id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
10446	Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0	jackieliu0406@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.2.1-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 0x00000002962bf000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x00000002952b3000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x00000002942a7000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000029329b000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000029228f000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x0000000291283000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x0000000290277000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000028f26b000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000028e25f000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000028d253000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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

Thread 0x000000028c247000 (most recent call first):
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 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 0x00000001dbdc5000 (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


{""app_name"":""ChimeraX"",""timestamp"":""2024-01-08 14:22:55.00 -0500"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.2.1 (23C71)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EED58CCD-2C98-4ED5-ADD0-815CF88D9A12""}
{
  ""uptime"" : 730000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 503,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,3"",
  ""coalitionID"" : 88308,
  ""osVersion"" : {
    ""train"" : ""macOS 14.2.1"",
    ""build"" : ""23C71"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-01-08 14:22:50.2654 -0500"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""EED58CCD-2C98-4ED5-ADD0-815CF88D9A12"",
  ""pid"" : 75645,
  ""translated"" : false,
  ""cpuType"" : ""ARM-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-01-08 11:51:47.1182 -0500"",
  ""procStartAbsTime"" : 17340648365482,
  ""procExitAbsTime"" : 17558163227509,
  ""procName"" : ""ChimeraX"",
  ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"",
  ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""},
  ""storeInfo"" : {""deviceIdentifierForVendor"":""4009FAF6-E9AB-50BF-9F04-0B89775FDB68"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""99DA3F3A-511F-2832-8536-7AEDB6E711CB"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""},
  ""wakeTime"" : 11363,
  ""sleepWakeUUID"" : ""B41793A7-447C-4392-97B2-81835EC9CF7E"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x18 is not in any region.  Bytes before following region: 105553653137384\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV  "",
  ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":75645},
  ""vmregioninfo"" : ""0x18 is not in any region.  Bytes before following region: 105553653137384\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV  "",
  ""extMods"" : {""caller"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""system"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""targeted"":{""thread_create"":0,""thread_set_state"":0,""task_for_pid"":0},""warnings"":0},
  ""faultingThread"" : 0,
  ""threads"" : [{""threadState"":{""x"":[{""value"":0},{""value"":0},{""value"":1},{""value"":6532705549},{""value"":5100731416},{""value"":14653896621418052622},{""value"":0},{""value"":6160720120},{""value"":4503198375180363156},{""value"":4503198382573073812},{""value"":78},{""value"":0},{""value"":49},{""value"":17},{""value"":10888413184},{""value"":0},{""value"":328},{""value"":8135078720},{""value"":0},{""value"":11},{""value"":7983616000,""symbolLocation"":0,""symbol"":""_main_thread""},{""value"":259},{""value"":7983616224,""symbolLocation"":224,""symbol"":""_main_thread""},{""value"":4773626496},{""value"":1},{""value"":32769},{""value"":32768},{""value"":7983622472,""symbolLocation"":0,""symbol"":""_NSConcreteStackBlock""},{""value"":1}],""flavor"":""ARM_THREAD_STATE64"",""lr"":{""value"":6532521152},""cpsr"":{""value"":1073745920},""fp"":{""value"":5100731216},""sp"":{""value"":5100731184},""esr"":{""value"":1442840704,""description"":"" Address size 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
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/TEST/Desktop/EMD/emd_12243.map

Opened emd_12243.map as #1, grid size 400,400,400, pixel 1.05, shown at level
0.00713, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.01363

> open 7BOH

7boh title:  
Complete Bacterial 30S ribosomal subunit assembly complex state E
(+RbfA)(Consensus Refinement) [more info...]  
  
Chain information for 7boh #2  
---  
Chain | Description | UniProt  
A | RNA (1527-MER) |  
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241  
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233  
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206  
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167  
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130  
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130  
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103  
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129  
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124  
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118  
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101  
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89  
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82  
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84  
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75  
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92  
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87  
V | 30S ribosome-binding factor | RBFA_ECOLI 1-133  
  
Non-standard residues in 7boh #2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 51997 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> set bgColor black

> set bgColor white

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting simple

> color #1 #b2b2b2cc models

> sequence chain #2/V

Alignment identifier is 2/V  

> select /V:84-104

173 atoms, 176 bonds, 21 residues, 1 model selected  

> select /V:6-84

614 atoms, 619 bonds, 79 residues, 1 model selected  

> select /V:78-104

225 atoms, 229 bonds, 27 residues, 1 model selected  

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> ui tool show ""Color Zone""

> color zone #1 near sel distance 4

> select add #2

52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected  

> select subtract #2

Nothing selected  

> volume #1 level 0.01493

> volume #1 level 0.01601

> open /Users/TEST/Desktop/cryosparc_P37_J127_009_volume_map.mrc

Opened cryosparc_P37_J127_009_volume_map.mrc as #3, grid size 384,384,384,
pixel 0.855, shown at level 0.0889, step 2, values float32  

