Crash changing Mac display configuration

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.7.4-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404300104 (2024-04-30 01:04:30 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 0x000000010f01b600 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 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 1006 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 1169 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, lxml._elementpath, lxml.etree, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.atom_search.ast, PIL._imagingmath, chimerax.chem_group._chem_group (total: 61)


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  "incident" : "363A5A07-0086-41A5-AA54-A9882CB611BA",
  "bug_type" : "309",
  "pid" : 25629,
  "procExitAbsTime" : 342769249936023,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
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  "crashReporterKey" : "1084A283-DC3B-E83B-EDB4-571ACCB1FA24",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404300104 (2024-04-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nageshpeddada/Downloads/cryo-em-data-
> analysis/011624_IRF4_15min_analysis/model_building/cryosparc_model_building/alphafold_MIDN_F.L_Psmd2_F.L/overlay_cryoem_str.cxs

Opened P24_J323_deepemhancer.mrc as #2, grid size 640,640,640, pixel 1.07,
shown at level 0.148, step 1, values float32  
Opened SA_jb100.mrc as #3, grid size 500,500,500, pixel 1.2, shown at level
0.0073, step 2, values float32  
opened ChimeraX session  

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4/A:413

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

686 atoms, 686 bonds, 38 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> color sel byhetero

> show #!1 models

> select clear

> hide #!1 models

> select #4/A:413

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

686 atoms, 686 bonds, 38 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross ignoreHiddenModels true color #424242

240 contacts  

> contacts sel restrict cross ignoreHiddenModels true color #424242

240 contacts  

> sele#B:464,8,11-12

Unknown command: sele#B:464,8,11-12  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> save /Users/nageshpeddada/Downloads/cryo-em-data-
> analysis/011624_IRF4_15min_analysis/model_building/cryosparc_model_building/alphafold_MIDN_F.L_Psmd2_F.L/overlay_cryoem_str2.cxs

> contacts sel select true makePseudobonds false

4758 contacts  

> show (#4 & sel-residues & sidechain) target ab

> ui tool show Contacts

> contacts sel restrict cross ignoreHiddenModels true color #424242

39 contacts  

> contacts sel restrict cross ignoreHiddenModels true color #424242

39 contacts  

> contacts sel select true makePseudobonds false

6460 contacts  

> ui tool show Contacts

> contacts sel restrict cross ignoreHiddenModels true color #424242

141 contacts  

> select clear

> ui tool show Contacts

Restriction atom specifier must not be blank  

> contacts sel restrict both ignoreHiddenModels true color #424242

No atoms match given atom specifier  

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  
Restriction atom specifier must not be blank  

> contacts sel ignoreHiddenModels true color #424242

31 contacts  

> select #4/B:438

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

> select #4/B:438

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

> select #4/A:389

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:389-390

35 atoms, 34 bonds, 2 residues, 1 model selected  

> select clear

> select #4/A:389

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:389

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:53-64,113-122,126-132,303-322,326-329,376-413

1534 atoms, 1533 bonds, 21 pseudobonds, 91 residues, 2 models selected  

> select clear

> select #4/A:391

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4/A:391

22 atoms, 21 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

33 contacts  

> select #4/B:464

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

> select #4/B:464

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

> show (sel-residues & sidechain) target ab

> select #4/A:395

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #4/A:395

19 atoms, 18 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

21 contacts  

> select #4/B:461

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #4/B:461

14 atoms, 14 bonds, 1 residue, 1 model selected  

> show (sel-residues & sidechain) target ab

> select #4/A:399

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #4/A:399

19 atoms, 18 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

26 contacts  

> select #4/A:402

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4/A:402

22 atoms, 21 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

34 contacts  

> select #4/A:409

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:409

24 atoms, 23 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

31 contacts  

> select #4/A:391

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4/A:391

22 atoms, 21 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

33 contacts  

> select #4/A:395

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #4/A:395

19 atoms, 18 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

21 contacts  

> select #4/A:399

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #4/A:399

19 atoms, 18 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

26 contacts  

> select #4/A:402

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #4/A:402

22 atoms, 21 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

34 contacts  

> select #4/A:409

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:409

24 atoms, 23 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true color #424242

