id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14970	Crash in QTabBar:paintEvent(). QPainter::begin: Paint device returned engine == 0, type: 3	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
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 0x0000000324e67000 (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 0x0000000323e64000 (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 0x0000000322e61000 (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 0x0000000321e5e000 (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 0x0000000320e5b000 (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 0x000000031fe58000 (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 0x000000031ee55000 (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 0x000000031de52000 (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 0x000000031ce4f000 (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 0x000000031be4c000 (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 0x000000031ae49000 (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 0x0000000319e46000 (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 0x0000000318e43000 (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 0x0000000204586240 (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"":""2024-04-17 19:11:11.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""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 14.3.1 (23D60)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""21D474CA-306F-41FC-B604-20E7D2D8C06E""}
{
  ""uptime"" : 1300000,
  ""procRole"" : ""Background"",
  ""version"" : 2,
  ""userID"" : 501,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro18,1"",
  ""coalitionID"" : 230639,
  ""osVersion"" : {
    ""train"" : ""macOS 14.3.1"",
    ""build"" : ""23D60"",
    ""releaseType"" : ""User""
  },
  ""captureTime"" : ""2024-04-17 18:29:28.1389 +0200"",
  ""codeSigningMonitor"" : 1,
  ""incident"" : ""21D474CA-306F-41FC-B604-20E7D2D8C06E"",
  ""pid"" : 24084,
  ""translated"" : true,
  ""cpuType"" : ""X86-64"",
  ""roots_installed"" : 0,
  ""bug_type"" : ""309"",
  ""procLaunch"" : ""2024-04-17 16:25:51.4503 +0200"",
  ""procStartAbsTime"" : 33345609699000,
  ""procExitAbsTime"" : 33523608044571,
  ""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"":""9550DBF0-DC1E-5AB0-81FB-E3F4CE21409E"",""thirdParty"":true},
  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""14C998C3-1AA5-72F8-4832-A833B8517703"",
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""wakeTime"" : 15219,
  ""sleepWakeUUID"" : ""B0C2B993-45F1-4B3B-B82F-4F4F9D7BA8D5"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0x18 is not in any region.  Bytes before following region: 140723103432680\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca6978000-7ffccf728000 [653.7M] r-x\/r-x SM=COW  ...t_id=8eef92bb"",
  ""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"":24084},
  ""vmregioninfo"" : ""0x18 is not in any region.  Bytes before following region: 140723103432680\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffca6978000-7ffccf728000 [653.7M] r-x\/r-x SM=COW  ...t_id=8eef92bb"",
  ""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"":{""flavor"":""x86_THREAD_STATE"",""rbp"":{""value"":15765584944734910341},""r12"":{""value"":259},""rosetta"":{""tmp2"":{""value"":140703412938648},""tmp1"":{""value"":140705834822220},""tmp0"":{""value"":18446744073709551615}},""rbx"":{""value"":8662835776,""symbolLocation"":0,""symbol"":""_main_thread""},""r8"":{""value"":1396816894187417},""r15"":{""value"":22},""r10"":{""value"":8662835776,""symbolLocation"":0,""symbol"":""_main_thread""},""rdx"":{""value"":0},""rdi"":{""value"":15765584944734910341},""r9"":{""value"":15765584944734910341},""r13"":{""value"":0},""rflags"":{""value"":647},""rax"":{""value"":0},""rsp"":{""value"":4504834184},""r11"":{""value"":140703413805339,""symbolLocation"":0,""symbol"":""-[__NSCFArray 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  ""reportNotes"" : [
  ""PC register does not match crashing frame (0x0 vs 0x7FF8A14D6A78)""
]
}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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 1F8A, 1PIN, 1ZCN, 2F21, 2ITK, 2Q5A, 2XP3, 2XP4, 2XP5, 2XP6, 2XP7, 2XP8,
> 2XP9, 2XPA, 2XPB, 2ZQS, 2ZQT, 2ZQU, 2ZQV, 2ZR4, 2ZR5, 2ZR6, 3I6C, 3IK8,
> 3IKD, 3IKG, 3JYJ, 3KAB, 3KAC, 3KAD, 3KAF, 3KAG, 3KAH, 3KAI, 3KCE, 3NTP,
> 3ODK, 3OOB, 3TC5, 3TCZ, 3TDB, 3WH0, 4GWT, 4GWV, 4QIB, 4TNS, 4TYO, 4U84,
> 4U85, 4U86, 5B3W, 5B3X, 5B3Y, 5B3Z, 5BMY, 5UY9, 5VTI, 5VTJ, 5VTK, 6DUN,
> 6O33, 6O34, 6VAJ, 7AOG, 7AXN, 7AYF, 7AZ1, 7AZ2, 7BDP, 7BDT, 7BDY, 7BFW,
> 7BG3, 7BGQ, 7BGR, 7BGV, 7BGW, 7EFJ, 7EFX, 7EKV, 7F0M, 7NIF, 7NIG, 7NJ6,
> 7NJ8, 7NJA, 7NRK, 7NRL, 7OQ9, 7OQA, 8C2G, 8C3C

'1F8A,' has no suffix  

> open 1F8A, 1PIN, 1ZCN, 2F21, 2ITK, 2Q5A, 2XP3, 2XP4, 2XP5, 2XP6, 2XP7, 2XP8,
> 2XP9, 2XPA, 2XPB, 2ZQS, 2ZQT, 2ZQU, 2ZQV, 2ZR4, 2ZR5, 2ZR6, 3I6C, 3IK8,
> 3IKD, 3IKG, 3JYJ, 3KAB, 3KAC, 3KAD, 3KAF, 3KAG, 3KAH, 3KAI, 3KCE, 3NTP,
> 3ODK, 3OOB, 3TC5, 3TCZ, 3TDB, 3WH0, 4GWT, 4GWV, 4QIB, 4TNS, 4TYO, 4U84,
> 4U85, 4U86, 5B3W, 5B3X, 5B3Y, 5B3Z, 5BMY, 5UY9, 5VTI, 5VTJ, 5VTK, 6DUN,
> 6O33, 6O34, 6VAJ, 7AOG, 7AXN, 7AYF, 7AZ1, 7AZ2, 7BDP, 7BDT, 7BDY, 7BFW,
> 7BG3, 7BGQ, 7BGR, 7BGV, 7BGW, 7EFJ, 7EFX, 7EKV, 7F0M, 7NIF, 7NIG, 7NJ6,
> 7NJ8, 7NJA, 7NRK, 7NRL, 7OQ9, 7OQA, 8C2G, 8C3C

'1F8A,' has no suffix  

> open 1f8a.pdb

No such file/path: 1f8a.pdb  

> open pdb 1f8a

'pdb' has no suffix  

> open pdb 1f8a.pdb

'pdb' has no suffix  

> fetch 7nif

Unknown command: fetch 7nif  

> open 1stp

**** TomG: Deleted several thousand lines to stay within Trac limit ****

---  
CA — calcium ion  
CL — chloride ion  
S6B — 3-chloranyl-4-imidazol-1-yl-benzaldehyde  
  
7axn mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7ayf title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound TCF521-110 [more
info...]  
  
