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Opened 7 months ago
Closed 7 months ago
#17300 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202311280534 (2023-11-28 05:34:38 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 0x00000001f7f84f40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1819 in new_bond
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 235 in molecule_from_atoms
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 100 in split_molecule
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py", line 63 in split
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.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_Daily.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_Daily.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, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/aleon/Downloads/emhancer5G01.mrc
Summary of feedback from opening /Users/aleon/Downloads/emhancer5G01.mrc
---
notes | open kw {}
Opened emhancer5G01.mrc as #1, grid size 512,512,512, pixel 0.833, shown at
level 8.22e-05, step 2, values float32
> volume #1 step 1
> volume #1 level 0.1393
> volume #1 level 0.1013
> volume flip #1
Opened emhancer5G01.mrc z flip as #2, grid size 512,512,512, pixel 0.833,
shown at step 1, values float32
> open
> /Users/aleon/Desktop/ModelBuilding/5G01new/cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc
Summary of feedback from opening
/Users/aleon/Desktop/ModelBuilding/5G01new/cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc
---
notes | open kw {}
Opened cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc as #3, grid
size 512,512,512, pixel 0.833, shown at level 0.0782, step 2, values float32
> volume #3 step 1
> volume #3 level 0.2023
> show #!1 models
> close #2
> volume #3 level 0.2732
> volume #3 level 0.2661
> volume #3 level 0.259
> volume #3 level 0.2448
> volume #3 level 0.3441
> open
> /Users/aleon/Desktop/ModelBuilding/5G01new/5G01_5TG8UniProtNumbering_ReadyToBuild-
> coot-0.pdb
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb #2
---
Chain | Description
A C E | No description available
B D F | No description available
H | No description available
L | No description available
> hide atoms
> show cartoons
> transparency #1.1 50
> volume #1 level 0.06757
> split #2
Split 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb (#2) into 8 models
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb F #2.6
---
Chain | Description
F | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H #2.7
---
Chain | Description
H | No description available
Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L #2.8
---
Chain | Description
L | No description available
> select add #2.8
815 atoms, 835 bonds, 107 residues, 1 model selected
> select add #2.7
1759 atoms, 1798 bonds, 230 residues, 2 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 56
shifted from previous position = 0.101
rotated from previous position = 0.196 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999580 -0.00163217 0.00239462 -0.27246777
0.00163650 0.99999703 -0.00180616 0.12169443
-0.00239166 0.00181007 0.99999550 0.25598900
Axis 0.52934418 0.70061640 0.47846777
Axis point 94.08668116 0.00000000 127.98856163
Rotation angle (degrees) 0.19570932
Shift along axis 0.06351437
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999580 -0.00163217 0.00239462 -0.27246777
0.00163650 0.99999703 -0.00180616 0.12169443
-0.00239166 0.00181007 0.99999550 0.25598900
Axis 0.52934418 0.70061640 0.47846777
Axis point 94.08668116 0.00000000 127.98856163
Rotation angle (degrees) 0.19570932
Shift along axis 0.06351437
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 28
shifted from previous position = 0.02
rotated from previous position = 0.0484 degrees
atoms outside contour = 551, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999301 -0.00217097 0.00304553 -0.32045454
0.00217653 0.99999597 -0.00182310 0.00304205
-0.00304156 0.00182972 0.99999370 0.38436186
Axis 0.43880597 0.73123026 0.52225628
Axis point 115.42840782 0.00000000 114.46891212
Rotation angle (degrees) 0.23847835
Shift along axis 0.06234248
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999301 -0.00217097 0.00304553 -0.32045454
0.00217653 0.99999597 -0.00182310 0.00304205
-0.00304156 0.00182972 0.99999370 0.38436186
Axis 0.43880597 0.73123026 0.52225628
Axis point 115.42840782 0.00000000 114.46891212
Rotation angle (degrees) 0.23847835
Shift along axis 0.06234248
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 36
shifted from previous position = 0.00657
rotated from previous position = 0.0412 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999541 -0.00177525 0.00245609 -0.25233398
0.00178001 0.99999654 -0.00193496 0.11436749
