id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9576	QPainter::begin: Paint device returned engine == 0	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-13.4-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

Current thread 0x00000001f3925e00 (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/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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  ""procRole"" : ""Background"",
  ""version"" : 2,
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  ""incident"" : ""5B661780-8568-4398-AFEC-5AC51F480DFB"",
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  ""procStartAbsTime"" : 617577234381,
  ""procExitAbsTime"" : 3385459284153,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"",
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  ""crashReporterKey"" : ""52E8BCBB-0ECD-E76A-418B-CCE1EDC18AAE"",
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  ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=8.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 4288K        8 \nCG image                          1568K       68 \nColorSync                          592K       30 \nCoreAnimation                     2816K      134 \nCoreGraphics                        48K        3 \nCoreGraphics (reserved)             32K        2         reserved VM address space (unallocated)\nCoreUI image data                 4576K       48 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             7.3G      818 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         680.0M        9         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        496K       31 \nStack                            151.7M       32 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      336.8M      584 \nVM_ALLOCATE (reserved)           192.0M        4         reserved VM address space (unallocated)\n__AUTH                            1850K      374 \n__AUTH_CONST                      28.9M      609 \n__CTF                               824        1 \n__DATA                            20.3M      755 \n__DATA_CONST                      39.1M      764 \n__DATA_DIRTY                      1983K      233 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       831.0M      154 \n__OBJC_RO                         66.3M        1 \n__OBJC_RW                         2011K        1 \n__TEXT                           853.2M      784 \ndyld private memory                272K        2 \nmapped file                      571.6M       97 \nshared memory                     3312K       32 \n===========                     =======  ======= \nTOTAL                             11.2G     5607 \nTOTAL, minus reserved VM space    10.2G     5607 \n"",
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  ""logWritingSignature"" : ""9f1e62e73396403fb285ecffa162ab2456cac1b0"",
  ""trialInfo"" : {
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      ""factorPackIds"" : {

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  ""experiments"" : [
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      ""experimentId"" : ""64a844035c85000c0f42398a"",
      ""deploymentId"" : 400000004
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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/rslack/Library/CloudStorage/OneDrive-
> EmoryUniversity/Documents/Data/Structures/A3G/Chimera/ClusPro_Docking_2_5.cxs
> format session

opened ChimeraX session  

> close session

> open /Users/rslack/Downloads/RT_Domains_Session.cxs

opened ChimeraX session  

> select /A/B

8209 atoms, 8064 bonds, 19 pseudobonds, 1310 residues, 3 models selected  

> hide sel surfaces

> select /B

3412 atoms, 3370 bonds, 2 pseudobonds, 529 residues, 2 models selected  

> show sel cartoons

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain /B

Alignment identifier is 1/B  

> select /B:233

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

> select /B:233-234

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

> select
> /B:27-44,77-84,97-103,112-118,121-129,134-138,154-175,196-211,235-239,254-268,276-284,296-312,363-384,394-405,420-427

1506 atoms, 1523 bonds, 180 residues, 1 model selected  

> select /B:210

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

> select /B:210-240

117 atoms, 121 bonds, 1 pseudobond, 13 residues, 2 models selected  

> select /B:210

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

> select /B:210-246

163 atoms, 168 bonds, 1 pseudobond, 19 residues, 2 models selected  

> name frozen HDX1 sel

> select
> /B:27-44,77-84,97-103,112-118,121-129,134-138,154-175,196-211,235-239,254-268,276-284,296-312,363-384,394-405,420-427

