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Opened 35 hours ago
Closed 33 hours ago
#20135 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x000000031e473000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d467000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c45b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b44f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a443000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000319437000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031842b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031741f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000316413000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000315407000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003143fb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003133ef000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003123e3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f088a0c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast (total: 62)
{"app_name":"ChimeraX","timestamp":"2026-04-03 18:31:30.00 -0400","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.6.1 (24G90)","roots_installed":0,"name":"ChimeraX","incident_id":"9F2F327E-7A28-45FF-A622-C2AE24F97A58"}
{
"uptime" : 2800000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1816534185,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 459761,
"osVersion" : {
"train" : "macOS 15.6.1",
"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2026-04-03 18:27:59.3865 -0400",
"codeSigningMonitor" : 1,
"incident" : "9F2F327E-7A28-45FF-A622-C2AE24F97A58",
"pid" : 61659,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-03-17 15:49:30.4754 -0400",
"procStartAbsTime" : 60473543095781,
"procExitAbsTime" : 68091359552862,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0C2BB12E-24B4-5BE2-9EF3-072FD0ADFDC2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FA6EEC6E-A890-96AC-901B-4A3BA4995AFD",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "52F873D9-CF35-4D9E-BD7E-324140C9F0A7",
"wakeTime" : 5864,
"sleepWakeUUID" : "68DA9BE4-907D-474B-AD6B-8834A1041833",
"sip" : "enabled",
"vmRegionInfo" : "0x5d790b31a318 is not in any region. Bytes after previous region: 102293423891225 Bytes before following region: 2778656038120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00005d790b31a318","rawCodes":[1,102774460228376],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005d790b31a318"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61659},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x5d790b31a318 is not in any region. Bytes after previous region: 102293423891225 Bytes before following region: 2778656038120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4697914008},{"value":99},{"value":116},{"value":1153027057775048320},{"value":1027},{"value":13469539983515972068},{"value":13469539991309472036},{"value":14757395258967641293},{"value":4294967286},{"value":4697913938},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8347587928},{"value":0},{"value":11},{"value":259},{"value":8330453408,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4357441072,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8291618816,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":8291618816,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTouchBarInputMethodCandidateList._list"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6485407884},"cpsr":{"value":1073745920},"fp":{"value":4697914080},"sp":{"value":4697914048},"esr":{"value":1442840704,"description":" Address 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_0.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_1.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_1.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_2.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_2.cif #3
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_3.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_3.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_4.cif
Chain information for fold_tcr_avavneefl_h_2kb_model_4.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_2.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_3.cif #9
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2db_model_4.cif #10
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_0.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_0.cif #11
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_1.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_1.cif #12
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_2.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_2.cif #13
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_3.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_3.cif #14
---
Chain | Description
A | .
B | .
C | .
D | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_4.cif
Chain information for fold_tcr_iskanvdvl_h2kb_model_4.cif #15
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-15 to #1
Computing secondary structure
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 fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_1.cif, chain D (#2), sequence alignment score =
1469.5
RMSD between 112 pruned atom pairs is 0.263 angstroms; (across all 274 pairs:
20.703)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_2.cif, chain D (#3), sequence alignment score =
1469.5
RMSD between 158 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
18.950)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_3.cif, chain D (#4), sequence alignment score =
1460.5
RMSD between 152 pruned atom pairs is 0.237 angstroms; (across all 274 pairs:
20.473)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_4.cif, chain D (#5), sequence alignment score =
1451.5
RMSD between 141 pruned atom pairs is 0.178 angstroms; (across all 274 pairs:
19.690)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_0.cif, chain D (#6), sequence alignment score =
1288.3
RMSD between 177 pruned atom pairs is 0.529 angstroms; (across all 274 pairs:
12.666)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_1.cif, chain D (#7), sequence alignment score =
1297.3
RMSD between 176 pruned atom pairs is 0.520 angstroms; (across all 274 pairs:
10.517)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_2.cif, chain D (#8), sequence alignment score =
1295.5
RMSD between 178 pruned atom pairs is 0.578 angstroms; (across all 274 pairs:
10.087)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_3.cif, chain D (#9), sequence alignment score =
1300.9
RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
10.467)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_4.cif, chain D (#10), sequence alignment score =
1284.7
RMSD between 176 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
13.215)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_0.cif, chain D (#11), sequence alignment score =
1449.7
RMSD between 179 pruned atom pairs is 0.451 angstroms; (across all 274 pairs:
7.791)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_1.cif, chain D (#12), sequence alignment score =
1453.3
RMSD between 179 pruned atom pairs is 0.374 angstroms; (across all 274 pairs:
10.016)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_2.cif, chain D (#13), sequence alignment score =
1464.1
RMSD between 181 pruned atom pairs is 0.296 angstroms; (across all 274 pairs:
8.969)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_3.cif, chain D (#14), sequence alignment score =
1471.3
RMSD between 172 pruned atom pairs is 0.272 angstroms; (across all 274 pairs:
15.272)
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_4.cif, chain D (#15), sequence alignment score =
1458.7
RMSD between 165 pruned atom pairs is 0.463 angstroms; (across all 274 pairs:
19.186)
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> color #1 bychain
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #1 models
> delete atoms #2-5
> delete bonds #2-5
> show #1 models
> hide #1 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> ui tool show "Color Actions"
> set bgColor white
> hide #7 models
> hide #8 models
> show #8 models
> show #7 models
> show #6-10 surfaces
> select /C
740 atoms, 730 bonds, 99 residues, 11 models selected
> hide sel & #!6-10 surfaces
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide sel & #!6 surfaces
> select clear
> hide #!6 surfaces
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!6-10 surfaces
