Opened 2 years ago

Closed 2 years ago

#10299 closed defect (duplicate)

Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.0-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 0x00000002b641b000 (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 0x00000002b540f000 (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 0x00000002b4403000 (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 0x00000002b33f7000 (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 0x00000002b23eb000 (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 0x00000002b13df000 (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 0x00000002b03d3000 (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 0x00000002af3c7000 (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 0x00000002ae3bb000 (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 0x00000002ad3af000 (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 0x00000002ac3a3000 (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 0x00000002ab397000 (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 0x00000002aa38b000 (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 0x00000002a937f000 (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 0x00000002a81f7000 (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 0x00000001e0662500 (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":"2023-12-06 17:07:55.00 -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 13.0 (22A8380)","roots_installed":0,"name":"ChimeraX","incident_id":"2B7C5097-62FC-42E4-9923-8E5D80A7B93A"}
{
  "uptime" : 110000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,6",
  "coalitionID" : 28358,
  "osVersion" : {
    "train" : "macOS 13.0",
    "build" : "22A8380",
    "releaseType" : "User"
  },
  "captureTime" : "2023-12-06 17:07:51.5155 -0500",
  "incident" : "2B7C5097-62FC-42E4-9923-8E5D80A7B93A",
  "pid" : 27217,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-12-06 11:47:17.9669 -0500",
  "procStartAbsTime" : 2412600158164,
  "procExitAbsTime" : 2870097164283,
  "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":"80EAF192-9463-5C86-BC34-BE503583011D","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "7210FCDD-56AE-A554-267C-574BE8139AF6",
  "wakeTime" : 3087,
  "sleepWakeUUID" : "94308F78-E7E2-4651-8885-8F3604FB3707",
  "sip" : "enabled",
  "vmRegionInfo" : "0x18 is not in any region.  Bytes before following region: 105556740145128\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 105556740145128\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO              6000d8000000-6000e0000000 [128.0M] 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" : [{"triggered":true,"id":2094287,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6525277773},{"value":6133533640},{"value":16487809229310873976},{"value":0},{"value":6133531528},{"value":12075225780863471380},{"value":12075225782480775700},{"value":78},{"value":0},{"value":49},{"value":4334052512},{"value":0},{"value":0},{"value":328},{"value":8141609656},{"value":0},{"value":11},{"value":8059757824,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8059758048,"symbolLocation":224,"symbol":"_main_thread"},{"value":4554519216},{"value":1},{"value":32769},{"value":32768},{"value":8059764256,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6525099244},"cpsr":{"value":1073745920},"fp":{"value":6133533440},"sp":{"value":6133533408},"esr":{"value":1442840704,"description":" Address size 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    "size" : 2555904,
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    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
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    "size" : 566452,
    "uuid" : "b7142778-f6ba-31ca-820c-34b24d90f149",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 6141591552,
    "size" : 154959872,
    "uuid" : "1b766dc4-2490-3425-8726-45387675bc14",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
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    "base" : 5545525248,
    "size" : 16384,
    "uuid" : "cfed1505-cef2-372b-abff-2a9183ec018e",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
    "name" : "_queue.cpython-39-darwin.so"
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    "size" : 32768,
    "uuid" : "ff7d40db-95e6-320a-b57f-faed8f2333d9",
    "path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
    "name" : "select.cpython-39-darwin.so"
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],
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  "legacyInfo" : {
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},
  "trialInfo" : {
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    {
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      "factorPackIds" : {

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      "factorPackIds" : {

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},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== 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 3suc 7w1e 40j5

Fetching url http://files.rcsb.org/download/40j5.cif failed:  
HTTP Error 404: Not Found  

> open 3suc 7w1e 4oj5

3suc title:  
Crystal structure of the pre-mature bacteriophage phi29 gene product 12 [more
info...]  
  
Chain information for 3suc #1  
---  
Chain | Description | UniProt  
A | Preneck appendage protein | B3VMP8_BPPH2 89-854  
  
Non-standard residues in 3suc #1  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
MG — magnesium ion  
  
3suc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  
7w1e title:  
Crystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide
lyase in complex with products [more info...]  
  