31 contacts  

> save /Users/nageshpeddada/Downloads/cryo-em-data-
> analysis/011624_IRF4_15min_analysis/model_building/cryosparc_model_building/alphafold_MIDN_F.L_Psmd2_F.L/overlay_cryoem_str3.cxs

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hbonds sel reveal true

6 hydrogen bonds found  

> hide #6 models

> show #6 models

> hide #5 models

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> sele#4/A:381arg

Unknown command: sele#4/A:381arg  

> sele#4/A:381

Unknown command: sele#4/A:381  

> sel#4/A:381

Unknown command: sel#4/A:381  

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #4/A:381, 391, 395, 399, 402, 409

130 atoms, 124 bonds, 6 residues, 1 model selected  

> select clear

> select #4/A:415

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select up

772 atoms, 784 bonds, 55 residues, 1 model selected  

> select clear

> select #4/A:415

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #4

20948 atoms, 21140 bonds, 35 pseudobonds, 1376 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #4/A:381, 391, 395, 399, 402, 409

130 atoms, 124 bonds, 6 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #4/B:438, 441

34 atoms, 32 bonds, 2 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true color #005493

48 contacts  

> contacts sel ignoreHiddenModels true color #005493

48 contacts  

> ui tool show Contacts

> ui tool show Distances

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select #4/B:438

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

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/B:438@OD1

1 atom, 1 residue, 1 model selected  

> select clear

Exactly two atoms must be selected!  

> select #4/B:438@OD2

1 atom, 1 residue, 1 model selected  

> select add #4/A:381@HH21

2 atoms, 2 residues, 1 model selected  

> distance #4/B:438@OD2 #4/A:381@HH21

Distance between ranked_0.pdb #4/B ASP 438 OD2 and /A ARG 381 HH21: 1.970Å  

> select clear

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel select true makePseudobonds false

39 contacts  

> ui tool show Contacts

> hide #7.1 models

> show #7.1 models

> ui tool show Contacts

> contacts sel ignoreHiddenModels true color #005493

43 contacts  

> select #4/B:438@OD1

1 atom, 1 residue, 1 model selected  

> select #4/A:381@HH21

1 atom, 1 residue, 1 model selected  

> select #4/B:438@OD1

1 atom, 1 residue, 1 model selected  

> select #4/A:381@HH21

1 atom, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select #4/A:381@HH21

1 atom, 1 residue, 1 model selected  

> select #4/B:438@OD1

1 atom, 1 residue, 1 model selected  

> select #4/A:381@HH21

1 atom, 1 residue, 1 model selected  

> hide #5 models

> ui mousemode right distance

> distance #4/B:438@OD1 #4/A:381@HH21

Distance between ranked_0.pdb #4/B ASP 438 OD1 and /A ARG 381 HH21: 1.923Å  

> ui mousemode right label

> label #4/B:400

> ui mousemode right "move label"

> ui mousemode right label

> label #4/B:438

> ui mousemode right "move label"

> ui mousemode right label

> label #4/A:381

> ui mousemode right "move label"

> select clear

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> distance style color #212121

> hbonds sel reveal true

5 hydrogen bonds found  

> contacts sel intraModel false intraMol false color #005493

8 contacts  

> hide #!7 models

> contacts sel intraModel false intraMol false select true color #005493
> reveal true

8 contacts  

> contacts sel intraModel false intraMol false select true color #005493
> reveal true

133 contacts  

> contacts sel intraModel false intraMol false color #005493

488 contacts  

> contacts sel intraModel false intraMol false color #005493

488 contacts  
Restriction atom specifier must not be blank  

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  
Restriction atom specifier must not be blank  

> select clear

> hide #7.1 models

> show #7.1 models

> hide #7.1 models

> hide #6 models

> show #6 models

> hide #6 models

> select #4/A:381

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #4/A:381, sel #4/B:438

36 atoms, 34 bonds, 4 pseudobonds, 2 residues, 3 models selected  
Restriction atom specifier must not be blank  

> ui tool show Contacts

> contacts sel restrict both select true makePseudobonds false

7 contacts  

> show #6 models

Restriction atom specifier must not be blank  

> contacts sel restrict both interModel false intraModel false intraMol false
> color #005493

No contacts  

> lighting soft

> lighting simple

> lighting full

> lighting soft

> ui tool show "Selection Inspector"