> select /D
24787 atoms, 25498 bonds, 3034 residues, 11 models selected
> show sel & #!6-10 surfaces
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> show #!7 models
> hide #!6 models
> show #!8 models
> hide #!7 models
> show #!10 models
> hide #!8 models
> show #11 models
> hide #!10 models
> hide #11 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide sel & #!6-10 surfaces
> hide #!6 models
> delete atoms (#!7-10 & sel)
> delete bonds (#!7-10 & sel)
> undo
> select clear
> hide #!6 models
> undo
> hide #!6 models
> delete atoms #7-10
> delete bonds #7-10
> show #!6 models
> show #11 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> show #11 models
> hide #15 models
> show #15 models
> hide #11 models
> show #11 models
> show #12 models
> hide #15 models
> show #13 models
> hide #12 models
> show #12 models
> hide #11 models
> show #14 models
> hide #12 models
> hide #13 models
> hide #14 models
> show #!6 models
> show #11 models
> show #12 models
> hide #!6 models
> hide #11 models
> hide #12 models
> show #11 models
> color #11 bychain
> show #15 models
> hide #11 models
> color #15 bychain
> show #!6 models
> hide #15 models
> color #!6 bychain
> show #1 models
> hide #1 models
> show #11 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> show #!6 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #6/B
Alignment identifier is 6/B
> select
> #6/A:4-7,10-14,19-25,32-37,43-48,52-56,59-64,69-74,83-90,97-99,103-108
501 atoms, 502 bonds, 62 residues, 1 model selected
> select #6/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> ui tool show "Color Actions"
> set bgColor indian red
> set bgColor white
> color sel brown target acsp
> color sel crimson target acsp
> color sel dark red target acsp
> select #6/B:5-7,10-14,19-24,31-37,44-50,53-56,65-67,73-78,87-94,106-111
465 atoms, 466 bonds, 55 residues, 1 model selected
> select #6/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> select #6/B:91
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/B:91-102
92 atoms, 93 bonds, 12 residues, 1 model selected
> color sel maroon target acsp
> select #6/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:87-99
99 atoms, 100 bonds, 13 residues, 1 model selected
> color sel medium slate blue target acsp
> color sel indigo target acsp
> color sel medium blue target acsp
> select clear
> select /A:87-:99
Expected an objects specifier or a keyword
> select /A:87-99
693 atoms, 700 bonds, 91 residues, 7 models selected
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> show #1 models
> color sel medium blue target acsp
> select /B:91-102
644 atoms, 651 bonds, 84 residues, 7 models selected
> color sel maroon target acsp
> hide #!6 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> show #!6 models
> hide #1 models
> show #11 models
> hide #!6 models
> show #12 models
> hide #11 models
> show #13 models
> hide #12 models
> show #14 models
> hide #13 models
> show #15 models
> hide #14 models
> show #!6 models
> hide #15 models
> show #15 models
> hide #15 models
> hide #!6 models
> show #12 models
> show #13 models
> show #14 models
> delete atoms (#12-14 & sel)
> delete bonds (#12-14 & sel)
> select clear
> undo
> show #11 models
> hide #!12 models
> hide #!13 models
> show #15 models
> hide #!14 models
> hide #15 models
> select clear
> show #!12 models
> hide #11 models
> show #!13 models
> show #!14 models
> delete atoms #12-14
> delete bonds #12-14
> show #!6 models
> show #11 models
> hide #!6 models
> show #!6 models
> hide #11 models
> show #11 models
> hide #!6 models
> show #15 models
> hide #11 models
> show #11 models
> hide #15 models
> show #15 models
> hide #11 models
> show #!6 models
> hide #15 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> peptide.cxs
opened ChimeraX session
> close session
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs
opened ChimeraX session
> hide #3 models
> hide #6 models
> show #6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> select #6/A:5,15
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95
109 atoms, 98 bonds, 13 residues, 1 model selected
> color sel magenta target acsp
> color sel violet target acsp
> color sel magenta target acsp
> color sel light steel blue target acsp
> color sel sky blue target acsp
> color sel cyan target acsp
> color sel magenta target acsp
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> ui tool show "Color Actions"
> color sel magenta target acsp
> select clear
> show #3,6 surfaces
> hide #!3 models
> show #!3 models
> hide #!3,6 surfaces
> show #!1 models
> hide #!1 models
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel atoms
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select #6/A:73
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select clear
> transparency #3,6 70
> transparency #3,6 40
Drag select of 1 residues
> hide sel surfaces
> select clear
> hide #!3,6 surfaces
> show #!3,6 surfaces
> hide #!3,6 surfaces
> select #6/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> color (#!6 & sel) blue
> show sel surfaces
> select clear
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.png"
> width 900 height 668 supersample 4 transparentBackground true
> select #6/G:49@OG1
1 atom, 1 residue, 1 model selected
Drag select of fold_hqba_hfqx6_co_model_0.cif_B SES surface, 234 of 122862
triangles
> select #6/A:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #6/A:98
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #6/A:102
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #6/A:103
35 atoms, 32 bonds, 4 residues, 2 models selected
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel surfaces
> hide #!3 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> show sel surfaces
> select clear
> hide #!6 surfaces
> show #!3 models
> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167
133 atoms, 122 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red target acsp
> select clear
> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167
133 atoms, 122 bonds, 15 residues, 1 model selected
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167
197 atoms, 183 bonds, 22 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select clear
> select #6/A:41
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!6 & sel) magenta
> select up
38 atoms, 38 bonds, 5 residues, 2 models selected
> select up
1311 atoms, 1341 bonds, 167 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!3,6 surfaces
> undo
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> select ~sel & ##selected
4717 atoms, 4800 bonds, 613 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.2.png"
> width 900 height 668 supersample 4 transparentBackground true
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif
Chain information for fold_hqba_yhbp_co_model_0.cif #4
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #5
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif
Chain information for fold_hqba_yhbp_co_model_2.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif
Chain information for fold_hqba_yhbp_co_model_3.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif
Chain information for fold_hqba_yhbp_co_model_4.cif #9
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #4-5,7-9#!3,6 surfaces
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4-5,7-9 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_2.cif, chain A (#7), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.278 angstroms; (across all 167 pairs:
0.278)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_3.cif, chain A (#8), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.296 angstroms; (across all 167 pairs:
0.296)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)
> hide #!3 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #!6 models
> hide #5 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #!3 models
> show #!6 models
> show #7 models
> hide #!6 models
> show #5 models
> show #8 models
> show #9 models
> color #4-5,7-9 bychain
> select clear
> hide #5 models
> hide #7 models
> show #5 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #5 models
> hide #4 models
> show #5 models
> show #7 models
> delete atoms #5,7-8
> delete bonds #5,7-8
> show #4 models
> show #9 models
> hide #9 models
> show #9 models
> hide #4 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif
Chain information for fold_hqba_yhbp_co_model_1.cif #5
---
Chain | Description
A | .