-0.00245265 0.00193932 0.99999511 0.24301384
Axis 0.53858494 0.68239068 0.49423601
Axis point 86.30670547 0.00000000 116.54915899
Rotation angle (degrees) 0.20607729
Shift along axis 0.06224622
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999541 -0.00177525 0.00245609 -0.25233398
0.00178001 0.99999654 -0.00193496 0.11436749
-0.00245265 0.00193932 0.99999511 0.24301384
Axis 0.53858494 0.68239068 0.49423601
Axis point 86.30670547 0.00000000 116.54915899
Rotation angle (degrees) 0.20607729
Shift along axis 0.06224622
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 40
shifted from previous position = 0.00216
rotated from previous position = 0.000596 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999542 -0.00176566 0.00245617 -0.25231218
0.00177042 0.99999655 -0.00193901 0.11655127
-0.00245274 0.00194335 0.99999510 0.24136057
Axis 0.54008155 0.68288782 0.49191071
Axis point 85.72735610 0.00000000 116.52952899
Rotation angle (degrees) 0.20593464
Shift along axis 0.06205014
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999542 -0.00176566 0.00245617 -0.25231218
0.00177042 0.99999655 -0.00193901 0.11655127
-0.00245274 0.00194335 0.99999510 0.24136057
Axis 0.54008155 0.68288782 0.49191071
Axis point 85.72735610 0.00000000 116.52952899
Rotation angle (degrees) 0.20593464
Shift along axis 0.06205014
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 36
shifted from previous position = 0.0166
rotated from previous position = 0.0314 degrees
atoms outside contour = 549, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999688 -0.00134332 0.00210700 -0.25644442
0.00134738 0.99999724 -0.00192292 0.20762260
-0.00210441 0.00192575 0.99999593 0.17514859
Axis 0.61014576 0.66765404 0.42656797
Axis point 71.43530146 0.00000000 138.28313613
Rotation angle (degrees) 0.18070499
Shift along axis 0.05686438
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999688 -0.00134332 0.00210700 -0.25644442
0.00134738 0.99999724 -0.00192292 0.20762260
-0.00210441 0.00192575 0.99999593 0.17514859
Axis 0.61014576 0.66765404 0.42656797
Axis point 71.43530146 0.00000000 138.28313613
Rotation angle (degrees) 0.18070499
Shift along axis 0.05686438
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 28
shifted from previous position = 0.0145
rotated from previous position = 0.0483 degrees
atoms outside contour = 551, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999455 -0.00201277 0.00261795 -0.24912033
0.00201778 0.99999613 -0.00191407 0.06141263
-0.00261409 0.00191934 0.99999474 0.28064599
Axis 0.50199222 0.68514424 0.52780790
Axis point 93.98833292 0.00000000 107.84631565
Rotation angle (degrees) 0.21876730
Shift along axis 0.06514721
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999455 -0.00201277 0.00261795 -0.24912033
0.00201778 0.99999613 -0.00191407 0.06141263
-0.00261409 0.00191934 0.99999474 0.28064599
Axis 0.50199222 0.68514424 0.52780790
Axis point 93.98833292 0.00000000 107.84631565
Rotation angle (degrees) 0.21876730
Shift along axis 0.06514721
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 28
shifted from previous position = 0.0164
rotated from previous position = 0.0673 degrees
atoms outside contour = 547, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999763 -0.00109636 0.00188279 -0.24763072
0.00109999 0.99999753 -0.00192894 0.26007809
-0.00188067 0.00193101 0.99999637 0.12770622
Axis 0.66308077 0.64650529 0.37729936
Axis point 0.00000000 -55.72870457 117.43016303
Rotation angle (degrees) 0.16676615
Shift along axis 0.05212617
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999763 -0.00109636 0.00188279 -0.24763072
0.00109999 0.99999753 -0.00192894 0.26007809
-0.00188067 0.00193101 0.99999637 0.12770622
Axis 0.66308077 0.64650529 0.37729936
Axis point 0.00000000 -55.72870457 117.43016303
Rotation angle (degrees) 0.16676615
Shift along axis 0.05212617
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 28
shifted from previous position = 0.0146
rotated from previous position = 0.0454 degrees
atoms outside contour = 551, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999569 -0.00170989 0.00238527 -0.24829433
0.00171453 0.99999664 -0.00194465 0.13112558
-0.00238194 0.00194873 0.99999526 0.22695890
Axis 0.55276001 0.67682041 0.48617950
Axis point 82.42457286 0.00000000 118.57538821
Rotation angle (degrees) 0.20178270
Shift along axis 0.06184406
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999569 -0.00170989 0.00238527 -0.24829433
0.00171453 0.99999664 -0.00194465 0.13112558
-0.00238194 0.00194873 0.99999526 0.22695890
Axis 0.55276001 0.67682041 0.48617950
Axis point 82.42457286 0.00000000 118.57538821
Rotation angle (degrees) 0.20178270
Shift along axis 0.06184406
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 36
