id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9409	Crash handling QTimer callback	edk4001@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000004005a7000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap

Current thread 0x00000001eb7dde00 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py"", line 147 in 
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in 
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main


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}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/edk4001/Library/Mobile Documents/com~apple~CloudDocs/bps2023
> site1.cxs""

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #19, grid size
340,340,340, pixel 0.815, shown at level 0.399, step 1, values float32  
Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #21, grid size
340,340,340, pixel 0.815, shown at level 0.147, step 1, values float32  
opened ChimeraX session  

> ui mousemode right ""play map series""

> ui mousemode right ""map eraser""

> volume erase #21 center 130.59,147.81,122.15 radius 2.0103

> volume erase #21 center 131.39,147.67,122.1 radius 2.0103

> volume erase #21 center 129.54,145.42,124.29 radius 2.0103

> volume erase #21 center 131.33,145.46,124.19 radius 2.0103

> volume erase #21 center 131.44,143.72,123.47 radius 1.0051

> volume erase #21 center 132.96,148.28,121.87 radius 1.0051

> volume erase #21 center 132.97,149.69,122.42 radius 1.0051

> open ""/Users/edk4001/Library/CloudStorage/Dropbox/ekim_nimigeanlab/final em
> maps/21july08_HCN1_WT_nanodisc_1mMDIPP/HCN1_21july08_j230_run_class001_highRes_mask.mrc""

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #23, grid size
340,340,340, pixel 0.815, shown at level 0.0458, step 2, values float32  

> volume #23 step 1

> volume #23 level 0.1705

> volume #23 level 0.1938

> volume #23 level 0.2094

> volume erase #23 center 131.87,148.61,121.88 radius 0.97001

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #24, grid size
340,340,340, pixel 0.815, shown at step 1, values float32  

> volume erase #24 center 131.95,148.41,121.24 radius 0.97001

> volume erase #24 center 132.15,148.36,122.56 radius 0.97001

> volume erase #24 center 132.53,148.17,123.23 radius 0.97001

> close #24

> open ""/Users/edk4001/Library/CloudStorage/Dropbox/ekim_nimigeanlab/final em
> maps/21july08_HCN1_WT_nanodisc_1mMDIPP/HCN1_21july08_j230_run_class001_highRes_mask.mrc""

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc as #24, grid size
340,340,340, pixel 0.815, shown at level 0.0458, step 2, values float32  

> show #!23 models

> hide #!23 models

> volume #24 step 1

> close #23

> volume #24 level 0.2912

> volume #24 level 0.2172

> volume erase #24 center 132.53,144.4,124.7 radius 0.97001

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #23, grid size
340,340,340, pixel 0.815, shown at step 1, values float32  

> volume erase #23 center 133.39,144.94,124.55 radius 0.97001

> volume erase #23 center 132.03,148.53,121.41 radius 0.97001

> volume erase #23 center 132.77,147.85,122.26 radius 0.97001

> volume erase #23 center 129.19,145.84,123.95 radius 6.3743 outside true

> volume erase #23 center 130.56,149.57,125.61 radius 2.0786

> volume erase #23 center 129.35,151.49,124.45 radius 2.0786

> volume erase #23 center 126.8,151.64,123.48 radius 2.0786

> ui tool show ""Side View""