> ui mousemode right pivot

> ui mousemode right clip

> ui mousemode right zone

> ui mousemode right "contour level"

> view sel

> hide #6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/B:436

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

> select #4/B:436

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

> select #4/A:381, sel #4/B:438, 436

47 atoms, 44 bonds, 5 pseudobonds, 3 residues, 3 models selected  

> show (#!4 & sel-residues & sidechain) target ab

> ui mousemode right distance

> show #6 models

> ui mousemode right distance

> select clear

> ui mousemode right distance

> select #4/A:381@HH11

1 atom, 1 residue, 1 model selected  

> select #4/B:436

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

> ui mousemode right distance

> select clear

> select #4/A:381@HH11

1 atom, 1 residue, 1 model selected  

> select #4/B:436

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

> ui mousemode right distance

> select #4/A:381@HH11

1 atom, 1 residue, 1 model selected  

> select #4/B:436

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

> ui mousemode right distance

> color #6 #424242ff models

> hide #!7 models

> ui mousemode right distance

> distance #4/A:381@HH11 #4/A:381@HH21

Distance between ranked_0.pdb #4/A ARG 381 HH11 and HH21: 3.334Å  

> ui mousemode right distance

> distance #4/A:381@HH21 #4/B:438@OD2

Distance already exists; modify distance properties with 'distance style'  

> show #!7 models

> hide #6 models

> ui tool show Distances

> show #7.1 models

> ~distance #4/A:381@HH11 #4/A:381@HH21

> color sel byhetero

> style sel stick

Changed 11 atom styles  

> lighting simple

Exactly two atoms must be selected!  

> select #4/A:381@HH22

1 atom, 1 residue, 1 model selected  

> select #4/B:436

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

> select #4/A:381@HH22

1 atom, 1 residue, 1 model selected  

> select #4/B:436

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

> select #4/A:381@HH22

1 atom, 1 residue, 1 model selected  

> select add #4/B:436

12 atoms, 10 bonds, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> ui mousemode right distance

> distance #4/A:381@HH11 #4/A:381@HH22

Distance between ranked_0.pdb #4/A ARG 381 HH11 and HH22: 2.196Å  

> ui mousemode right distance

> distance #4/A:381@HH22 #4/B:436@CA

Distance between ranked_0.pdb #4/A ARG 381 HH22 and /B SER 436 CA: 5.389Å  

> ~distance #4/B:438@OD1 #4/A:381@HH21

> ~distance #4/A:381@HH11 #4/A:381@HH22

> show #6 models

> ui mousemode right distance

> ~distance #4/A:381@HH22 #4/B:436@CA

> ui mousemode right label

> label #4/B:436

> ui mousemode right label

> label delete residues

> ui mousemode right label

> label #4/B:438

> label #4/A:381

> label #4/B:436

> ui mousemode right "move label"

> view

> select #4/A:381, sel #4/B:438, 436

47 atoms, 44 bonds, 4 pseudobonds, 3 residues, 3 models selected  

> view sel

> lighting soft

> ui mousemode right "move label"

> select clear

> lighting soft

> lighting full

> lighting soft

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting flat

> lighting full

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> hide #!7 models

> view

> select #4/A:381, sel #4/B:438, 436

47 atoms, 44 bonds, 4 pseudobonds, 3 residues, 3 models selected  

> view sel

> ui tool show "Side View"

> view sel

> view orient

> view

> view sel

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting full

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> view sel

> lighting soft

> lighting flat

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> view sel

> hide (#!4 & sel) target a

> hide #* target a

> show (#!4 & sel) target ab

> lighting soft

> view sel

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> select clear

> ui mousemode right "move label"

> save /Users/nageshpeddada/Desktop/image22.png supersample 3

> save /Users/nageshpeddada/Downloads/cryo-em-data-
> analysis/011624_IRF4_15min_analysis/model_building/cryosparc_model_building/alphafold_MIDN_F.L_Psmd2_F.L/overlay_cryoem_str4.cxs

> select #4/A:381, 391, 395, 398, 402, 409

130 atoms, 124 bonds, 6 residues, 1 model selected  

> hide #* target a

> show sel target ab

> select #4/B:468, 464, 465, 457, 423, 458, 459, 315, 316

120 atoms, 115 bonds, 9 residues, 1 model selected  

> hide #* target a

> show sel target ab

> select #4/B:468, 464, 465, 457, 423, 458, 459, 315, 316, sel #4/A:381, 391,
> 395, 398, 402, 409