shifted from previous position = 0.0141
rotated from previous position = 0.0285 degrees
atoms outside contour = 548, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999697 -0.00131750 0.00208084 -0.25656893
0.00132158 0.99999721 -0.00195709 0.22092705
-0.00207826 0.00195983 0.99999592 0.16331478
Axis 0.62239907 0.66088173 0.41935038
Axis point 67.24968512 0.00000000 139.79112949
Rotation angle (degrees) 0.18028882
Shift along axis 0.05480450
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999697 -0.00131750 0.00208084 -0.25656893
0.00132158 0.99999721 -0.00195709 0.22092705
-0.00207826 0.00195983 0.99999592 0.16331478
Axis 0.62239907 0.66088173 0.41935038
Axis point 67.24968512 0.00000000 139.79112949
Rotation angle (degrees) 0.18028882
Shift along axis 0.05480450
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 40
shifted from previous position = 0.0145
rotated from previous position = 0.0398 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999512 -0.00185994 0.00251123 -0.25162157
0.00186472 0.99999645 -0.00190390 0.09065496
-0.00250768 0.00190858 0.99999503 0.26061481
Axis 0.52075660 0.68554735 0.50876064
Axis point 90.77702586 0.00000000 113.58549600
Rotation angle (degrees) 0.20973273
Shift along axis 0.06370524
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999512 -0.00185994 0.00251123 -0.25162157
0.00186472 0.99999645 -0.00190390 0.09065496
-0.00250768 0.00190858 0.99999503 0.26061481
Axis 0.52075660 0.68554735 0.50876064
Axis point 90.77702586 0.00000000 113.58549600
Rotation angle (degrees) 0.20973273
Shift along axis 0.06370524
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 40
shifted from previous position = 0.0014
rotated from previous position = 0.00857 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999554 -0.00174323 0.00242474 -0.25078302
0.00174793 0.99999659 -0.00193992 0.12231065
-0.00242135 0.00194415 0.99999518 0.23581029
Axis 0.54516924 0.68019885 0.49002042
Axis point 84.60086957 0.00000000 117.52840739
Rotation angle (degrees) 0.20410311
Shift along axis 0.06202823
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999554 -0.00174323 0.00242474 -0.25078302
0.00174793 0.99999659 -0.00193992 0.12231065
-0.00242135 0.00194415 0.99999518 0.23581029
Axis 0.54516924 0.68019885 0.49002042
Axis point 84.60086957 0.00000000 117.52840739
Rotation angle (degrees) 0.20410311
Shift along axis 0.06202823
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 40
shifted from previous position = 0.000881
rotated from previous position = 0.0033 degrees
atoms outside contour = 550, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999537 -0.00178584 0.00246283 -0.25170210
0.00179060 0.99999653 -0.00193332 0.11156410
-0.00245937 0.00193773 0.99999510 0.24469577
Axis 0.53679736 0.68256059 0.49594318
Axis point 86.68261574 0.00000000 115.96190715
Rotation angle (degrees) 0.20659128
Shift along axis 0.06239144
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999537 -0.00178584 0.00246283 -0.25170210
0.00179060 0.99999653 -0.00193332 0.11156410
-0.00245937 0.00193773 0.99999510 0.24469577
Axis 0.53679736 0.68256059 0.49594318
Axis point 86.68261574 0.00000000 115.96190715
Rotation angle (degrees) 0.20659128
Shift along axis 0.06239144
> fitmap sel inMap #1
Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7),
5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 1759 atoms
average map value = 0.237, steps = 28
shifted from previous position = 0.0187
rotated from previous position = 0.0282 degrees
atoms outside contour = 547, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999664 -0.00149755 0.00211768 -0.23264751
0.00150122 0.99999737 -0.00173413 0.13321376
-0.00211507 0.00173730 0.99999625 0.21382791
Axis 0.55616145 0.67813373 0.48043635
Axis point 86.40837525 0.00000000 126.72067157
Rotation angle (degrees) 0.17881361
Shift along axis 0.06367787
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999664 -0.00149755 0.00211768 -0.23264751
0.00150122 0.99999737 -0.00173413 0.13321376
-0.00211507 0.00173730 0.99999625 0.21382791
Axis 0.55616145 0.67813373 0.48043635
Axis point 86.40837525 0.00000000 126.72067157
Rotation angle (degrees) 0.17881361
Shift along axis 0.06367787
> select clear
> select add #2.7
944 atoms, 963 bonds, 123 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map
emhancer5G01.mrc (#1) using 944 atoms
average map value = 0.2481, steps = 60
shifted from previous position = 0.0597
rotated from previous position = 0.385 degrees
atoms outside contour = 278, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99996119 -0.00356284 0.00805717 -1.25941691
0.00355764 0.99999345 0.00065965 -0.89108197
-0.00805947 -0.00063096 0.99996732 1.94358221
Axis -0.07305309 0.91226010 0.40304435