B | .
Computing secondary structure
> color #5,9 bychain
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #5 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
> hide #9 models
> show #4 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif
Chain information for fold_hqba_yhbq_co_model_0.cif #7
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif
Chain information for fold_hqba_yhbq_co_model_1.cif #8
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif
Chain information for fold_hqba_yhbq_co_model_2.cif #10
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif
Chain information for fold_hqba_yhbq_co_model_3.cif #11
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif
Chain information for fold_hqba_yhbq_co_model_4.cif #12
---
Chain | Description
A | .
B | .
Computing secondary structure
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4-5,7-12 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_0.cif, chain A (#7), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
0.202)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_1.cif, chain A (#8), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.376 angstroms; (across all 167 pairs:
0.376)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
> hide #4 models
> hide #5 models
> hide #8 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #8 models
> hide #7 models
> show #10 models
> hide #8 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> show #4 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #12 models
> show #12 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #12 models
> select clear
> show #7 models
> hide #7 models
> show #4 models
> hide #!6 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #5 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #7 models
> color #7#!3 bychain
> hide #7 models
> color #3 lime
> show #7 models
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #11 models
> hide #11 models
> show #12 models
> hide #12 models
> show #9 models
> hide #!3 models
> hide #7 models
> show #5 models
> hide #9 models
> show #9 models
> hide #5 models
> delete atoms #9
> delete bonds #9
> show #7 models
> show #!3 models
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #8 models
> show #10 models
> show #11 models
> show #12 models
> hide #7 models
> hide #!3 models
> show #4 models
> hide #8 models
> hide #10 models
> hide #12 models
> hide #11 models
> show #!6 models
> show #5 models
> hide #4 models
> hide #!6 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif
Chain information for fold_hqba_ubiu_model_0.cif #9
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif
Chain information for fold_hqba_ubiu_model_1.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif
Chain information for fold_hqba_ubiu_model_2.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif
Chain information for fold_hqba_ubiu_model_3.cif #15
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif
Chain information for fold_hqba_ubiu_model_4.cif #16
---
Chain | Description
A | .
B | .
Computing secondary structure
> show #!6 models
> hide #5 models
> hide #9 models
> ui tool show Matchmaker
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #9-16 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)
> show #9 models
> hide #!6 models
> show #!6 models
> hide #9 models
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> show #9 models
> hide #!6 models
> ui tool show Matchmaker
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> matchmaker #9-16 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)
> show #!6 models
> hide #!6 models
> show #13 models
> show #14 models
> show #15 models
> show #16 models
> hide #9 models
> delete atoms #13-16
> delete bonds #13-16
> show #9 models
> color #9 bychain
> show #!6 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #9 models
> select clear
> select #6/A:164
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:23,24,27
24 atoms, 22 bonds, 3 residues, 1 model selected
> select #6/A:23,24,27,167
36 atoms, 34 bonds, 4 residues, 1 model selected
> color (#!6 & sel) cyan
> select clear
> show #9 models
> hide #!6 models
> show #7 models
> hide #9 models
> show #!6 models
> hide #!6 models
> show #8 models
> show #10 models
> show #11 models
> show #12 models
> hide #8 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #!6 models
> hide #7 models
> show #4 models
> show #5 models
> hide #!6 models
> hide #5 models
> show #5 models
> hide #4 models
> show #!6 models
> hide #5 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_0.cif
Chain information for fold_hqba_yhbq_model_0.cif #13
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_1.cif
Chain information for fold_hqba_yhbq_model_1.cif #14
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_2.cif
Chain information for fold_hqba_yhbq_model_2.cif #15
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_3.cif
Chain information for fold_hqba_yhbq_model_3.cif #16
---
Chain | Description
A | .
B | .
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_4.cif
Chain information for fold_hqba_yhbq_model_4.cif #17
---
Chain | Description
A | .
B | .