250 atoms, 239 bonds, 15 residues, 1 model selected  

> show (sel-residues & sidechain) target ab

> view sel

> select clear

> select #4/A:241

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

> select up

1505 atoms, 1528 bonds, 112 residues, 1 model selected  

> select up

6897 atoms, 6971 bonds, 468 residues, 1 model selected  

> select down

1505 atoms, 1528 bonds, 112 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/A:448

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select up

772 atoms, 784 bonds, 55 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #4/A:374

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

672 atoms, 678 bonds, 46 residues, 1 model selected  

> select up

2298 atoms, 2317 bonds, 147 residues, 1 model selected  

> select down

672 atoms, 678 bonds, 46 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select #4/A:329

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

57 atoms, 56 bonds, 4 residues, 1 model selected  

> select up

940 atoms, 951 bonds, 63 residues, 1 model selected  

> select up

3948 atoms, 3976 bonds, 255 residues, 1 model selected  

> select down

940 atoms, 951 bonds, 63 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/A:154

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

123 atoms, 124 bonds, 7 residues, 1 model selected  

> select up

2322 atoms, 2339 bonds, 154 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save /Users/nageshpeddada/Downloads/cryo-em-data-
> analysis/011624_IRF4_15min_analysis/model_building/cryosparc_model_building/alphafold_MIDN_F.L_Psmd2_F.L/overlay_cryoem_str5.cxs

> hide #6 models

> select #4/B:468, 464, 465, 457, 423, 458, 459, 315, 316, sel #4/A:381, 391,
> 395, 398, 402, 409

250 atoms, 239 bonds, 15 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both interModel false intraModel false intraMol false
> color #797979

No contacts  

> contacts sel restrict both intraModel false intraMol false color #797979

No contacts  
Restriction atom specifier must not be blank  

> contacts sel intraModel false intraMol false color #797979

1191 contacts  

> select #4/A:381, 391, 395, 398, 402, 409

130 atoms, 124 bonds, 6 residues, 1 model selected  

> ui tool show Contacts

> contacts sel intraModel false intraMol false color #797979

678 contacts  

> hide #5 models

> show #5 models

> ui tool show Contacts

> contacts sel intraModel false intraMol false color #797979

678 contacts  

> contacts sel intraModel false intraMol false color #797979

678 contacts  

> select clear

> hide #7.1 models

> hide #5 models

> ui mousemode right label

> label #4/A:391

> label #4/A:395

> label #4/A:398

> label #4/A:402

> label #4/A:409

> ui mousemode right "move label"

> lighting shadows true intensity 0.5

> lighting soft

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting flat

> save /Users/nageshpeddada/Desktop/image23.png supersample 3

> select #4/B:468, 464, sel #4/A:391

44 atoms, 41 bonds, 3 residues, 1 model selected  

> view sel

> ui tool show H-Bonds

> hbonds sel color #424242 showDist true restrict cross reveal true

5 hydrogen bonds found  

> show #!6 models

> hbonds sel color #424242 showDist true restrict cross intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> hbonds sel color #424242 showDist true restrict cross intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hbonds sel color #424242 showDist true restrict both intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> hbonds sel color #424242 showDist true restrict cross intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> ui tool show Contacts

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> contacts sel restrict cross intraModel false intraMol false color #797979

166 contacts  

> show #5 models

> hide #6 models

> select subtract #6

44 atoms, 41 bonds, 3 residues, 1 model selected  

> contacts sel restrict cross intraModel false intraMol false color #797979

166 contacts  

> contacts sel restrict cross intraModel false intraMol false select true
> color #797979 reveal true

166 contacts  

> contacts sel restrict cross intraModel false intraMol false select true
> color #797979 name contacts2 reveal true

637 contacts  

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts2

1252 contacts  

> close #8

> contacts sel restrict both intraModel false intraMol false color #797979
> name contacts2