Chain information for 7ayf #66  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7ayf #66  
---  
CA — calcium ion  
S9E — 6-(2-bromanylimidazol-1-yl)pyridine-3-carbaldehyde  
  
7ayf mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7az1 title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1013 [more
info...]  
  
Chain information for 7az1 #67  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7az1 #67  
---  
CA — calcium ion  
CL — chloride ion  
SGH — 1-[4-methyl-3-(trifluoromethyl)phenyl]-2-phenyl-imidazole  
  
7az1 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7az2 title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1014 [more
info...]  
  
Chain information for 7az2 #68  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN
116-132  
  
Non-standard residues in 7az2 #68  
---  
CA — calcium ion  
CL — chloride ion  
SFW — 1-[4-methyl-2-(trifluoromethyl)phenyl]-2-phenyl-imidazole  
  
7az2 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bdp title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1017 [more
info...]  
  
Chain information for 7bdp #69  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bdp #69  
---  
MG — magnesium ion  
TJB — 2-chloranyl-4-(2-phenylimidazol-1-yl)benzaldehyde (LvD1017)  
  
7bdp mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bdt title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1009 [more
info...]  
  
Chain information for 7bdt #70  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bdt #70  
---  
MG — magnesium ion  
TJ8 — 2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde (LvD1009)  
  
7bdt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bdy title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound PC2068B [more
info...]  
  
Chain information for 7bdy #71  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bdy #71  
---  
CA — calcium ion  
CL — chloride ion  
MG — magnesium ion  
TJK — 2-bromanyl-4-[2-(5-bromanyl-2-fluoranyl-
phenyl)imidazol-1-yl]benzaldehyde (PC2068B)  
  
7bdy mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bfw title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound PC2068A [more
info...]  
  
Chain information for 7bfw #72  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bfw #72  
---  
CA — calcium ion  
CL — chloride ion  
TKH — [4-[2-[2,4-bis(fluoranyl)phenyl]imidazol-1-yl]-2-bromanyl-
phenyl]methanol  
  
7bfw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bg3 title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound PC2046 [more
info...]  
  
Chain information for 7bg3 #73  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bg3 #73  
---  
CA — calcium ion  
CL — chloride ion  
TKK — 1-(3-bromanyl-4-methyl-phenyl)-2-(2-bromophenyl)imidazole  
  
7bg3 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bgq title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1019 [more
info...]  
  
Chain information for 7bgq #74  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bgq #74  
---  
CA — calcium ion  
CL — chloride ion  
TL8 — 2-methoxy-4-(2-phenylimidazol-1-yl)benzaldehyde  
  
7bgq mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bgr title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1016 [more
info...]  
  
Chain information for 7bgr #75  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bgr #75  
---  
CA — calcium ion  
CL — chloride ion  
TQK — 2-methyl-4-(2-phenylimidazol-1-yl)benzaldehyde  
  
7bgr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bgv title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1012 [more
info...]  
  
Chain information for 7bgv #76  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bgv #76  
---  
CA — calcium ion  
CL — chloride ion  
MG — magnesium ion  
TLK — 3-methoxy-4-(2-phenylimidazol-1-yl)benzaldehyde  
  
7bgv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7bgw title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1011 [more
info...]  
  
Chain information for 7bgw #77  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7bgw #77  
---  
CA — calcium ion  
CL — chloride ion  
NA — sodium ion  
TLQ — 4-(2-phenylimidazol-1-yl)naphthalene-1-carbaldehyde  
  
7bgw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7efj title:  
Crystal Structure Analysis of human PIN1 [more info...]  
  
Chain information for 7efj #78  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 1-163  
  
Non-standard residues in 7efj #78  
---  
J2C —
8-(2-chloroacetyl)-4-(furan-2-ylmethyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one  
PE8 — 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol  
  
7efx title:  
Crystal Structure of human PIN1 complexed with covalent inhibitor [more
info...]  
  
Chain information for 7efx #79  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 1-163  
  
Non-standard residues in 7efx #79  
---  
J3X —
4-((5-bromofuran-2-yl)methyl)-8-(2-chloroacetyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one  
  
7ekv title:  
Crystal Structure of human Pin1 complexed with a covalent inhibitor [more
info...]  
  
Chain information for 7ekv #80  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 1-163  
  
Non-standard residues in 7ekv #80  
---  
J50 —
8-(2-chloroacetyl)-4-((5-phenylfuran-2-yl)methyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one  
PE8 — 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol  
  
7f0m title:  
Crystal Structure of human Pin1 complexed with a potent covalent inhibitor
[more info...]  
  
Chain information for 7f0m #81  
---  
Chain | Description | UniProt  
A B C D | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN
1-163  
  
Non-standard residues in 7f0m #81  
---  
0BF —
8-(2-chloranylethanoyl)-4-[(5-naphthalen-1-ylfuran-2-yl)methyl]-1-thia-4,8-diazaspiro[4.5]decan-3-one  
P33 — 3,6,9,12,15,18-hexaoxaicosane-1,20-diol (heptaethylene glycol; PEG330)  
  
7f0m mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  
7nif title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound TCF521-011 [more
info...]  
  
Chain information for 7nif #82  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nif #82  
---  
CA — calcium ion  
CL — chloride ion  
P5N — 1-(4-methylphenyl)imidazole  
  
7nif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7nig title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1008 [more
info...]  
  
Chain information for 7nig #83  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nig #83  
---  
CA — calcium ion  
CL — chloride ion  
UFH — 2-bromanyl-4-imidazol-1-yl-benzaldehyde  
  
7nig mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7nj6 title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1005 [more
info...]  
  
