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Opened 13 months ago
Closed 13 months ago
#16014 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.2-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001dc3d1ec0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.surface._surface, chimerax.map._map, 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, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 59)
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"procLaunch" : "2024-09-24 10:09:29.9790 +1000",
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"procExitAbsTime" : 2699342918924,
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"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":12311},
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===== Log before crash start =====
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/chunyiqian/Desktop/Honours/Thesis/Figures/Bessie_Figures
> 1&2/MainFig2/FIG2_PANEL_A.cxs"
Opened NPA_MAP as #1, grid size 296,296,296, pixel 1.11, shown at level 0.282,
step 1, values float32
Opened NPA_SHARP as #2, grid size 250,250,250, pixel 1, shown at level 1.86,
step 1, values float32
Opened WT_SHARP as #5, grid size 327,327,327, pixel 1, shown at level 2.3,
step 1, values float32
Opened TRP_SHARP as #8, grid size 327,327,327, pixel 0.872, shown at level
1.73, step 1, values float32
Opened IAA_SHARP as #9, grid size 327,327,327, pixel 1, shown at level 2.28,
step 1, values float32
Opened 5HT_SHARP as #10, grid size 217,217,217, pixel 1, shown at level 2.05,
step 1, values float32
Log from Tue Sep 17 12:02:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /home/charles/Desktop/Bessie_Figures/MainFig1/FIG1_PANEL_A.cxs
Opened cryosparc_P13_J2195_005_volume_map.mrc as #1, grid size 296,296,296,
pixel 1.11, shown at level 0.282, step 1, values float32
Opened J1898.emready.mrc as #2, grid size 250,250,250, pixel 1, shown at level
1.86, step 1, values float32
Log from Tue Sep 17 11:10:51 2024 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: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/charles/Downloads/cryosparc_P13_J2195_005_volume_map.mrc
Opened cryosparc_P13_J2195_005_volume_map.mrc as #1, grid size 296,296,296,
pixel 1.11, shown at level 0.245, step 2, values float32
> volume #1 step 1
> volume #1 level 0.2732
> volume #1 level 0.4101
> volume #1 level 0.3235
> volume #1 level 0.424
> volume #1 level 0.2732
> volume #1 level 0.2648
> open /home/charles/Desktop/Bessie_Figures/J1898.emready.mrc
Opened J1898.emready.mrc as #2, grid size 250,250,250, pixel 1, shown at level
0.555, step 1, values float32
> volume zflip #1
Expected a density maps specifier or a keyword
> volume flip #1
Opened cryosparc_P13_J2195_005_volume_map.mrc z flip as #3, grid size
296,296,296, pixel 1.11, shown at step 1, values float32
> volume #2 level 4.005
> volume #1 level 0.3905
> close #3
> fitmap #2 inMap #1
Fit map J1898.emready.mrc in map cryosparc_P13_J2195_005_volume_map.mrc using
45095 points
correlation = 0.9533, correlation about mean = 0.4078, overlap = 1.612e+05
steps = 140, shift = 24.2, angle = 10.4 degrees
Position of J1898.emready.mrc (#2) relative to
cryosparc_P13_J2195_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.98356155 -0.18057282 -0.00036263 32.34339736
0.18057271 0.98356158 -0.00033307 -26.87146429
0.00041681 0.00026211 0.99999988 24.04588210
Axis 0.00164803 -0.00215822 0.99999631
Axis point 163.45479285 164.01494976 0.00000000
Rotation angle (degrees) 10.40316225
Shift along axis 24.15709080
> select clear
> volume #1 level 0.1531
> volume #1 color #deddda
> volume #1 color white
[Repeated 1 time(s)]
> volume #1 color #ffffff7d
> volume #1 color #ffffff38
> lighting soft
> set bgColor white
> graphics silhouettes true
> volume #1 level 0.262
> volume #1 level 0.2816
> open /home/charles/Desktop/Bessie_Figures/NPA_model.init.pdb
Summary of feedback from opening
/home/charles/Desktop/Bessie_Figures/NPA_model.init.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 39
ARG A 41 1 3
Start residue of secondary structure not found: HELIX 2 2 LEU A 42 ARG A 61 1
20
Start residue of secondary structure not found: HELIX 3 3 GLN A 69 LYS A 71 1
3
Start residue of secondary structure not found: HELIX 4 4 GLY A 72 PHE A 80 1
9
Start residue of secondary structure not found: HELIX 5 5 ALA A 81 VAL A 92 1
12
167 messages similar to the above omitted
Chain information for NPA_model.init.pdb
---
Chain | Description
3.1/A 3.1/B | No description available
3.3/A 3.3/C | No description available
3.2/B 3.5/B | No description available
> close #3.4#3#3.1-3,5
> open "/home/charles/Desktop/Bessie_Figures/NPA_model.init (1).pdb"