Chain information for 7w1e #2  
---  
Chain | Description | UniProt  
A B C D E F | K1 LYASE | A0A068Q5Q5_9CAUD 1-651  
  
Non-standard residues in 7w1e #2  
---  
98U — 3-O-acetyl-6-deoxy-alpha-L-galactopyranose  
98X — 2,6-anhydro-4,5-O-[(1R)-1-carboxyethylidene]-3-deoxy-L-threo-
hex-2-enonic acid  
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IMD — imidazole  
  
7w1e mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
4oj5 title:  
Crystal Structure of a Putative Tailspike Protein (TSP1, orf210) from
Escherichia coli O157:H7 Bacteriohage CBA120 [more info...]  
  
Chain information for 4oj5 #3  
---  
Chain | Description | UniProt  
A B C | Tailspike protein | G3M189_9CAUD 1-770  
  
Non-standard residues in 4oj5 #3  
---  
ZN — zinc ion  
  

> set bgColor white

> hide atoms

> show cartoons

Drag select of 83 residues  

> select up

957 atoms, 969 bonds, 130 residues, 1 model selected  

> select up

9554 atoms, 9758 bonds, 1264 residues, 1 model selected  

> select up

11313 atoms, 9844 bonds, 2945 residues, 1 model selected  

> select up

34354 atoms, 30103 bonds, 8765 residues, 1 model selected  

> select down

11313 atoms, 9844 bonds, 2945 residues, 1 model selected  

> select up

34354 atoms, 30103 bonds, 8765 residues, 1 model selected  

> select down

11313 atoms, 9844 bonds, 2945 residues, 1 model selected  

> delete sel

Drag select of 1333 residues  

> select up

10710 atoms, 10930 bonds, 1413 residues, 1 model selected  

> select down

10101 atoms, 1333 residues, 1 model selected  

> select clear

Drag select of 737 residues  

> select up

6233 atoms, 6359 bonds, 822 residues, 1 model selected  

> select up

14509 atoms, 14820 bonds, 1918 residues, 1 model selected  

> select up

17032 atoms, 14960 bonds, 4315 residues, 1 model selected  

> select up

23041 atoms, 20256 bonds, 5820 residues, 1 model selected  

> select down

17032 atoms, 14960 bonds, 4315 residues, 1 model selected  

> delete sel

> select clear

Drag select of 42 residues  

> select up

1476 atoms, 1482 bonds, 100 residues, 1 model selected  

> select up

22550 atoms, 22758 bonds, 1514 residues, 1 model selected  

> select up

24100 atoms, 22758 bonds, 3064 residues, 1 model selected  

> select up

36271 atoms, 34133 bonds, 4721 residues, 1 model selected  

> select down

24100 atoms, 22758 bonds, 3064 residues, 1 model selected  

> delete sel

> select clear

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3suc, chain A (#1) with 7w1e, chain E (#2), sequence alignment
score = 275.5  
RMSD between 76 pruned atom pairs is 1.103 angstroms; (across all 517 pairs:
24.890)  
  
Matchmaker 3suc, chain A (#1) with 4oj5, chain C (#3), sequence alignment
score = 238.2  
RMSD between 29 pruned atom pairs is 1.320 angstroms; (across all 631 pairs:
30.404)  
  

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3suc, chain A (#1) with 7w1e, chain E (#2), sequence alignment
score = 275.5  
RMSD between 76 pruned atom pairs is 1.103 angstroms; (across all 517 pairs:
24.890)  
  
Matchmaker 3suc, chain A (#1) with 4oj5, chain C (#3), sequence alignment
score = 238.2  
RMSD between 29 pruned atom pairs is 1.320 angstroms; (across all 631 pairs:
30.404)  
  

