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Opened 21 hours ago

#19875 new defect

ChimeraX bug report submission

Reported by:	disha-gajanan.hiregange@…	Owned by:
Priority:	normal	Milestone:
Component:	Unassigned	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:
Project:

Description

The following bug report has been submitted:
Platform:        Linux-5.14.0-427.20.1.el9_4.x86_64-x86_64-with-glibc2.34
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: Segmentation fault

Current thread 0x0000146f4aa6a740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/libexec/UCSF-ChimeraX/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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.mmcif.mmcif_write (total: 53)
===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
Registration file '/yonath_group/disha/.local/share/ChimeraX/registration' has
expired  
  
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  

> open
> /yonath_group/disha/Downloads/cryosparc_P7_J27_class_02_final_volume.mrc

Opened cryosparc_P7_J27_class_02_final_volume.mrc as #1, grid size
256,256,256, pixel 0.731, shown at level 0.0494, step 1, values float32  

> volume #1 level 0.1967

> volume #1 level 0.1867

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_01_final_volume.mrc

Opened cryosparc_P16_J79_class_01_final_volume.mrc as #2, grid size
256,256,256, pixel 0.731, shown at level 0.0402, step 1, values float32  

> volume #2 level 0.2499

> hide #!1 models

> show #!1 models

> close #2

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_02_final_volume.mrc

Opened cryosparc_P16_J79_class_02_final_volume.mrc as #2, grid size
256,256,256, pixel 0.731, shown at level 0.0279, step 1, values float32  

> volume #2 level 0.2515

> hide #!1 models

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_02_final_volume.mrc

Opened cryosparc_P16_J79_class_02_final_volume.mrc as #3, grid size
256,256,256, pixel 0.731, shown at level 0.0279, step 1, values float32  

> volume #3 level 0.1969

> close #3

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_01_final_volume.mrc

Opened cryosparc_P16_J79_class_01_final_volume.mrc as #3, grid size
256,256,256, pixel 0.731, shown at level 0.0402, step 1, values float32  

> volume #3 level 0.253

> close #3

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_00_final_volume.mrc

Opened cryosparc_P16_J79_class_00_final_volume.mrc as #3, grid size
256,256,256, pixel 0.731, shown at level 0.0287, step 1, values float32  

> volume #3 level 0.2394

> close #3

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J77_class_00_final_volume(1).mrc

Opened cryosparc_P16_J77_class_00_final_volume(1).mrc as #3, grid size
256,256,256, pixel 0.731, shown at level 0.0437, step 1, values float32  

> volume #3 level 0.04367

> volume #3 level 0.2108

> show #!1 models

> hide #!2 models

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.85999,-0.4012,0.31536,20.089,-0.21895,-0.8483,-0.48213,245.06,0.46095,0.34558,-0.81737,104.53

> ui tool show "Fit in Map"

> fitmap #3 inMap #1

Fit map cryosparc_P16_J77_class_00_final_volume(1).mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 38548 points  
correlation = 0.8584, correlation about mean = 0.3273, overlap = 2657  
steps = 176, shift = 11.2, angle = 28.8 degrees  
  
Position of cryosparc_P16_J77_class_00_final_volume(1).mrc (#3) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90127074 -0.39395040 -0.18031683 66.87233688  
-0.42971634 -0.75971525 -0.48803343 254.23932195  
0.05527152 0.51733533 -0.85399605 119.91675477  
Axis 0.97304248 -0.22801332 -0.03461594  
Axis point 0.00000000 117.79064354 97.60327569  
Rotation angle (degrees) 148.89480766  
Shift along axis 2.94864182  
  

> hide #!1 models

> select clear

> show #!1 models

> select subtract #3

Nothing selected  

> select add #3

2 models selected  

> view matrix models
> #3,0.89295,-0.39889,0.20864,29.409,-0.18823,-0.75186,-0.63189,245.08,0.40892,0.52497,-0.74645,75.194

> view matrix models
> #3,0.77939,-0.60763,-0.15274,95.999,-0.54369,-0.53479,-0.64684,259.3,0.31136,0.58718,-0.74717,78.51

> view matrix models
> #3,0.82065,-0.53147,-0.20995,90.539,-0.49655,-0.48142,-0.72227,257.28,0.28279,0.69698,-0.65898,61.938

> view matrix models
> #3,-0.87667,0.36488,-0.31354,175.04,0.41039,0.90729,-0.091629,-23.449,0.25104,-0.209,-0.94514,179.91

> view matrix models
> #3,0.62284,-0.7725,-0.12372,123.59,-0.099187,0.078897,-0.99194,193.23,0.77603,0.63009,-0.027482,-40.967

> view matrix models
> #3,0.40196,-0.86038,0.31331,109.26,-0.5802,-0.50404,-0.63977,259.1,0.70837,0.075378,-0.7018,85.487

> fitmap #3 inMap #1

Fit map cryosparc_P16_J77_class_00_final_volume(1).mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 38548 points  
correlation = 0.8584, correlation about mean = 0.3271, overlap = 2657  
steps = 216, shift = 1.13, angle = 50.7 degrees  
  
Position of cryosparc_P16_J77_class_00_final_volume(1).mrc (#3) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90122484 -0.39409116 -0.18023866 66.88673357  
-0.42980207 -0.75973589 -0.48792579 254.24483416  
0.05535346 0.51719779 -0.85407404 119.92599006  
Axis 0.97303083 -0.22806987 -0.03457068  
Axis point 0.00000000 117.80025224 97.59807135  
Rotation angle (degrees) 148.90282419  
Shift along axis 2.95134541  
  

> select clear

> set bgColor white

> set bgColor #ffffff00

> select subtract #3

Nothing selected  

> select clear

> hide #!1 models

> movie record

> turn y 2 180

> wait 180

> movie encode /yonath_group/disha/Desktop/movie7.mp4

Movie saved to /yonath_group/disha/Desktop/movie7.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /yonath_group/disha/Desktop/movie8.mp4

Movie saved to /yonath_group/disha/Desktop/movie8.mp4  
  

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode /yonath_group/disha/Desktop/movie9.mp4

Movie saved to /yonath_group/disha/Desktop/movie9.mp4  
  

> select clear

> volume #3 level 0.2602

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J77_class_02_final_volume.mrc

Opened cryosparc_P16_J77_class_02_final_volume.mrc as #4, grid size
256,256,256, pixel 0.731, shown at level 0.047, step 1, values float32  

> volume #4 level 0.2545

> hide #!3 models

> volume #4 level 0.2045

> show #!1 models

> select add #4

2 models selected  

> view matrix models
> #4,-0.70246,0.67928,-0.21242,110.57,-0.0054951,-0.30363,-0.95277,203.09,-0.7117,-0.66812,0.21702,194.04