Axis point 237.39561134 0.00000000 156.88712111
Rotation angle (degrees) 0.50612090
Shift along axis 0.06245561
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map
emhancer5G01.mrc (#1) using 944 atoms
average map value = 0.2481, steps = 40
shifted from previous position = 0.0124
rotated from previous position = 0.0326 degrees
atoms outside contour = 278, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99996295 -0.00355914 0.00783717 -1.21390513
0.00355819 0.99999366 0.00013478 -0.75252091
-0.00783760 -0.00010689 0.99996928 1.79689355
Axis -0.01403674 0.91044210 0.41339830
Axis point 224.71263675 0.00000000 155.81910716
Rotation angle (degrees) 0.49322684
Shift along axis 0.07474528
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map
emhancer5G01.mrc (#1) using 944 atoms
average map value = 0.2481, steps = 44
shifted from previous position = 0.0153
rotated from previous position = 0.0334 degrees
atoms outside contour = 278, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99995988 -0.00381995 0.00810195 -1.22155969
0.00381532 0.99999255 0.00058690 -0.93022822
-0.00810413 -0.00055596 0.99996701 1.93994519
Axis -0.06366544 0.90279235 0.42533832
Axis point 235.44900774 0.00000000 151.44358394
Rotation angle (degrees) 0.51426680
Shift along axis 0.06310124
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map
emhancer5G01.mrc (#1) using 944 atoms
average map value = 0.2481, steps = 40
shifted from previous position = 0.00154
rotated from previous position = 0.0159 degrees
atoms outside contour = 278, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99995860 -0.00366850 0.00832736 -1.30534798
0.00366420 0.99999315 0.00053099 -0.88300432
-0.00832925 -0.00050046 0.99996519 1.97794611
Axis -0.05658458 0.91377191 0.40226743
Axis point 233.78521022 0.00000000 157.49059909
Rotation angle (degrees) 0.52221302
Shift along axis 0.06266132
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map
emhancer5G01.mrc (#1) using 944 atoms
average map value = 0.2481, steps = 40
shifted from previous position = 0.0123
rotated from previous position = 0.0372 degrees
atoms outside contour = 278, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99996350 -0.00360409 0.00774711 -1.18284326
0.00360230 0.99999348 0.00024451 -0.79038502
-0.00774794 -0.00021660 0.99996996 1.79775254
Axis -0.02697348 0.90640485 0.42154795
Axis point 227.44457516 0.00000000 153.49824654
Rotation angle (degrees) 0.48974355
Shift along axis 0.07333548
> select add #2.8
1759 atoms, 1798 bonds, 230 residues, 2 models selected
> select subtract #2.7
815 atoms, 835 bonds, 107 residues, 1 model selected
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 815 atoms
average map value = 0.2252, steps = 40
shifted from previous position = 0.0693
rotated from previous position = 0.158 degrees
atoms outside contour = 260, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999597 -0.00230000 0.00166696 -0.00725415
0.00230719 0.99998798 -0.00432575 0.62250308
-0.00165699 0.00432958 0.99998925 -0.39883307
Axis 0.83600220 0.32105405 0.44499956
Axis point 0.00000000 94.14831450 142.43417593
Rotation angle (degrees) 0.29659967
Shift along axis 0.01631211
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 815 atoms
average map value = 0.2252, steps = 28
shifted from previous position = 0.00904
rotated from previous position = 0.045 degrees
atoms outside contour = 261, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999398 -0.00292874 0.00185970 0.06441551
0.00293756 0.99998438 -0.00475504 0.60402438
-0.00184575 0.00476047 0.99998697 -0.44360852
Axis 0.80799998 0.31464469 0.49813127
Axis point 0.00000000 95.73948955 125.31589554
Rotation angle (degrees) 0.33737735
Shift along axis 0.02112552
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 815 atoms
average map value = 0.2252, steps = 40
shifted from previous position = 0.00472
rotated from previous position = 0.0111 degrees
atoms outside contour = 261, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999364 -0.00298014 0.00196156 0.04825343
0.00298913 0.99998496 -0.00459933 0.55793122
-0.00194782 0.00460516 0.99998750 -0.39234187
Axis 0.79033112 0.33567310 0.51254296
Axis point 0.00000000 88.22723548 119.24302275
Rotation angle (degrees) 0.33364605
Shift along axis 0.02432662
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 815 atoms
average map value = 0.2252, steps = 28
shifted from previous position = 0.0169
rotated from previous position = 0.0437 degrees
atoms outside contour = 261, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999580 -0.00229050 0.00177495 -0.04182500
0.00229818 0.99998797 -0.00433342 0.63147239
-0.00176500 0.00433748 0.99998904 -0.37105302
Axis 0.83139268 0.33942150 0.43997643
Axis point 0.00000000 87.56440037 144.20098396