> view all

> tile

3 models tiled  

> tile columns 3

3 models tiled  

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
3suc #1/A HIS 88  
4oj5 #3/C LYS 269  
4oj5 #3/C LYS 291  
4oj5 #3/C LYS 298  
4oj5 #3/C LYS 583  
4oj5 #3/C ARG 621  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -4) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/8t/ntwqvzc54xg6vsp4ddfj1_3w0000gn/T/tmpw5ywa6kd/ante.in.mol2 -fi
mol2 -o
/var/folders/8t/ntwqvzc54xg6vsp4ddfj1_3w0000gn/T/tmpw5ywa6kd/ante.out.mol2 -fo
mol2 -c bcc -nc -4 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file
(/var/folders/8t/ntwqvzc54xg6vsp4ddfj1_3w0000gn/T/tmpw5ywa6kd/ante.in.mol2);
atoms read (13), bonds read (12).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 56; net charge: -4`  
(HIS) ``  
(HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(HIS) ``  
(HIS) `Running:
/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS) ``  
Charges for residue HIS determined  
Coulombic values for 3suc_A SES surface #1.2: minimum, -32.28, mean -2.34,
maximum 12.12  
Coulombic values for 7w1e_E SES surface #2.1: minimum, -16.13, mean -1.75,
maximum 9.36  
Coulombic values for 4oj5_C SES surface #3.1: minimum, -16.86, mean -0.17,
maximum 12.52  
To also show corresponding color key, enter the above coulombic command and
add key true  

> ui tool show "Color Actions"

> color dark gray

> coulombic

Coulombic values for 3suc_A SES surface #1.2: minimum, -32.28, mean -2.34,
maximum 12.12  
Coulombic values for 7w1e_E SES surface #2.1: minimum, -16.13, mean -1.75,
maximum 9.36  
Coulombic values for 4oj5_C SES surface #3.1: minimum, -16.86, mean -0.17,
maximum 12.52  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 40

> ui mousemode right zoom

> lighting flat

> tile columns 3 spacingFactor facotr 0.7

Invalid "spacingFactor" argument: Expected a number  

> tile columns 3 spacingFactor 0.7

3 models tiled  

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.cxs

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.png width
> 2000 height 2000 supersample 4 transparentBackground true

> close

> open 2x3h 4ru4

2x3h title:  
Coliphage K5A lyase [more info...]  
  
Chain information for 2x3h #1  
---  
Chain | Description | UniProt  
A B C | K5 LYASE | Q9AZ47_9CAUD 1-505  
  
Non-standard residues in 2x3h #1  
---  
BR — bromide ion  
  
4ru4 title:  
Crystal structure of the tailspike protein gp49 from Pseudomonas phage LKA1
[more info...]  
  
Chain information for 4ru4 #2  
---  
Chain | Description | UniProt  
A B C D E F | tail spike protein gp49 | Q0E5W5_9CAUD 168-769  
  
Non-standard residues in 4ru4 #2  
---  
CA — calcium ion  
EDO — ethane-1,2-diol (ethylene glycol)  
NA — sodium ion  
  