> volume erase #23 center 131.89,149.95,126.39 radius 2.0786

> volume erase #23 center 130.76,151.99,126.98 radius 2.0786

> volume erase #23 center 126.87,149.85,128.3 radius 2.0786

> volume erase #23 center 127.03,148.83,128.95 radius 2.0786

> volume erase #23 center 126.16,151.47,123.57 radius 2.0786

> volume erase #23 center 130.82,145.39,128.5 radius 2.0786

> volume erase #23 center 130.36,144.33,128.79 radius 2.0786

> volume erase #23 center 131.67,146.02,128.05 radius 2.0786

> volume erase #23 center 131.48,146.52,127.65 radius 2.0786

> volume erase #23 center 131.36,147.05,127.43 radius 2.0786

> volume erase #23 center 131.71,148.37,125.28 radius 2.0786

> volume erase #23 center 132.57,144.72,128.65 radius 2.0786

> volume erase #23 center 129.4,140.93,123.21 radius 2.0786

> volume erase #23 center 128.17,140.73,125.55 radius 2.0786

> volume erase #23 center 127.34,141.06,125.18 radius 2.0786

> volume erase #23 center 130.26,140.29,123.68 radius 2.0786

> volume erase #23 center 129.95,140.14,122.22 radius 2.0786

> volume erase #23 center 127.4,141.47,119.9 radius 2.0786

> volume erase #23 center 126.22,143.71,120.64 radius 2.0786

> volume erase #23 center 126.14,141.51,121.83 radius 2.0786

> volume erase #23 center 125.83,145.18,120.08 radius 2.0786

> volume erase #23 center 132.34,143.94,119.7 radius 2.0786

> volume erase #23 center 134.08,142.97,123.95 radius 2.0786

> volume erase #23 center 134.58,142.73,124.53 radius 2.0786

> volume erase #23 center 135.68,145.34,125.45 radius 2.0786

> volume erase #23 center 133.06,149.87,120.48 radius 2.0786

> volume erase #23 center 133.39,150.29,121.73 radius 2.0786

> volume erase #23 center 131.96,142,125.33 radius 2.0786

> volume erase #23 center 133.94,146.56,124.48 radius 2.0786

> volume erase #23 center 133.76,147.34,123.92 radius 2.0786

> show #!21 models

> color #23 #941100ff models

> select add #23

4 models selected  

> ui tool show ""Color Actions""

> color sel fire brick

> color sel maroon

> color sel dark red

> color sel fire brick

> color #23 #9411003e models

> color #23 #94110029 models

> color #23 #94110028 models

> color #23 #94110026 models

> select clear

> color #21 #b2b2b22a models

> color #21 #b2b2b227 models

> color #21 #b2b2b222 models

> color #21 #b2b2b21c models

> color #21 #b2b2b218 models

> color #21 #b2b2b21a models

> hide #!23 models

> hide #!21 models

> select #1/C:380

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

> select add #1/C:383

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #1/C:384

20 atoms, 17 bonds, 3 residues, 2 models selected  

> select add #1/B:357

28 atoms, 24 bonds, 4 residues, 2 models selected  

> select add #1/B:386

40 atoms, 36 bonds, 5 residues, 3 models selected  

> select add #1/B:389

51 atoms, 47 bonds, 6 residues, 3 models selected  

> select add #1/B:302

59 atoms, 54 bonds, 7 residues, 3 models selected  

> select add #1/B:305

67 atoms, 61 bonds, 8 residues, 3 models selected  

> select add #1/B:306

75 atoms, 68 bonds, 9 residues, 3 models selected  

> select add #1/B:309

81 atoms, 73 bonds, 10 residues, 3 models selected  

> select add #1/B:353

89 atoms, 80 bonds, 11 residues, 3 models selected  

> ui tool show ""Color Actions""

> color sel dark slate blue

> select #1/?:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1/C:384

8 atoms, 6 bonds, 2 residues, 2 models selected  

> select add #1/C:383

13 atoms, 10 bonds, 3 residues, 3 models selected  

> select add #1/C:380

21 atoms, 17 bonds, 4 residues, 3 models selected  

> select add #1/B:357

29 atoms, 24 bonds, 5 residues, 3 models selected  

> select add #1/B:353

37 atoms, 31 bonds, 6 residues, 4 models selected  

> select add #1/B:309

43 atoms, 36 bonds, 7 residues, 4 models selected  

> select add #1/B:306

51 atoms, 43 bonds, 8 residues, 4 models selected  

> select add #1/B:305

59 atoms, 50 bonds, 9 residues, 4 models selected  

> select add #1/B:302

67 atoms, 57 bonds, 10 residues, 4 models selected  

> select add #1/B:389

78 atoms, 68 bonds, 11 residues, 4 models selected  

> select add #1/B:386

90 atoms, 80 bonds, 12 residues, 4 models selected  

> select up

102 atoms, 95 bonds, 12 residues, 4 models selected  

> size sel stickRadius 0.27

Changed 95 bond radii  

> select clear

> show #!21 models

> show #!23 models

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 3000 height
> 2481 supersample 4 transparentBackground true

> graphics silhouettes width 6

> lighting soft

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> volume #23 level 0.2021

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> open /Users/edk4001/Desktop/phenix_HCN1_21july08/21july08_isolde5-coot-5.pdb

Chain information for 21july08_isolde5-coot-5.pdb #22  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!1 models

