id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17383	Out of bounds string index when showing a tool window	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00000001fc308c40 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2696 in shown
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2419 in _mw_set_shown
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2083 in _tool_window_request_shown
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 2309 in shown
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 271 in text_changed
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.segment._segment (total: 64)


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===== Log before crash start =====
Startup Messages  
---  
warning | Registration file '/Users/abdel104/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/abdel104/Downloads/cryosparc_P1024_J45_006_volume_map.mrc

Opened cryosparc_P1024_J45_006_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.09, shown at level 0.0192, step 1, values float32  

> set bgColor white

> graphics silhouettes true

> volume #1 level 0.05512

> volume #1 level 0.1078

> open ""/Users/abdel104/Documents/Aihara Lab/Model Building/A3A-nbE11-NabFab-
> nbElbow/model_building.cxs""

Opened cryosparc_P32_J58_011_volume_map.mrc as #1, grid size 180,180,180,
pixel 1.33, shown at level 0.0876, step 1, values float32  
opened ChimeraX session  

> open /Users/abdel104/Downloads/cryosparc_P1024_J45_006_volume_map.mrc

Opened cryosparc_P1024_J45_006_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.09, shown at level 0.0192, step 1, values float32  

> volume #6 level 0.1054

> show #!1 models

> select clear

> select add #6

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,-0.99764,0.051474,-0.045369,273.86,-0.05774,-0.98702,0.14983,276.41,-0.037068,0.15209,0.98767,-15.325

> ui mousemode right ""move picked models""

> select clear

> select add #6

2 models selected  

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models
> #6,-0.99764,0.051474,-0.045369,258.38,-0.05774,-0.98702,0.14983,240.09,-0.037068,0.15209,0.98767,-36.836

> ui tool show ""Fit in Map""

> fitmap #6 inMap #1

Fit map cryosparc_P1024_J45_006_volume_map.mrc in map
cryosparc_P32_J58_011_volume_map.mrc using 36873 points  
correlation = 0.5672, correlation about mean = 0.2162, overlap = 662.4  
steps = 264, shift = 7.47, angle = 20.1 degrees  
  
Position of cryosparc_P1024_J45_006_volume_map.mrc (#6) relative to
cryosparc_P32_J58_011_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.91466341 0.21644389 -0.34138378 272.11753526  
-0.27077513 -0.95514627 0.11990178 269.64804012  
-0.30011944 0.20210800 0.93224496 -0.82698846  
Axis 0.16579668 -0.08322351 -0.98264200  
Axis point 153.39143826 117.67313348 0.00000000  
Rotation angle (degrees) 165.64596450  
Shift along axis 23.48775969  
  

> ui mousemode right ""rotate selected models""

> close #6

> open /Users/abdel104/Downloads/cryosparc_P1024_J46_map.mrc

Opened cryosparc_P1024_J46_map.mrc as #6, grid size 256,256,256, pixel 1.09,
shown at level 0.0192, step 1, values float32  

> volume #6 level 0.0623

> select add #6

2 models selected  

> view matrix models
> #6,-0.97639,-0.19737,-0.087817,321.17,-0.19151,0.97893,-0.070774,40.583,0.099935,-0.052285,-0.99362,287.36

> ui mousemode right ""translate selected models""

> view matrix models
> #6,-0.97639,-0.19737,-0.087817,324.35,-0.19151,0.97893,-0.070774,30.079,0.099935,-0.052285,-0.99362,246.89

> view matrix models
> #6,-0.97639,-0.19737,-0.087817,290.71,-0.19151,0.97893,-0.070774,19.811,0.099935,-0.052285,-0.99362,247.5

> fitmap #6 inMap #1

Fit map cryosparc_P1024_J46_map.mrc in map
cryosparc_P32_J58_011_volume_map.mrc using 68623 points  
correlation = 0.6547, correlation about mean = 0.3736, overlap = 1073  
steps = 276, shift = 7.07, angle = 29.9 degrees  
  
Position of cryosparc_P1024_J46_map.mrc (#6) relative to
cryosparc_P32_J58_011_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.90126839 0.17195848 -0.39767520 271.45549393  
0.24188402 0.96120800 -0.13255680 -35.41934372  
0.35945432 -0.21566053 -0.90790040 223.22710470  
Axis -0.10864942 -0.98986748 0.09142031  
Axis point 115.49688768 0.00000000 137.51680437  
Rotation angle (degrees) 157.51510618  
Shift along axis 25.97446637  
  

