,0.01000
> cartoon style #1,4 xsection rectangle modeHelix default
> cartoon style (#1,4 & coil) xsection oval
> cartoon style #1,4 xsection barbell modeHelix default
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting full
> lighting soft
> lighting simple
> save ../Fig2/fig2a_apo2lip_colorlip_Calpha_show_withoutlip.tiff format tiff
> width 1000 height 750 supersample 6
> lighting full
> save ../Fig2/fig2a_apo2lip_colorlip_Calpha_show_withoutlip_lightingFull.tiff
> format tiff width 1000 height 750 supersample 6
> show #1/:117
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1/901
> show #1 atoms
> hide #1 atoms
> select #1/901
Nothing selected
> show #1 atoms
> hide #1 atoms
> select #1:901
164 atoms, 176 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> color sel black
> color sel byhetero
> color sel dark gray
> color sel byhetero
> select clear
> select #1:901
164 atoms, 176 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 164 atom styles
> style sel ball
Changed 164 atom styles
> color sel byhetero
> select clear
> size #1:901 ballScale 0.4 stickRadius 0.5
Changed 176 bond radii, 1 ball scales
> size #1:901 ballScale 0.3 stickRadius 0.5
Changed 176 bond radii, 1 ball scales
> size #1:901 ballScale 0.35 stickRadius 0.5
Changed 176 bond radii, 1 ball scales
> lighting simple
> save ../Fig2/fig2a_apo2lip_colorlip_Calpha_show_withlip_lightingSimple.tiff
> format tiff width 1000 height 750 supersample 6
> select #1:901
164 atoms, 176 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dim gray
> color sel byhetero
> select clear
> save ../Fig2/fig2a_apo2lip_colorlip_Calpha_show_withlip_lightingSimple.tiff
> format tiff width 1000 height 750 supersample 6
> save /dls/industrial/cryoem/Staff/kmani/HMG-
> CoA/EMDB_deposition/asymmetric_model_deposition/figures_revised/Fig2/Fig2a_chimerax_session.cxs
> close session
> ui mousemode right translate
Traceback (most recent call last):
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149,
in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line
1069, in proxy_handler
s._changes_cb(*args)
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line
1255, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91, in
get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
N10atomstruct9StructureE
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++
N10atomstruct9StructureE
File "/dls_sw/apps/EM/chimerax_industry/1.8/rhel8/usr/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91, in
get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
===== Log before crash end =====
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
OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
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 8.10 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 6.5Gi 33Gi 1.5Gi 21Gi 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: 0.7.16
appdirs: 1.4.4
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: 2024.6.2
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-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-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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
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: 1.2
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
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
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: 24.1
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
pycollada: 0.8
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
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
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