Chain information for NPA_model.init (1).pdb #3
---
Chain | Description
B | No description available
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #3
4474 atoms, 4583 bonds, 1 pseudobond, 571 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-3.8186,0,1,0,-4.1877,0,0,1,24.584
> fitmap #3 inMap #1
Fit molecule NPA_model.init (1).pdb (#3) to map
cryosparc_P13_J2195_005_volume_map.mrc (#1) using 4474 atoms
average map value = 0.4378, steps = 96
shifted from previous position = 2.89
rotated from previous position = 11 degrees
atoms outside contour = 1068, contour level = 0.2816
Position of NPA_model.init (1).pdb (#3) relative to
cryosparc_P13_J2195_005_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.98172728 -0.18252641 0.05381140 24.39018336
0.18323148 0.98303363 -0.00843213 -26.27737719
-0.05135933 0.01813799 0.99851551 29.55902652
Axis 0.06964562 0.27567362 0.95872496
Axis point 187.53350670 106.15426354 0.00000000
Rotation angle (degrees) 10.99668790
Shift along axis 22.79366629
> select clear
> select #2
2 models selected
> select clear
> select #2
2 models selected
> select clear
> select #2
2 models selected
> select clear
> hide #!2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel atoms
> volume #2 level 1.86
> volume #2 color #deddda
> volume #2 color #bf404081
> volume #2 color #d3d3d381
> show sel atoms
> hide sel atoms
> combine #3
> select add #4
4496 atoms, 4607 bonds, 1 pseudobond, 572 residues, 3 models selected
> view matrix models
> #3,0.98173,-0.18253,0.053811,41.679,0.18323,0.98303,-0.0084321,-59.731,-0.051359,0.018138,0.99852,34.002,#4,0.98173,-0.18253,0.053811,41.679,0.18323,0.98303,-0.0084321,-59.731,-0.051359,0.018138,0.99852,34.002
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98029,0.05909,-0.18854,340.9,-0.098315,-0.97359,0.20604,313.77,-0.17139,0.22051,0.96021,21.166,#4,-0.98029,0.05909,-0.18854,340.9,-0.098315,-0.97359,0.20604,313.77,-0.17139,0.22051,0.96021,21.166
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.98029,0.05909,-0.18854,345.01,-0.098315,-0.97359,0.20604,313.15,-0.17139,0.22051,0.96021,21.532,#4,-0.98029,0.05909,-0.18854,345.01,-0.098315,-0.97359,0.20604,313.15,-0.17139,0.22051,0.96021,21.532
> fitmap #4 inMap #2
Fit molecule copy of NPA_model.init (1).pdb (#4) to map J1898.emready.mrc (#2)
using 4474 atoms
average map value = 4.804, steps = 108
shifted from previous position = 6.17
rotated from previous position = 15.1 degrees
atoms outside contour = 941, contour level = 1.8598
Position of copy of NPA_model.init (1).pdb (#4) relative to J1898.emready.mrc
(#2) coordinates:
Matrix rotation and translation
-0.99879913 0.00579831 -0.04864867 334.59095701
-0.00672310 -0.99979939 0.01886771 326.39111829
-0.04852951 0.01917213 0.99863774 4.79852373
Axis 0.02430315 -0.00951330 -0.99965937
Axis point 167.86502425 162.64867932 0.00000000
Rotation angle (degrees) 179.64116346
Shift along axis 0.22966888
> hide #!3 models
> show #!3 models
> undo
[Repeated 3 time(s)]
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> select add #3
8948 atoms, 9166 bonds, 2 pseudobonds, 1142 residues, 4 models selected
> select subtract #3
4474 atoms, 4583 bonds, 1 pseudobond, 571 residues, 2 models selected
> select clear
> select add #3
4474 atoms, 4583 bonds, 1 pseudobond, 571 residues, 2 models selected
> view matrix models
> #3,0.98173,-0.18253,0.053811,25.971,0.18323,0.98303,-0.0084321,-25.412,-0.051359,0.018138,0.99852,29.596
> select add #4
8948 atoms, 9166 bonds, 2 pseudobonds, 1142 residues, 4 models selected
> select subtract #3
4474 atoms, 4583 bonds, 1 pseudobond, 571 residues, 2 models selected
> view matrix models
> #4,0.98173,-0.18253,0.053811,47.258,0.18323,0.98303,-0.0084321,-69.172,-0.051359,0.018138,0.99852,35.308
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.96187,0.18416,-0.20221,322.53,-0.22306,-0.95604,0.19035,322.99,-0.15826,0.2282,0.96067,18.926
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.96187,0.18416,-0.20221,322.29,-0.22306,-0.95604,0.19035,330,-0.15826,0.2282,0.96067,18.248
> fitmap #3 inMap #2
Fit molecule NPA_model.init (1).pdb (#3) to map J1898.emready.mrc (#2) using
4474 atoms
average map value = 4.81, steps = 88
shifted from previous position = 1.82
rotated from previous position = 0.306 degrees
atoms outside contour = 962, contour level = 1.8598
Position of NPA_model.init (1).pdb (#3) relative to J1898.emready.mrc (#2)
coordinates:
Matrix rotation and translation
0.99884315 -0.00548327 0.04777337 -6.51282795
0.00632873 0.99982571 -0.01756402 1.44815970
-0.04766873 0.01784605 0.99870377 4.88786290
Axis 0.34552428 0.93130464 0.11525903