1506 atoms, 1523 bonds, 180 residues, 1 model selected  

> select /B:380

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

> select /B:380-386

57 atoms, 58 bonds, 7 residues, 1 model selected  

> select /B:381

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:381-382

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

> select /B:380

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

> select /B:380-394

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

> name frozen HDX2 sel

> select /B:410

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select /B:410-414

52 atoms, 56 bonds, 5 residues, 1 model selected  

> select /B:409

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /B:409-414

59 atoms, 63 bonds, 6 residues, 1 model selected  

> name frozen HDX3 sel

> lighting soft

> lighting full

> lighting soft

> show sel surfaces

> hide sel surfaces

> select /A:61

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

> select /A:61-65

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

> select /A:63

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

> select /A:63-64

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

> select /A:62

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

> select /A:62-72

95 atoms, 96 bonds, 11 residues, 1 model selected  

> name frozen HDX4 sel

> select /A:534

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

> select /A:534-555

157 atoms, 160 bonds, 22 residues, 1 model selected  

> name frozen HDX5 sel

> select HDX1, HDX2, HDX3, HDX4, HDX5

Expected an objects specifier or a keyword  

> select HDX1

3281 atoms, 168 bonds, 1 pseudobond, 398 residues, 2 models selected  

> select HDX1

3281 atoms, 168 bonds, 1 pseudobond, 398 residues, 2 models selected  

> select /B:327

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

> select /B:325-327

21 atoms, 20 bonds, 3 residues, 1 model selected  

> select /B:210

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

> select /B:210-247

170 atoms, 176 bonds, 1 pseudobond, 20 residues, 2 models selected  

> name frozen HDX1 sel

> select HDX1

3281 atoms, 176 bonds, 1 pseudobond, 398 residues, 2 models selected  

> select /B:394

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

> select /B:394

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

> select #1/B:210-247,380-394

295 atoms, 305 bonds, 1 pseudobond, 35 residues, 2 models selected  

> select #1/B:210-247,380-394,409-415

363 atoms, 377 bonds, 1 pseudobond, 42 residues, 2 models selected  

> ui tool show ""Volume Viewer""

> ui tool show ""Measure Volume and Area""

> ui tool show ""Measure and Color Blobs""

> ui tool show ""Surface Zone""

No surface chosen for zoning  

> molmap #1/B:210-247,380-394,409-415

Missing or invalid ""resolution"" argument: Expected a number  

> molmap #1 3.5

Opened 5J2M.pdb map 3.5 as #2, grid size 84,115,91, pixel 1.17, shown at level
0.103, step 1, values float32  

> hide #!2 models

> select #2/B:210-247,380-394,409-415

Nothing selected  

> show surfaces

> show #!2 models

> hide #!2 models

> hide surfaces

> show #!2 models

> select /A

4797 atoms, 4694 bonds, 17 pseudobonds, 781 residues, 2 models selected  

> close #2

> molmap #2/B:210-247,380-394,409-415 3.5

No atoms specified  

> molmap #1/B:210-247,380-394,409-415 3.5

Opened 5J2M.pdb map 3.5 as #2, grid size 42,63,63, pixel 1.17, shown at level
0.0798, step 1, values float32  

> select clear

> select add #2

2 models selected  

> transparency #2.1 50

No visible atoms or bonds selected  

> select /B:61

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

> select /B:61-76

138 atoms, 140 bonds, 16 residues, 1 model selected  

> select /A:61-62

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

> select /A:61-76

138 atoms, 140 bonds, 16 residues, 1 model selected  

> select /A:535-536

21 atoms, 22 bonds, 2 residues, 1 model selected  

> select /A:535-555

152 atoms, 155 bonds, 21 residues, 1 model selected  

> molmap #1/A:61-76,535-555

Missing or invalid ""resolution"" argument: Expected a number  

> molmap #1/A:61-76,535-555 3.5

Opened 5J2M.pdb map 3.5 as #3, grid size 62,87,44, pixel 1.17, shown at level
0.0857, step 1, values float32  

> volume #3 level 0.1343

> volume #3 level 0.07757

> volume #3 style image

> volume #3 colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 30,43,21 imageMode orthoplanes

> volume #3 style mesh

> volume #3 style image maximumIntensityProjection true colorMode auto8
> imageMode ""full region""