Computing secondary structure
> select #6/A
1311 atoms, 1341 bonds, 167 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #13-17 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
> matchmaker #13-17 to #6 & sel
Computing secondary structure
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)
> hide #!6 models
> show #7 models
> show #8 models
> hide #8 models
> show #8 models
> show #10 models
> show #11 models
> hide #11 models
> show #11 models
> show #12 models
> hide #!3 models
> hide #7 models
> hide #13 models
> delete atoms #8,10-12,14-17
> delete bonds #8,10-12,14-17
> show #4 models
> show #5 models
> hide #5 models
> show #7 models
> show #9 models
> hide #7 models
> hide #4 models
> show #13 models
> show #!6 models
[deleted to fit within ticket limits]
> hide #5 models
> show #1 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #4 models
> show #3 models
> hide #!2 models
> hide #1 models
> show #!6 models
> hide #3#!6 surfaces
> show #7 models
> hide #!6 models
> hide #3 models
> show #8 models
> hide #7 models
> show #9 models
> hide #8 models
> rainbow #9
> show #10 models
> hide #9 models
> show #11 models
> hide #10 models
> show #1 models
> hide #1 models
> show #1 models
> hide #11 models
> show #11 models
> show #12 models
> hide #11 models
> hide #1 models
> matchmaker #8-10,12 to #7/A pairing bs
Computing secondary structure
[Repeated 4 time(s)] Parameters
---
Chain pairing | bs
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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
chain A (#12), sequence alignment score = 124
RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
29.841)
> show #7 models
> hide #12 models
> show #8 models
> show #9 models
> hide #8 models
> hide #7 models
> show #8 models
> hide #9 models
> show #12 models
> hide #8 models
> rainbow #12
> show #7 models
> hide #12 models
> show #8 models
> hide #7 models
> show #5 models
> hide #8 models
> color #5 bychain
> show #!6 models
> hide #5 models
> show #11 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #5 models
> select /A
32114 atoms, 32801 bonds, 4077 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs
Computing secondary structure
[Repeated 6 time(s)] Parameters
---
Chain pairing | bs
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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1083.2
RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
0.359)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)
> show #1 models
> hide #1 models
> show #5 models
> hide #11 models
> show #11 models
> hide #5 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ~sel & ##selected
4938 atoms, 5055 bonds, 624 residues, 2 models selected
> rainbow sel & #11
> select clear
> show #1 models
> hide #11 models
> open 9H2I fromDatabase pdb format mmcif
Summary of feedback from opening 9H2I fetched from pdb
---
note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif
9h2i title:
Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
dehydrogenase complex [more info...]
Chain information for 9h2i #13
---
Chain | Description | UniProt
A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379
B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474
Non-standard residues in 9h2i #13
---
FAD — flavin-adenine dinucleotide
> ui tool show Matchmaker
> matchmaker #13 to #1/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
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 fold_azor_monomer_model_0.cif, chain A (#1) with 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
18.939)
> undo
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> hide #11 models
> hide #1 models
> show #4 models
> hide #13 models
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> show #13 models
> hide #4 models
> color sel & #13 bychain
> undo
> select clear
> color #13 bychain
> undo
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #4/A & sel pairing bs
No 'to' chains specified
> matchmaker #13 & sel to #6 & sel
No matrix compatible with both reference structure and all match structures
> select clear
> select ::name="FAD"
265 atoms, 290 bonds, 5 residues, 4 models selected
> matchmaker #13 to #6 & sel
No matrix compatible with both reference structure and all match structures
> matchmaker #13 to #6
Computing secondary structure
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 9h2i, chain B
(#13), sequence alignment score = 64.3
RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
18.887)
> show #!6 models
> hide #13 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open 8RX4 fromDatabase pdb format mmcif
Summary of feedback from opening 8RX4 fetched from pdb
---
notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
8rx4 title:
Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
and redox co-factor NADP(H) [more info...]
Chain information for 8rx4 #14
---
Chain | Description | UniProt
A B | Mycothione reductase | X8E6Y0_MYCXE 1-459
Non-standard residues in 8rx4 #14
---
FAD — flavin-adenine dinucleotide
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)
> hide #!6 models
> matchmaker #14 to #13
Computing secondary structure
[Repeated 1 time(s)] 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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #13-14 bychain
> select clear
> hide #14 models
> show #14 models
> hide #13 models
> show #13 models
> hide #14 models
> show #14 models
> hide #13 models
> select #14/B
3646 atoms, 3705 bonds, 481 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #13 models
> hide #14 models
> select #13/C
3803 atoms, 3650 bonds, 693 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> hide sel atoms
> select #13/B