Axis point 99.64991645 0.00000000 136.29392862
Rotation angle (degrees) 2.93718354
Shift along axis -0.33829195
> fitmap #4 inMap #2
Fit molecule copy of NPA_model.init (1).pdb (#4) to map J1898.emready.mrc (#2)
using 4474 atoms
average map value = 4.804, steps = 100
shifted from previous position = 5.55
rotated from previous position = 13.8 degrees
atoms outside contour = 941, contour level = 1.8598
Position of copy of NPA_model.init (1).pdb (#4) relative to J1898.emready.mrc
(#2) coordinates:
Matrix rotation and translation
-0.99879478 0.00536479 -0.04878742 334.69534555
-0.00628890 -0.99980335 0.01880782 326.34652276
-0.04867692 0.01909198 0.99863210 4.84019323
Axis 0.02437473 -0.00947827 -0.99965796
Axis point 167.88240739 162.66243088 0.00000000
Rotation angle (degrees) 179.66603023
Shift along axis 0.22636969
> select clear
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> view name side_view
> view side_view
> select clear
> show #!1 models
> hide #!1 models
> view list
Named views: side_view
> ui tool show Log
> view side_view
[Repeated 1 time(s)]
> select clear
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select
8948 atoms, 9166 bonds, 2 pseudobonds, 1142 residues, 8 models selected
> color (#!3 & sel) #4079bfff
> color (#!3 & sel) #417abfff
> color (#!3 & sel) #57a3ffff
[Repeated 3 time(s)]
> show #!4 models
> select
8948 atoms, 9166 bonds, 2 pseudobonds, 1142 residues, 8 models selected
> color #4 #57a3ffff
> select clear
[Repeated 3 time(s)]
> select #3/B:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select :371-900
3700 atoms, 3788 bonds, 2 pseudobonds, 470 residues, 4 models selected
> select :371-429
978 atoms, 998 bonds, 122 residues, 2 models selected
> select :371-900
3700 atoms, 3788 bonds, 2 pseudobonds, 470 residues, 4 models selected
> color (#!3-4 & sel) #bf8640ff
> color (#!3-4 & sel) #bf761dff
> color (#!3-4 & sel) #ff9d26ff
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> select #3/B:234
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/B:93
16 atoms, 14 bonds, 2 residues, 1 model selected
> select :93-234
2278 atoms, 2340 bonds, 284 residues, 2 models selected
> select add #3/B:267
2287 atoms, 2348 bonds, 285 residues, 2 models selected
> select add #3/B:370
2295 atoms, 2355 bonds, 286 residues, 2 models selected
> select :93-234,267-370
3892 atoms, 3988 bonds, 492 residues, 2 models selected
> name transporter sel
> color sel #aa557f
> select clear
> select transporter
Nothing selected
> select :93-234,267-370
3892 atoms, 3988 bonds, 492 residues, 2 models selected
> name transporter sel
> select clear
> select transporter
Nothing selected
> name transporter :93-234,267-370
> select transporter
3892 atoms, 3988 bonds, 492 residues, 2 models selected
> select clear
> select transporter
3892 atoms, 3988 bonds, 492 residues, 2 models selected
> select ~sel
5056 atoms, 5170 bonds, 2 pseudobonds, 650 residues, 8 models selected
> select clear
> show atoms
> hide atoms
> show atoms
> select :E70
Nothing selected
> select :E7O
68 atoms, 72 bonds, 4 residues, 2 models selected
> color sel #40a3bfff
> color sel #40babfff
> color sel #40bdbfff
> color sel #51bf40ff
> color sel #60bf40ff
> color sel #7dbf40ff
> color sel #80bf40ff
> color sel #82bf40ff
> color sel #8abf40ff
> color sel #8cbf40ff
> color sel #b3bf40ff
> color sel #b6bf40ff
> color sel #b8bf40ff
> color sel #bebf40ff
> color sel #bbbf40ff
> color sel #51bf40ff
> color sel #40abbfff
> color sel #408cbfff
> color sel #6040bfff
> color sel #8240bfff
> color sel #9740bfff
> color sel #a140bfff
> color sel #ab40bfff
> color sel #bf40beff
> color sel #bf40b1ff
> color sel #bf40acff
> color sel #bf40aaff
> color sel #bf40a7ff
> color sel #bf409dff
> color sel #bf408dff
> color sel #bf4083ff
> color sel #bf4079ff
> color sel #bf406cff
> color sel #bf4064ff
> color sel #bf4057ff
> color sel #bf4042ff
> color sel #bf4040ff
> color sel #bf4042ff
> color sel #bf4095ff
> color sel #404ebfff
> color sel #40bf86ff
> color sel #40bf6fff
> color sel #40bf6aff
> color sel #40bf65ff
> color sel #40bf50ff
> color sel #44bf40ff
> color sel #47bf40ff
> color sel #44bf40ff
> color sel #40bf46ff
> color sel #2ec27eff
> select clear
> select :402
84 atoms, 86 bonds, 6 residues, 2 models selected
> select clear
> select #3/A:402@C14
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete sel
> select #4/A:402@C06
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> delete sel
> select clear
> view side_view
> color #2 zone #3,4 dist 4
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> scolor #2 zone #3,4 dist 4
Unknown command: scolor #2 zone #3,4 dist 4