Chain information for 7nj6 #93  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nj6 #93  
---  
CA — calcium ion  
UG5 — 4-[4-(trifluoromethyl)imidazol-1-yl]benzaldehyde  
  
7nj6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7nj8 title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1007 [more
info...]  
  
Chain information for 7nj8 #94  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nj8 #94  
---  
CA — calcium ion  
JFS — [4-(1H-benzimidazol-1-yl)phenyl]methanol  
MG — magnesium ion  
  
7nj8 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7nja title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1006 [more
info...]  
  
Chain information for 7nja #95  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nja #95  
---  
CL — chloride ion  
UG2 — [4-(2-phenylimidazol-1-yl)phenyl]methanol  
  
7nja mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7nrk title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1002F1 [more
info...]  
  
Chain information for 7nrk #96  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nrk #96  
---  
CA — calcium ion  
CL — chloride ion  
PEG — di(hydroxyethyl)ether  
UPQ — 4-(4-methylimidazol-1-yl)benzaldehyde  
  
7nrk mmCIF Assemblies  
---  
1| author_defined_assembly  
  
7nrl title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound LvD1032 [more
info...]  
  
Chain information for 7nrl #97  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7nrl #97  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
PEG — di(hydroxyethyl)ether  
UPK — 2-(hydroxymethyl)-5-(2-phenylimidazol-1-yl)phenol  
  
7nrl mmCIF Assemblies  
---  
1| author_defined_assembly  
  
7oq9 title:  
Ternary complex of 14-3-3 sigma, Pin1pS72 phosphopeptide, and WQ136 [more
info...]  
  
Chain information for 7oq9 #98  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7oq9 #98  
---  
0AW — ~{N}-[(5-carbamimidoyl-3-phenyl-
thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-5-carboxamide  
CL — chloride ion  
  
7oq9 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
7oqa title:  
Ternary complex of 14-3-3 sigma, Pin1pS72 phosphopeptide, and WQ162 [more
info...]  
  
Chain information for 7oqa #99  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-248  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 7oqa #99  
---  
09W — ~{N}-[(5-carbamimidoyl-3-phenyl-
thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-7-carboxamide  
CL — chloride ion  
  
7oqa mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
8c2g title:  
14-3-3 σ with Pin1 binding site pS72 and covalently bound CV1040 [more
info...]  
  
Chain information for 8c2g #100  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-231  
P | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN
116-132  
  
Non-standard residues in 8c2g #100  
---  
MG — magnesium ion  
T85 — 2-iodanyl-4-(2-phenylimidazol-1-yl)benzaldehyde  
  
8c2g mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
8c3c title:  
14-3-3 σ with Pin1 binding site pS72 and bound Fusicoccin A [more info...]  
  
Chain information for 8c3c #101  
---  
Chain | Description | UniProt  
A | 14-3-3 protein sigma | 1433S_HUMAN 1-231  
B | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 61-77  
  
Non-standard residues in 8c3c #101  
---  
FSC — fusicoccin  
MG — magnesium ion  
  
8c3c mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #64-77

> close #82-101

> close #51-54

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX.cxs

> select #56/B

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

> select add #56

1337 atoms, 1280 bonds, 1 pseudobond, 236 residues, 2 models selected  

> select subtract #56

Nothing selected  

> select add #56

1337 atoms, 1280 bonds, 1 pseudobond, 236 residues, 2 models selected  

> select subtract #56

Nothing selected  

> select #5/B

49 atoms, 51 bonds, 6 residues, 1 model selected  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> select #9/A

1314 atoms, 1219 bonds, 1 pseudobond, 267 residues, 2 models selected  

> select #55/A

3349 atoms, 3077 bonds, 732 residues, 1 model selected  

> select add #55

3372 atoms, 3101 bonds, 734 residues, 1 model selected  

> hide #55 models

> show #55 models

> hide #55 models

> show #55 models

> hide #55 models

> show #55 models

> hide #55 models

> show #55 models

> close #55

> select .a

Expected an objects specifier or a keyword  

> select #1:.a

Expected an objects specifier or a keyword  

> select #1:/a

Expected an objects specifier or a keyword  

> select #1:\a

Nothing selected  

> select #1:113\a

Nothing selected  

> select #1:113aa

Nothing selected  

> select #1:113.a

Expected an objects specifier or a keyword  

> select #1:/A

Expected an objects specifier or a keyword  

> select #1:113/A

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

> select #1:*/A

1446 atoms, 1322 bonds, 1 pseudobond, 314 residues, 2 models selected  

> show #!1 target m

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX.cxs

> hide #23-27,29,43-44,46-47,57-60#!2-22,28,30-42,45,48-50,56,61-63,78-81
> target m

> show #!50 models

> select :*/A

91945 atoms, 85654 bonds, 51 pseudobonds, 17782 residues, 110 models selected  

> show #46 models

> show #23-27,29,43-44,46-47,57-60#!1-22,28,30-42,45,48-50,56,61-63,78-81
> target m

> show #!81 target m

> view #81 clip false

> hide #23-27,29,43-44,46-47,57-60#!1-22,28,30-42,45,48-50,56,61-63,78-80
> target m

> select :*/A

91945 atoms, 85654 bonds, 51 pseudobonds, 17782 residues, 110 models selected  

> select :#/A

Expected an objects specifier or a keyword  

> select #:/A

Expected an objects specifier or a keyword  

> select #81:/A

Expected an objects specifier or a keyword  

> select #81

5346 atoms, 4984 bonds, 4 pseudobonds, 1070 residues, 2 models selected  

> select #81/A

1336 atoms, 1246 bonds, 1 pseudobond, 267 residues, 2 models selected  

> select /A

75784 atoms, 70409 bonds, 47 pseudobonds, 14936 residues, 108 models selected  

> show #!80 models

> show #!79 models

> show #!78 models

> show #!63 models

> show #!62 models

> show #!61 models

> hide #!61 models

> show #23-27,29,43-44,46-47,57-60#!1-22,28,30-42,45,48-50,56,61 target m

> select ~sel

16161 atoms, 15245 bonds, 4 pseudobonds, 2846 residues, 18 models selected  

> delete atoms (#23-27,29,46-47,60#!1,5-6,56,61-62,81 & sel)

> delete bonds (#23-27,29,46-47,60#!1,5-6,56,61-62,81 & sel)