4ru4 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> show atoms

> hide atoms

> show cartoons

Drag select of 161 residues  

> select up

4937 atoms, 5022 bonds, 679 residues, 1 model selected  

> select up

12873 atoms, 13110 bonds, 1770 residues, 1 model selected  

> select up

15733 atoms, 13134 bonds, 4606 residues, 1 model selected  

> select up

31500 atoms, 26266 bonds, 9246 residues, 1 model selected  

> select down

15733 atoms, 13134 bonds, 4606 residues, 1 model selected  

> delete sel

Drag select of 116 residues  

> select clear

Drag select of 15 residues  

> select up

179 atoms, 180 bonds, 26 residues, 1 model selected  

> select up

3616 atoms, 3672 bonds, 498 residues, 1 model selected  

> select up

3910 atoms, 3672 bonds, 792 residues, 1 model selected  

> select #1/B:23

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

> select clear

Drag select of 7 residues  

> select up

153 atoms, 155 bonds, 17 residues, 1 model selected  

> select up

7232 atoms, 7344 bonds, 996 residues, 1 model selected  

> select up

7833 atoms, 7344 bonds, 1597 residues, 1 model selected  

> select up

11734 atoms, 11016 bonds, 2380 residues, 1 model selected  

> select down

7833 atoms, 7344 bonds, 1597 residues, 1 model selected  

> delete sel

Drag select of 111 residues  

> select up

4219 atoms, 4290 bonds, 580 residues, 1 model selected  

> select up

8574 atoms, 8732 bonds, 1178 residues, 1 model selected  

> select up

10490 atoms, 8747 bonds, 3079 residues, 1 model selected  

> select up

15767 atoms, 13132 bonds, 4640 residues, 1 model selected  

> select down

10490 atoms, 8747 bonds, 3079 residues, 1 model selected  

> delete sel

> select clear

> ui tool show Matchmaker

> matchmaker #!2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2x3h, chain A (#1) with 4ru4, chain B (#2), sequence alignment
score = 258.5  
RMSD between 45 pruned atom pairs is 1.336 angstroms; (across all 463 pairs:
20.299)  
  

> view all

> tile spacingFactor 0.7

2 models tiled  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 2x3h_A SES surface #1.1: minimum, -15.71, mean -0.95,
maximum 9.85  
Coulombic values for 4ru4_B SES surface #2.2: minimum, -20.73, mean -2.82,
maximum 12.43  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting flat

> transparency 40

> tile

2 models tiled  

> tile spacingFactor 0.8

2 models tiled  

> lighting flat

> ui tool show "Color Actions"

> color dark gray target acpf

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_endo.png width
> 2000 height 2000 supersample 4 transparentBackground true

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_endo.cxs

> lighting soft

> lighting flat

> close

> open /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.cxs format
> session

opened ChimeraX session  

> lighting flat

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.cxs

> tile spacingFactor 0.8

3 models tiled  

> tile spacingFactor 0.8 columns 3

3 models tiled  

> lighting flat

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.cxs

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_PL_exo.png width
> 2000 height 2000 supersample 4 transparentBackground true

> close

> open 2xc1 2x6w 3riq 2v5i

2xc1 title:  
Full-length Tailspike Protein Mutant Y108W of Bacteriophage P22 [more info...]  
  
Chain information for 2xc1 #1  
---  
Chain | Description | UniProt  
A B C | BIFUNCTIONAL TAIL PROTEIN | TSPE_BPP22 1-666  
  
Non-standard residues in 2xc1 #1  
---  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PE4 — 2-{2-[2-(2-{2-[2-(2-ethoxy-
ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol (polyethylene glycol
PEG4000)  
SO4 — sulfate ion  
  
2x6w title:  
Tailspike protein mutant E372Q of E.coli bacteriophage HK620 in complex with
hexasaccharide [more info...]  
  
Chain information for 2x6w #2  
---  
Chain | Description | UniProt  
A | TAIL SPIKE PROTEIN | Q9AYY6_BPHK6 110-709  
  
Non-standard residues in 2x6w #2  
---  
GLA — alpha-D-galactopyranose  
GLC — alpha-D-glucopyranose  
NA — sodium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
NDG — 2-acetamido-2-deoxy-alpha-D-glucopyranose  
RAM — alpha-L-rhamnopyranose  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
2x6w mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
3riq title:  
Siphovirus 9NA tailspike receptor binding domain [more info...]  
  
Chain information for 3riq #3  
---  
Chain | Description  
A | Tailspike protein  
  
Non-standard residues in 3riq #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3riq mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
2v5i title:  
Structure of the receptor-binding protein of bacteriophage Det7: a podoviral
tailspike in a myovirus [more info...]  
  