3924 atoms, 3668 bonds, 798 residues, 1 model selected
> rainbow sel
> select clear
> show #4 models
> hide #13 models
> show #14 models
> show #13 models
> hide #14 models
> hide #4 models
> show #!6 models
> hide #13 models
> show #13 models
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/B:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "move picked models"
> view matrix models
> #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123
> select clear
> show #3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> hide #13 models
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> color sel & #3 bychain
> select clear
> show #13 models
> select #13/B:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908
> view matrix models
> #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524
Drag select of 1 residues
> view matrix models
> #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933
> view matrix models
> #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363
> view matrix models
> #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081
> view matrix models
> #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262
> view matrix models
> #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418
> view matrix models
> #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733
> view matrix models
> #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879
> select clear
> select #13/B:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27
> view matrix models
> #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67
> view matrix models
> #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714
> view matrix models
> #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802
> view matrix models
> #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54
> select clear
[Repeated 1 time(s)]Drag select of 5 residues, 1 bonds
> show #5 models
> hide #3 models
> show #3 models
> hide #5 models
> show #14 models
> matchmaker #14 to #13
Computing secondary structure
[Repeated 1 time(s)] 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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)
> hide #13 models
> show #13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> show sel & #3,13-14 surfaces
> hide #!14 models
> hide sel & #!3,13 surfaces
> show #!14 models
> hide #!13 models
> hide sel & #!3,14 surfaces
> select clear
> hide #!3 models
> select ::name="NAD"
88 atoms, 96 bonds, 2 residues, 2 models selected
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> show #!13 models
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> select ::name="FAD"
371 atoms, 406 bonds, 7 residues, 5 models selected
> select ~sel & ##selected
21835 atoms, 21626 bonds, 3388 residues, 5 models selected
> rainbow sel & #!14
> select clear
> select ::name="NAP"
96 atoms, 104 bonds, 2 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.051654 seconds
| QMMM: Dspev diag routine = 0.044332 seconds
| QMMM: Dspevd diag routine = 0.032116 seconds
| QMMM: Dspevx diag routine = 0.153242 seconds
| QMMM: Dsyev diag routine = 0.047097 seconds
| QMMM: Dsyevd diag routine = 0.033935 seconds
| QMMM: Dsyevr diag routine = 0.038554 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.022789 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n
(NAP) ``
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`
(NAP) ``
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(NAP) ``
(NAP) ``
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(NAP) `Info: Total number of electrons: 384; net charge: -3`
(NAP) ``
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 217
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.050281 seconds
| QMMM: Dspev diag routine = 0.043968 seconds
| QMMM: Dspevd diag routine = 0.032120 seconds
| QMMM: Dspevx diag routine = 0.153124 seconds
| QMMM: Dsyev diag routine = 0.047103 seconds
| QMMM: Dsyevd diag routine = 0.033926 seconds
| QMMM: Dsyevr diag routine = 0.039887 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.024004 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 P 17.4620 0.4650 57.8060
QMMM: 2 2 O 16.5620 -0.5740 58.3900
QMMM: 3 3 O 18.0440 0.2210 56.4520
QMMM: 4 4 O 18.6480 0.7880 58.8450
QMMM: 5 5 C 18.2700 1.3930 60.1070
QMMM: 6 6 C 19.4870 1.8540 60.8730
QMMM: 7 7 O 19.0230 2.6210 62.0160
QMMM: 8 8 C 20.3910 0.7570 61.4600
QMMM: 9 9 O 21.7470 1.1830 61.4090
QMMM: 10 10 C 19.8810 0.6600 62.8920
QMMM: 11 11 O 20.8230 0.1440 63.8270
QMMM: 12 12 C 19.6340 2.1310 63.1840
QMMM: 13 13 N 18.7140 2.3450 64.2950
QMMM: 14 14 C 17.4200 1.8950 64.3780
QMMM: 15 15 N 16.8230 2.2310 65.4940
QMMM: 16 16 C 17.7860 2.9360 66.2020
QMMM: 17 17 C 17.7680 3.5530 67.4670
QMMM: 18 18 N 16.7090 3.5600 68.2720
QMMM: 19 19 N 18.9020 4.1690 67.8780
QMMM: 20 20 C 19.9640 4.1590 67.0630
QMMM: 21 21 N 20.0960 3.6140 65.8570
QMMM: 22 22 C 18.9590 3.0090 65.4750
QMMM: 23 23 O 16.6940 1.8750 57.8220
QMMM: 24 24 P 16.8310 3.1760 56.8950
QMMM: 25 25 O 16.1610 4.3450 57.5500
QMMM: 26 26 O 18.2590 3.2930 56.4770
QMMM: 27 27 O 15.9430 2.7150 55.6410
QMMM: 28 28 C 14.5280 2.4980 55.8770
QMMM: 29 29 C 13.9670 1.5170 54.8750
QMMM: 30 30 O 14.0230 2.0920 53.5500
QMMM: 31 31 C 14.6700 0.1520 54.7880
QMMM: 32 32 O 13.7350 -0.9120 54.6620
QMMM: 33 33 C 15.5640 0.2940 53.5490
QMMM: 34 34 O 15.7840 -0.9330 52.8700
QMMM: 35 35 C 14.7120 1.2110 52.6690
QMMM: 36 36 N 15.5520 2.0170 51.7640
QMMM: 37 37 C 15.9700 1.4830 50.5670
QMMM: 38 38 C 16.8040 2.2160 49.7300
QMMM: 39 39 C 17.2170 1.5960 48.4310
QMMM: 40 40 O 16.7920 0.4660 48.1440
QMMM: 41 41 N 18.0490 2.2680 47.6420
QMMM: 42 42 C 17.1960 3.4950 50.0970
QMMM: 43 43 C 16.7690 4.0240 51.3000
QMMM: 44 44 C 15.9580 3.2770 52.1340
QMMM: 45 45 P 20.6860 -1.4490 64.0240