> view matrix models
> #4,-0.69808,0.71492,0.03966,85.08,-0.5685,-0.58707,0.57633,148.12,0.43531,0.37977,0.81626,-58.694

> view matrix models
> #4,0.59636,0.79373,-0.11981,-26.093,-0.76871,0.60768,0.19952,88.802,0.23117,-0.026885,0.97254,-16.167

> view matrix models
> #4,-0.95426,0.10569,-0.27967,192.16,-0.086622,-0.99305,-0.079725,198.48,-0.28615,-0.051852,0.95678,34.539

> view matrix models
> #4,-0.96323,0.14855,-0.22388,184.2,-0.22213,-0.90906,0.35251,165.67,-0.15115,0.38927,0.90864,-14.233

> view matrix models
> #4,0.8776,0.47527,0.062718,-38.104,-0.35587,0.55821,0.74951,8.2407,0.32121,-0.68009,0.65902,62.978

> help help:user/tools/modelpanel.html

> fitmap #4 inMap #1

Fit map cryosparc_P16_J77_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 41793 points  
correlation = 0.8586, correlation about mean = 0.3621, overlap = 2729  
steps = 128, shift = 3.38, angle = 22.5 degrees  
  
Position of cryosparc_P16_J77_class_02_final_volume.mrc (#4) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93911177 0.31374969 0.14010788 -33.65669748  
-0.34088529 0.79942801 0.49468381 8.10688494  
0.04320073 -0.51232410 0.85770490 56.98221648  
Axis -0.83569758 0.08042148 -0.54326968  
Axis point 0.00000000 102.06922855 24.64239030  
Rotation angle (degrees) 37.04882841  
Shift along axis -2.17792210  
  

> view matrix models
> #4,-0.9125,0.38527,0.13749,128.35,-0.34944,-0.90888,0.22765,189.45,0.21267,0.15969,0.96399,-29.566

> fitmap #4 inMap #1

Fit map cryosparc_P16_J77_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 41793 points  
correlation = 0.8762, correlation about mean = 0.2256, overlap = 2920  
steps = 100, shift = 6.48, angle = 11.5 degrees  
  
Position of cryosparc_P16_J77_class_02_final_volume.mrc (#4) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.93045758 0.36148348 -0.05981949 152.85558229  
-0.36505580 -0.90063650 0.23577138 191.88868304  
0.03135184 0.24121273 0.96996571 -26.49425280  
Axis 0.00743092 -0.12450719 -0.99219088  
Axis point 94.70952291 83.00069082 0.00000000  
Rotation angle (degrees) 158.52293337  
Shift along axis 3.53169215  
  

> select clear

> volume #4 level 0.192

> volume #1 level 0.1568

> select clear

> volume #1 level 0.1936

> hide #3.1 models

> hide #!1 models

> volume #4 level 0.192

> lighting soft

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J77_class_01_final_volume.mrc

Opened cryosparc_P16_J77_class_01_final_volume.mrc as #5, grid size
256,256,256, pixel 0.731, shown at level 0.0477, step 1, values float32  

> volume #5 level 0.1868

> hide #!4 models

> fitmap #5 inMap #1

Fit map cryosparc_P16_J77_class_01_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 47804 points  
correlation = 0.788, correlation about mean = 0.04834, overlap = 2376  
steps = 152, shift = 13.3, angle = 7.73 degrees  
  
Position of cryosparc_P16_J77_class_01_final_volume.mrc (#5) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99113912 -0.13096813 0.02214913 12.67298003  
0.13140308 0.99113779 -0.01947102 -14.85242477  
-0.01940275 0.02220896 0.99956505 -12.41643049  
Axis 0.15500691 0.15453050 0.97575262  
Axis point 105.43125961 104.36127273 -0.00000000  
Rotation angle (degrees) 7.72656036  
Shift along axis -12.44611776  
  

> show #!1 models

> show #!4 models

> select add #5

2 models selected  

> view matrix models
> #5,-0.1339,0.72142,-0.67942,110.18,0.77654,-0.34955,-0.52421,96.105,-0.61567,-0.5978,-0.51341,249.2

> view matrix models
> #5,0.92068,0.2871,-0.26442,8.6431,0.32677,-0.93747,0.11989,131.1,-0.21346,-0.19679,-0.95693,216.57

> view matrix models
> #5,-0.90562,-0.39454,0.15553,206.38,-0.37034,0.55701,-0.74336,143.83,0.20665,-0.7308,-0.65056,195.78

> view matrix models
> #5,-0.91493,-0.38333,0.12635,209.08,-0.35087,0.60068,-0.71838,135.5,0.19948,-0.7016,-0.68408,197.03

> view matrix models
> #5,-0.74912,-0.35728,0.55783,148.81,-0.62392,0.66349,-0.41292,126.26,-0.22258,-0.65737,-0.71995,236.99

> fitmap #5 inMap #1

Fit map cryosparc_P16_J77_class_01_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 47804 points  
correlation = 0.8288, correlation about mean = 0.3821, overlap = 2672  
steps = 568, shift = 10.8, angle = 67.4 degrees  
  
Position of cryosparc_P16_J77_class_01_final_volume.mrc (#5) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.87350214 0.44464443 -0.19820524 156.51026581  
0.45951556 0.61864043 -0.63728286 56.63939311  
-0.16074650 -0.64774634 -0.74470478 240.14299773  
Axis -0.25129144 -0.89961078 0.35714571  
Axis point 68.94561833 0.00000000 132.21347308  
Rotation angle (degrees) 178.80704917  
Shift along axis -4.51705688  
  

> view matrix models
> #5,0.97198,-0.18322,-0.14725,32.217,-0.10655,-0.90182,0.41876,148.99,-0.20952,-0.39134,-0.89608,235.84

> view matrix models
> #5,0.96274,-0.19231,-0.19011,38.109,-0.16742,-0.97598,0.1394,188.83,-0.21235,-0.10238,-0.97182,216.76

> fitmap #5 inMap #1

Fit map cryosparc_P16_J77_class_01_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 47804 points  
correlation = 0.8983, correlation about mean = 0.2635, overlap = 3239  
steps = 144, shift = 7.24, angle = 31.3 degrees  
  
Position of cryosparc_P16_J77_class_01_final_volume.mrc (#5) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96268689 0.26941507 0.02548436 -24.08002956  
0.27060987 -0.95909692 -0.08308650 168.56546300  
0.00205722 0.08688261 -0.99621642 174.08279738  
Axis 0.99061042 0.13653759 0.00696350  
Axis point 0.00000000 82.16628964 90.78124643  
Rotation angle (degrees) 175.07854037  
Shift along axis 0.37381954  
  

> hide #!4 models

> show #!4 models

> hide #!4 models

> select subtract #5

Nothing selected  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #5 level 0.2241