Rotation angle (degrees) 0.29878093
Shift along axis 0.01630772
> fitmap sel inMap #1
Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map
emhancer5G01.mrc (#1) using 815 atoms
average map value = 0.2252, steps = 44
shifted from previous position = 0.0165
rotated from previous position = 0.0252 degrees
atoms outside contour = 260, contour level = 0.06757
Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8)
relative to emhancer5G01.mrc (#1) coordinates:
Matrix rotation and translation
0.99999480 -0.00262945 0.00186654 0.00538842
0.00263801 0.99998595 -0.00459763 0.62394266
-0.00185442 0.00460253 0.99998769 -0.41217089
Axis 0.81885345 0.33118137 0.46882611
Axis point 0.00000000 91.72652073 134.14614433
Rotation angle (degrees) 0.32187268
Shift along axis 0.01781403
> select clear
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #2
13444 atoms, 13704 bonds, 1721 residues, 9 models selected
> hide #!1 models
> combine sel
> save /Users/aleon/Desktop/ModelBuilding/5G01new/5G01_EMhancer_Fit.pdb models
> #4 relModel #1
> close
> open /Users/aleon/Desktop/ModelBuilding/6H4new/emhancer6H4.mrc
Summary of feedback from opening
/Users/aleon/Desktop/ModelBuilding/6H4new/emhancer6H4.mrc
---
notes | open kw {}
Opened emhancer6H4.mrc as #1, grid size 512,512,512, pixel 0.833, shown at
level 6.59e-05, step 2, values float32
> open
> /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_5TG8UniProtNumbering_ReadyToBuild-
> Refit-coot-3.pdb
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb
#2
---
Chain | Description
A C E | No description available
B D F | No description available
H | No description available
L | No description available
> volume #1 step 1
> volume #1 level 0.06129
> volume flip #1
Opened emhancer6H4.mrc z flip as #3, grid size 512,512,512, pixel 0.833, shown
at step 1, values float32
> hide atoms
> show cartoons
> transparency #3.1 50
> volume #1 level 0.05484
> volume #3 level 0.03229
> split #2
Split 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb (#2) into 8
models
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb A
#2.1
---
Chain | Description
A | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb B
#2.2
---
Chain | Description
B | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb C
#2.3
---
Chain | Description
C | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb D
#2.4
---
Chain | Description
D | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb E
#2.5
---
Chain | Description
E | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb F
#2.6
---
Chain | Description
F | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H
#2.7
---
Chain | Description
H | No description available
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L
#2.8
---
Chain | Description
L | No description available
> select add #2.7
1776 atoms, 1800 bonds, 119 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map emhancer6H4.mrc z flip (#3) using 1776 atoms
average map value = 0.1735, steps = 44
shifted from previous position = 0.0434
rotated from previous position = 0.517 degrees
atoms outside contour = 545, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to emhancer6H4.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99995934 0.00563431 0.00704100 -3.26382830
-0.00563512 0.99998412 0.00009586 1.23296795
-0.00704035 -0.00013553 0.99997521 1.54295019
Axis -0.01282825 0.78068676 -0.62479086
Axis point 221.10775476 0.00000000 464.74942199
Rotation angle (degrees) 0.51673266
Shift along axis 0.04040980
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map emhancer6H4.mrc z flip (#3) using 1776 atoms
average map value = 0.1735, steps = 40
shifted from previous position = 0.00324
rotated from previous position = 0.0112 degrees
atoms outside contour = 545, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to emhancer6H4.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99995847 0.00573222 0.00708490 -3.29773953
-0.00573419 0.99998353 0.00025773 1.21198079
-0.00708331 -0.00029834 0.99997487 1.59072854
Axis -0.03049432 0.77696654 -0.62880291
Axis point 226.64496659 0.00000000 466.60777071
Rotation angle (degrees) 0.52241001
Shift along axis 0.04197612
> select add #2.8
3508 atoms, 3555 bonds, 232 residues, 2 models selected
> select subtract #2.7
1732 atoms, 1755 bonds, 113 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8)
to map emhancer6H4.mrc z flip (#3) using 1732 atoms
average map value = 0.1623, steps = 40
shifted from previous position = 0.0645
rotated from previous position = 0.374 degrees
atoms outside contour = 607, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8)
relative to emhancer6H4.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99997982 -0.00622110 -0.00128438 1.69159387
0.00622299 0.99997955 0.00147382 -1.82335538