> show #!1 models

> select add #22

14613 atoms, 14977 bonds, 4 pseudobonds, 1941 residues, 2 models selected  

> hide #!23 models

> hide #!21 models

> select #22/A,D

7300 atoms, 7482 bonds, 2 pseudobonds, 970 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select #22/b

3663 atoms, 3754 bonds, 1 pseudobond, 486 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light slate gray

> color sel slate gray

> color sel light slate gray

> select #22/C

3650 atoms, 3741 bonds, 1 pseudobond, 485 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel pale goldenrod

> hide #!1 models

> show #!1 models

> select #22/B:601@C7

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark red

> color sel maroon

> color sel fire brick

> color sel maroon

> select #22/B:302

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

> select add #22/B:305

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #22/B:306

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select add #22/B:309

30 atoms, 26 bonds, 4 residues, 1 model selected  

> select add #22/B:357

38 atoms, 33 bonds, 5 residues, 1 model selected  

> select add #1/B:354

44 atoms, 38 bonds, 6 residues, 2 models selected  

> select subtract #1/B:354

38 atoms, 33 bonds, 5 residues, 2 models selected  

> select add #1/B:353

46 atoms, 40 bonds, 6 residues, 2 models selected  

> select add #22/B:353

54 atoms, 47 bonds, 7 residues, 3 models selected  

> select subtract #1/B:353

46 atoms, 40 bonds, 6 residues, 2 models selected  

> select subtract #22/B:353

38 atoms, 33 bonds, 5 residues, 1 model selected  

> select add #22/B:353

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select subtract #22/B:357

38 atoms, 33 bonds, 5 residues, 1 model selected  

> select add #1/B:357

46 atoms, 40 bonds, 6 residues, 2 models selected  

> select subtract #1/B:357

38 atoms, 33 bonds, 5 residues, 2 models selected  

> select add #22/B:357

46 atoms, 40 bonds, 6 residues, 1 model selected  

> select add #22/C:380

54 atoms, 47 bonds, 7 residues, 1 model selected  

> select add #22/C:384

61 atoms, 53 bonds, 8 residues, 1 model selected  

> select add #22/C:383

66 atoms, 57 bonds, 9 residues, 1 model selected  

> select add #22/B:389

77 atoms, 68 bonds, 10 residues, 1 model selected  

> select add #22/B:386

89 atoms, 80 bonds, 11 residues, 1 model selected  

> show sel atoms

> ui tool show ""Color Actions""

> color sel dark slate blue

> hide #!1 models

> select add #22/B:601@C1

90 atoms, 80 bonds, 12 residues, 1 model selected  

> select up

102 atoms, 95 bonds, 12 residues, 1 model selected  

> size sel stickRadius 0.27

Changed 95 bond radii  

> show #!23 models

> show #!21 models

> select clear

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> lighting shadows false

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> volume #23 level 0.1672

> volume #23 level 0.1486

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.cxs"" includeMaps true

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> volume #23 level 0.09513

> hide #!21 models

> show #!21 models

> hide #!21 models

> ui mousemode right ""map eraser""

> volume erase #23 center 124.31,151.58,122.4 radius 2.6818

> volume erase #23 center 128.65,152.95,123.27 radius 2.6818

> volume erase #23 center 132.01,152.78,124.92 radius 2.6818

> surface dust #23 size 8.15

> show #!21 models

> graphics silhouettes width 6

> color #23 #ff2600ff models

> color #23 #ff26002a models

> color #23 #ff260024 models

> color #23 #ff26001b models

> color #23 #ff260027 models

> color #23 #ff260026 models

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.png"" width 4000 height
> 3307 supersample 4 transparentBackground true

> save ""/Users/edk4001/Desktop/HCN1 pfl site 1 zoom.cxs"" includeMaps true

> show #!24 models

> hide #!24 models

> show #!24 models

> hide #!24 models

> open /Users/edk4001/Desktop/phenix_HCN1_21july08/21july08_isolde5-coot-5.pdb

Chain information for 21july08_isolde5-coot-5.pdb #25  
---  
Chain | Description  
A B C D | No description available  
  