Chain information for 2v5i #4  
---  
Chain | Description  
A | SALMONELLA TYPHIMURIUM DB7155 BACTERIOPHAGE DET7 TAILSPIKE  
  
Non-standard residues in 2v5i #4  
---  
NA — sodium ion  
  
2v5i mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> hide atoms

> show cartoons

> hide #!4 models

> show #!4 models

> hide #3 models

> show #3 models

> hide #!2 models

> show #!2 models

Drag select of 77 residues  

> select up

923 atoms, 939 bonds, 117 residues, 1 model selected  

> select up

15064 atoms, 15376 bonds, 1982 residues, 1 model selected  

> select clear

Drag select of 11 residues  

> select up

180 atoms, 182 bonds, 21 residues, 1 model selected  

> select up

10048 atoms, 10256 bonds, 1322 residues, 1 model selected  

> delete sel

> ui tool show Matchmaker

> matchmaker #3#!2,4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2xc1, chain A (#1) with 3riq, chain A (#3), sequence alignment
score = 1171.6  
RMSD between 366 pruned atom pairs is 0.951 angstroms; (across all 536 pairs:
2.874)  
  
Matchmaker 2xc1, chain A (#1) with 2x6w, chain A (#2), sequence alignment
score = 154.3  
RMSD between 27 pruned atom pairs is 1.062 angstroms; (across all 453 pairs:
20.416)  
  
Matchmaker 2xc1, chain A (#1) with 2v5i, chain A (#4), sequence alignment
score = 1912.7  
RMSD between 530 pruned atom pairs is 0.736 angstroms; (across all 553 pairs:
1.049)  
  

> matchmaker #3#!2,4 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2xc1, chain A (#1) with 3riq, chain A (#3), sequence alignment
score = 1171.6  
RMSD between 366 pruned atom pairs is 0.951 angstroms; (across all 536 pairs:
2.874)  
  
Matchmaker 2xc1, chain A (#1) with 2x6w, chain A (#2), sequence alignment
score = 154.3  
RMSD between 27 pruned atom pairs is 1.062 angstroms; (across all 453 pairs:
20.416)  
  
Matchmaker 2xc1, chain A (#1) with 2v5i, chain A (#4), sequence alignment
score = 1912.7  
RMSD between 530 pruned atom pairs is 0.736 angstroms; (across all 553 pairs:
1.049)  
  

> view all

> tile spacingFactor 0.8 columns 3

4 models tiled  

> tile spacingFactor 0.8 columns 4

4 models tiled  

> lighting flat

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
2x6w #2/A GLN 113  
3riq #3/A ARG 134  
3riq #3/A ASP 267  
3riq #3/A ASP 654  

Using Amber 20 recommended default charges and atom types for standard
residues  

There are UNK residues in the structure. Charges in those regions will be
inaccurate.  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 2xc1_A SES surface #1.2: minimum, -14.50, mean -1.82,
maximum 11.16  
Coulombic values for 2x6w_A SES surface #2.2: minimum, -14.72, mean -1.78,
maximum 9.92  
Coulombic values for 3riq_A SES surface #3.1: minimum, -16.22, mean -2.45,
maximum 9.06  
Coulombic values for 2v5i_A SES surface #4.2: minimum, -16.04, mean -2.42,
maximum 12.97  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting flat

> transparency 40

> ui tool show "Color Actions"

> color dark gray target acpf

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_GH_endo.png width
> 2000 height 2000 supersample 4 transparentBackground true

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_GH_endo.cxs

> close

> fetch 5jsd

Unknown command: fetch 5jsd  

> open 5jsd

5jsd title:  
Crystal structure of phiAB6 tailspike in complex with five-repeated
oligosaccharides of Acinetobacter baumannii surface polysaccharide [more
info...]  
  