0.00127518 -0.00148179 0.99999809 0.01313887
Axis -0.22658991 -0.19622703 0.95401885
Axis point 294.30086023 270.48536533 0.00000000
Rotation angle (degrees) 0.37368186
Shift along axis -0.01297176
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8)
to map emhancer6H4.mrc z flip (#3) using 1732 atoms
average map value = 0.1623, steps = 40
shifted from previous position = 0.012
rotated from previous position = 0.0397 degrees
atoms outside contour = 609, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8)
relative to emhancer6H4.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99997994 -0.00616294 -0.00146069 1.72985251
0.00616606 0.99997870 0.00214204 -1.99287718
0.00144746 -0.00215100 0.99999664 0.10407725
Axis -0.32097352 -0.21743060 0.92179170
Axis point 325.07881845 278.27480266 0.00000000
Rotation angle (degrees) 0.38316956
Shift along axis -0.02598681
> select clear
> select add #2
15193 atoms, 15461 bonds, 1723 residues, 9 models selected
> combine sel
> save /Users/aleon/Desktop/ModelBuilding/6H4new/EMhancer6H4_FitinMap.pdb
> models #4 relModel #3
> save /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_EMHancerMap.mrc models #3
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #2.7/H #4/H
Alignment identifier is 1
> select #2.7/H:1 #4/H:1
34 atoms, 32 bonds, 2 residues, 2 models selected
> select #2.7/H:1-2 #4/H:1-2
66 atoms, 64 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [1-2] RMSD: 0.000
> delete atoms sel
> delete bonds sel
> select #2.7/H:118 #4/H:118
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #2.7/H:118-119 #4/H:118-119
46 atoms, 44 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [118-119] RMSD: 0.000
> delete atoms sel
> delete bonds sel
> select add #2.7
1720 atoms, 1744 bonds, 115 residues, 1 model selected
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms
average map value = 0.1766, steps = 76
shifted from previous position = 0.0148
rotated from previous position = 0.0971 degrees
atoms outside contour = 528, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to 6H4_EMHancerMap.mrc (#3) coordinates:
Matrix rotation and translation
0.99995069 0.00592546 0.00796941 -3.59102572
-0.00591628 0.99998181 -0.00117582 1.65046679
-0.00797623 0.00112861 0.99996755 1.47852023
Axis 0.11525058 0.79748071 -0.59223460
Axis point 185.51020105 0.00000000 452.13554805
Rotation angle (degrees) 0.57282454
Shift along axis 0.02671680
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms
average map value = 0.1766, steps = 36
shifted from previous position = 0.00154
rotated from previous position = 0.0102 degrees
atoms outside contour = 528, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to 6H4_EMHancerMap.mrc (#3) coordinates:
Matrix rotation and translation
0.99995114 0.00595014 0.00789336 -3.57567490
-0.00594230 0.99998183 -0.00101626 1.61270024
-0.00789926 0.00096930 0.99996833 1.49765050
Axis 0.09993239 0.79483494 -0.59854068
Axis point 189.90057564 0.00000000 454.52892265
Rotation angle (degrees) 0.56921607
Shift along axis 0.02810001
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms
average map value = 0.1766, steps = 44
shifted from previous position = 0.00235
rotated from previous position = 0.00679 degrees
atoms outside contour = 528, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to 6H4_EMHancerMap.mrc (#3) coordinates:
Matrix rotation and translation
0.99995002 0.00603993 0.00796669 -3.61581683
-0.00603221 0.99998131 -0.00099239 1.62757059
-0.00797254 0.00094428 0.99996777 1.52079226
Axis 0.09640714 0.79345217 -0.60094868
Axis point 191.09060147 0.00000000 455.41495959
Rotation angle (degrees) 0.57550175
Shift along axis 0.02889075
> ui mousemode right "rotate selected models"
> view matrix models
> #2.7,0.98464,-0.11414,0.1321,-8.1577,0.12924,0.98526,-0.11203,6.526,-0.11736,0.12738,0.98489,1.308
> fitmap sel inMap #3
Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms
average map value = 0.1766, steps = 92
shifted from previous position = 0.336
rotated from previous position = 12.1 degrees
atoms outside contour = 527, contour level = 0.032288
Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7)
relative to 6H4_EMHancerMap.mrc (#3) coordinates:
Matrix rotation and translation
0.99995430 0.00549588 0.00782213 -3.45421867
-0.00548303 0.99998358 -0.00166319 1.67847744
-0.00783114 0.00162022 0.99996802 1.32821793
Axis 0.16925178 0.80688885 -0.56593658
Axis point 169.10100723 0.00000000 442.97350230
Rotation angle (degrees) 0.55576465
Shift along axis 0.01802498
> select #3
2 models selected
> select clear
> open
> /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_J604_WA79_modelangeloFinal.cif
Summary of feedback from opening