> ui tool show Matchmaker

> matchmaker #23-27,29,43-44,46-47#!2-22,28,30-42,45 to #63

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 6vaj, chain A (#63) with 3i6c, chain A (#23), sequence alignment
score = 583.1  
RMSD between 111 pruned atom pairs is 0.344 angstroms; (across all 113 pairs:
0.445)  
  
Matchmaker 6vaj, chain A (#63) with 3ik8, chain A (#24), sequence alignment
score = 580.1  
RMSD between 111 pruned atom pairs is 0.450 angstroms; (across all 113 pairs:
0.537)  
  
Matchmaker 6vaj, chain A (#63) with 3ikd, chain A (#25), sequence alignment
score = 563.3  
RMSD between 111 pruned atom pairs is 0.439 angstroms; (across all 113 pairs:
0.520)  
  
Matchmaker 6vaj, chain A (#63) with 3ikg, chain A (#26), sequence alignment
score = 583.1  
RMSD between 111 pruned atom pairs is 0.409 angstroms; (across all 113 pairs:
0.493)  
  
Matchmaker 6vaj, chain A (#63) with 3jyj, chain A (#27), sequence alignment
score = 583.1  
RMSD between 112 pruned atom pairs is 0.439 angstroms; (across all 113 pairs:
0.480)  
  
Matchmaker 6vaj, chain A (#63) with 3kac, chain A (#29), sequence alignment
score = 589.4  
RMSD between 111 pruned atom pairs is 0.449 angstroms; (across all 113 pairs:
0.541)  
  
Matchmaker 6vaj, chain A (#63) with 4gwt, chain A (#43), sequence alignment
score = 178.6  
RMSD between 33 pruned atom pairs is 0.844 angstroms; (across all 33 pairs:
0.844)  
  
Matchmaker 6vaj, chain A (#63) with 4gwv, chain A (#44), sequence alignment
score = 178.6  
RMSD between 33 pruned atom pairs is 0.829 angstroms; (across all 33 pairs:
0.829)  
  
Matchmaker 6vaj, chain A (#63) with 4tns, chain A (#46), sequence alignment
score = 581.6  
RMSD between 111 pruned atom pairs is 0.430 angstroms; (across all 113 pairs:
0.522)  
  
Matchmaker 6vaj, chain A (#63) with 4tyo, chain A (#47), sequence alignment
score = 583.1  
RMSD between 111 pruned atom pairs is 0.382 angstroms; (across all 113 pairs:
0.473)  
  
Matchmaker 6vaj, chain A (#63) with 1pin, chain A (#2), sequence alignment
score = 797.2  
RMSD between 149 pruned atom pairs is 0.368 angstroms; (across all 150 pairs:
0.443)  
  
Matchmaker 6vaj, chain A (#63) with 1zcn, chain A (#3), sequence alignment
score = 770  
RMSD between 143 pruned atom pairs is 0.285 angstroms; (across all 143 pairs:
0.285)  
  
Matchmaker 6vaj, chain A (#63) with 2f21, chain A (#4), sequence alignment
score = 783  
RMSD between 146 pruned atom pairs is 0.402 angstroms; (across all 148 pairs:
0.486)  
  
Matchmaker 6vaj, chain A (#63) with 2itk, chain A (#5), sequence alignment
score = 777.1  
RMSD between 138 pruned atom pairs is 0.414 angstroms; (across all 145 pairs:
0.827)  
  
Matchmaker 6vaj, chain A (#63) with 2q5a, chain A (#6), sequence alignment
score = 777.1  
RMSD between 138 pruned atom pairs is 0.499 angstroms; (across all 145 pairs:
0.878)  
  
Matchmaker 6vaj, chain A (#63) with 2xp3, chain A (#7), sequence alignment
score = 777.7  
RMSD between 138 pruned atom pairs is 0.529 angstroms; (across all 145 pairs:
0.940)  
  
Matchmaker 6vaj, chain A (#63) with 2xp4, chain A (#8), sequence alignment
score = 783.1  
RMSD between 138 pruned atom pairs is 0.519 angstroms; (across all 144 pairs:
0.862)  
  
Matchmaker 6vaj, chain A (#63) with 2xp5, chain A (#9), sequence alignment
score = 784.3  
RMSD between 138 pruned atom pairs is 0.464 angstroms; (across all 145 pairs:
0.902)  
  
Matchmaker 6vaj, chain A (#63) with 2xp6, chain A (#10), sequence alignment
score = 780.1  
RMSD between 138 pruned atom pairs is 0.424 angstroms; (across all 145 pairs:
0.841)  
  
Matchmaker 6vaj, chain A (#63) with 2xp7, chain A (#11), sequence alignment
score = 784.3  
RMSD between 138 pruned atom pairs is 0.499 angstroms; (across all 145 pairs:
0.899)  
  
Matchmaker 6vaj, chain A (#63) with 2xp8, chain A (#12), sequence alignment
score = 784.3  
RMSD between 137 pruned atom pairs is 0.591 angstroms; (across all 145 pairs:
0.953)  
  
Matchmaker 6vaj, chain A (#63) with 2xp9, chain A (#13), sequence alignment
score = 783.1  
RMSD between 137 pruned atom pairs is 0.515 angstroms; (across all 144 pairs:
0.935)  
  
Matchmaker 6vaj, chain A (#63) with 2xpa, chain A (#14), sequence alignment
score = 785.5  
RMSD between 139 pruned atom pairs is 0.532 angstroms; (across all 146 pairs:
1.085)  
  
Matchmaker 6vaj, chain A (#63) with 2xpb, chain A (#15), sequence alignment
score = 785.5  
RMSD between 138 pruned atom pairs is 0.450 angstroms; (across all 146 pairs:
1.030)  
  
Matchmaker 6vaj, chain A (#63) with 2zqs, chain A (#16), sequence alignment
score = 783.7  
RMSD between 149 pruned atom pairs is 0.279 angstroms; (across all 150 pairs:
0.369)  
  
Matchmaker 6vaj, chain A (#63) with 2zqt, chain A (#17), sequence alignment
score = 807.4  
RMSD between 149 pruned atom pairs is 0.265 angstroms; (across all 150 pairs:
0.321)  
  