> hide #!23 models

> hide #!22 models

> hide #!21 models

> show #!23 models

> hide #!23 models

> show #!24 models

> volume #24 level 0.1549

> surface dust #24 size 8.15

> color #24 #d6d6d6ff models

> color #24 #d6d6d616 models

> color #24 #d6d6d631 models

> color #24 #d6d6d61f models

> color #24 #d6d6d61a models

> color #24 #d6d6d672 models

> color #24 #d6d6d62c models

> color #24 #d6d6d62e models

> color #24 #d6d6d634 models

> color #24 #d6d6d633 models

> hide #!24 models

> select #25/B

3663 atoms, 3754 bonds, 1 pseudobond, 486 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light slate gray

> lighting soft

> lighting full

> lighting simple

> lighting full

> select clear

> select #25/A,C,D

10950 atoms, 11223 bonds, 3 pseudobonds, 1455 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> select #25/B:602@C1

1 atom, 1 residue, 1 model selected  

> select up

13 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show ""Color Actions""

> color sel maroon

> size sel stickRadius 0.27

Changed 13 bond radii  

> select clear

> show #!24 models

> volume #24 level 0.1705

> color #24 #d6d6d6ff models

> show #!1 models

> hide #!24 models

> hide #!25 models

> hide #!1 models

> show #!25 models

> show #!24 models

> show #!23 models

> hide #!23 models

> hide #!24 models

> show #!24 models

> hide #!25 models

> ui mousemode right ""map eraser""

> volume erase #24 center 146.24,181.09,136.81 radius 7.6004 outside true

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #27, grid size
340,340,340, pixel 0.815, shown at step 1, values float32  

> volume erase #27 center 145.13,182.93,142.46 radius 2.4943

> volume erase #27 center 145.05,182.34,142.37 radius 2.4943

> volume erase #27 center 140.81,178.09,139.5 radius 2.4943

> volume erase #27 center 139.76,177.9,137.68 radius 2.4943

> volume erase #27 center 144.01,180.05,142.55 radius 2.4943

> volume erase #27 center 143.96,179.97,142.41 radius 2.4943

> volume erase #27 center 141.89,176.39,132.27 radius 2.4943

> color #27 #ff2600ff models

> color #27 #ff260010 models

> color #27 #ff260025 models

> color #27 #ff260026 models

> color #27 #ff260027 models

> show #!25 models

> color #27 #ff260026 models

> show #!24 models

> hide #!24 models

> hide #!25 models

> hide #!27 models

> show #!24 models

> ui mousemode right ""map eraser""

> volume erase #24 center 145.88,164.03,135.58 radius 18.953 outside true

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #28, grid size
340,340,340, pixel 0.815, shown at step 1, values float32  