/Users/aleon/Desktop/ModelBuilding/6H4new/6H4_J604_WA79_modelangeloFinal.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 6H4_J604_WA79_modelangeloFinal.cif #5
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Da | No description available
Db | No description available
Dc | No description available
Dd | No description available
De | No description available
Df | No description available
Dg | No description available
Dh | No description available
Ea | No description available
Eb | No description available
Ec | No description available
Ed | No description available
Ee | No description available
Ef | No description available
Eg | No description available
> show atoms
> hide atoms
> show cartoons
> hide #4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 74 residues
> select up
684 atoms, 699 bonds, 85 residues, 1 model selected
Drag select of 1333 residues
> select up
12113 atoms, 12301 bonds, 1549 residues, 1 model selected
> select up
12701 atoms, 12903 bonds, 1626 residues, 1 model selected
Drag select of 90 residues
> select down
11982 atoms, 12903 bonds, 1536 residues, 1 model selected
> select down
11982 atoms, 12903 bonds, 1536 residues, 1 model selected
> select clear
Drag select of 1465 residues
> select up
11869 atoms, 12053 bonds, 1523 residues, 1 model selected
> delete sel
Drag select of 16 residues
> delete sel
Drag select of 86 residues
> view matrix models
> #5,0.96969,0.17483,-0.17069,16.703,-0.15978,0.98224,0.09837,11.229,0.18485,-0.068115,0.9804,-20.241
> show sel atoms
> style sel stick
Changed 690 atom styles
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> hide #2.4 models
> show #2.8 models
> hide #2.8 models
> show #2.7 models
> hide #2.7 models
> select clear
> hide #!5 models
> show #2.7 models
> select aromatic-ring
2464 atoms, 2524 bonds, 392 residues, 10 models selected
> show sel & #2.7 atoms
> style sel & #2.7 stick
Changed 119 atom styles
> select up
5148 atoms, 5280 bonds, 392 residues, 10 models selected
> show sel & #2.7 atoms
> style sel & #2.7 stick
Changed 383 atom styles
> show #!5 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
24 atoms, 25 bonds, 1 residue, 1 model selected
> select up
137 atoms, 141 bonds, 7 residues, 1 model selected
> select up
1720 atoms, 1744 bonds, 115 residues, 1 model selected
> view matrix models
> #2.7,0.95455,-0.1456,-0.26006,115.62,0.19967,0.9602,0.19533,-89.62,0.22127,-0.23838,0.94563,20.297
> select clear
> mmaker #2.7/H to #5/Ba
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 6H4_J604_WA79_modelangeloFinal.cif, chain Ba (#5) with
6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H, chain H (#2.7),
sequence alignment score = 43.8
RMSD between 10 pruned atom pairs is 0.474 angstroms; (across all 18 pairs:
13.657)
> hide #!2 models
> show #!2 models
> show #2.1 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #2.7 models
> show #2.8 models
> hide #!5 models
> select aromatic-ring
2464 atoms, 2524 bonds, 392 residues, 10 models selected
> select up
5148 atoms, 5280 bonds, 392 residues, 10 models selected
> show sel & #2.8 atoms
> style sel & #2.8 stick
Changed 308 atom styles
> show #!5 models
> select clear
Drag select of 5 atoms, 3 residues, 7 bonds
> select clear
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> hide #!5 models
> show #2.8 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> show #2.7 models
> hide #2.7 models
> show #2.7 models
> hide #4 models
> show #!5 models
> hide #2.8 models
> show #2.8 models
> hide #2.7 models
> show #2.7 models
> hide #2.7 models
> show #2.7 models
> hide #2.8 models
> show #2.8 models
> hide #2.7 models
> hide #!5 models
> select ::name="HIS"
722 atoms, 734 bonds, 68 residues, 10 models selected
> select clear
> show #!5 models
> hide #!5 models
> select ::name="LYS"
1960 atoms, 1786 bonds, 180 residues, 10 models selected
> select up
13598 atoms, 13712 bonds, 1568 residues, 10 models selected
> select down
1960 atoms, 1786 bonds, 180 residues, 10 models selected
> show sel & #2.8 atoms
> style sel & #2.8 stick
Changed 177 atom styles
> show #!5 models
> select clear
> select #2.8/L:86
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select add #2.8
1732 atoms, 1755 bonds, 113 residues, 1 model selected
> view matrix models
> #2.8,0.9912,0.12169,-0.05206,-8.0691,-0.12143,0.99257,0.0081145,25.827,0.052661,-0.0017216,0.99861,-10.923
> ui mousemode right "translate selected models"
> view matrix models
> #2.8,0.9912,0.12169,-0.05206,-10.356,-0.12143,0.99257,0.0081145,26.822,0.052661,-0.0017216,0.99861,-10.205
> ui mousemode right "rotate selected models"
> view matrix models
> #2.8,0.97637,0.17441,0.12758,-68.999,-0.16616,0.98341,-0.07275,61.469,-0.13815,0.049832,0.98916,23.877
> ui mousemode right "translate selected models"
> view matrix models