> color zone #2 near #3,4 distance 4
> color zone #2 near #3,4 distance 5
> color zone #2 near #3,4 distance 1
> hide #!3 models
> hide #!4 models
> color zone #2 near #3,4 distance 2
> color zone #2 near #3,4 distance 5
> lighting soft
> ui tool show "Side View"
> save /home/charles/Desktop/Bessie_Figures/MainFig1/FIG1_PANEL_A.cxs
> includeMaps true
——— End of log from Tue Sep 17 11:10:51 2024 ———
opened ChimeraX session
> color zone #2 near #3,4 distance 5
> hide #!2 models
> show #!2 models
> hide #!1 models
> color zone #2 near #3,4 distance 5
[Repeated 1 time(s)]
> view name slab_ligands
> select clear
> ui tool show "Side View"
> open
> /home/charles/projects/lychos/MAPS_MODELS/WT/J603_005_volume_map_WT_EMREADY.flip.mrc
Opened J603_005_volume_map_WT_EMREADY.flip.mrc as #5, grid size 327,327,327,
pixel 1, shown at level 0.000375, step 2, values float32
> volume #5 level 2.299
> volume #5 step 1
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.23197,0.53515,-0.81228,241.36,0.5624,0.75513,0.33689,-104.77,0.79366,-0.37868,-0.47613,163.28
> view matrix models
> #5,-0.736,0.67688,0.011545,171.7,0.6766,0.73491,0.04615,-74.643,0.022754,0.041778,-0.99887,302.5
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.736,0.67688,0.011545,171.78,0.6766,0.73491,0.04615,-74.571,0.022754,0.041778,-0.99887,314.48
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.88648,0.46254,-0.014765,235.84,0.46119,0.88563,0.054368,-65.304,0.038223,0.041387,-0.99841,311.93
> fitmap #5 inMap #2
Fit map J603_005_volume_map_WT_EMREADY.flip.mrc in map J1898.emready.mrc using
71285 points
correlation = 0.8096, correlation about mean = 0.3542, overlap = 1.895e+06
steps = 76, shift = 1.89, angle = 6.34 degrees
Position of J603_005_volume_map_WT_EMREADY.flip.mrc (#5) relative to
J1898.emready.mrc (#2) coordinates:
Matrix rotation and translation
-0.84355623 0.53704064 -0.00049373 214.33839440
0.53704083 0.84355613 -0.00044051 -62.37040215
0.00017992 -0.00063675 -0.99999978 303.04152120
Axis -0.27968224 -0.96009258 0.00028016
Axis point 116.22599888 0.00000000 151.53124150
Rotation angle (degrees) 179.97989909
Shift along axis 0.01961747
> select clear
> color zone #5 near #3,4 distance 5
> color zone #5 near #3,4 distance 15
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view list
Named views: side_view, slab_ligands
> view slab_ligands
> hide #!5 models
> show #!5 models
> color zone #5 near #3,4 distance 15
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> color zone #5 near #3,4 distance 15
> color zone #5 near #3,4 distance 12
> hide #!5 models
> show #!3 models
> show #!4 models
> select :E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> select ~sel
8880 atoms, 9094 bonds, 2 pseudobonds, 1138 residues, 10 models selected
> select up
8904 atoms, 9118 bonds, 2 pseudobonds, 1140 residues, 10 models selected
> select up
8904 atoms, 9118 bonds, 2 pseudobonds, 1140 residues, 10 models selected
> select clear
> select :E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> select ~sel
8880 atoms, 9094 bonds, 2 pseudobonds, 1138 residues, 10 models selected
> show #!5 models
> hide #!3 models
> hide #!4 models
> color zone #5 near #3,4 distance 12
> select subtract #2
8880 atoms, 9094 bonds, 2 pseudobonds, 1138 residues, 8 models selected
> select subtract #1
8880 atoms, 9094 bonds, 2 pseudobonds, 1138 residues, 6 models selected
> select clear
> show #!3 models
> show #!4 models
> hide #!5 models
> select clear
> select :E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> select ~sel
8880 atoms, 9094 bonds, 2 pseudobonds, 1138 residues, 10 models selected
> color zone #5 near #3,4 distance 12
> select clear
> show #!5 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!5 models
> combine #3 #4
Remapping chain ID 'B' in copy of NPA_model.init (1).pdb #4 to 'D'
Remapping chain ID 'C' in copy of NPA_model.init (1).pdb #4 to 'E'
> hide #!4 models
> hide #!3 models
> select #6 & :E7O
24 atoms, 24 bonds, 2 residues, 1 model selected
> delete sel
> select clear
> show #!3 models
> hide #!3 models
> show #!5 models
> color zone #5 near #6 distance 12
> select clear
> hide #!6 models
> save /home/charles/Desktop/Bessie_Figures/MainFig1/FIG1_PANEL_C.cxs
> includeMaps true
> save /home/charles/Desktop/Bessie_Figures/MainFig1/PANEL_C_wt_map.png width
> 1404 height 807 supersample 3
> show #!2 models
> hide #!5 models
> color zone #2 near #3,4 distance 5
> save /home/charles/Desktop/Bessie_Figures/MainFig1/PANEL_C_NPA_map.png width
> 1404 height 807 supersample 3
> hide #!2 models
> show #!3 models
> show #!4 models
> open
> /home/charles/projects/lychos/MAPS_MODELS/WT/J603_model_13_real_space_refined_050.pdb