Matchmaker 6vaj, chain A (#63) with 2zqu, chain A (#18), sequence alignment
score = 780.2  
RMSD between 149 pruned atom pairs is 0.316 angstroms; (across all 150 pairs:
0.406)  
  
Matchmaker 6vaj, chain A (#63) with 2zqv, chain A (#19), sequence alignment
score = 763.4  
RMSD between 143 pruned atom pairs is 0.498 angstroms; (across all 150 pairs:
0.895)  
  
Matchmaker 6vaj, chain A (#63) with 2zr4, chain A (#20), sequence alignment
score = 795.1  
RMSD between 149 pruned atom pairs is 0.332 angstroms; (across all 150 pairs:
0.404)  
  
Matchmaker 6vaj, chain A (#63) with 2zr5, chain A (#21), sequence alignment
score = 793  
RMSD between 149 pruned atom pairs is 0.438 angstroms; (across all 150 pairs:
0.487)  
  
Matchmaker 6vaj, chain A (#63) with 2zr6, chain A (#22), sequence alignment
score = 721  
RMSD between 149 pruned atom pairs is 0.563 angstroms; (across all 150 pairs:
0.594)  
  
Matchmaker 6vaj, chain A (#63) with 3kab, chain A (#28), sequence alignment
score = 784.3  
RMSD between 138 pruned atom pairs is 0.436 angstroms; (across all 145 pairs:
0.834)  
  
Matchmaker 6vaj, chain A (#63) with 3kad, chain A (#30), sequence alignment
score = 780.1  
RMSD between 136 pruned atom pairs is 0.426 angstroms; (across all 145 pairs:
0.988)  
  
Matchmaker 6vaj, chain A (#63) with 3kaf, chain A (#31), sequence alignment
score = 776.5  
RMSD between 136 pruned atom pairs is 0.637 angstroms; (across all 145 pairs:
1.126)  
  
Matchmaker 6vaj, chain A (#63) with 3kag, chain A (#32), sequence alignment
score = 784.3  
RMSD between 137 pruned atom pairs is 0.442 angstroms; (across all 145 pairs:
0.909)  
  
Matchmaker 6vaj, chain A (#63) with 3kah, chain A (#33), sequence alignment
score = 766.3  
RMSD between 136 pruned atom pairs is 0.422 angstroms; (across all 145 pairs:
1.104)  
  
Matchmaker 6vaj, chain A (#63) with 3kai, chain A (#34), sequence alignment
score = 784.3  
RMSD between 138 pruned atom pairs is 0.543 angstroms; (across all 145 pairs:
0.943)  
  
Matchmaker 6vaj, chain A (#63) with 3kce, chain A (#35), sequence alignment
score = 785.5  
RMSD between 139 pruned atom pairs is 0.475 angstroms; (across all 146 pairs:
0.864)  
  
Matchmaker 6vaj, chain A (#63) with 3ntp, chain A (#36), sequence alignment
score = 783.1  
RMSD between 139 pruned atom pairs is 0.436 angstroms; (across all 147 pairs:
0.889)  
  
Matchmaker 6vaj, chain A (#63) with 3odk, chain A (#37), sequence alignment
score = 762.7  
RMSD between 137 pruned atom pairs is 0.533 angstroms; (across all 145 pairs:
0.960)  
  
Matchmaker 6vaj, chain A (#63) with 3oob, chain A (#38), sequence alignment
score = 780.4  
RMSD between 139 pruned atom pairs is 0.487 angstroms; (across all 146 pairs:
0.951)  
  
Matchmaker 6vaj, chain A (#63) with 3tc5, chain A (#39), sequence alignment
score = 787.3  
RMSD between 138 pruned atom pairs is 0.570 angstroms; (across all 144 pairs:
0.889)  
  
Matchmaker 6vaj, chain A (#63) with 3tcz, chain A (#40), sequence alignment
score = 770.7  
RMSD between 139 pruned atom pairs is 0.422 angstroms; (across all 146 pairs:
0.849)  
  
Matchmaker 6vaj, chain A (#63) with 3tdb, chain A (#41), sequence alignment
score = 748.5  
RMSD between 139 pruned atom pairs is 0.441 angstroms; (across all 146 pairs:
0.846)  
  
Matchmaker 6vaj, chain A (#63) with 3wh0, chain A (#42), sequence alignment
score = 779.2  
RMSD between 135 pruned atom pairs is 0.590 angstroms; (across all 145 pairs:
0.982)  
  
Matchmaker 6vaj, chain A (#63) with 4qib, chain A (#45), sequence alignment
score = 767.5  
RMSD between 136 pruned atom pairs is 0.549 angstroms; (across all 145 pairs:
0.957)  
  

> hide #57 models

> show #57 models

> hide #!56 models

> show #!56 models

> hide #!56 models

> show #!56 models

> ui tool show Matchmaker

> matchmaker #60 to #63

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 6vaj, chain A (#63) with 6dun, chain A (#60), sequence alignment
score = 592  
RMSD between 111 pruned atom pairs is 0.311 angstroms; (across all 115 pairs:
0.837)  
  

> matchmaker #60 to #63

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 6vaj, chain A (#63) with 6dun, chain A (#60), sequence alignment
score = 592  
RMSD between 111 pruned atom pairs is 0.311 angstroms; (across all 115 pairs:
0.837)  
  

> show #60 target m

> view #60 clip false

> select add #60

1812 atoms, 1755 bonds, 187 residues, 1 model selected  

> select subtract #60

Nothing selected  

> matchmaker #!79 to #63

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 6vaj, chain A (#63) with 7efx, chain A (#79), sequence alignment
score = 785.6  
RMSD between 141 pruned atom pairs is 0.486 angstroms; (across all 147 pairs:
0.757)  
  

> matchmaker #!48 to #63

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 6vaj, chain A (#63) with 4u84, chain A (#48), sequence alignment
score = 784.5  
RMSD between 135 pruned atom pairs is 0.572 angstroms; (across all 145 pairs:
0.997)  
  

> matchmaker #!49-50 to #63

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 6vaj, chain A (#63) with 4u85, chain A (#49), sequence alignment
score = 777.3  
RMSD between 138 pruned atom pairs is 0.464 angstroms; (across all 145 pairs:
0.859)  
  
Matchmaker 6vaj, chain A (#63) with 4u86, chain A (#50), sequence alignment
score = 776.8  
RMSD between 136 pruned atom pairs is 0.615 angstroms; (across all 145 pairs:
1.012)  
  