QMMM: 46 46 O 21.7060 -1.8020 65.0890
QMMM: 47 47 O 21.0090 -2.0990 62.6800
QMMM: 48 48 O 19.2630 -1.7280 64.4740
QMMM: 49 49 H 17.7290 0.6600 60.7060
QMMM: 50 50 H 17.6220 2.2480 59.9150
QMMM: 51 51 H 20.0850 2.5010 60.2310
QMMM: 52 52 H 20.2560 -0.1860 60.9310
QMMM: 53 53 H 22.3250 0.4250 61.5240
QMMM: 54 54 H 18.9490 0.0970 62.9320
QMMM: 55 55 H 20.5770 2.6470 63.3660
QMMM: 56 56 H 16.9410 1.3200 63.5990
QMMM: 57 57 H 15.8540 3.1050 67.9850
QMMM: 58 58 H 16.7600 4.0200 69.1700
QMMM: 59 59 H 20.8400 4.6670 67.4390
QMMM: 60 60 H 14.0000 3.4470 55.7840
QMMM: 61 61 H 14.3870 2.1050 56.8840
QMMM: 62 62 H 12.9200 1.3420 55.1230
QMMM: 63 63 H 15.2870 -0.0020 55.6730
QMMM: 64 64 H 13.8800 -1.5500 55.3640
QMMM: 65 65 H 16.5100 0.7710 53.8050
QMMM: 66 66 H 16.3180 -1.5120 53.4190
QMMM: 67 67 H 13.9980 0.6220 52.0930
QMMM: 68 68 H 15.6500 0.4930 50.2770
QMMM: 69 69 H 18.3800 3.1810 47.9180
QMMM: 70 70 H 18.3500 1.8650 46.7660
QMMM: 71 71 H 17.8320 4.0750 49.4450
QMMM: 72 72 H 17.0690 5.0210 51.5890
QMMM: 73 73 H 15.6420 3.6860 53.0820
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.2168E+07 DeltaE = -0.4757E+03 DeltaP = 0.9525E+00
QMMM: Smallest DeltaE = 0.8289E-07 DeltaP = 0.1057E-04 Step = 3
Failure running ANTECHAMBER for residue NAP Check reply log for details
> color bfactor sel
96 atoms, 2 residues, atom bfactor range 41.3 to 73.2
> select clear
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> show #!6 models
> select #14/A:97
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454
> view matrix models
> #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003
> view matrix models
> #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104
> view matrix models
> #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309
> hide #!6 models
> show #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #4 models
> show #5 models
> hide #!6 models
> show #!6 models
> hide #5 models
> select #14/A:60
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425
> view matrix models
> #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602
> view matrix models
> #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335
> select clear
> select #14/A:91
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913
> select clear
> hide #!6 models
> show #!6 models
> select clear
Drag select of 26 atoms, 132 residues, 25 bonds
Drag select of 40 atoms, 192 residues, 36 bonds
> hide sel cartoons
> view matrix models
> #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964
> select clear
[Repeated 1 time(s)]
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> select #14/A
3671 atoms, 3705 bonds, 506 residues, 1 model selected
> show sel cartoons
> select clear
> hide #!3 models
> open 3w78 fromDatabase pdb format mmcif
Summary of feedback from opening 3w78 fetched from pdb
---
notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif
Fetching CCD CBD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif
Fetching CCD FMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif
3w78 title:
Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
Cibacron Blue [more info...]
Chain information for 3w78 #15
---
Chain | Description | UniProt
A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211
Non-standard residues in 3w78 #15
---
CBD — cibacron blue
FMN — flavin mononucleotide (riboflavin monophosphate)
3w78 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> matchmaker #15 to #6
Computing secondary structure
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 3w78, chain A
(#15), sequence alignment score = 709.3
RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
1.539)
> hide #!6 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> select #15/C
1697 atoms, 1735 bonds, 217 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #15/D
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show #!3 models
> hide #!14 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> rainbow sel
> select clear
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> rainbow sel
> select clear
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> select #3/B:169
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select clear
> show #15 models
> hide #15 models
> show #15 models
> select #3/B:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> hide sel atoms
> select clear
> select #3/A:184
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #15 models
> select clear
> show #15 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #15/A:186
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select clear
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> show #!3 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/A
1698 atoms, 1735 bonds, 218 residues, 1 model selected
> select #15/B
1696 atoms, 1735 bonds, 216 residues, 1 model selected
> color sel light gray
> color sel gray
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #15/B:52
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #!3 models
> hide #!3 models
> show #!3 models
> select #3/A:147
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide sel atoms
> select clear
> hide #!3 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> select #3/B:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> select #3/B:124
12 atoms, 12 bonds, 1 residue, 1 model selected
> style sel stick
Changed 12 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> open 4m0C fromDatabase pdb format mmcif
Summary of feedback from opening 4m0C fetched from pdb
---
note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif
4m0c title:
The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
anthracis str. Ames Ancestor in complex with FMN. [more info...]