> #2.8,0.97637,0.17441,0.12758,-69.179,-0.16616,0.98341,-0.07275,61.355,-0.13815,0.049832,0.98916,23.746
> select clear
> mmaker #2.8/L to #5/Bb
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 6H4_J604_WA79_modelangeloFinal.cif, chain Bb (#5) with
6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L, chain L (#2.8),
sequence alignment score = 30.6
RMSD between 4 pruned atom pairs is 1.201 angstroms; (across all 28 pairs:
9.863)
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #2.7 models
> show #!3 models
> hide #!3 models
> select add #2.8
1732 atoms, 1755 bonds, 113 residues, 1 model selected
> select subtract #2.8
Nothing selected
> select add #2.7
1720 atoms, 1744 bonds, 115 residues, 1 model selected
> save
> /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainAromaticModelAngeloMMFit.pdb
> models #2.7 relModel #3
> select clear
> select #2.7/H:11
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.7
1720 atoms, 1744 bonds, 115 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2.7,0.96576,0.12525,0.22718,-82.907,-0.14725,0.98565,0.082539,12.423,-0.21358,-0.11317,0.97035,79.872
> ui mousemode right "translate selected models"
> view matrix models
> #2.7,0.96576,0.12525,0.22718,-84.052,-0.14725,0.98565,0.082539,13.719,-0.21358,-0.11317,0.97035,82.032
> ui mousemode right "rotate selected models"
> view matrix models
> #2.7,0.93161,0.29151,0.2171,-111.04,-0.24367,0.94409,-0.22206,129.72,-0.2697,0.15398,0.95056,39.96
> view matrix models
> #2.7,0.95482,0.29232,0.053593,-70.367,-0.25536,0.89922,-0.35524,179.76,-0.15203,0.32551,0.93324,-19.429
> view matrix models
> #2.7,0.95494,0.2484,0.16246,-91.116,-0.19682,0.93966,-0.27981,136.68,-0.22216,0.23523,0.94621,12.539
> view matrix models
> #2.7,0.98298,0.10585,0.15015,-61.791,-0.081007,0.98332,-0.16287,68.691,-0.16488,0.14794,0.97516,11.471
> ui mousemode right "translate selected models"
> view matrix models
> #2.7,0.98298,0.10585,0.15015,-62.422,-0.081007,0.98332,-0.16287,69.016,-0.16488,0.14794,0.97516,11.602
> select add #2
15137 atoms, 15405 bonds, 1719 residues, 9 models selected
> select subtract #2
Nothing selected
> select add #2
15137 atoms, 15405 bonds, 1719 residues, 9 models selected
> select subtract #2
Nothing selected
> close #1
> volume #3 level 0.0267
> save /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainFit.pdb models #2.7
> relModel #3
> close #2
> close #5
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> close #4
> open
> /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_5TG8UniProtNumbering_ReadyToBuild-
> Refit-coot-3.pdb
Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb
#1
---
Chain | Description
A C E | No description available
B D F | No description available
H | No description available
L | No description available
> hide atoms
> show cartoons
> open /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainFit.pdb
Chain information for HeavyChainFit.pdb #2
---
Chain | Description
H | No description available
> split #1
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Max
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 Pro
Model Identifier: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 3 days, 17 hours, 18 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LS24D36xG:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
biopython: 1.85
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: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.2
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: 1.51
ChimeraX-AtomicLibrary: 12.1.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
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: 1.4
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: 1.8.dev202311280534
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-crai: 0.4
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
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.2
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: 1.14.1
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: 0.2.0
contourpy: 1.2.0
cripser: 0.0.15
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: 4.45.1
fsspec: 2025.3.2
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
mpmath: 1.3.0
mrcfile: 1.5.4
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
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: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
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: 25.1.1
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
sympy: 1.13.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
torch: 2.2.0
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 7 months ago
| 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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