> matchmaker #!80 to #63

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 6vaj, chain A (#63) with 7ekv, chain A (#80), sequence alignment
score = 780.2  
RMSD between 140 pruned atom pairs is 0.462 angstroms; (across all 146 pairs:
0.786)  
  

> matchmaker #57-59 to #63

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 6vaj, chain A (#63) with 5vti, chain A (#57), sequence alignment
score = 154.5  
RMSD between 27 pruned atom pairs is 0.556 angstroms; (across all 31 pairs:
1.225)  
  
Matchmaker 6vaj, chain A (#63) with 5vtj, chain A (#58), sequence alignment
score = 171.2  
RMSD between 31 pruned atom pairs is 0.881 angstroms; (across all 33 pairs:
1.320)  
  
Matchmaker 6vaj, chain A (#63) with 5vtk, chain A (#59), sequence alignment
score = 177.2  
RMSD between 33 pruned atom pairs is 0.772 angstroms; (across all 33 pairs:
0.772)  
  

> matchmaker #!56 to #63

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 6vaj, chain A (#63) with 5uy9, chain A (#56), sequence alignment
score = 771.4  
RMSD between 141 pruned atom pairs is 0.572 angstroms; (across all 146 pairs:
0.837)  
  

> matchmaker #!81 to #63

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 6vaj, chain A (#63) with 7f0m, chain A (#81), sequence alignment
score = 798.8  
RMSD between 140 pruned atom pairs is 0.481 angstroms; (across all 146 pairs:
0.814)  
  

> matchmaker #!78 to #63

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 6vaj, chain A (#63) with 7efj, chain A (#78), sequence alignment
score = 772.4  
RMSD between 141 pruned atom pairs is 0.474 angstroms; (across all 147 pairs:
0.776)  
  

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

> select :133/A

75784 atoms, 70409 bonds, 47 pseudobonds, 14936 residues, 108 models selected  

> select :133

406 atoms, 406 bonds, 56 residues, 56 models selected  

> select clear

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!63 models

> hide #23-27,29,43-44,46-47,57-60#!2-22,28,30-42,45,48-50,56,61-62 target m

> hide #!78-80 target m

> show #!78 models

> hide #!78 models

> show #!78 models

> hide #!78 models

> show #!79 models

> hide #!79 models

> show #!79 models

> hide #!79 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!79 models

> hide #!79 models

> hide #!81 models

> show #!78 models

> hide #!78 models

> show #!78 models

> hide #!78 models

> show #!78 models

> hide #!78 models

> select #63/A:115

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

> select up

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

> select up

914 atoms, 930 bonds, 117 residues, 1 model selected  

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66622 atoms, 67975 bonds, 47 pseudobonds, 8092 residues, 108 models selected  

> select #63

1366 atoms, 1257 bonds, 1 pseudobond, 286 residues, 2 models selected  

> select intersect
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

1177 atoms, 1202 bonds, 1 pseudobond, 150 residues, 2 models selected  

> surface (#!63 & sel)

> select clear

> show #!81 models

> hide #!81 models

> hide #!63 models

> show #!81 models

> show #!63 models

> hide #!81 models

> show #!81 models

> hide #63.2 models

> hide #63.1 models

> show #!80 models

> hide #!80 models

> show #!80 models

> show #63.2 models

> hide #!63 models

> show #!63 models

> show #!79 models

> show #!78 models

> hide #!63 models

> show #!63 models

> hide #!63 models

> show #!63 models

> show #!62 models

> hide #!62 models

> show #!62 models

> hide #!62 models

> show #!61 models

> hide #!61 models

> show #!61 models

> hide #!61 models

> close #61-62

> open 6o33 6o34

6o33 title:  
Crystal Structure Analysis of PIN1 [more info...]  
  
Chain information for 6o33 #1  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 1-163  
B | peptide |  
  
Non-standard residues in 6o33 #1  
---  
ACE — acetyl group  
NH2 — amino group  
SO4 — sulfate ion  
YCP — (2S)-piperidine-2-carboxylic acid  
  
6o34 title:  
Crystal Structure Analysis of PIN1 [more info...]  
  
Chain information for 6o34 #51  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | PIN1_HUMAN 1-163  
B | peptide |  
  
Non-standard residues in 6o34 #51  
---  
2PE — nonaethylene glycol  
ACE — acetyl group  
CIR — citrulline  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MEA — N-methylphenylalanine  
NH2 — amino group  
SO4 — sulfate ion  
YCP — (2S)-piperidine-2-carboxylic acid  
  

> show #63.1 models

> hide #63.1 models

> hide #!63 models

> show #!63 models

> copy m51 m52

Unknown command: copy m51 m52  

> copy #51 #52

Unknown command: copy #51 #52  

> copy :WAT

Unknown command: copy :WAT  

> select :WAT

Nothing selected  

> select :HOH

7142 atoms, 418 bonds, 6724 residues, 61 models selected  

> hide (#!1,51,63,78-81 & sel) target ab

> select :SO4

110 atoms, 88 bonds, 22 residues, 17 models selected  

> hide (#!1,51,63 & sel) target a

> select clear

> hide #!80 models

> show #!80 models

> hide #!80 models

> hide #!79 models

> hide #!78 models

> hide #!63 models

> show #!63 models

> hide #!81 models

> hide #!51 models

> hide #!1 models

> select #63/A:201@C2

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 16 atom styles  

> select #63/A:135@OE2

1 atom, 1 residue, 1 model selected  

> select clear

> select #63/A:114@CB

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

48 atoms, 47 bonds, 7 residues, 2 models selected  

> select up

914 atoms, 930 bonds, 117 residues, 2 models selected  

> color (#!63 & sel) dark gray

> ui tool show ""Color Actions""

> select #63/A:201@C2

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

914 atoms, 930 bonds, 117 residues, 1 model selected  

> select up

965 atoms, 983 bonds, 123 residues, 2 models selected  

> color #63 #b8938aff

> color #63 #b88189ff

> select #63/A:201@C2

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

914 atoms, 930 bonds, 117 residues, 1 model selected  

> select up

965 atoms, 983 bonds, 123 residues, 2 models selected  

> select down

914 atoms, 930 bonds, 117 residues, 2 models selected  

> select down

16 atoms, 16 bonds, 1 residue, 2 models selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