Chain information for 4m0c #16
---
Chain | Description | UniProt
A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220
Non-standard residues in 4m0c #16
---
FMN — flavin mononucleotide (riboflavin monophosphate)
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
> hide #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #!16 models
> show #15 models
> hide #15 models
> matchmaker #!16 to #3
Computing secondary structure
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
> show #!16 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> select #3/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #3/A:28
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> show #!16 models
> select #3/A:24@NZ
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) blue
> select clear
> hide #!3 models
> show #!3 models
> select #3/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #!16 bypolymer
> color #!16 bychain
> undo
> show #!14 models
> hide #!14 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612
> show #!3 models
> hide #!3 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041
> show #!3 models
> hide #!3 models
> show #15 models
> hide #!16 models
> hide #15 models
> show #15 models
> show #!16 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #!16 models
> show #!3 models
> hide #15 models
> view matrix models
> #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471
> select #/B
Expected an objects specifier or a keyword
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select #3/A:85
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #5 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #5 models
> hide #!3 models
> hide #!6 models
> show #8 models
> rainbow #8
> show #9 models
> hide #9 models
> show #9 models
> hide #8 models
> show #10 models
> hide #9 models
> rainbow #10
> show #9 models
> show #11 models
> hide #11 models
> ui tool show Matchmaker
> matchmaker #8-10 to #7
Computing secondary structure
[Repeated 3 time(s)] 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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)
> view matrix models
> #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815
> hide #9 models
> show #11 models
> hide #10 models
> show #12 models
> hide #11 models
> hide #12 models
> show #7 models
> rainbow #7
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #7 models
> show #7 models
> hide #!6 models
> show #!6 models
> hide #7 models
> show #7 models
> select #7/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931
> ui mousemode right "rotate selected models"
> select #7/A:168
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882
> view matrix models
> #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624
> view matrix models
> #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657
> view matrix models
> #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396
> view matrix models
> #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757
> view matrix models
> #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601
> view matrix models
> #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434
> view matrix models
> #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31
> select clear
> hide #7 models
> show #8 models
> select #8/A:495
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568
> ui mousemode right "rotate selected models"
> select #8/A:464
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42
> view matrix models
> #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86
> view matrix models
> #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983
> view matrix models
> #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383
> view matrix models
> #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657
> view matrix models
> #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89
> view matrix models
> #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004
> view matrix models
> #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708
> view matrix models
> #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> hide #8 models
> show #!13 models
> hide #!13 models
> show #!14 models
> hide #!14 models
> show #!16 models
> open 1v4B fromDatabase pdb format mmcif
Summary of feedback from opening 1v4B fetched from pdb
---
notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif
1v4b title:
The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
form [more info...]
Chain information for 1v4b #17
---
Chain | Description | UniProt
A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200
Non-standard residues in 1v4b #17
---
EDO — 1,2-ethanediol (ethylene glycol)
FMN — flavin mononucleotide (riboflavin monophosphate)
IPA — isopropyl alcohol (2-propanol)
1v4b mmCIF Assemblies
---
1| author_defined_assembly
> open 2B3D fromDatabase pdb format mmcif
Summary of feedback from opening 2B3D fetched from pdb
---
note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif
2b3d title:
Crystal structure of Modulator of Drug activity B in complex with flavin
adenine dinucleotide [more info...]
Chain information for 2b3d #18
---
Chain | Description | UniProt
A B | Modulator of drug activity B | MDAB_ECOLI 13-204
Non-standard residues in 2b3d #18
---
FAD — flavin-adenine dinucleotide
> hide #!16 models
> hide #!17 models
> matchmaker #!18 to #3
Computing secondary structure
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain B
(#18), sequence alignment score = 156.9
RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
6.190)
> show #!3 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> select /A
43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected
> hide #!3 models
> show #!3 models
> show #7 models
> hide #7 models
> hide #!6 models
> matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel to #3 & sel
Computing secondary structure
[Repeated 12 time(s)] 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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
0.436)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085
RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
0.263)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1081.4
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1074.2
RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
0.269)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4
RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
23.782)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8
RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
22.736)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4
RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
32.226)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3
RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
21.293)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2
RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
17.171)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
(#13), sequence alignment score = 24
RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
11.957)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
(#14), sequence alignment score = 51.5
RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
29.959)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
(#15), sequence alignment score = 716.5
RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
1.461)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
(#17), sequence alignment score = 427.4
RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
2.701)
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
(#18), sequence alignment score = 150.4
RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
6.224)
> show #!6 models
> hide #!6 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!6 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> hide #!3 models
> show #!18 models
> hide #!18 models
> show #!17 models
> show #!16 models
> hide #!16 models
> show #!18 models
> hide #!17 models
> view matrix models
> #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!6 models
> hide #1 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> select clear
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #4 models
> show #1 models
> hide #!3 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #1 models
> hide #!3 models
> show #1 models
> hide #1 models
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> show #!6 models
> hide #!6 models