Chain information for J603_model_13_real_space_refined_050.pdb #7
---
Chain | Description
A B | No description available
> fitmap #7 to #3
Expected a keyword
> mmaker #7 to #3
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 NPA_model.init (1).pdb, chain B (#3) with
J603_model_13_real_space_refined_050.pdb, chain B (#7), sequence alignment
score = 2797.9
RMSD between 386 pruned atom pairs is 0.693 angstroms; (across all 551 pairs:
3.656)
> select clear
> hide #!3 models
> show #!3 models
> hide #!3-4,7 atoms
> select :E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> show sel
> select clear
> color #7 #dedddaff
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!1 models
> rename #1 NPA_MAP
> rename #2 NPA_SHARP
> rename #3 NPA_CHAIN_A
> rename #4 NPA_CHAIN_B
> hide #!1 models
> hide #!7 models
> select add #4
4452 atoms, 4559 bonds, 1 pseudobond, 570 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!5 models
> hide #!4 models
> hide #!3 models
> rename #5 WT_SHARP
> show #!7 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> rename #7 WT_MODEL
> show #!5 models
> hide #!5 models
> select clear
> select /A:E7O
Nothing selected
> select A/:E7O
Expected an objects specifier or a keyword
> select :E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> show #!7 atoms
> select clear
> show #!7 atoms
> hide #!7 models
> show #!3 models
> show #!4 models
> select /C:E7O
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #3/C:402@C16
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> select clear
> view name pocket
> view list
Named views: pocket, side_view, slab_ligands
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!5 models
> show #!7 models
> hide #!7 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!2 models
> view ligand_pocket
Expected an objects specifier or a view name or a keyword
> view slab_ligands
> view pocket
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> color zone #2 near #3,4 distance 5
> lighting flat
> lighting soft
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> color zone #2 near #3,4 distance 5
> save /home/charles/projects/lychos/MAPS_MODELS/WT/PANEL_D_01_NPA.png width
> 929 height 801 supersample 3
> show #!5 models
> hide #!2 models
> color zone #5 near #6 distance 12
color zone: No atoms specified.
> combine #3 #4
Remapping chain ID 'B' in NPA_CHAIN_B #4 to 'D'
Remapping chain ID 'C' in NPA_CHAIN_B #4 to 'E'
> select clear
> select #6/C:402@C14
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> delete sel
> color zone #5 near #6 distance 12
> save /home/charles/projects/lychos/MAPS_MODELS/WT/PANEL_D_02_WT.png width
> 929 height 801 supersample 3
> save /home/charles/Desktop/Bessie_Figures/MainFig1/FIG1_PANEL_D.cxs
> includeMaps true
> hide #!6 models
> hide #!5 models
> show #!6 models
> select #6/B:663
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select #6/B:259
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/B:336
11 atoms, 11 bonds, 1 residue, 1 model selected
> open
> /home/charles/projects/lychos/MAPS_MODELS/TRP/J1174_004_volume_map_EMREADY_TRP.scaled.mrc
Opened J1174_004_volume_map_EMREADY_TRP.scaled.mrc as #8, grid size
327,327,327, pixel 0.872, shown at level 0.0569, step 2, values float32
> rename #8 TRP
> rename #8 TRP_SHARP
> volume #8 level 1.733
> volume #8 step 1
> select add #8
11 atoms, 11 bonds, 1 residue, 3 models selected
> select add #6
8892 atoms, 9106 bonds, 2 pseudobonds, 1139 residues, 4 models selected
> select add #5
8892 atoms, 9106 bonds, 2 pseudobonds, 1139 residues, 6 models selected
> show #!5 models
> select subtract #5
8892 atoms, 9106 bonds, 2 pseudobonds, 1139 residues, 4 models selected
> select clear
> select #8
2 models selected
> view matrix models
> #8,0.48956,0.87028,-0.054251,-43.284,-0.87008,0.48347,-0.095987,212.83,-0.057307,0.094194,0.9939,-4.3562
> view matrix models
> #8,0.30675,-0.93751,0.16427,208.08,-0.9463,-0.28189,0.15829,294.4,-0.10209,-0.20401,-0.97363,344.82
> view matrix models
> #8,0.2788,-0.96035,7.9058e-05,240.38,-0.95477,-0.27719,-0.10757,335.5,0.10333,0.029915,-0.9942,285.16
> view matrix models
> #8,0.28425,-0.95045,0.12586,219.01,-0.95853,-0.28452,0.016189,318.2,0.020422,-0.12524,-0.99192,318.84
> view matrix models
> #8,0.16324,-0.97831,0.12752,240.03,-0.98656,-0.1628,0.013912,305.14,0.0071497,-0.12807,-0.99174,321.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.16324,-0.97831,0.12752,260.1,-0.98656,-0.1628,0.013912,324.46,0.0071497,-0.12807,-0.99174,323.35
> fitmap #8 inMap #5
Fit map TRP_SHARP in map WT_SHARP using 107903 points
correlation = 0.8746, correlation about mean = 0.5616, overlap = 3.609e+06