> show #!4 models

> hide #!5 models

> volume #4 level 0.2282

> show #!5 models

> show #!2 models

> hide #!4 models

> hide #!5 models

> fitmap #2 inMap #1

Fit map cryosparc_P16_J79_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 26177 points  
correlation = 0.9292, correlation about mean = 0.3552, overlap = 2830  
steps = 108, shift = 3.17, angle = 18.1 degrees  
  
Position of cryosparc_P16_J79_class_02_final_volume.mrc (#2) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96016647 -0.25738504 -0.10878092 39.39855353  
0.27011868 0.95460611 0.12555110 -32.81702593  
0.07152796 -0.14993371 0.98610528 5.74365645  
Axis -0.44302798 -0.28996835 0.84831867  
Axis point 145.82720285 125.22592241 0.00000000  
Rotation angle (degrees) 18.11415832  
Shift along axis -3.06631178  
  

> select add #2

2 models selected  

> view matrix models
> #2,0.66032,-0.69869,0.27533,75.666,0.1223,0.46178,0.87852,-39.484,-0.74096,-0.54643,0.39037,175.29

> view matrix models
> #2,-0.71261,-0.40805,0.57069,151.06,0.69945,-0.35027,0.62295,7.4672,-0.0543,0.84309,0.53502,-37.395

> view matrix models
> #2,0.064443,-0.79562,0.60236,111.91,0.66686,0.48339,0.56713,-64.992,-0.74239,0.36514,0.56172,71.715

> view matrix models
> #2,-0.21016,0.70549,-0.67684,108.94,-0.60992,0.44646,0.65474,51.814,0.76409,0.55042,0.33646,-68.745

> view matrix models
> #2,0.38183,0.77486,-0.50378,30.327,-0.2961,0.61891,0.72751,-1.2563,0.87552,-0.12861,0.46576,-25.392

> fitmap #2 inMap #1

Fit map cryosparc_P16_J79_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 26177 points  
correlation = 0.9292, correlation about mean = 0.3553, overlap = 2830  
steps = 304, shift = 4.87, angle = 79.5 degrees  
  
Position of cryosparc_P16_J79_class_02_final_volume.mrc (#2) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96040678 -0.25665744 -0.10837787 39.25458383  
0.26935905 0.95477577 0.12589246 -32.79066002  
0.07116533 -0.15010054 0.98610614 5.79287158  
Axis -0.44474452 -0.28932204 0.84764088  
Axis point 146.02977179 125.11410477 0.00000000  
Rotation angle (degrees) 18.07626426  
Shift along axis -3.06092591  
  

> view matrix models
> #2,-0.92937,0.12406,-0.34768,203.53,-0.17878,-0.97528,0.12988,196.04,-0.32297,0.18286,0.92857,16.226

> view matrix models
> #2,0.57378,0.80022,-0.17445,-20.257,-0.79124,0.48661,-0.37034,158.2,-0.21146,0.35052,0.91237,-9.101

> view matrix models
> #2,-0.55724,0.71479,-0.42256,117.88,-0.73791,-0.65964,-0.14272,243.33,-0.38075,0.23228,0.89503,19.977

> view matrix models
> #2,-0.71337,0.47227,-0.51776,164.8,-0.54138,-0.84052,-0.020754,231.1,-0.44499,0.2655,0.85528,26.47

> view matrix models
> #2,0.59293,0.76899,0.23891,-56.582,-0.70536,0.63912,-0.30658,129.52,-0.38845,0.013262,0.92138,39.496

> view matrix models
> #2,0.68218,0.5837,-0.44038,14.534,-0.69824,0.69879,-0.15542,109.35,0.21701,0.41351,0.88426,-53.31

> view matrix models
> #2,0.047247,0.86003,-0.50804,54.22,-0.98694,0.1186,0.10899,168.85,0.15399,0.49626,0.85441,-52.62

> view matrix models
> #2,-0.84736,0.50567,-0.16211,142,-0.53081,-0.79804,0.28525,198.2,0.014874,0.32776,0.94464,-31.313

> view matrix models
> #2,-0.84771,0.50553,-0.16071,141.92,-0.53013,-0.79656,0.29063,197.51,0.018902,0.33156,0.94324,-31.936

> view matrix models
> #2,0.48022,0.87671,-0.027598,-32.107,-0.8669,0.47917,0.13741,120.01,0.13369,-0.042063,0.99013,-10.955

> view matrix models
> #2,0.46618,0.87784,0.10986,-43.362,-0.71998,0.30429,0.62373,78.826,0.51411,-0.36987,0.77388,4.2696

> fitmap #2 inMap #1

Fit map cryosparc_P16_J79_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 26177 points  
correlation = 0.9292, correlation about mean = 0.3553, overlap = 2830  
steps = 252, shift = 3.82, angle = 83.1 degrees  
  
Position of cryosparc_P16_J79_class_02_final_volume.mrc (#2) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96040300 -0.25666463 -0.10839430 39.25674884  
0.26936848 0.95477350 0.12588955 -32.79075986  
0.07118061 -0.15010271 0.98610470 5.79215335  
Axis -0.44472689 -0.28936244 0.84763635  
Axis point 146.02677597 125.11833286 0.00000000  
Rotation angle (degrees) 18.07695535  
Shift along axis -3.06047792  
  

> view matrix models
> #2,0.67414,-0.65212,0.34681,63.347,0.65809,0.7435,0.11883,-48.615,-0.33534,0.14812,0.93038,20.596

> fitmap #2 inMap #1

Fit map cryosparc_P16_J79_class_02_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 26177 points  
correlation = 0.9292, correlation about mean = 0.3552, overlap = 2830  
steps = 144, shift = 2.56, angle = 39.2 degrees  
  
Position of cryosparc_P16_J79_class_02_final_volume.mrc (#2) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.96023322 -0.25711721 -0.10882499 39.37074853  
0.26986029 0.95467693 0.12556817 -32.80059387  
0.07160697 -0.14994227 0.98609824 5.73765822  
Axis -0.44335386 -0.29035273 0.84801689  
Axis point 145.88498463 125.27414900 0.00000000  
Rotation angle (degrees) 18.10212504  
Shift along axis -3.06580032  
  

> select clear

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> volume #5 level 0.2399

> show #!4 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!4 models

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_01_final_volume.mrc

Opened cryosparc_P16_J79_class_01_final_volume.mrc as #6, grid size
256,256,256, pixel 0.731, shown at level 0.0402, step 1, values float32  

> volume #6 level 0.2597

> close #6

> open
> /yonath_group/disha/Downloads/cryosparc_P16_J79_class_00_final_volume.mrc

Opened cryosparc_P16_J79_class_00_final_volume.mrc as #6, grid size
256,256,256, pixel 0.731, shown at level 0.0287, step 1, values float32  