> open /Users/TEST/Desktop/cryosparc_P37_J130_007_volume_map.mrc

Opened cryosparc_P37_J130_007_volume_map.mrc as #4, grid size 384,384,384,
pixel 0.855, shown at level 0.0922, step 2, values float32  

> volume #4 color #929292

> Volume flip#3

Unknown command: Volume flip#3  

> Volume flip #3

Unknown command: Volume flip #3  

> Flip volume#3

Unknown command: Flip volume#3  

> flip volume#3

Unknown command: flip volume#3  

> volume flip#3

Expected a density maps specifier or a keyword  

> volume flip #3

Opened cryosparc_P37_J127_009_volume_map.mrc z flip as #5, grid size
384,384,384, pixel 0.855, shown at step 1, values float32  

> ui mousemode right select

> select #5

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.4933,-0.77976,0.38553,144.83,0.70356,0.6183,0.35031,-116.89,-0.51153,0.098429,0.85361,95.286

> view matrix models
> #5,0.54346,-0.51885,0.65988,52.265,-0.0768,0.75207,0.65459,-53.281,-0.83592,-0.40642,0.36887,305.74

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.54346,-0.51885,0.65988,92.871,-0.0768,0.75207,0.65459,-2.5794,-0.83592,-0.40642,0.36887,356.62

> fitmap #2 inMap #5

Fit molecule 7boh (#2) to map cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) using 52154 atoms  
average map value = 0.1072, steps = 172  
shifted from previous position = 6.88  
rotated from previous position = 15.1 degrees  
atoms outside contour = 25183, contour level = 0.088917  
  
Position of 7boh (#2) relative to cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.67315578 -0.23783323 -0.70021187 220.00709757  
-0.42476837 0.65073060 -0.62938185 246.63226221  
0.60533720 0.72109988 0.33701903 -184.55574865  
Axis 0.71543201 -0.69162846 -0.09903087  
Axis point 0.00000000 410.98082186 169.39766307  
Rotation angle (degrees) 70.70374472  
Shift along axis 5.09894631  
  

> ui mousemode right select

> select clear

> volume #5 color darkgrey

> volume #5 color #a9a9a9a3

> volume #5 color #a9a9a9e6

> volume #5 level 0.1057

> volume #5 level 0.8

> volume #5 level 0.08

Drag select of 18 residues, 48 shapes, 5 cryosparc_P37_J127_009_volume_map.mrc
z flip  

> ui mousemode right select

> select clear

> ui mousemode right ""translate selected models""

> fitmap #2 inMap #5

Fit molecule 7boh (#2) to map cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) using 52154 atoms  
average map value = 0.1072, steps = 60  
shifted from previous position = 0.00785  
rotated from previous position = 0.00599 degrees  
atoms outside contour = 22210, contour level = 0.08  
  
Position of 7boh (#2) relative to cryosparc_P37_J127_009_volume_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.67321205 -0.23775232 -0.70018525 219.97767516  
-0.42479011 0.65071717 -0.62938106 246.63894830  
0.60525937 0.72113868 0.33707581 -184.56527011  
Axis 0.71546537 -0.69158590 -0.09908708  
Axis point 0.00000000 410.96888656 169.40982950  
Rotation angle (degrees) 70.70072116  
Shift along axis 5.10242367  
  

> volume flip #4

Opened cryosparc_P37_J130_007_volume_map.mrc z flip as #6, grid size
384,384,384, pixel 0.855, shown at step 1, values float32  

> ui mousemode right select

> select #6

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #6,1,0,0,58.857,0,1,0,32.855,0,0,1,40.286

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,0.49673,0.53209,-0.68567,168.71,-0.071775,-0.76213,-0.64343,455.64,-0.86493,0.36882,-0.34038,349.95

> ui mousemode right ""translate selected models""

> view matrix models
> #6,0.49673,0.53209,-0.68567,161.56,-0.071775,-0.76213,-0.64343,456.91,-0.86493,0.36882,-0.34038,344.48

> fitmap #2 inMap #6

Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms  
average map value = 0.1092, steps = 148  
shifted from previous position = 13.8  
rotated from previous position = 4.92 degrees  
atoms outside contour = 25285, contour level = 0.092213  
  
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:  
Matrix rotation and translation  
0.68529294 -0.24480885 -0.68588790 216.20271485  
0.37897532 -0.68436668 0.62291248 97.43482379  
-0.62189331 -0.68681211 -0.37621514 517.29154942  
Axis -0.90195504 -0.04407052 0.42957526  
Axis point 0.00000000 164.45628448 286.65330045  
Rotation angle (degrees) 133.44393362  
Shift along axis 22.91651852  
  

> volume #6 level 0.089

> volume #6 level 0.08

> volume #6 color #929292d7

> volume #6 color #929292cc

> view matrix models
> #6,0.49673,0.53209,-0.68567,153.81,-0.071775,-0.76213,-0.64343,434.01,-0.86493,0.36882,-0.34038,352.92