steps = 120, shift = 15.3, angle = 15 degrees
Position of TRP_SHARP (#8) relative to WT_SHARP (#5) coordinates:
Matrix rotation and translation
-0.31529590 0.94899340 0.00017884 73.32190208
-0.94899342 -0.31529589 -0.00006662 344.90669528
-0.00000683 -0.00019073 0.99999999 4.70748161
Axis -0.00006539 0.00009783 -0.99999999
Axis point 161.08702636 146.00260507 0.00000000
Rotation angle (degrees) 108.37867789
Shift along axis -4.67853472
> select clear
> open
> /home/charles/projects/lychos/MAPS_MODELS/AUXIN/consensus/J1099_003_volume_map_EMREADY_auxin.flip.scaled.mrc
Opened J1099_003_volume_map_EMREADY_auxin.flip.scaled.mrc as #9, grid size
327,327,327, pixel 1, shown at level 0.0104, step 2, values float32
> volume #9 level 2.285
> volume #9 step 1
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.12789,0.99178,-0.0028085,-18.738,-0.98689,0.12754,0.098898,287.79,0.098444,-0.0098762,0.99509,-13.696
> view matrix models
> #9,-0.0010844,-0.99494,0.10049,309.9,-0.99225,0.013553,0.12348,303.05,-0.12422,-0.099577,-0.98725,383.8
> fitmap #9 inMap #5
Fit map J1099_003_volume_map_EMREADY_auxin.flip.scaled.mrc in map WT_SHARP
using 75893 points
correlation = 0.8738, correlation about mean = 0.5702, overlap = 2.683e+06
steps = 80, shift = 4.52, angle = 9.81 degrees
Position of J1099_003_volume_map_EMREADY_auxin.flip.scaled.mrc (#9) relative
to WT_SHARP (#5) coordinates:
Matrix rotation and translation
-0.31186456 0.95012656 0.00011185 59.31130093
-0.95012656 -0.31186456 0.00003354 371.00818858
0.00006675 -0.00009581 0.99999999 -17.62017529
Axis -0.00006807 0.00002373 -1.00000000
Axis point 164.00866293 164.02515022 0.00000000
Rotation angle (degrees) 108.17163397
Shift along axis 17.62494315
> select clear
> rename #9 IAA_SHARP
> open
> /home/charles/Desktop/Bessie_Figures/5HT_cryosparc_P13_J2129_005_volume_map.emready.mrc
Opened 5HT_cryosparc_P13_J2129_005_volume_map.emready.mrc as #10, grid size
217,217,217, pixel 1, shown at level 1.44, step 1, values float32
> volume #10 level 2.051
> select add #10
2 models selected
> view matrix models
> #10,0.9998,0.020143,-0.00072598,-3.1597,-0.020115,0.99479,-0.099927,19.078,-0.0012906,0.099922,0.99499,-15.418
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.10271,0.98567,0.13382,-0.37193,-0.98999,-0.11439,0.082681,332.95,0.096804,-0.12399,0.98755,6.2769
> fitmap #10 inMap #5
Fit map 5HT_cryosparc_P13_J2129_005_volume_map.emready.mrc in map WT_SHARP
using 83494 points
correlation = 0.8595, correlation about mean = 0.5835, overlap = 2.409e+06
steps = 120, shift = 14.4, angle = 9.29 degrees
Position of 5HT_cryosparc_P13_J2129_005_volume_map.emready.mrc (#10) relative
to WT_SHARP (#5) coordinates:
Matrix rotation and translation
-0.23490746 -0.97201765 -0.00042549 362.03922954
-0.97201774 0.23490746 0.00004238 284.89361854
0.00005876 0.00042354 -0.99999990 312.87631528
Axis 0.61850241 -0.78578289 -0.00014698
Axis point 293.11112670 0.00000000 156.44700363
Rotation angle (degrees) 179.98234538
Shift along axis 0.01161516
> select clear
> view pocket
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!2 models
> show #!9 models
> hide #!9 models
> ui tool show "Side View"
> show #!9 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> view name pocket2
> show #!3 models
> hide #!9 models
> hide #!2 models
> select clear
> show #!3 atoms
> select #3/B:328
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:327
7 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select clear
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view name pocket2
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> view pocket2
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> show #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!8 models
> color zone #8 near #6 distance 12
> hide #!8 models
> show #!10 models
> color zone #10 near #6 distance 12
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!10 models
> hide #!10 models
> show #!8 models
> open
> /home/charles/projects/lychos/MAPS_MODELS/TRP/J1174_model_14_real_space_refined_012.pdb
Chain information for J1174_model_14_real_space_refined_012.pdb #11
---
Chain | Description
A C | No description available
> select add #11
8884 atoms, 9096 bonds, 8 pseudobonds, 1132 residues, 2 models selected
> view matrix models
> #11,0.017408,0.99806,-0.059805,6.8653,-0.9981,0.020885,0.058002,274.06,0.059138,0.058682,0.99652,-16.328
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.017408,0.99806,-0.059805,24.115,-0.9981,0.020885,0.058002,292.52,0.059138,0.058682,0.99652,-17.422