> volume #6 level 0.09379

> select clear

> hide #!1 models

> volume mask #1 surfaces #2.4 modelId #3

No surfaces specified  

> volume all transparency 0.5

> hide #!4 models

> show #!4 models

> fitmap #4 inMap #6

Fit molecule 7pij (#4) to map cryosparc_P1024_J46_map.mrc (#6) using 4200
atoms  
average map value = 0.12, steps = 176  
shifted from previous position = 1.81  
rotated from previous position = 17.1 degrees  
atoms outside contour = 2071, contour level = 0.093791  
  
Position of 7pij (#4) relative to cryosparc_P1024_J46_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.54489237 0.76624670 0.34052651 36.96032172  
-0.80819452 -0.37173000 -0.45676955 427.04521352  
-0.22341424 -0.52410190 0.82182922 172.99115655  
Axis -0.04022852 0.33693316 -0.94066876  
Axis point 139.51244726 234.11413225 0.00000000  
Rotation angle (degrees) 123.18858967  
Shift along axis -20.32854449  
  

> fitmap #3 inMap #6

Fit molecule 7pij (#3) to map cryosparc_P1024_J46_map.mrc (#6) using 5122
atoms  
average map value = 0.1065, steps = 356  
shifted from previous position = 3.37  
rotated from previous position = 15.3 degrees  
atoms outside contour = 2619, contour level = 0.093791  
  
Position of 7pij (#3) relative to cryosparc_P1024_J46_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.49942333 0.78342600 0.36989190 17.71857477  
-0.82264427 -0.29492154 -0.48608402 419.79211904  
-0.27172177 -0.54705115 0.79177162 195.73594197  
Axis -0.03522966 0.37075439 -0.92806253  
Axis point 138.56400109 243.78310922 0.00000000  
Rotation angle (degrees) 120.08515935  
Shift along axis -26.63964172  
  

> hide #!2 models

> show #!2 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> fitmap #5 inMap #6

Fit molecule A3A-A10_for_Allision.pdb (#5) to map cryosparc_P1024_J46_map.mrc
(#6) using 862 atoms  
average map value = 0.1612, steps = 104  
shifted from previous position = 8.27  
rotated from previous position = 12.9 degrees  
atoms outside contour = 323, contour level = 0.093791  
  
Position of A3A-A10_for_Allision.pdb (#5) relative to
cryosparc_P1024_J46_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.41953668 0.68094929 -0.60024748 -18.34521228  
0.14921806 0.60052551 0.78555909 -177.24864049  
0.89538983 -0.41913862 0.15033255 94.90370849  
Axis -0.60454693 -0.75054757 -0.26683581  
Axis point -29.64862984 0.00000000 117.75997739  
Rotation angle (degrees) 85.11262549  
Shift along axis 118.80037138  
  

> show #!5 models

> hide #!4 models

> hide #!3 models

> open ""/Users/abdel104/Documents/Aihara Lab/Model
> Building/Borf2-A3B-B10-B1/RealSpaceRefine_11/A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb""

Chain information for
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb
#7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #!7 to #2

Computing secondary structure  
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
A3A_nbG11-coot-2_real_space_refined_004-coot-0_real_space_refined_005-coot-0.pdb,
chain A (#2) with
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb,
chain C (#7), sequence alignment score = 803  
RMSD between 172 pruned atom pairs is 0.535 angstroms; (across all 180 pairs:
1.354)  
  

> select clear

> select #7/D:237

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

127 atoms, 129 bonds, 15 residues, 1 model selected  

> select up

317 atoms, 323 bonds, 41 residues, 1 model selected  

> select up

360 atoms, 365 bonds, 47 residues, 1 model selected  

> select up

4583 atoms, 4700 bonds, 579 residues, 1 model selected  

> select up

4611 atoms, 4728 bonds, 582 residues, 1 model selected  

> select up

5373 atoms, 5502 bonds, 675 residues, 1 model selected  

> select up

8747 atoms, 8957 bonds, 1099 residues, 1 model selected  

> select down

5373 atoms, 5502 bonds, 675 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #7/B:20