> volume #6 level 0.2386

> hide #!2 models

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 27804 points  
correlation = 0.9167, correlation about mean = 0.5117, overlap = 2693  
steps = 148, shift = 4.64, angle = 33.5 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84978281 -0.26254971 -0.45709608 86.27782120  
0.34297505 0.93387546 0.10121631 -34.95634478  
0.40029650 -0.24278443 0.88363931 -5.04807519  
Axis -0.31142847 -0.77620899 0.54818967  
Axis point 58.01269473 0.00000000 167.98161127  
Rotation angle (degrees) 33.52459783  
Shift along axis -2.50324381  
  

> show #!4 models

> select add #6

2 models selected  

> view matrix models
> #6,-0.86045,0.34183,-0.37787,180.99,-0.11623,-0.85371,-0.50761,233.94,-0.49611,-0.39285,0.7743,102.89

> view matrix models
> #6,-0.90676,-0.31594,-0.27923,239.89,0.41179,-0.80596,-0.42528,172.69,-0.090683,-0.50061,0.86091,67.682

> view matrix models
> #6,-0.48565,-0.82415,-0.29142,250.51,0.85542,-0.37942,-0.35255,83.718,0.17998,-0.4205,0.88926,32.156

> view matrix models
> #6,0.059625,-0.99211,-0.11031,199.65,0.93367,0.094521,-0.34543,30.158,0.35313,-0.0824,0.93194,-20.352

> view matrix models
> #6,-0.050661,-0.9986,0.015073,199.48,0.14702,-0.022385,-0.98888,171.94,0.98784,-0.047881,0.14795,-13.579

> view matrix models
> #6,0.11052,-0.98682,-0.11823,195.09,0.99272,0.11534,-0.034728,-4.8837,0.047906,-0.11353,0.99238,5.827

> view matrix models
> #6,0.91383,-0.36697,-0.17392,65.26,0.34619,0.92784,-0.13878,-13.421,0.2123,0.066607,0.97493,-25.334

> view matrix models
> #6,0.94157,0.33291,-0.051113,-15.569,-0.33611,0.91896,-0.20624,57.199,-0.021689,0.21137,0.97717,-17.588

> view matrix models
> #6,0.92418,0.37839,-0.052015,-18.241,-0.37306,0.92347,0.089583,34.019,0.081932,-0.063386,0.99462,-2.3785

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 27804 points  
correlation = 0.9167, correlation about mean = 0.5118, overlap = 2693  
steps = 168, shift = 0.966, angle = 46.4 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84977236 -0.26251933 -0.45713296 86.29395510  
0.34294525 0.93388821 0.10119964 -34.95321889  
0.40034422 -0.24276824 0.88362215 -5.05013189  
Axis -0.31139240 -0.77626980 0.54812405  
Axis point 58.01918887 0.00000000 167.99804016  
Rotation angle (degrees) 33.52536929  
Shift along axis -2.50625216  
  

> view matrix models
> #6,-0.90446,-0.41315,-0.10614,233.71,0.39771,-0.90671,0.14038,133.6,-0.15424,0.084749,0.98439,6.3529

> view matrix models
> #6,-0.14747,-0.77087,0.61969,133.08,0.9869,-0.073247,0.14374,-1.9963,-0.065416,0.63277,0.77157,-35.846

> view matrix models
> #6,-0.90869,0.24005,0.34154,131.59,0.031169,-0.77684,0.62892,112.1,0.4163,0.58214,0.69843,-69.532

> view matrix models
> #6,-0.56128,0.80794,0.17944,58.814,-0.4606,-0.48508,0.74333,119.87,0.68761,0.33457,0.64441,-66.285

> view matrix models
> #6,-0.7438,0.61212,-0.26847,134.39,-0.61062,-0.4589,0.64541,140.05,0.27186,0.64399,0.7151,-63.457

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 27804 points  
correlation = 0.9157, correlation about mean = 0.375, overlap = 2371  
steps = 172, shift = 4.23, angle = 22.6 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.54203568 0.83606074 -0.08485147 76.94666622  
-0.75592974 -0.44097972 0.48384618 163.35594583  
0.36710702 0.32640364 0.87102991 -58.97755177  
Axis -0.09470944 -0.27187528 -0.95766067  
Axis point 87.31224650 68.46294265 0.00000000  
Rotation angle (degrees) 123.77911972  
Shift along axis 4.78046159  
  

> select subtract #6

Nothing selected  

> hide #!4 models

> show #!5 models

> show #!4 models

> hide #!6 models

> hide #!5 models

> show #!6 models

> select add #6

2 models selected  

> view matrix models
> #6,-0.67969,-0.64453,0.35015,193.79,0.7334,-0.58924,0.339,51.213,-0.012171,0.48721,0.8732,-39.187

> view matrix models
> #6,-0.93028,0.048599,-0.36361,213.72,-0.21974,-0.86751,0.44625,157.61,-0.29374,0.49504,0.81771,-8.7005

> view matrix models
> #6,-0.89649,-0.4399,0.052925,220.68,0.3663,-0.66865,0.64709,65.89,-0.24927,0.5995,0.76057,-17.852

> view matrix models
> #6,-0.89265,-0.44643,0.062227,220.13,0.37613,-0.66168,0.64861,64.165,-0.24839,0.60239,0.75857,-18.035

> view matrix models
> #6,-0.7433,0.46788,0.47811,81.339,-0.60265,-0.77858,-0.17501,239.87,0.29037,-0.41822,0.86069,20.778

> view matrix models
> #6,0.5523,0.76239,0.33723,-55.657,-0.62983,0.64662,-0.43035,127.86,-0.54615,0.025285,0.83731,58.372

> view matrix models
> #6,0.31919,0.78703,0.52793,-53.124,-0.76005,0.54534,-0.35345,142.97,-0.56607,-0.28843,0.77225,96.19

> view matrix models
> #6,0.47557,0.8327,0.28361,-50.502,-0.87644,0.4209,0.23386,113.81,0.075358,-0.35979,0.92999,29.118

> view matrix models
> #6,0.97065,0.11236,0.21264,-21.174,-0.18289,0.91901,0.34925,-9.1871,-0.15617,-0.37789,0.91258,54.048

> view matrix models
> #6,0.96521,-0.18177,0.18798,9.8267,0.091706,0.90853,0.40764,-39.023,-0.24488,-0.37622,0.89358,63.864

> view matrix models
> #6,0.92587,-0.34855,0.14587,33.285,0.25667,0.86351,0.43414,-52.46,-0.27728,-0.36451,0.88896,66.176

> view matrix models
> #6,0.88949,-0.42536,0.16696,42.211,0.31195,0.83223,0.45834,-56.761,-0.33391,-0.3556,0.87296,72.03

> view matrix models
> #6,0.87055,-0.42179,0.25345,35.978,0.34847,0.89209,0.28765,-50.82,-0.34742,-0.1621,0.92359,50.185