Chain information for 5jsd #1  
---  
Chain | Description  
A B C | phiAB6 tailspike  
  
Non-standard residues in 5jsd #1  
---  
1GN — 2-amino-2-deoxy-beta-D-galactopyranose  
6PZ — 5,7-bisacetamido-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-
non-2-ulopyranosonic acid (Pseudaminic acid)  
ACY — acetic acid  
BGC — beta-D-glucopyranose  
GAL — beta-D-galactopyranose  
MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;
methanedicarboxylic acid)  
  

> show atoms

> hide atoms

Drag select of 62 residues  

> select up

819 atoms, 825 bonds, 109 residues, 1 model selected  

> select up

8376 atoms, 8562 bonds, 1096 residues, 1 model selected  

> select up

10323 atoms, 8590 bonds, 3015 residues, 1 model selected  

> select up

16005 atoms, 13434 bonds, 4584 residues, 1 model selected  

> select down

10323 atoms, 8590 bonds, 3015 residues, 1 model selected  

> delete sel

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 5jsd_A SES surface #1.1: minimum, -14.75, mean -0.88,
maximum 11.44  
To also show corresponding color key, enter the above coulombic command and
add key true  

> lighting flat

> transparency 40

> ui tool show "Color Actions"

> color dark gray target acpf

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_GH_exo.cxs

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_GH_exo.png width
> 2000 height 2000 supersample 4 transparentBackground true

> close

> open /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/tsp_GH_endo.cxs format
> session

opened ChimeraX session  

> close

> open 7O12

Summary of feedback from opening 7O12 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7o12 from
http://files.rcsb.org/download/7o12.cif  
Fetching CCD ANP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ANP/ANP.cif  
  
7o12 title:  
ABC transporter NosDFY, AMPPNP-bound in GDN [more info...]  
  
Chain information for 7o12 #1  
---  
Chain | Description | UniProt  
A | Probable ABC transporter binding protein NosD | NOSD_PSEST 1-436  
B C | Probable ABC transporter ATP-binding protein NosF | NOSF_PSEST 1-308  
D E | Probable ABC transporter permease protein NosY | NOSY_PSEST 1-276  
  
Non-standard residues in 7o12 #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
  

> hide atoms

> show cartoons

> select ::name="ANP"::name="HOH"::name="MG"

66 atoms, 66 bonds, 7 pseudobonds, 6 residues, 2 models selected  

> show sel atoms

> select clear

Drag select of 38 atoms, 502 residues, 6 pseudobonds, 35 bonds  

> select up

3892 atoms, 3935 bonds, 6 pseudobonds, 506 residues, 2 models selected  

> select up

4309 atoms, 4368 bonds, 6 pseudobonds, 557 residues, 2 models selected  

> select up

4654 atoms, 4726 bonds, 6 pseudobonds, 600 residues, 2 models selected  

> select up

11691 atoms, 11912 bonds, 17 pseudobonds, 1517 residues, 2 models selected  

> lighting flat

> ui tool show "Color Actions"

> color sel dark gray target acpf

> select clear

> select /A:333

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

> select add /A:310

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select add /A:289

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

> select add /A:252

34 atoms, 31 bonds, 4 residues, 1 model selected  

> select add /A:229

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select add /A:207

49 atoms, 45 bonds, 6 residues, 1 model selected  

> select add /A:185

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

> select add /A:163

71 atoms, 67 bonds, 8 residues, 1 model selected  

> select add /A:133

82 atoms, 78 bonds, 9 residues, 1 model selected  

> select add /A:110

93 atoms, 89 bonds, 10 residues, 1 model selected  

> select add /A:82

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

> select add /A:57

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

> select up

464 atoms, 467 bonds, 55 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium blue target acpf

> select clear

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/nosD_rhbh.png width 2000
> height 2000 supersample 4 transparentBackground true

> save /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/nosD_rhbh.cxs

> close

> fetch 6kqs

Unknown command: fetch 6kqs  

> open 6kqs

6kqs title:  
Crystal Structure of GH136 lacto-N-biosidase from Eubacterium ramulus -
selenomethionine derivative [more info...]  
  
Chain information for 6kqs #1  
---  
Chain | Description | UniProt  
A | lacto-N-biosidase | U2PDT9_EUBRA 1-663  
  
Non-standard residues in 6kqs #1  
---  
GAL — beta-D-galactopyranose  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
  

> close

> open 7v6i

7v6i title:  
Crystal structure of lacto-N-biosidase BsaX from Bifidobacterium saguini,
lacto-N-biose complex [more info...]  
  