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

50 atoms, 49 bonds, 7 residues, 1 model selected  

> select up

842 atoms, 858 bonds, 111 residues, 1 model selected  

> select up

3374 atoms, 3455 bonds, 424 residues, 1 model selected  

> select down

842 atoms, 858 bonds, 111 residues, 1 model selected  

> hide sel target a

> cartoon hide sel

> hide #!2 models

> select add #7

3374 atoms, 3455 bonds, 4 pseudobonds, 424 residues, 3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,-0.29005,-0.89688,-0.33389,467.43,-0.23452,-0.27164,0.93339,75.429,-0.92783,0.34903,-0.13154,206.72

> view matrix models
> #7,-0.19085,-0.64561,-0.73944,444.59,-0.060699,-0.74408,0.66533,207.86,-0.97974,0.17186,0.10282,227.3

> ui mousemode right ""translate selected models""

> view matrix models
> #7,-0.19085,-0.64561,-0.73944,446.39,-0.060699,-0.74408,0.66533,200.98,-0.97974,0.17186,0.10282,244.34

> fitmap #7 inMap #6

Fit molecule
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb
(#7) to map cryosparc_P1024_J46_map.mrc (#6) using 3374 atoms  
average map value = 0.06714, steps = 288  
shifted from previous position = 11.3  
rotated from previous position = 47.2 degrees  
atoms outside contour = 2413, contour level = 0.093791  
  
Position of
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb
(#7) relative to cryosparc_P1024_J46_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.27947117 0.49822109 0.82077500 -207.22874860  
0.68818628 -0.70004744 0.19061275 124.92188414  
0.66954873 0.51157533 -0.53851200 -23.59492241  
Axis 0.79750407 0.37575584 0.47201144  
Axis point -0.00000000 108.88957923 60.58983182  
Rotation angle (degrees) 168.39113798  
Shift along axis -129.46271653  
  

> cartoon (#!7 & sel)

> select #7/B:71

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

48 atoms, 48 bonds, 6 residues, 1 model selected  

> select up

842 atoms, 858 bonds, 111 residues, 1 model selected  

> select up

3374 atoms, 3455 bonds, 424 residues, 1 model selected  

> select down

842 atoms, 858 bonds, 111 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> fitmap #7 inMap #6

Fit molecule
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb
(#7) to map cryosparc_P1024_J46_map.mrc (#6) using 2532 atoms  
average map value = 0.08745, steps = 180  
shifted from previous position = 5.43  
rotated from previous position = 27.2 degrees  
atoms outside contour = 1544, contour level = 0.093791  
  
Position of
A3B-B1-B10_aligned_real_space_refined_003_aligned_borf2_real_space_refined_004-coot-1_real_space_refined_009-coot-0_real_space_refined_010-coot-0_real_space_refined_011_alignedtoOrf61A3Bctd.pdb
(#7) relative to cryosparc_P1024_J46_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.66666137 0.41992048 0.61581605 -239.65946826  
0.46203655 -0.88113078 0.10065171 242.47555661  
0.58488019 0.21742891 -0.78143447 122.60137793  
Axis 0.91277590 0.24180664 0.32919555  
Axis point 0.00000000 150.14063184 109.27814629  
Rotation angle (degrees) 176.33239003  
Shift along axis -119.76335780  
  

> volume #6 level 0.1297

> volume #6 level 0.07943

> ui tool show ""Segment Map""

Segmenting cryosparc_P1024_J46_map.mrc, density threshold 0.079430  
Showing 13 region surfaces  
974 watershed regions, grouped to 13 regions  
Showing cryosparc_P1024_J46_map.seg - 13 regions, 13 surfaces  

> select add #6

2 models selected  

> select subtract #6

Nothing selected  

> select add #8

14 models selected  

> select subtract #8

Nothing selected  

> close #8

> select clear

> hide #!6 models

> show #!6 models

Segmenting cryosparc_P1024_J46_map.mrc, density threshold 0.079430  
Showing 13 region surfaces  
974 watershed regions, grouped to 13 regions  
Showing cryosparc_P1024_J46_map.seg - 13 regions, 13 surfaces  

> select add #8

14 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.9657,0.15913,-0.20521,291.07,0.17993,0.97983,-0.086927,-9.081,0.18724,-0.12087,-0.97485,286.54