637 contacts  

> hide #* target a

> show (#!4 & sel) target ab

> show (#!4 & sel-residues & sidechain) target ab

> select clear

> select #4/B:468, 464, sel #4/A:391

44 atoms, 41 bonds, 3 residues, 1 model selected  

> hide #* target a

> show sel target ab

> ui tool show Contacts

> contacts sel restrict both intraModel false intraMol false color #797979

No contacts  

> contacts sel restrict both intraModel false intraMol false color #797979
> name contacts2

No contacts  

> ui tool show H-Bonds

> hbonds sel color #424242 showDist true restrict cross intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> hbonds sel color #424242 showDist true restrict cross intraModel false
> saltOnly true reveal true

0 hydrogen bonds found  

> select clear

> ui tool show Distances

> ui tool show Contacts

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts2

No atoms match given atom specifier  
Exactly two atoms must be selected!  

> select #4/A:391

22 atoms, 21 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts3

110 contacts  

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts3

110 contacts  

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts3

110 contacts  

> contacts sel restrict cross intraModel false intraMol false color #797979
> name contacts3

110 contacts  

> contacts sel restrict cross select true makePseudobonds false

143 contacts  

> ui tool show Contacts

> contacts sel restrict cross intraModel false intraMol false color #797979

408 contacts  

> hide #9 models

> show #9 models

> select add #9

64 atoms, 110 pseudobonds, 16 residues, 5 models selected  

> hide #* target a

> show (#!4 & sel) target ab

> show (#!4 & sel-residues & sidechain) target ab

> hide #9 models

> show #9 models

> contacts sel restrict cross intraModel false intraMol false color #212121

408 contacts  

> select clear

> ui mousemode right label

> label #4/A:389

> ui mousemode right "move label"

> ui mousemode right label

> label #4/B:468

> ui mousemode right label

> label #4/B:464

> ui mousemode right distance

> distance #4/B:468@OD2 #4/A:391@HZ3

Distance between ranked_0.pdb #4/B ASP 468 OD2 and /A LYS 391 HZ3: 1.745Å  

> distance #4/B:468@OD2 #4/A:391@HZ3

Distance already exists; modify distance properties with 'distance style'  

> show #!7 models

> color #7 black models

> distance #4/B:468@OD1 #4/A:391@HZ1

Distance between ranked_0.pdb #4/B ASP 468 OD1 and /A LYS 391 HZ1: 2.357Å  

> ui mousemode right distance

> select clear

> color #7 #212121ff models

> distance #4/A:391@HZ1 #4/A:391@HE3

Distance between ranked_0.pdb #4/A LYS 391 HZ1 and HE3: 2.503Å  

> ~distance #4/A:391@HZ1 #4/A:391@HE3

> distance #4/A:391@HE3 #4/A:391@CE

Distance between ranked_0.pdb #4/A LYS 391 HE3 and CE: 1.090Å  

> ui mousemode right distance

> distance #4/A:391@HE3 #4/A:391@HE2

Distance between ranked_0.pdb #4/A LYS 391 HE3 and HE2: 1.781Å  

> ui mousemode right distance

> ~distance #4/A:391@HE3 #4/A:391@HE2

> ui mousemode right distance

> distance #4/A:391@HE3 #4/A:391@CE

Distance already exists; modify distance properties with 'distance style'  

> distance #4/B:464@CB #4/A:391@HD3

Distance between ranked_0.pdb #4/B ALA 464 CB and /A LYS 391 HD3: 4.843Å  

> color #7 black models

> ui mousemode right "move label"

> save /Users/nageshpeddada/Desktop/image24.png supersample 3

> hide #9 models

> show #9 models

> hide #9 models

> hide #8 models

> show #8 models

> hide #8 models


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

Log:
UCSF ChimeraX version: 1.8.dev202404300104 (2024-04-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 526.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.33f12

Software:

    System Software Overview:

      System Version: macOS 12.7.4 (21H1123)
      Kernel Version: Darwin 21.6.0
      Time since boot: 3 days 23:13

Graphics/Displays:

    AMD Radeon R9 M380:

      Chipset Model: AMD Radeon R9 M380
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6640
      Revision ID: 0x0080
      ROM Revision: 113-C6005R-800
      VBIOS Version: 113-C6005T-009
      EFI Driver Version: 01.00.800
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: YMYH137E1E4S
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.4
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    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.dev202404300104
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.38
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10