Chain information for 7v6i #1  
---  
Chain | Description | UniProt  
A | Lacto-N-biosidase | A0A087D8U9_9BIFI 34-641  
  
Non-standard residues in 7v6i #1  
---  
GAL — beta-D-galactopyranose (beta-D-galactose; D-galactose; galactose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> close

> open 3lyc

3lyc title:  
Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides
distasonis ATCC 8503 at 2.30 A resolution [more info...]  
  
Chain information for 3lyc #1  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N O P | Putative pectinase | A6LGH6_PARD8 27-266  
  
3lyc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
5| author_and_software_defined_assembly  
6| author_and_software_defined_assembly  
7| author_and_software_defined_assembly  
8| author_and_software_defined_assembly  
  

> hide atoms

> show cartoons

> close

> open 4urr

4urr title:  
Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen
octasaccharide fragment [more info...]  
  
Chain information for 4urr #1  
---  
Chain | Description | UniProt  
A B C D E F | BIFUNCTIONAL TAIL PROTEIN | TSPE_BPSFV 109-622  
  
Non-standard residues in 4urr #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
MN — manganese (II) ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
PO4 — phosphate ion  
RAM — alpha-L-rhamnopyranose  
  
4urr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> hide atoms

> show cartoons

Drag select of 1275 residues  

> select up

10590 atoms, 10772 bonds, 1408 residues, 1 model selected  

> select up

11430 atoms, 11640 bonds, 1524 residues, 1 model selected  

> select up

12191 atoms, 11657 bonds, 2268 residues, 1 model selected  

> select up

24991 atoms, 23895 bonds, 4656 residues, 1 model selected  

> select down

12191 atoms, 11657 bonds, 2268 residues, 1 model selected  

> delete sel

> select
> ::name="EDO"::name="HOH"::name="MN"::name="NAG"::name="PO4"::name="RAM"

1362 atoms, 590 bonds, 15 pseudobonds, 862 residues, 2 models selected  

> show sel atoms

> select clear

> delete solvent

Drag select of 214 atoms, 231 bonds  

> select up

221 atoms, 232 bonds, 21 residues, 1 model selected  

> select up

233 atoms, 250 bonds, 21 residues, 1 model selected  

> select up

267 atoms, 288 bonds, 24 residues, 1 model selected  

> select up

11995 atoms, 12238 bonds, 1583 residues, 1 model selected  

> select down

267 atoms, 288 bonds, 24 residues, 1 model selected  

> delete sel

> select clear

> select ::name="EDO"::name="MN"::name="NAG"::name="PO4"::name="RAM"

290 atoms, 302 bonds, 33 residues, 1 model selected  

> show sel surfaces

> ui tool show "Color Actions"

> color sel orange target acpf

> color sel yellow

> color sel orange

> select clear

> select /A:1626@P

1 atom, 1 residue, 1 model selected  

> select /B:1625@C1

1 atom, 1 residue, 1 model selected  

> select add /A:1626@P

2 atoms, 2 residues, 2 models selected  

> select add /B:1623@O1

3 atoms, 3 residues, 3 models selected  

> select add /A:1623@MN

4 atoms, 4 residues, 3 models selected  

> select add /C:1623@MN

5 atoms, 5 residues, 3 models selected  

> select up

16 atoms, 11 bonds, 5 residues, 4 models selected  

> select up

11461 atoms, 11662 bonds, 1535 residues, 4 models selected  

> select down

16 atoms, 11 bonds, 5 residues, 4 models selected  

> delete sel

> select clear

Drag select of 256 residues  

> select up

2197 atoms, 2232 bonds, 305 residues, 1 model selected  

> select up

11438 atoms, 11648 bonds, 1526 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark gray