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 27804 points  
correlation = 0.9167, correlation about mean = 0.5118, overlap = 2693  
steps = 176, shift = 5.28, angle = 44.2 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.84973461 -0.26250743 -0.45720998 86.30033476  
0.34295888 0.93388239 0.10120725 -34.95599124  
0.40041269 -0.24280352 0.88358143 -5.05201934  
Axis -0.31139535 -0.77631208 0.54806249  
Axis point 58.02624941 -0.00000000 167.97701900  
Rotation angle (degrees) 33.52974210  
Shift along axis -2.50558731  
  

> view matrix models
> #6,0.68194,-0.63829,-0.35712,129.29,0.73004,0.62388,0.27896,-57.052,0.044748,-0.45094,0.89143,47.537

> view matrix models
> #6,-0.028914,-0.93857,-0.34387,223.48,0.90951,-0.16742,0.38049,-6.666,-0.41468,-0.30175,0.85848,79.049

> view matrix models
> #6,0.27408,-0.9615,0.020127,165.12,0.95322,0.27438,0.12683,-30.807,-0.12747,-0.015576,0.99172,12.854

> view matrix models
> #6,-0.9059,0.38702,-0.17192,162.66,-0.41589,-0.88959,0.18887,203.72,-0.07984,0.2426,0.96684,-14.242

> view matrix models
> #6,-0.87843,-0.25374,0.40493,170.67,0.44364,-0.74797,0.49369,82.737,0.17761,0.61331,0.76961,-56.523

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 27804 points  
correlation = 0.8898, correlation about mean = 0.2619, overlap = 2329  
steps = 120, shift = 8.27, angle = 22.2 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.95799129 -0.28531561 0.02911546 210.33148493  
0.25578317 -0.80406204 0.53671148 96.09018009  
-0.12972153 0.52161217 0.84326336 -25.67858521  
Axis -0.02676557 0.28155990 0.95917028  
Axis point 97.52897469 67.59121658 0.00000000  
Rotation angle (degrees) 163.61644720  
Shift along axis -3.20463605  
  

> select clear

> select subtract #6

Nothing selected  

> hide #!4 models

> show #!4 models

> hide #!6 models

> volume #4 level 0.2082

> show #!1 models

> hide #!4 models

> show #!6 models

> hide #!1 models

> volume #6 level 0.2136

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!6 models

> transparency #4.1 50

> graphics silhouettes true

> show #!1 models

> select add #1

2 models selected  

> view matrix models
> #1,-0.75921,0.34162,-0.55398,187.7,-0.63106,-0.17808,0.75502,107.54,0.15927,0.92281,0.35078,-46.477

> view matrix models
> #1,0.87614,-0.35268,-0.32864,75.335,0.36784,0.92973,-0.0171,-27.501,0.31158,-0.1059,0.9443,-15.151

> view matrix models
> #1,0.99091,-0.11718,-0.066012,18.059,0.12425,0.98547,0.11576,-21.017,0.051488,-0.12291,0.99108,7.6242

> view matrix models
> #1,0.68729,0.04114,-0.72522,91.152,-0.065587,0.99783,-0.0055531,7.0865,0.72341,0.051382,0.6885,-47.56

> view matrix models
> #1,-0.93605,-0.29924,-0.18512,233.73,-0.016543,-0.4881,0.87263,67.108,-0.35149,0.81989,0.45193,4.1174

> view matrix models
> #1,-0.5677,-0.82321,0.0067041,231.24,0.69723,-0.47646,0.53559,26.592,-0.43771,0.30872,0.84445,26.731

> view matrix models
> #1,-0.86119,-0.50635,-0.044339,233.84,0.22416,-0.45664,0.86095,41.697,-0.45619,0.7315,0.50676,17.929

> view matrix models
> #1,-0.96392,-0.26082,0.053256,211.48,0.13415,-0.30314,0.94346,28.312,-0.22993,0.91656,0.32719,-5.8971

> view matrix models
> #1,-0.99618,0.067078,-0.055858,192.77,-0.086988,-0.70967,0.69914,110.78,0.0072554,0.70133,0.7128,-42.641

> view matrix models
> #1,-0.91759,-0.29801,-0.2631,238.77,0.22221,-0.93329,0.28212,139.42,-0.32963,0.20041,0.9226,19.677

> view matrix models
> #1,0.86029,-0.37111,-0.34953,80.516,0.21915,0.88825,-0.40371,25.446,0.46029,0.27071,0.84549,-57.084

> view matrix models
> #1,-0.77949,-0.32028,-0.53834,252.03,-0.29046,-0.57663,0.76363,112.01,-0.555,0.75161,0.35645,39.014

> view matrix models
> #1,-0.77688,-0.57297,-0.26107,251.38,0.25216,-0.66305,0.70483,72.779,-0.57695,0.48174,0.65959,40.105

> volume flip #1

Opened cryosparc_P7_J27_class_02_final_volume.mrc z flip as #7, grid size
256,256,256, pixel 0.731, shown at step 1, values float32  

> select subtract #1

Nothing selected  

> select add #7

2 models selected  

> view matrix models
> #7,0.994,0.086344,0.067105,-16.349,0.062911,0.050418,-0.99674,187.89,-0.089446,0.99499,0.044683,3.0061

> view matrix models
> #7,-0.93326,-0.28349,0.22059,191.89,-0.19001,0.91077,0.36659,-2.902,-0.30483,0.30021,-0.90385,183.09

> view matrix models
> #7,-0.94108,0.18103,0.28565,141.59,0.28495,0.87937,0.38146,-47.541,-0.18213,0.44038,-0.87914,155.25

> view matrix models
> #7,0.9052,-0.28359,0.31654,3.6762,-0.074984,-0.83969,-0.53786,242.43,0.41833,0.46313,-0.78135,85.123

> view matrix models
> #7,0.99492,-0.047208,0.088903,-5.6941,0.043394,-0.59577,-0.80198,233.09,0.090826,0.80176,-0.5907,65.841

> view matrix models
> #7,-0.89299,-0.10787,0.43696,150.03,0.094003,0.90474,0.41546,-34.709,-0.44015,0.41208,-0.79778,175.18

> fitmap #6 inMap #1

Fit map cryosparc_P16_J79_class_00_final_volume.mrc in map
cryosparc_P7_J27_class_02_final_volume.mrc using 32876 points  
correlation = 0.9089, correlation about mean = 0.5243, overlap = 2881  
steps = 80, shift = 5.38, angle = 6.02 degrees  
  
Position of cryosparc_P16_J79_class_00_final_volume.mrc (#6) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.85958848 -0.25097388 -0.44510646 83.08147756  
0.32660862 0.93976286 0.10085917 -33.99872453  
0.39298151 -0.23207298 0.88977956 -5.97357944  
Axis -0.31088869 -0.78259811 0.53934073  
Axis point 58.54054080 0.00000000 166.48160781  
Rotation angle (degrees) 32.37459266  
Shift along axis -2.44354905  
  