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.016856,0.99785,-0.063314,24.758,-0.99424,0.023433,0.10463,284.5,0.10588,0.061186,0.99249,-23.855
> view matrix models
> #11,0.10743,0.99194,-0.067175,13.233,-0.98859,0.11375,0.098733,271.67,0.10558,0.055802,0.99284,-23.094
> view matrix models
> #11,-0.098365,0.99348,-0.057662,41.009,-0.98954,-0.091499,0.11157,299.22,0.10557,0.068033,0.99208,-24.726
> view matrix models
> #11,0.41482,0.89895,-0.14077,-6.2856,0.64995,-0.40101,-0.64556,224,-0.63678,0.1763,-0.75062,331.33
> view matrix models
> #11,0.43352,0.89391,0.11394,-47.018,0.76514,-0.43193,0.47749,40.943,0.47605,-0.11982,-0.87122,232.85
> view matrix models
> #11,0.27491,0.96146,0.0041131,-17.26,0.83783,-0.24166,0.48954,1.4836,0.47167,-0.13113,-0.87197,235.21
> view matrix models
> #11,0.14785,0.93841,0.31231,-42.726,0.97502,-0.19123,0.11299,31.995,0.16576,0.2878,-0.94324,229.9
> view matrix models
> #11,0.15997,0.95415,0.25299,-37.678,0.98165,-0.18072,0.060838,37.487,0.10377,0.23861,-0.96555,249.2
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.15997,0.95415,0.25299,-36.433,0.98165,-0.18072,0.060838,39.42,0.10377,0.23861,-0.96555,249.09
> view matrix models
> #11,0.15997,0.95415,0.25299,-34.854,0.98165,-0.18072,0.060838,33.826,0.10377,0.23861,-0.96555,266.12
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.16526,0.97575,0.14351,-22.025,0.98175,-0.14886,-0.11839,56.555,-0.094157,0.16046,-0.98254,308.21
> view matrix models
> #11,0.10807,0.99372,-0.02892,9.8293,0.99406,-0.10839,-0.009979,32.504,-0.013051,-0.02767,-0.99953,326.11
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.10807,0.99372,-0.02892,9.9375,0.99406,-0.10839,-0.009979,38.468,-0.013051,-0.02767,-0.99953,326.23
> fitmap #11 inMap #8
Fit molecule J1174_model_14_real_space_refined_012.pdb (#11) to map TRP_SHARP
(#8) using 8884 atoms
average map value = 7.7, steps = 60
shifted from previous position = 2.14
rotated from previous position = 3.06 degrees
atoms outside contour = 891, contour level = 1.7335
Position of J1174_model_14_real_space_refined_012.pdb (#11) relative to
TRP_SHARP (#8) coordinates:
Matrix rotation and translation
-0.99999998 -0.00014859 0.00011480 286.17308640
0.00014860 -0.99999999 0.00009015 286.11652427
0.00011479 0.00009016 0.99999999 -0.03170280
Axis 0.00005051 0.00004149 1.00000000
Axis point 143.07591500 143.06889390 0.00000000
Rotation angle (degrees) 179.99148603
Shift along axis -0.00537784
> select clear
> rename #11 TRP_MODEL
> rename #10 5HT_SHARP
> hide #!8 models
> show #!8 models
> select clear
> hide #!11 models
> hide #!8 models
> open
> /home/charles/projects/lychos/MAPS_MODELS/AUXIN/consensus/J1099_consensus_model_06_real_space_refined_041.pdb
Chain information for J1099_consensus_model_06_real_space_refined_041.pdb #12
---
Chain | Description
A C | No description available
> mmaker #12 to #11
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 TRP_MODEL, chain A (#11) with
J1099_consensus_model_06_real_space_refined_041.pdb, chain A (#12), sequence
alignment score = 2467.5
RMSD between 491 pruned atom pairs is 0.499 angstroms; (across all 500 pairs:
0.887)
> show #!11 models
> hide #!11 models
> rename #12 IAA_MODEL
> show #!7 models
> hide #!12 models
> show #!10 models
> view pocket2
> select clear
> select #10
4 models selected
> transparency #10.1 40
> select clear
> select #10
4 models selected
> select clear
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!7 atoms
> show #!7 cartoons
> hide #!7 models
> show #!6 models
> hide #!6 models
> close #6
> show #!3 models
> show #!4 models
> hide #!3-4 atoms
> select clear
> select transporter
15524 atoms, 15906 bonds, 2 pseudobonds, 1962 residues, 6 models selected
> show #!7 models
> show #!11 models
> show #!12 models
> color sel #AA557F
> select ~sel
19028 atoms, 19440 bonds, 22 pseudobonds, 2430 residues, 22 models selected
> color sel #57a3ff
> select clear
> select #7/B:371
8 atoms, 7 bonds, 1 residue, 1 model selected
> select :371-800
13604 atoms, 13912 bonds, 22 pseudobonds, 1712 residues, 10 models selected
> name gpcr :371-800
> select clear
> select gpcr
13604 atoms, 13912 bonds, 22 pseudobonds, 1712 residues, 10 models selected
> color gpcr #ff9d26
> select clear
> select :NAG
28 atoms, 28 bonds, 2 residues, 1 model selected
> delete sel
> select :IAA
Nothing selected
> select clear
> show atoms
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select :IAC :E7O
50 atoms, 52 bonds, 4 residues, 3 models selected
> color sel #33d17aff
> color sel #2ec27eff
> select clear
> save /home/charles/Desktop/Bessie_Figures/MainFig2/FIG2_PANEL_A.cxs
> includeMaps true
——— End of log from Tue Sep 17 12:02:46 2024 ———
opened ChimeraX session