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.9657,0.15913,-0.20521,268.45,0.17993,0.97983,-0.086927,-35.553,0.18724,-0.12087,-0.97485,237.4

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.88638,0.076738,-0.45655,305.61,0.15873,0.97677,-0.14399,-23.012,0.43489,-0.2001,-0.87797,197.55

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.88638,0.076738,-0.45655,290.89,0.15873,0.97677,-0.14399,-21.208,0.43489,-0.2001,-0.87797,204.29

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.86065,0.13351,-0.49138,284.65,0.21919,0.96817,-0.12085,-32.313,0.4596,-0.21172,-0.86252,200.17

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.86065,0.13351,-0.49138,282.93,0.21919,0.96817,-0.12085,-32.4,0.4596,-0.21172,-0.86252,201.69

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.8937,0.1382,-0.42686,277.44,0.20498,0.97205,-0.11446,-31.835,0.39911,-0.18979,-0.89705,212.56

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.8937,0.1382,-0.42686,277.11,0.20498,0.97205,-0.11446,-33.088,0.39911,-0.18979,-0.89705,213.04

> hide #!5 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> view matrix models
> #8,-0.8937,0.1382,-0.42686,277.34,0.20498,0.97205,-0.11446,-33.23,0.39911,-0.18979,-0.89705,213.24

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.89695,0.12013,-0.4255,280.07,0.1947,0.97136,-0.13618,-28.428,0.39695,-0.20499,-0.89465,215.27

> view matrix models
> #8,-0.90918,0.099693,-0.4043,281.48,0.16273,0.97877,-0.12458,-26.566,0.3833,-0.17906,-0.9061,215.37

> view matrix models
> #8,-0.90754,0.11096,-0.40505,279.82,0.16939,0.97925,-0.11126,-29.557,0.3843,-0.16958,-0.9075,214.14

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.90754,0.11096,-0.40505,281.35,0.16939,0.97925,-0.11126,-29.22,0.3843,-0.16958,-0.9075,213.39

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.90703,0.10668,-0.40733,282.2,0.16883,0.97835,-0.11973,-27.765,0.38574,-0.17737,-0.9054,213.94

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.90703,0.10668,-0.40733,281.82,0.16883,0.97835,-0.11973,-28.869,0.38574,-0.17737,-0.9054,214.05

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select clear

> select #8.3

1 model selected  

> select add #8.7

2 models selected  

> select add #8.1

3 models selected  

> select #8.1

1 model selected  
Ungrouped to 8 regions  

> select #8.3

1 model selected  

> select add #8.7

2 models selected  

> select add #8.19

3 models selected  

> select add #8.21

4 models selected  

> select add #8.15

5 models selected  

> select add #8.18

6 models selected  
Grouped 6 regions  

> select add #8.16

2 models selected  
Grouped 2 regions  

> select add #8.20

2 models selected  
Grouped 2 regions  
Grouped 12 regions  
Ungrouped to 12 regions  

> select #8.13

1 model selected  

> select add #8.11

2 models selected  

> select add #8.5

3 models selected  

> select add #8.1

4 models selected  
Grouped 4 regions  
Ungrouped to 4 regions  

> select #8.13

1 model selected  

> select #8.13

1 model selected  
Ungrouped to 3 regions  

> select #8.1

1 model selected  

> select add #8.16

2 models selected  

> select add #8.5

3 models selected  

> select add #8.11

4 models selected  

> select add #8.2

5 models selected  
Grouped 5 regions  
Ungrouped to 5 regions  

> select #8.13

1 model selected  
Ungrouped to 5 regions  

> select #8.18

1 model selected  

> select add #8.2

2 models selected  

> select add #8.16

3 models selected  

> select add #8.5

4 models selected  
Grouped 4 regions  

> select add #8.11

2 models selected  

> select add #8.19

3 models selected  
Grouped 3 regions  

> select add #8.20

2 models selected  
Grouped 2 regions  

> select add #8.17

2 models selected  
Grouped 2 regions  


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

Log:
Startup Messages  
---  
warning | Registration file '/Users/abdel104/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14V0016ELL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E248)
      Kernel Version: Darwin 24.4.0
      Time since boot: 3 days, 23 hours, 46 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      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


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		can't reproduce		Tom Goddard				all	ChimeraX