914 atoms, 930 bonds, 117 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel byhetero target acpf

> ui tool show ""Color Actions""

> select clear

> show #!78 models

> show #!79 models

> show #!80 models

> show #!81 models

> hide #!78 models

> hide #!79 models

> hide #!80 models

> hide #63.2 models

> hide #!63 models

> select #81/A:201@C29

1 atom, 1 residue, 1 model selected  

> select up

30 atoms, 34 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #39ff3b interModel false distSlop 0.6 angleSlop 45.0
> twoColors true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.6 angstroms and 45 degrees
    Models used:
    	81 7f0m
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7f0m #81/A GLN 131 N  7f0m #81/A 0BF 201 O14  no hydrogen  2.580  N/A
    

  
1 hydrogen bonds found  
1 strict hydrogen bonds found  

> style sel ball

Changed 30 atom styles  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

30 atoms, 34 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #39ff3b interModel false distSlop 0.8 angleSlop 60.0
> twoColors true reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 60 degrees
    Models used:
    	81 7f0m
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7f0m #81/A ARG 68 NH1  7f0m #81/A 0BF 201 O13  no hydrogen  3.264  N/A
    7f0m #81/A GLN 131 N   7f0m #81/A 0BF 201 O14  no hydrogen  2.580  N/A
    

  
2 hydrogen bonds found  
1 strict hydrogen bonds found  

> show #!80 models

> hide #!80 models

> show #!80 models

> show #!79 models

> show #!78 models

> hide #!78 models

> hide #!79 models

> hide #!80 models

> hbonds sel color #39ff3b interModel false distSlop 0.8 angleSlop 60.0 reveal
> true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 60 degrees
    Models used:
    	81 7f0m
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    7f0m #81/A ARG 68 NH1  7f0m #81/A 0BF 201 O13  no hydrogen  3.264  N/A
    7f0m #81/A GLN 131 N   7f0m #81/A 0BF 201 O14  no hydrogen  2.580  N/A
    

  
2 hydrogen bonds found  

> show #!63 models

> select #63/A:201@C5

1 atom, 1 residue, 1 model selected  

> select up

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

> hbonds sel color #39ff3b dashes 6 interModel false distSlop 0.8 angleSlop
> 60.0 reveal true retainCurrent true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.8 angstroms and 60 degrees
    Models used:
    	63 6vaj
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6vaj #63/A GLN 131 N    6vaj #63/A QT7 201 O3  no hydrogen  2.914  N/A
    6vaj #63/A HIS 157 NE2  6vaj #63/A QT7 201 O2  no hydrogen  3.198  N/A
    

  
2 hydrogen bonds found  

> hide #!81 models

> show #63.2 models

> select clear

> hide #63.2 models

> select clear

> ui tool show ""Color Actions""

> set bgColor white

> show #63.2 models

> show #!81 models

> hide #63.3 models

> show #63.3 models

> hide #63.2 models

> show #63.2 models

> hide #!63 models

> select #81/A:129

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

> select up

38 atoms, 37 bonds, 5 residues, 1 model selected  

> select up

921 atoms, 941 bonds, 114 residues, 1 model selected  

> select up

968 atoms, 990 bonds, 119 residues, 1 model selected  

> select up

1195 atoms, 1225 bonds, 147 residues, 1 model selected  

> select up

1336 atoms, 1246 bonds, 267 residues, 1 model selected  

> select up

75883 atoms, 70510 bonds, 14951 residues, 61 models selected  

> select up

75883 atoms, 70510 bonds, 3 pseudobonds, 14951 residues, 64 models selected  

> select up

75883 atoms, 70510 bonds, 3 pseudobonds, 14951 residues, 64 models selected  

> select up

75883 atoms, 70510 bonds, 3 pseudobonds, 14951 residues, 64 models selected  

> select up

75883 atoms, 70510 bonds, 3 pseudobonds, 14951 residues, 64 models selected  

> select down

75883 atoms, 70510 bonds, 14951 residues, 62 models selected  

> select down

1336 atoms, 1246 bonds, 267 residues, 2 models selected  

> select down

1195 atoms, 1225 bonds, 147 residues, 1 model selected  

> select down

968 atoms, 990 bonds, 119 residues, 1 model selected  

> select down

921 atoms, 941 bonds, 114 residues, 1 model selected  

> select clear

> show #!80 models

> hide #!81 models

> select #80/A:109

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

> select up

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select up

917 atoms, 936 bonds, 114 residues, 1 model selected  

> select down

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select up

917 atoms, 936 bonds, 114 residues, 1 model selected  

> select down

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select up

917 atoms, 936 bonds, 114 residues, 1 model selected  

> select down

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select up

917 atoms, 936 bonds, 114 residues, 1 model selected  

> select down

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select down

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

> select down

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

> select down

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

> select down

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

> select down

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

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

> select #78,79,80,81

5299 atoms, 4949 bonds, 6 pseudobonds, 1055 residues, 9 models selected  

> select intersect
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

4668 atoms, 4768 bonds, 4 pseudobonds, 586 residues, 8 models selected  

> surface (#!80 & sel)

> show #!79 models

> show #!78 models

> hide #!78 models

> hide #!79 models

> hide #!80 models

> show #!78 models

> hide #!78 models

> show #!78 models

> show #!80 models

> hide #!80 models

> show #!80 models

> show #!79 models

> hide #!80 models

> hide #!79 models

> show #!79 models

> hide #!78 models

> show #!78 models

> hide #!79 models

> hide #!78 models

> show #63.1 models

> show #!78 models

> hide #!78 models

> show #!79 models

> hide #!79 models

> show #!80 models

> hide #!80 models

> show #!80 models

> select clear

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #!80 models

> show #!80 models

> hide #63.2 models

> show #63.2 models

> hide #63.2 models

> show #63.2 models

> hide #63.2 models

> show #63.2 models

> hide #63.2 models

> show #63.2 models

> hide #63.2 models

> hide #!80 models

> show #!80 models

> hide #80.2 models

> select #80/A:201@C20

1 atom, 1 residue, 1 model selected  

> select up

26 atoms, 29 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 26 atom styles  