> lighting flat

> select clear

> select add /C:530

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

> select add /C:512

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

> select clear

> select add /C:530

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

> select add /C:512

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

> select add /C:492

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

> select add /C:469

31 atoms, 27 bonds, 4 residues, 1 model selected  

> select add /C:435

39 atoms, 34 bonds, 5 residues, 1 model selected  

> select add /C:406

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

> select add /C:384

58 atoms, 52 bonds, 7 residues, 1 model selected  

> select add /C:350

69 atoms, 62 bonds, 8 residues, 1 model selected  

> select add /C:321

79 atoms, 72 bonds, 9 residues, 1 model selected  

> select add /C:298

91 atoms, 84 bonds, 10 residues, 1 model selected  

> select add /C:267

99 atoms, 91 bonds, 11 residues, 1 model selected  

> select add /C:241

110 atoms, 101 bonds, 12 residues, 1 model selected  

> select add /C:213

118 atoms, 108 bonds, 13 residues, 1 model selected  

> select up

578 atoms, 573 bonds, 74 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium blue

> select up

3814 atoms, 3884 bonds, 509 residues, 1 model selected  

> select up

11712 atoms, 11939 bonds, 1554 residues, 1 model selected  

> select down

3814 atoms, 3884 bonds, 509 residues, 6 models selected  

> select down

578 atoms, 573 bonds, 74 residues, 1 model selected  

> select clear

> save
> /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/4urr_tsp_noncleftbinding.cxs

> select /A:213

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

> select add /A:240

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

> select add /A:267

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

> select add /A:298

36 atoms, 33 bonds, 4 residues, 1 model selected  

> select add /A:320

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

> select add /A:349

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

> select add /A:384

64 atoms, 59 bonds, 7 residues, 1 model selected  

> select add /A:406

71 atoms, 65 bonds, 8 residues, 1 model selected  

> select add /A:435

79 atoms, 72 bonds, 9 residues, 1 model selected  

> select add /A:468

87 atoms, 79 bonds, 10 residues, 1 model selected  

> select add /A:492

95 atoms, 86 bonds, 11 residues, 1 model selected  

> select add /A:513

107 atoms, 98 bonds, 12 residues, 1 model selected  

> select add /A:531

116 atoms, 106 bonds, 13 residues, 1 model selected  

> select up

578 atoms, 573 bonds, 74 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium blue

> select clear

> select add /B:531

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

> select add /B:513

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select add /B:493

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

> select add /B:469

34 atoms, 31 bonds, 4 residues, 1 model selected  

> select add /B:435

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

> select add /B:406

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

> select add /B:383

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

> select add /B:349

64 atoms, 57 bonds, 8 residues, 1 model selected  

> select add /B:320

72 atoms, 64 bonds, 9 residues, 1 model selected  

> select add /B:298

84 atoms, 76 bonds, 10 residues, 1 model selected  

> select add /B:266

88 atoms, 79 bonds, 11 residues, 1 model selected  

> select add /B:240

96 atoms, 86 bonds, 12 residues, 1 model selected  

> select add /B:213

104 atoms, 93 bonds, 13 residues, 1 model selected  

> select up

578 atoms, 573 bonds, 74 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium blue

> select clear

> save
> /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/4urr_tsp_noncleftbinding.cxs

> save
> /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/4urr_tsp_noncleftbinding.png
> width 2000 height 2000 supersample 4 transparentBackground true

> lighting flat

> lighting soft

> lighting flat

> select /B:1624@MN

1 atom, 1 residue, 1 model selected  

> delete sel

> save
> /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/4urr_tsp_noncleftbinding.cxs

> save
> /Users/aburnim_m2/Desktop/JIANG_LAB/rhbh_local/4urr_tsp_noncleftbinding.png
> width 2000 height 2000 supersample 4 transparentBackground true

> lighting simple

> lighting soft

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
OpenGL renderer: Apple M2 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: Mac14,6
      Model Number: MNWE3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A8380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 3 days, 14 hours, 46 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      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
        LG HDR 4K:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 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

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0

comment:2 by Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: accepted → closed
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