> fitmap #7 inMap #1

Fit map cryosparc_P7_J27_class_02_final_volume.mrc z flip in map
cryosparc_P7_J27_class_02_final_volume.mrc using 43313 points  
correlation = 0.8607, correlation about mean = 0.2633, overlap = 2864  
steps = 204, shift = 6, angle = 30 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc z flip (#7) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99767290 0.06595270 0.01729254 -7.77850117  
0.06076820 -0.74510204 -0.66417630 222.96170092  
-0.03091951 0.66368153 -0.74737596 102.12076494  
Axis 0.99933390 0.03628395 -0.00390180  
Axis point 0.00000000 92.19576233 93.45960763  
Rotation angle (degrees) 138.36587696  
Shift along axis -0.08184299  
  

> view matrix models
> #7,0.72514,-0.63995,0.25424,65.503,-0.43451,-0.71166,-0.55204,264.16,0.53421,0.28983,-0.79412,85.44

> view matrix models
> #7,-0.75375,-0.59914,-0.26998,256.44,-0.62826,0.77747,0.028643,83.135,0.19274,0.19121,-0.96244,144.53

> view matrix models
> #7,-0.23305,0.36474,0.90147,-0.94548,0.88032,0.47299,0.036209,-35.073,-0.41318,0.80202,-0.43132,93.029

> view matrix models
> #7,0.53759,-0.81176,0.22812,102.84,0.010837,-0.26387,-0.9645,217.79,0.84314,0.52098,-0.13306,-31.148

> view matrix models
> #7,0.99992,0.0043011,-0.011522,2.5441,0.00091805,-0.96035,-0.27881,219.18,-0.012265,0.27878,-0.96028,155.83

> view matrix models
> #7,-0.92946,0.34504,-0.13058,169.05,0.31496,0.92645,0.20615,-40.255,0.19211,0.15048,-0.96977,149.23

> view matrix models
> #7,0.9717,0.23616,-0.0061973,-17.559,0.20421,-0.85286,-0.48054,208.66,-0.11877,0.46567,-0.87695,140.1

> view matrix models
> #7,0.85137,0.34486,-0.39528,21.504,0.042431,-0.79634,-0.60336,230.9,-0.52285,0.49691,-0.69261,158.49

> view matrix models
> #7,0.94317,0.26441,0.20129,-37.674,0.32753,-0.84205,-0.42857,190.56,0.05618,0.47014,-0.8808,123.02

> fitmap #7 inMap #1

Fit map cryosparc_P7_J27_class_02_final_volume.mrc z flip in map
cryosparc_P7_J27_class_02_final_volume.mrc using 43313 points  
correlation = 0.8856, correlation about mean = 0.5935, overlap = 3193  
steps = 312, shift = 7.57, angle = 46.3 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc z flip (#7) relative to
cryosparc_P7_J27_class_02_final_volume.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99526447 -0.09566577 0.01722491 194.43498620  
-0.09559274 0.99540789 0.00501634 8.96763050  
-0.01762570 0.00334603 -0.99983906 187.86282757  
Axis -0.04787269 0.99885125 0.00209308  
Axis point 98.25272955 0.00000000 93.07297290  
Rotation angle (degrees) 179.00040464  
Shift along axis 0.04241615  
  

> view matrix models
> #7,0.83228,-0.49959,0.24024,46.875,-0.19564,-0.6702,-0.71593,247.92,0.51868,0.54886,-0.65553,53.685

> view matrix models
> #7,0.60192,-0.067442,0.79571,-26.33,0.7052,-0.42262,-0.56928,122.16,0.37468,0.90379,-0.20682,-10.108

> view matrix models
> #7,0.41824,0.0037376,0.90833,-26.261,0.90766,0.036793,-0.41808,43.51,-0.034983,0.99932,0.011996,-0.71611

> show #!1 models

> view matrix models
> #7,0.32592,0.49873,0.80315,-54.73,0.94081,-0.087531,-0.32744,43.447,-0.093001,0.86233,-0.49774,67.676

> select subtract #7

Nothing selected  

> hide #!7 models

> select add #1

2 models selected  

> view matrix models
> #1,0.1694,-0.95181,0.25567,149.7,0.97255,0.11945,-0.19968,7.9842,0.15951,0.28248,0.94592,-37.907

> view matrix models
> #1,0.3127,0.67838,-0.66484,60.84,-0.93963,0.32334,-0.11202,166.6,0.13897,0.65973,0.73854,-53.747

> view matrix models
> #1,0.76611,-0.64109,-0.045639,88.58,0.63401,0.76547,-0.10991,-29.303,0.1054,0.055266,0.99289,-14.945

> view matrix models
> #1,0.81566,-0.57832,-0.015393,75.014,0.57644,0.81469,-0.063285,-32.599,0.04914,0.042746,0.99788,-8.7096

> select subtract #1

Nothing selected  

> fitmap #1 inMap #4

Fit map cryosparc_P7_J27_class_02_final_volume.mrc in map
cryosparc_P16_J77_class_02_final_volume.mrc using 43313 points  
correlation = 0.9097, correlation about mean = 0.2739, overlap = 3105  
steps = 108, shift = 2.07, angle = 33.2 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc (#1) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.94340860 -0.32771983 0.05079327 209.00224009  
0.33073063 -0.91845265 0.21693777 130.60757068  
-0.02444360 0.22145984 0.97486310 -12.95470702  
Axis 0.00682318 0.11352219 0.99351203  
Axis point 93.37125559 83.97618991 0.00000000  
Rotation angle (degrees) 160.64773551  
Shift along axis 3.38225914  
  

> show #!7 models

> color #7 #aaffffff models

> fitmap #7 inMap #4

Fit map cryosparc_P7_J27_class_02_final_volume.mrc z flip in map
cryosparc_P16_J77_class_02_final_volume.mrc using 43313 points  
correlation = 0.8847, correlation about mean = 0.3967, overlap = 2849  
steps = 196, shift = 9.52, angle = 44.9 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc z flip (#7) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.91946248 -0.38830765 0.06169233 210.43444660  
-0.29316589 0.78164471 0.55053185 -6.34251478  
-0.26199721 0.48810729 -0.83253154 147.19551499  
Axis -0.18193804 0.94340184 0.27729320  
Axis point 111.39121988 0.00000000 64.92051521  
Rotation angle (degrees) 170.12179030  
Shift along axis -3.45325614  
  

> hide #!1 models

> select add #7

2 models selected  

> view matrix models
> #7,-0.90999,0.38861,0.14454,135.3,0.26072,0.80738,-0.5293,43.608,-0.32239,-0.44397,-0.83603,239.52