> volume #3 style surface maximumIntensityProjection false

> hide #!3 models

> show #!3 models

> set bgColor black

> hide #!3 models

> show #!3 models

> hide #3.1 models

> show #3.1 models

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> show #3.2 models

> hide #3.2 models

> volume #3 step 4

> volume #3 step 2

> volume #3 step 1

> volume #3 change image level 0,0 level 0.09808,0.8 level 1.504,1

> volume #3 level 0.07757

> volume #3 style image colorMode opaque8 imageMode ""box faces""

> volume #3 style surface

> close #3

> molmap #1/A:61-76,535-555 3.5

Opened 5J2M.pdb map 3.5 as #3, grid size 62,87,44, pixel 1.17, shown at level
0.0857, step 1, values float32  

> hide #!2 models

> show #!2 models

> set bgColor white

> volume #3 region 0,0,4,61,86,43

> color #3 #531b93ff models

> color #3 #531b9380 models

> volume #3 region 0,0,1,61,86,43

> volume #3 level 0.0798

> color #3 #fffb00ff models

> color #3 #fffb0075 models

> color #3 #fffb007d models

> color #3 #fffb0080 models

> color #3 #9437ffff models

> color #3 #9437ff7d models

> color #3 #9437ff80 models

> color #2 #9437ffff models

> color #2 #9437ff80 models

> select clear

> lighting soft

> open /Users/rslack/Downloads/5J2M_8CX2_docked_prot-prot-
> docking_3_pose_1_-_prepared.pdb

5J2M_8CX2_docked_prot-prot-docking_3_pose_1_-_prepared.pdb title:  
prot-prot-docking_3_pose_1 - prepared [more info...]  
  
Chain information for 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
F G | No description available  
K | No description available  
L | No description available  
P | No description available  
T | No description available  
  
Non-standard residues in 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb #4  
---  
MG — (MG)  
ZN — (ZN)  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> select add #4

30265 atoms, 30826 bonds, 19 pseudobonds, 1774 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select #4/A

9147 atoms, 9261 bonds, 10 pseudobonds, 561 residues, 2 models selected  

> select #4/A:427-560

2072 atoms, 2084 bonds, 132 residues, 1 model selected  

> color sel orange

> select #4/A:319-426

1829 atoms, 1862 bonds, 108 residues, 1 model selected  

> color sel yellow

> select #4/A:1-85,118-155

2035 atoms, 2060 bonds, 123 residues, 1 model selected  

> color sel blue

> select #4/A:86-117,156-236

1862 atoms, 1890 bonds, 113 residues, 1 model selected  

> color sel red

> select #4/A:237-318

1346 atoms, 1359 bonds, 82 residues, 1 model selected  

> color sel lime

> select #4/B

6628 atoms, 6718 bonds, 2 pseudobonds, 398 residues, 2 models selected  

> color (#!4 & sel) white

> ui tool show Matchmaker

> matchmaker #!4 to #1 cutoffDistance 1.5 bring #1.3

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 | 1.5  
  
Matchmaker 5J2M.pdb, chain A (#1) with 5J2M_8CX2_docked_prot-prot-
docking_3_pose_1_-_prepared.pdb, chain A (#4), sequence alignment score =
2862.7  
RMSD between 558 pruned atom pairs is 0.207 angstroms; (across all 558 pairs:
0.207)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4/P

556 atoms, 594 bonds, 1 pseudobond, 17 residues, 2 models selected  

> show #!1 models

> hide #!1 models

> color (#!4 & sel) cyan

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4/T

786 atoms, 847 bonds, 24 residues, 1 model selected  

> show #!1 models

> hide #!1 models

> color sel magenta

> show #!1 models

> hide #!1 models

> show #!1 models

> color sel hot pink

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!2 models

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4/P:816

35 atoms, 37 bonds, 1 residue, 1 model selected  

> select #4/P:816

35 atoms, 37 bonds, 1 residue, 1 model selected  

> select #4/P:816

35 atoms, 37 bonds, 1 residue, 1 model selected  

> select #4/T:709

31 atoms, 32 bonds, 1 residue, 1 model selected  

> select clear

> select #4/P:818

32 atoms, 33 bonds, 1 residue, 1 model selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!4 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie1.mp4