> show #!27 models

> show #!24 models

> color #28 #fffc79ff models

> hide #!27 models

> hide #!24 models

> volume erase #28 center 140.65,178.1,137.91 radius 5.8201

> volume erase #28 center 142.43,180.15,140.89 radius 5.8201

> volume erase #28 center 132.71,175.9,130.96 radius 5.8201

> volume erase #28 center 133.14,177.14,137.65 radius 5.8201

> volume erase #28 center 133.89,177.06,140.13 radius 5.8201

> volume erase #28 center 134.09,177.26,141.05 radius 5.8201

> volume erase #28 center 138.02,180.64,133.77 radius 5.8201

> volume erase #28 center 133.47,172.71,133.77 radius 5.1272

> volume erase #28 center 134.21,175.85,137.09 radius 5.1272

> volume erase #28 center 136.35,177.14,135.72 radius 5.1272

> volume erase #28 center 135.61,176.86,128.88 radius 5.1272

> volume erase #28 center 137.17,173.83,125.71 radius 5.1272

> volume erase #28 center 142.08,176.32,129.09 radius 5.1272

> volume erase #28 center 148.5,168.2,148.12 radius 5.1272

> volume erase #28 center 136.19,167.82,148.77 radius 5.1272

> volume erase #28 center 131.52,172.79,144.77 radius 5.1272

> volume erase #28 center 131.84,171.09,148.14 radius 5.1272

> volume erase #28 center 126.52,167.55,138.8 radius 5.1272

> volume erase #28 center 128.13,160.02,139.17 radius 4.0186

> volume erase #28 center 129.42,167,134.45 radius 4.0186

> volume erase #28 center 128.32,163.71,134.03 radius 4.0186

> volume erase #28 center 129.01,165.62,131.38 radius 4.0186

> volume erase #28 center 129.5,167.34,128.3 radius 4.0186

> volume erase #28 center 131.42,169.69,125.91 radius 4.0186

> volume erase #28 center 132.47,170.27,123.91 radius 4.0186

> surface dust #28 size 8.15

> volume erase #28 center 140.26,152.03,120.22 radius 4.0186

> volume erase #28 center 153.87,148.28,142.38 radius 14.827

> volume erase #28 center 155.39,146.15,138.27 radius 14.827

> show #!27 models

> show #!24 models

> show #!25 models

> color #24 #d6d6d61b models

> color #24 #d6d6d621 models

> color #24 #d6d6d61e models

> color #24 #d6d6d61b models

> color #24 #d6d6d618 models

> color #24 #d6d6d619 models

> color #24 #d6d6d61a models

> color #28 #fffc794a models

> color #28 #fffc7928 models

> color #28 #fffc7924 models

> color #28 #fffc7923 models

> color #28 #fffc7926 models

> hide #!24 models

> hide #!27 models

> hide #!28 models

> select #25/B:219

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #25/B:220

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select add #25/B:221

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select add #25/B:222

35 atoms, 34 bonds, 4 residues, 1 model selected  

> select add #25/B:223

42 atoms, 40 bonds, 5 residues, 1 model selected  

> select add #25/B:218

47 atoms, 44 bonds, 6 residues, 1 model selected  

> show sel atoms

> ui tool show ""Color Actions""

> color sel dark slate blue

> size sel stickRadius 0.27

Changed 49 bond radii  

> select clear

> show #!24 models

> hide #!25 models

> color #24 #d6d6d6ff models

> ui mousemode right ""map eraser""

> surface dust #24 size 8.15

> volume erase #24 center 140.78,168.83,138.18 radius 3.1748

Opened HCN1_21july08_j230_run_class001_highRes_mask.mrc copy as #29, grid size
340,340,340, pixel 0.815, shown at step 1, values float32  

> surface dust #29 size 8.15

> volume erase #29 center 146.23,177.22,134.83 radius 3.0486

> volume erase #29 center 147.49,177.85,136.46 radius 3.0486

> volume erase #29 center 146.14,177.23,137.89 radius 3.0486

> volume erase #29 center 145.13,179.91,138.37 radius 3.0486

> volume erase #29 center 143.8,179.27,141.63 radius 3.0486

> volume erase #29 center 143.19,179.37,141.67 radius 3.0486

> volume erase #29 center 122.83,190.28,141.38 radius 3.0486

> volume erase #29 center 138.56,164.03,133.03 radius 3.0486

> volume erase #29 center 137.84,164.09,134.7 radius 3.0486

> volume erase #29 center 135.89,163.85,136.88 radius 3.0486

> volume erase #29 center 138.1,164.94,127.97 radius 3.0486

> volume erase #29 center 138.02,159.54,131.18 radius 3.0486

> show #!28 models

> show #!27 models

> show #!25 models

> color #29 #d6d6d627 models

> color #29 #d6d6d61a models

> set bgColor black

> set bgColor white

> ui tool show ""Side View""

> hide #!28 models

> show #!28 models

> hide #!27 models

> hide #!28 models

> hide #!29 models

> ui tool show Rotamers

No residues selected  

> select #25/B:218@CA

1 atom, 1 residue, 1 model selected  

> select clear

> show #!28 models

> show #!27 models

> show #!29 models

> save ""/Users/edk4001/Desktop/HCN1 pfl site 2 zoom.png"" width 4000 height
> 3301 supersample 4 transparentBackground true

> hide #!25 models

> hide #!28 models

> hide #!29 models

> ui mousemode right ""map eraser""

> volume erase #27 center 143.51,182.72,140.9 radius 1.4669

> volume #23 color #ff260050

> volume #23 color #ff260043

> volume #23 color #ff260042

> color #27 #ff260080 models

> color #27 #ff260071 models

> color #27 #ff260066 models

> color #27 #ff26005c models

> color #27 #ff260058 models

> show #!25 models

> color #27 #ff260059 models

> show #!28 models

> color #28 #fffc7985 models

> color #28 #fffc795c models

> color #28 #fffc795a models

> show #!29 models


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

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000HSLL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Time since boot: 5 days, 10 hours, 57 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      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
        G236HL:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    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: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

}}}
"	defect	closed	normal		Core		duplicate		Tom Goddard				all	ChimeraX