> view matrix models
> #7,-0.90424,0.21928,0.36642,129.48,0.12226,0.9551,-0.26988,17.635,-0.40914,-0.19924,-0.89045,229.68

> view matrix models
> #7,-0.92125,0.29979,-0.24782,183.09,0.38825,0.74721,-0.53939,37.975,0.023468,-0.59313,-0.80476,217.2

> view matrix models
> #7,-0.42506,-0.72227,-0.54557,262.2,-0.90105,0.39502,0.17907,127.52,0.08618,0.5677,-0.81871,100.64

> view matrix models
> #7,-0.52293,-0.83576,-0.16748,245.9,-0.80121,0.54901,-0.238,143.51,0.29086,0.0097265,-0.95672,147.88

> view matrix models
> #7,-0.6864,-0.72722,0.002243,234.85,-0.72677,0.68586,-0.037394,103.59,0.025655,-0.027297,-0.9993,181.39

> fitmap #7 inMap #4

Fit map cryosparc_P7_J27_class_02_final_volume.mrc z flip in map
cryosparc_P16_J77_class_02_final_volume.mrc using 43313 points  
correlation = 0.881, correlation about mean = 0.4247, overlap = 2787  
steps = 144, shift = 11, angle = 27.1 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc z flip (#7) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99735307 -0.02822267 -0.06701016 10.67341326  
-0.04356609 -0.96980253 -0.23996890 210.37565622  
-0.05821405 0.24225309 -0.96846507 168.28335363  
Axis 0.99932812 -0.01822853 -0.03179677  
Axis point 0.00000000 94.97261555 97.20154205  
Rotation angle (degrees) 166.03830807  
Shift along axis 1.48053657  
  

> view matrix models
> #7,0.6298,0.5418,0.5566,-79.543,0.75208,-0.24613,-0.61139,107.02,-0.19426,0.80366,-0.56249,83.383

> view matrix models
> #7,-0.85386,-0.021992,0.52005,122.69,0.32314,0.76086,0.56273,-62.371,-0.40806,0.64854,-0.64256,126.91

> view matrix models
> #7,0.94855,0.1703,0.26694,-46.619,0.31419,-0.61091,-0.72669,195.97,0.039323,0.77317,-0.63298,70.443

> fitmap #7 inMap #4

Fit map cryosparc_P7_J27_class_02_final_volume.mrc z flip in map
cryosparc_P16_J77_class_02_final_volume.mrc using 43313 points  
correlation = 0.8847, correlation about mean = 0.3969, overlap = 2849  
steps = 156, shift = 10.3, angle = 28.5 degrees  
  
Position of cryosparc_P7_J27_class_02_final_volume.mrc z flip (#7) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.91937031 -0.38850250 0.06183897 210.43612773  
-0.29323291 0.78156244 0.55061295 -6.33460346  
-0.26224552 0.48808398 -0.83246702 147.21234291  
Axis -0.18201581 0.94337878 0.27732061  
Axis point 111.40206671 0.00000000 64.91544413  
Rotation angle (degrees) 170.10937231  
Shift along axis -3.45361760  
  

> show #!1 models

> select subtract #7

Nothing selected  

> hide #!7 models

> open
> /yonath_group/disha/protoribosome/CryoEM_data_processing/A1P1_50um_03022025/models/P1(1).pdb

Chain information for P1(1).pdb #8  
---  
Chain | Description  
0 | No description available  
  

> select add #8

1534 atoms, 1715 bonds, 72 residues, 1 model selected  

> view matrix models
> #8,-0.35716,0.42181,-0.83338,113.8,0.40272,-0.73549,-0.54486,240.8,-0.84276,-0.53022,0.092815,205.51

> view matrix models
> #8,0.020845,0.40385,-0.91459,102.26,0.57296,-0.75449,-0.3201,210.12,-0.81932,-0.51735,-0.24712,237.45

> view matrix models
> #8,0.16599,-0.951,-0.26087,189.21,0.075817,-0.25145,0.9649,47.277,-0.98321,-0.17994,0.030364,178.29

> view matrix models
> #8,0.29462,0.063642,0.95349,-64.04,0.20764,0.96968,-0.12888,5.6123,-0.93278,0.23596,0.27247,100.78

> view matrix models
> #8,-0.41115,0.60042,0.6859,-59.957,0.41568,0.79314,-0.44512,47.039,-0.81128,0.1021,-0.57568,196.56

> view matrix models
> #8,-0.76148,-0.52367,0.382,126.17,0.52724,-0.15758,0.83498,23.368,-0.37705,0.83722,0.39609,-16.158

> view matrix models
> #8,-0.54919,-0.44865,0.70506,71.736,0.75592,0.093055,0.64802,-0.7633,-0.35634,0.88885,0.28804,-12.466

> fitmap #8 inMap #4

Fit molecule P1(1).pdb (#8) to map cryosparc_P16_J77_class_02_final_volume.mrc
(#4) using 1534 atoms  
average map value = 0.1589, steps = 428  
shifted from previous position = 38.6  
rotated from previous position = 61.2 degrees  
atoms outside contour = 1012, contour level = 0.20824  
  
Position of P1(1).pdb (#8) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
0.72077538 0.51395318 -0.46511825 37.91616735  
-0.60791816 0.79108962 -0.06791697 35.61100191  
0.33304408 0.33170672 0.88263939 -47.12138199  
Axis 0.27874529 -0.55673374 -0.78252707  
Axis point 87.70134978 -11.14833148 0.00000000  
Rotation angle (degrees) 45.79303912  
Shift along axis 27.61686383  
  

> view matrix models
> #8,0.6968,-0.30182,-0.65068,153.81,-0.71529,-0.22511,-0.66157,238.67,0.053203,0.92641,-0.37275,21.137

> view matrix models
> #8,0.25573,-0.0089729,0.96671,-21.365,0.88388,0.40723,-0.23004,25.795,-0.39161,0.91328,0.11207,-0.93896

> view matrix models
> #8,0.3844,-0.42967,0.81708,36.922,0.88884,0.41136,-0.20184,22.119,-0.24939,0.80384,0.54004,-39.958

> view matrix models
> #8,0.2611,-0.61048,0.74776,72.787,0.91943,0.39325,1.6057e-05,1.8332,-0.29407,0.68751,0.66397,-36.156

> view matrix models
> #8,-0.0020543,-0.95677,0.29085,176.28,0.88761,0.13222,0.44121,-10.305,-0.46059,0.25907,0.84896,5.7904

> view matrix models
> #8,0.80312,-0.48141,0.35107,66.448,0.58484,0.52431,-0.61892,69.025,0.11388,0.70239,0.70263,-65.629

> view matrix models
> #8,0.94193,-0.26365,0.20798,47.006,0.31156,0.91721,-0.2483,0.026381,-0.1253,0.29868,0.94609,-28.407