> undo

> ui mousemode right select

> select clear

> fitmap #2 inMap #6

Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms  
average map value = 0.1092, steps = 48  
shifted from previous position = 0.00906  
rotated from previous position = 0.00769 degrees  
atoms outside contour = 21358, contour level = 0.08  
  
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:  
Matrix rotation and translation  
0.68536512 -0.24470339 -0.68585341 216.16552790  
0.37897767 -0.68438745 0.62288823 97.44035501  
-0.62181233 -0.68682899 -0.37631817 517.29721270  
Axis -0.90198033 -0.04410402 0.42951871  
Axis point 0.00000000 164.44866357 286.63938718  
Rotation angle (degrees) 133.44597052  
Shift along axis 22.91426777  
  
Drag select of 417 residues, 488 shapes, 6
cryosparc_P37_J130_007_volume_map.mrc z flip  

> select clear

> volume #6 level 0.09

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> color zone #6 near sel distance 5.13

> color zone #6 near sel distance 5

> color zone #6 near sel distance 5.5

> ui mousemode right ""rotate selected models""

> view matrix models
> #2,0.96853,-0.012704,0.24858,-34.336,0.060076,0.9811,-0.18393,34.798,-0.24154,0.19307,0.95099,17.402

> view matrix models
> #2,0.96815,-0.012668,0.25004,-34.581,0.06066,0.98083,-0.18518,35.009,-0.2429,0.19445,0.95036,17.501

> ui mousemode right select

> select clear

> fitmap #2 inMap #6

Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms  
average map value = 0.1092, steps = 44  
shifted from previous position = 0.0361  
rotated from previous position = 0.16 degrees  
atoms outside contour = 24622, contour level = 0.09  
  
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:  
Matrix rotation and translation  
0.68538534 -0.24467747 -0.68584246 216.16016140  
0.37902882 -0.68433422 0.62291559 97.41975345  
-0.62175887 -0.68689127 -0.37629283 517.29428287  
Axis -0.90198394 -0.04413045 0.42950840  
Axis point 0.00000000 164.44598994 286.63791018  
Rotation angle (degrees) 133.44207273  
Shift along axis 22.91006921  
  
Drag select of 46 residues, 33 shapes, 6 cryosparc_P37_J130_007_volume_map.mrc
z flip  

> select clear

> ui mousemode right translate

> fitmap #2 inMap #6

Fit molecule 7boh (#2) to map cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) using 52154 atoms  
average map value = 0.1092, steps = 48  
shifted from previous position = 0.0175  
rotated from previous position = 0.00505 degrees  
atoms outside contour = 24610, contour level = 0.09  
  
Position of 7boh (#2) relative to cryosparc_P37_J130_007_volume_map.mrc z flip
(#6) coordinates:  
Matrix rotation and translation  
0.68533362 -0.24474155 -0.68587127 216.17412593  
0.37901688 -0.68434110 0.62291530 97.42157257  
-0.62182315 -0.68686158 -0.37624079 517.29503805  
Axis -0.90196716 -0.04410621 0.42954614  
Axis point 0.00000000 164.44948982 286.64636235  
Rotation angle (degrees) 133.44233126  
Shift along axis 22.92323105  
  

> volume #6 level 0.04764

> volume #6 level 0.08199

> volume #5 level 0.08872

> volume #6 level 0.08886

No atoms selected for color zoning  

> volume #6 level 0.09229

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> select add #2

52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> show #!2 models

> volume #6 level 0.1014

> select /V:6-8

22 atoms, 22 bonds, 3 residues, 1 model selected  

> select /V

783 atoms, 792 bonds, 99 residues, 1 model selected  

> select add #2

52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected  

> select subtract #2

Nothing selected  

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  

> open 7BOH

7boh title:  
Complete Bacterial 30S ribosomal subunit assembly complex state E
(+RbfA)(Consensus Refinement) [more info...]  
  
Chain information for 7boh #1  
---  
Chain | Description | UniProt  
A | RNA (1527-MER) |  
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241  
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233  
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206  
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167  
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130  
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130  
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103  
K | 30S ribosomal protein S11 | RS11_ECOLI 1-129  
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124  
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118  
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101  
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89  
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82  
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84  
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75  
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92  
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87  
V | 30S ribosome-binding factor | RBFA_ECOLI 1-133  
  
Non-standard residues in 7boh #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> sequence chain #1/V

Alignment identifier is 1/V  

> select /V:104

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

> select /V:101-104

29 atoms, 28 bonds, 4 residues, 1 model selected  

> select add #1

52154 atoms, 56194 bonds, 1667 pseudobonds, 4129 residues, 4 models selected  

> select subtract #1

Nothing selected  




OpenGL version: 4.1 Metal - 88
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: MKGP3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 19 days, 21 hours, 41 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      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
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 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-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		Window Toolkit		duplicate		Eric Pettersen				all	ChimeraX