> hide #!4 models
> hide #!7 models
> hide #!11 models
> hide #!12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #4/B
Alignment identifier is 1
> select
> #3/B:39-61,67-92,95-97,100-124,127-142,146-158,163-195,203-215,218-233,239-250,252-264,273-301,307-321,327-336,340-369,372-403,406-408,412-435,440-473,481-502,512-514,517-543
> #4/B:39-61,67-92,95-97,100-124,127-142,146-158,163-195,203-215,218-233,239-250,252-264,273-301,307-321,327-336,340-369,372-403,406-408,412-435,440-473,481-502,512-514,517-543
6582 atoms, 6706 bonds, 844 residues, 2 models selected
> select #3/B:327 #4/B:327
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:327-328 #4/B:327-328
22 atoms, 22 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [293-294] RMSD: 33.952
> select #3/B:39 #4/B:39
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:39-61 #4/B:39-61
352 atoms, 358 bonds, 46 residues, 2 models selected
1 [ID: 1] region 2 chains [5-27] RMSD: 30.314
> select #3/B:66 #4/B:66
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #3/B:66-92 #4/B:66-92
408 atoms, 414 bonds, 54 residues, 2 models selected
1 [ID: 1] region 2 chains [32-58] RMSD: 20.397
> select #3/B:95 #4/B:95
22 atoms, 22 bonds, 2 residues, 2 models selected
> select #3/B:95-97 #4/B:95-97
50 atoms, 50 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [61-63] RMSD: 44.967
> select #3/B:100 #4/B:100
28 atoms, 30 bonds, 2 residues, 2 models selected
> select #3/B:100-142 #4/B:100-142
672 atoms, 692 bonds, 86 residues, 2 models selected
1 [ID: 1] region 2 chains [66-108] RMSD: 66.610
> set bgColor black
> select #3/B:39 #4/B:39
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:39-61 #4/B:39-61
352 atoms, 358 bonds, 46 residues, 2 models selected
1 [ID: 1] region 2 chains [5-27] RMSD: 30.314
> select #3/B:66-67 #4/B:66-67
26 atoms, 24 bonds, 4 residues, 2 models selected
> select #3/B:67-93 #4/B:67-93
410 atoms, 416 bonds, 54 residues, 2 models selected
1 [ID: 1] region 2 chains [33-59] RMSD: 21.295
> select #3/B:100-101 #4/B:100-101
40 atoms, 42 bonds, 4 residues, 2 models selected
> select #3/B:100-124 #4/B:100-124
402 atoms, 412 bonds, 50 residues, 2 models selected
1 [ID: 1] region 2 chains [66-90] RMSD: 67.873
> select #3/B:127 #4/B:127
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:127-158 #4/B:127-158
502 atoms, 518 bonds, 64 residues, 2 models selected
1 [ID: 1] region 2 chains [93-124] RMSD: 49.617
> select #3/B:162-163 #4/B:162-163
38 atoms, 40 bonds, 4 residues, 2 models selected
> select #3/B:163-195 #4/B:163-195
558 atoms, 576 bonds, 66 residues, 2 models selected
1 [ID: 1] region 2 chains [129-161] RMSD: 53.446
> select #3/B:202-203 #4/B:202-203
34 atoms, 32 bonds, 4 residues, 2 models selected
> select #3/B:203-234 #4/B:203-234
508 atoms, 516 bonds, 64 residues, 2 models selected
1 [ID: 1] region 2 chains [169-200] RMSD: 52.870
> select #3/B:239 #4/B:239
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #3/B:239-264 #4/B:239-264
396 atoms, 404 bonds, 52 residues, 2 models selected
1 [ID: 1] region 2 chains [205-230] RMSD: 20.248
> select #3/B:273-274 #4/B:273-274
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #3/B:273-301 #4/B:273-301
452 atoms, 454 bonds, 58 residues, 2 models selected
1 [ID: 1] region 2 chains [239-267] RMSD: 64.226
> select #3/B:307 #4/B:307
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #3/B:307-336 #4/B:307-336
460 atoms, 476 bonds, 60 residues, 2 models selected
1 [ID: 1] region 2 chains [273-302] RMSD: 46.285
> select clear
> open "/Users/chunyiqian/Desktop/Honours/Thesis/Figures/Lignd binding/PIN8 vs
> LYCHOS.cxs" format session
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 81, in msgpack_deserialize
return next(stream)
^^^^^^^^^^^^
TypeError: NoneType takes no arguments
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15Y00041X/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.2 (23B92)
Kernel Version: Darwin 23.1.0
Time since boot: 2 days, 20 hours, 53 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
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: 2022.12.7
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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-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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
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
setuptools-scm: 7.0.5
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: 1.0.8
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: 0.5.0
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 13 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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