> view matrix models
> #8,0.59526,-0.44089,-0.67177,178.51,-0.56845,-0.82194,0.035737,230.03,-0.56791,0.3606,-0.73989,162.66

> view matrix models
> #8,0.13143,-0.88843,0.43979,145.19,0.19697,0.45819,0.86675,-52.78,-0.97156,-0.027286,0.23522,132.69

> view matrix models
> #8,-0.4439,-0.87456,-0.1952,241.82,-0.038446,-0.19905,0.97924,27.993,-0.89525,0.44218,0.054734,90.566

> view matrix models
> #8,-0.89339,-0.31324,0.32209,147.65,0.051868,0.64019,0.76646,-56.016,-0.44628,0.70145,-0.55569,95.909

> view matrix models
> #8,0.42791,-0.20495,0.88028,0.88708,0.68733,0.70625,-0.16969,-4.804,-0.58692,0.67765,0.44308,4.6776

> view matrix models
> #8,0.2738,-0.16025,0.94834,-2.4977,0.63788,0.76821,-0.054352,-21.181,-0.71982,0.61982,0.31256,32.701

> view matrix models
> #8,0.65391,-0.4363,0.61809,42.289,0.66723,0.7177,-0.19927,-1.998,-0.35666,0.54272,0.76043,-25.142

> view matrix models
> #8,0.31143,0.89145,0.32912,-67.245,0.38412,0.19869,-0.90165,148.4,-0.86917,0.40722,-0.28054,127.51

> view matrix models
> #8,-0.0038565,0.66952,-0.74278,87.602,-0.99944,0.0222,0.025199,154.83,0.033361,0.74246,0.66906,-62.4

> view matrix models
> #8,-0.67523,0.036049,-0.73673,201.77,-0.73692,0.010017,0.6759,74.33,0.031746,0.9993,0.019801,-26.466

> select subtract #8

Nothing selected  

> hide #8 models

> hide #!1 models

> transparency #4.1 0

> show #8 models

> select add #8

1534 atoms, 1715 bonds, 72 residues, 1 model selected  

> view matrix models
> #8,0.19788,0.34598,0.91714,-55.258,-0.072659,0.93824,-0.33826,28.348,-0.97753,0.00029746,0.2108,132.16

> view matrix models
> #8,0.22499,0.31245,0.92291,-53.408,-0.13601,0.94799,-0.28778,25.712,-0.96482,-0.060781,0.25578,134.14

> view matrix models
> #8,-0.94723,-0.017803,0.32005,115.89,0.18813,0.77752,0.60005,-63.248,-0.25953,0.6286,-0.73315,112.04

> view matrix models
> #8,-0.79096,0.055409,-0.60935,193.19,-0.50024,0.51492,0.69615,-1.8937,0.35234,0.85545,-0.37956,13.232

> view matrix models
> #8,0.26969,-0.60103,0.75235,70.544,0.4671,0.76488,0.4436,-62.191,-0.84207,0.23179,0.48703,68.687

> fitmap #8 inMap #4

Fit molecule P1(1).pdb (#8) to map cryosparc_P16_J77_class_02_final_volume.mrc
(#4) using 1534 atoms  
average map value = 0.1853, steps = 328  
shifted from previous position = 20.6  
rotated from previous position = 56.2 degrees  
atoms outside contour = 949, contour level = 0.20824  
  
Position of P1(1).pdb (#8) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
0.44796061 0.07034225 -0.89128182 149.27453878  
-0.66794701 -0.63632016 -0.38593196 248.32473535  
-0.59428790 0.76821134 -0.23806147 49.62229375  
Axis 0.82327087 -0.21185102 -0.52663481  
Axis point 0.00000000 125.26026628 136.58530154  
Rotation angle (degrees) 135.49673453  
Shift along axis 44.15270210  
  

> view matrix models
> #8,0.16235,-0.31756,-0.93424,220.23,-0.98064,0.053083,-0.18846,163.15,0.10944,0.94675,-0.30279,-9.4566

> view matrix models
> #8,0.079021,-0.11128,-0.99064,206.18,-0.96281,-0.26606,-0.046914,185.78,-0.25835,0.95751,-0.12817,-7.2605

> fitmap #8 inMap #4

Fit molecule P1(1).pdb (#8) to map cryosparc_P16_J77_class_02_final_volume.mrc
(#4) using 1534 atoms  
average map value = 0.1979, steps = 196  
shifted from previous position = 7  
rotated from previous position = 40.8 degrees  
atoms outside contour = 902, contour level = 0.20824  
  
Position of P1(1).pdb (#8) relative to
cryosparc_P16_J77_class_02_final_volume.mrc (#4) coordinates:  
Matrix rotation and translation  
0.78753008 0.35396885 0.50448236 -46.52762836  
0.38914917 0.34912682 -0.85245141 122.01885985  
-0.47786956 0.86765002 0.13720118 -3.14061381  
Axis 0.86822867 0.49584640 0.01775742  
Axis point 0.00000000 76.60659160 72.98463370  
Rotation angle (degrees) 82.12981822  
Shift along axis 20.05022224  
  

> volume #4 level 0.2003

> close session

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/male_mutant/new_maps/Class_45/Models/pdb_extract_out_0436460302.cif

Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/male_mutant/new_maps/Class_45/Models/pdb_extract_out_0436460302.cif  
---  
warnings | Unknown polymer entity '1' near line 2185  
Unknown polymer entity '2' near line 4160  
Unknown polymer entity '3' near line 7394  
Unknown polymer entity '4' near line 83434  
Unknown polymer entity '5' near line 85995  
74 messages similar to the above omitted  
Expected gap or connection between A /At:76 and PHE /At:77  
Expected gap or connection between A /Pt:77 and MET /Pt:78  
Atom ? is not in the residue template for ASN /LA:257  
Atom ? is not in the residue template for ALA /LB:403  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
note | Combining 2 symmetry atoms into ASN /LA:257 ?  
  
Chain information for pdb_extract_out_0436460302.cif #1  
---  
Chain | Description  
At | No description available  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Pt | No description available  
S2 | No description available  
SA | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sg | No description available  
mR | No description available  
  
Drag select of 1 atoms  

> delete sel

> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/male_mutant/new_maps/Class_45/Models/pdb_extract_out_0436460302_corrected.cif
> relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> close session

> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/New_maps/class2_blush/models/RPS9_MWT_class2_8_10_25_fromcootbackup.cif-
> coot-0.cif


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

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
Registration file '/yonath_group/disha/.local/share/ChimeraX/registration' has
expired  
  
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: 3.3.0 NVIDIA 550.90.07
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=plasmax11
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.4 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        44Gi        11Gi       252Mi       8.0Gi        18Gi
	Swap:           31Gi       3.2Gi        28Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    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-Clipper: 0.22.4
    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-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    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
    distro: 1.7.0
    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: 23.2
    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
    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

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