Movie saved to /Users/rslack/Desktop/movie1.mp4  
  

> volume #3 region 0,0,1,61,86,43

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie1.mp4

Movie saved to /Users/rslack/Desktop/movie1.mp4  
  

> lighting soft

> set bgColor black

> set bgColor white

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie1.mp4

Movie saved to /Users/rslack/Desktop/movie1.mp4  
  

> open /Users/rslack/Downloads/8cx0.pdb

8cx0.pdb title:  
Cryo-em structure of human APOBEC3G/hiv-1 vif/cbfbeta/elob/eloc monomeric
complex [more info...]  
  
Chain information for 8cx0.pdb #5  
---  
Chain | Description | UniProt  
A | DNA DC->du-editing enzyme apobec-3G | ABC3G_HUMAN 1-384  
B | virion infectivity factor | Q77YG0_9HIV1 1-192  
C | core-binding factor subunit β | PEBB_HUMAN 1-182  
D | elongin-B | ELOB_HUMAN 1-118  
E | elongin-C | ELOC_HUMAN 1-112  
K | RNA (5'-R(P*ap*ap*ap*ap*ap*ap*ap*A)-3') |  
  
Non-standard residues in 8cx0.pdb #5  
---  
ZN — zinc ion  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> select add #4

30265 atoms, 30826 bonds, 19 pseudobonds, 1774 residues, 3 models selected  

> select subtract #4

Nothing selected  

> select add #5

7575 atoms, 7802 bonds, 12 pseudobonds, 900 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> select #5/A

3202 atoms, 3307 bonds, 6 pseudobonds, 378 residues, 2 models selected  

> show sel cartoons

> ui tool show ""Show Sequence Viewer""

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:7-13

62 atoms, 62 bonds, 7 residues, 1 model selected  

> select #5/A:21

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

> select #5/A:21-27

65 atoms, 67 bonds, 7 residues, 1 model selected  

> select #5/A:7-13

62 atoms, 62 bonds, 7 residues, 1 model selected  

> select #5/A:21-27

65 atoms, 67 bonds, 7 residues, 1 model selected  

> molmap #5/A:1-13, 21-27, 86-91, 108-119, 124-135, 165-181, 235-260, 264-276,
> 282-289, 340-373 3.5

Opened 8cx0.pdb map 3.5 as #6, grid size 67,58,79, pixel 1.17, shown at level
0.0875, step 1, values float32  

> volume #6 level 0.0798

> volume #6 color #9437ff

> volume #6 color #9437ff81

> volume #6 color #9437ff80

> select clear

> volume #6 region 0,0,0,66,57,78

> volume #6 level 0.05

> volume #6 level 0.0798

> volume #6 level 0.1

> volume #6 level 0.0798

> select #5/A:7

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

> select clear

> volume #6 region 0,0,0,66,57,78

> select Zn

5 atoms, 5 residues, 2 models selected  

> show sel & #!5 atoms

> color (#!5 & sel) black

> select clear

> select #5/B:201@ZN

1 atom, 1 residue, 1 model selected  

> hide sel target a

> save /Users/rslack/Downloads/A3G_HDX.tif width 687 height 581 supersample 4

> hide #!6 models

> molmap #5/A:1-13, 21-27, 235-260, 340-373 3.5

Opened 8cx0.pdb map 3.5 as #7, grid size 46,57,75, pixel 1.17, shown at level
0.0885, step 1, values float32  