> select clear

> show #!78 models

> hide #!63 models

> hide #63.3 models

> hide #!78 models

> hide #!80 models

> show #!81 models

> hide #!81 models

> show #!80 models

> hide #!80 models

> show #!81 models

> select #81/A:115

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

> select up

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

> select up

921 atoms, 941 bonds, 114 residues, 1 model selected  

> select subtract #81/A:201@C27

920 atoms, 939 bonds, 114 residues, 1 model selected  

> select up

921 atoms, 941 bonds, 114 residues, 1 model selected  

> select down

920 atoms, 939 bonds, 114 residues, 1 model selected  

> select down

920 atoms, 939 bonds, 114 residues, 1 model selected  

> show #!80 models

> show #!79 models

> hide #!81 models

> hide #!80 models

> select #79/A:125

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

> select up

36 atoms, 36 bonds, 5 residues, 1 model selected  

> select up

916 atoms, 934 bonds, 115 residues, 1 model selected  

> select clear

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> surface (#!79 & sel)

> select subtract #63.2

65494 atoms, 66823 bonds, 46 pseudobonds, 7946 residues, 109 models selected  

> show #!80 models

> hide #!79 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> surface (#!80 & sel)

> show #!81 models

> hide #!80 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> surface (#!81 & sel)

> show #!80 models

> show #!79 models

> show #!78 models

> hide #!79 models

> hide #!80 models

> hide #!81 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> surface (#!78 & sel)

> show #!79 models

> show #!80 models

> show #!81 models

> hide #!79 models

> show #!79 models

> hide #!79 models

> hide #!80 models

> hide #!81 models

> hide #!78 models

> show #!79 models

> show #!63 models

> show #63.2 models

> hide #79.2 models

> hide #!63 models

> select #79/A:201@C11

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 21 atom styles  

> show #!80 models

> hide #80.2 models

> show #79.2 models

> show #80.2 models

> hide #80.2 models

> show #80.2 models

> hide #80.2 models

> show #80.2 models

> hide #80.2 models

> show #80.2 models

> hide #79.2 models

> show #79.2 models

> hide #79.2 models

> show #79.2 models

> hide #79.2 models

> show #79.2 models

> hide #79.2 models

> show #79.2 models

> hide #63.2 models

> show #63.2 models

> hide #!63 models

> show #!63 models

> hide #63.1 models

> show #63.1 models

> hide #63.2 models

> hide #80.2 models

> hide #79.2 models

> select clear

> select #80/A:69

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

> show sel atoms

> show #!81 models

> hide #81.3 models

> select #79/A:68

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

> show sel atoms

> hide #81.1 models

> show #81.1 models

> hide #!81 models

> show #!81 models

> hide #!81 models

> show #!81 models

> hide #!81 models

> show #!81 models

> hide #!63 models

> hide #!79 models

> hide #!80 models

> hide #!81 models

> show #!81 models

> select #81/A:69

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

> show sel atoms

> hide #!81 models

> show #!80 models

> select #80/A:69

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

> select #80/A:68

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

> show sel atoms

> show #!78 models

> hide #78.1 models

> hide #78.2 models

> hide #!80 models

> show #!63 models

> hide #!63 models

> show #!63 models

> select #63/A:68

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

> show sel atoms

> hide #!78 models

> show #!78 models

> hide #79.1 models

> show #79.1 models

> hide #79.1 models

> hide #!79 models

> hide #!63 models

> select #78/A:69

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

> select add #78/A:68

22 atoms, 20 bonds, 2 residues, 2 models selected  

> show sel atoms

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

> show #!63 models

> hide #63.1 models

> show #80.2 models

> select clear

> show #!1 models

> select #1/B:5@O

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

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

> style sel ball

Changed 47 atom styles  

> hide #!63 models

> hide #!80 models

> hide #!78 models

> hide #80.1 models

> show #80.1 models

> hide #!80 models

> hide #81.1 models

> select #1/A:68

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

> show sel atoms

> select up

159 atoms, 162 bonds, 18 residues, 1 model selected  

> select up

908 atoms, 923 bonds, 116 residues, 1 model selected  

> select down

159 atoms, 162 bonds, 18 residues, 1 model selected  

> select down

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

> select down

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

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> select #1/B

49 atoms, 49 bonds, 8 residues, 1 model selected  

> select ~sel

75834 atoms, 70461 bonds, 51 pseudobonds, 14943 residues, 110 models selected  

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> show #1.2 models

> hide #!1 models

> show #!51 models

> select #51/B:6@N

1 atom, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 49 atom styles  

> show #!1 models

> hide #!1 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CSD""::name=""CSO""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""NAL""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

66671 atoms, 68025 bonds, 47 pseudobonds, 8096 residues, 108 models selected  

> surface (#!51 & sel)

> select clear

> close #1.2

> close #51.3

> show #!1 models

> hide #!51 models

> select #1/A

1307 atoms, 1217 bonds, 1 pseudobond, 265 residues, 2 models selected  

> surface (#!1 & sel)

> select clear

> hide #1.2 models

> show #!51 models

> hide #51.1 models

> hide #51.2 models

> select #51/A:68

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

> select add #51/A:69

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

> show sel atoms

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #1.2 models

> show #!50 models

> show #51.2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #51.1 models

> hide #51.1 models

> hide #51.2 models

> show #51.2 models

> hide #51.2 models

> show #!63 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!51 models

> hide #!1 models

> show #!1 models

> show #!51 models

> hide #80.1 models

> hide #80.2 models

> hide #81.2 models

> show #!78 models

> hide #!78 models

> show #!78 models

> hide #!63 models

> show #78.2 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> style sel ball

Changed 20 atom styles  

> hide #!1 models

> select clear

> hide #!51 models

> show #!63 models

> show #!80 models

> show #!81 models

> show #81.2 models

> show #81.3 models

> hide #81.3 models

> show #81.3 models

> hide #81.3 models

> show #81.3 models

> hide #!81 models

> show #!81 models

> hide #!80 models

> hide #!78 models

> hide #81.3 models

> show #63.3 models

> select #81/A:157

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

> show sel atoms

> save /Users/adaina/Documents/PROJETS/Quantro/PIN1/CoX-chimeraX-chainA-
> only.cxs

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


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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 - 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: MacBookPro18,1
      Model Number: Z14V00074SM/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.81.1
      OS Loader Version: 10151.81.1

Software:

    System Software Overview:

      System Version: macOS 14.3.1 (23D60)
      Kernel Version: Darwin 23.3.0
      Time since boot: 55 days, 13 hours, 5 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2719DC:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    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		can't reproduce						all	ChimeraX