> volume #7 color #d783ff

> volume #7 color #d783ff80

> color #7 #d783ffff models

> color #7 #d783ff80 models

> color #7 #7a81ffff models

> color #7 #7a81ff80 models

> save /Users/rslack/Downloads/A3G_HDX2.tif width 687 height 581 supersample 4

> select #5/A:180,270

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

> show sel atoms

> color sel byhetero

> style sel stick

Changed 18 atom styles  

> style sel sphere

Changed 18 atom styles  

> style sel ball

Changed 18 atom styles  

> style sel sphere

Changed 18 atom styles  

> color sel dark gray

> color sel lime

> color sel cyan

> color sel byhetero

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 2

> save /Users/rslack/Downloads/A3G_Xlink.tif width 687 height 581 supersample
> 3

> hide #!7 models

> hide #!5 models

> show #!7 models

> show #!5 models

> hide #!5 models

> hide #!7 models

> show #!1 models

> show #!2 models

> show #!3 models

> select #1/B:154,201,275

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

> select #1/B:154,201,275

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

> show sel atoms

> style sel sphere

Changed 27 atom styles  

> color (#!1 & sel) cyan

> color (#!1 & sel) byhetero

> label (#!1 & sel) attribute label_one_letter_code

> label (#!1 & sel) text ""{0.label_one_letter_code}
> {0.number}{0.insertion_code}""

> label height 2

> label height 3

> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 3

> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 4

> label height 5

> select clear

> save /Users/rslack/Downloads/RT_Xlink.tif width 687 height 581 supersample 4

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!4 models

> show #!2 models

> show #!3 models

> volume #3 region 0,0,1,56,86,43

> select #4/B:154,201,275

66 atoms, 63 bonds, 3 residues, 1 model selected  

> style sel sphere

Changed 66 atom styles  

> style sel sphere

Changed 66 atom styles  

> show sel atoms

> color sel cyan

> color sel byhetero

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 5

> select #4/F:180,270

44 atoms, 42 bonds, 2 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> color sel cyan

> color sel byhetero

> select #4/G:180,270

44 atoms, 42 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel cyan

> color sel byhetero

> select #4/F

6274 atoms, 6379 bonds, 6 pseudobonds, 379 residues, 2 models selected  

> color (#!4 & sel) hot pink

> select #4/G

6276 atoms, 6383 bonds, 377 residues, 1 model selected  

> color sel hot pink

> select #4/G:180,270

44 atoms, 42 bonds, 2 residues, 1 model selected  

> color sel cyan

> color sel byhetero

> select #4/F:180,270

44 atoms, 42 bonds, 2 residues, 1 model selected  

> color sel cyan

> color sel byhetero

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 5

> select #4/G:180,270

44 atoms, 42 bonds, 2 residues, 1 model selected  

> label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}""

> label height 5

> select #4/K,L

598 atoms, 644 bonds, 18 residues, 1 model selected  

> color sel blue

> color sel cornflower blue

> select clear

> save /Users/rslack/Downloads/A3G_RT_Dock.tif width 921 height 685
> supersample 4

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie2.mp4

Movie saved to /Users/rslack/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie2.mp4

Movie saved to /Users/rslack/Desktop/movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie1.mp4

Movie saved to /Users/rslack/Desktop/movie1.mp4  
  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!6 models

> hide #!6 models

> show #!7 models

> show #!5 models

> select #5/A:180,270

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

> hide sel atoms

> color sel hot pink

> ui tool show ""Color Actions""

> color sel salmon

> ~label sel residues

> select clear

> volume #7 region 0,0,0,45,56,74

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/rslack/Desktop/movie1.mp4

Movie saved to /Users/rslack/Desktop/movie1.mp4  
  

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


===== 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 Pro
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: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 4 days, 23 hours, 8 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: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        C32F391:
          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-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-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-OpenCommands: 1.1
    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
    MolecularDynamicsViewer: 1.4
    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		Window Toolkit		duplicate		Tom Goddard				all	ChimeraX