> color sel & #!18 bychain
> undo
> select clear
> color #!18 bychain
> undo
> show #!3 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!3 models
> show #!3 models
> hide #!18 models
> show #!18 models
> hide #!3 models
> show #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #!3 models
> show #!18 models
> show #1 models
> hide #!6 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!3 models
> hide #1 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel goldenrod
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> select ::name="FAD"
477 atoms, 522 bonds, 9 residues, 6 models selected
> select ~sel & ##selected
25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected
> color sel dark goldenrod
> color sel salmon
> color sel dark goldenrod
> color sel peru
> color sel dark orange
> color sel saddle brown
> color sel dark goldenrod
> color sel slate gray
> color sel steel blue
> color sel cadet blue
> color sel dark olive green
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> rainbow sel
> select clear
> show #1 models
> hide #!3 models
> show #!13 models
> hide #!13 models
> show #!6 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #4 models
> hide #1 models
> show #1 models
> hide #4 models
> show #4 models
> hide #1 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
> 600 height 489 supersample 4 transparentBackground true
> show #4 models
> hide #1 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #4 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
> width 600 height 489 supersample 4 transparentBackground true
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> select clear
> select #3/B
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> hide #!3 models
> show #1 models
> show #!6 models
> hide #1 models
> show #1 models
> show #!3 models
> hide #!6 models
> hide #1 models
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
> width 600 height 489 supersample 4 transparentBackground true
> show #11 models
> hide #!3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #12 models
> hide #12 models
> show #!6 models
> hide #11 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!6 models
> hide #!3 surfaces
> select add #3/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
> width 600 height 489 supersample 4 transparentBackground true
> select #3/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/B:124
23 atoms, 23 bonds, 2 residues, 2 models selected
> select add #3/A:148
35 atoms, 35 bonds, 3 residues, 2 models selected
> select add #3/A:184
43 atoms, 42 bonds, 4 residues, 3 models selected
> select add #3/A:101@CA
44 atoms, 42 bonds, 5 residues, 3 models selected
> select add #3/A:102@CB
45 atoms, 43 bonds, 6 residues, 3 models selected
> select subtract #3/A:102
44 atoms, 43 bonds, 5 residues, 3 models selected
> select add #3/A:102
52 atoms, 50 bonds, 6 residues, 3 models selected
> select subtract #3/A:101
51 atoms, 49 bonds, 5 residues, 3 models selected
> select add #3/A:101
59 atoms, 56 bonds, 6 residues, 3 models selected
> select add #3/A:100
73 atoms, 71 bonds, 7 residues, 3 models selected
> select add #3/A:99
81 atoms, 78 bonds, 8 residues, 3 models selected
> select add #3/A:183
91 atoms, 88 bonds, 9 residues, 3 models selected
> select add #3/A:143
97 atoms, 93 bonds, 10 residues, 3 models selected
> select add #3/A:98
104 atoms, 100 bonds, 11 residues, 3 models selected
> select add #3/A:19
110 atoms, 105 bonds, 12 residues, 3 models selected
> select add #3/A:18
118 atoms, 112 bonds, 13 residues, 3 models selected
> select add #3/A:17
124 atoms, 117 bonds, 14 residues, 3 models selected
> select add #3/A:16
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:9
136 atoms, 127 bonds, 16 residues, 3 models selected
> select subtract #3/A:9
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:8
138 atoms, 129 bonds, 16 residues, 3 models selected
> select subtract #3/A:8
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10@CB
132 atoms, 123 bonds, 16 residues, 3 models selected
> select subtract #3/A:10@CB
131 atoms, 123 bonds, 15 residues, 3 models selected
> select add #3/A:10
141 atoms, 133 bonds, 16 residues, 3 models selected
> select add #3/B:57
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 148 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select subtract #3/B:52
149 atoms, 140 bonds, 17 residues, 3 models selected
> select add #3/B:52
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CG
158 atoms, 147 bonds, 19 residues, 3 models selected
> select subtract #3/B:60@CG
157 atoms, 147 bonds, 18 residues, 3 models selected
> select add #3/B:60@CB
158 atoms, 147 bonds, 19 residues, 3 models selected
> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> select #3/B:197
6 atoms, 5 bonds, 1 residue, 1 model selected
> label height 3
> label height 2
> label height 1
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> show #5 models
> hide #!3 models
> select #5/B:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:122
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #5/B:124
23 atoms, 23 bonds, 2 residues, 1 model selected
> select add #5/A:100
37 atoms, 39 bonds, 3 residues, 1 model selected
> select add #5/A:101
45 atoms, 45 bonds, 4 residues, 1 model selected
> select add #5/A:16
52 atoms, 51 bonds, 5 residues, 1 model selected
> select add #5/A:10
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:11
69 atoms, 68 bonds, 7 residues, 1 model selected
> select subtract #5/A:11
62 atoms, 61 bonds, 6 residues, 1 model selected
> select add #5/A:12
73 atoms, 72 bonds, 7 residues, 1 model selected
> select add #5/B:60
87 atoms, 87 bonds, 8 residues, 1 model selected
> select add #5/B:57
95 atoms, 94 bonds, 9 residues, 1 model selected
> select add #5/B:58
102 atoms, 100 bonds, 10 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
[Repeated 1 time(s)]
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #5/B:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel stick
Changed 8 atom styles
> show sel atoms
> show #4 models
> hide #4 models
> show #!3 models
> hide #!5 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!3 models
> hide sel atoms
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> hide #!5 models
> show #7 models
> hide #7 models
> show #11 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select add #11/A:101
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #11/A:143
14 atoms, 13 bonds, 2 residues, 1 model selected
> select add #11/A:19
20 atoms, 18 bonds, 3 residues, 1 model selected
> select add #11/A:18
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #11/A:17
34 atoms, 30 bonds, 5 residues, 1 model selected
> select add #11/A:10
44 atoms, 40 bonds, 6 residues, 1 model selected
> select add #11/A:100
58 atoms, 55 bonds, 7 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> select clear
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!5 models
> hide #!11 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true
> ~label #5 residues
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.png
> width 600 height 489 supersample 4 transparentBackground true
> show #15 models
> hide #5 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select ::name="CBD"
204 atoms, 224 bonds, 4 residues, 1 model selected
> color sel pale turquoise
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/3w78.AzrC.CBD.FMN.png
> width 600 height 489 supersample 4 transparentBackground true
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> show #!3 models
> hide #15 models
> select #3/B:126
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #15 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!3 models
> hide #15 models
> show #15 models
> hide #!3 models
> select #15/B:60
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> select clear
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #15 models
> undo
> hide #!16 models
> show #!16 models
> hide #15 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
> show #!6 models
> hide #!16 models
> show #1 models
> hide #!6 models
> show #!16 models
> hide #1 models
> show #!6 models
> hide #!16 models
> show #!16 models
> hide #!6 models
> show #1 models
> hide #!16 models
> show #!16 models
> hide #1 models
> show #!3 models
> hide #!16 models
> show #!16 models
> hide #!3 models
> select #16/B:126
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> show #5 models
> hide #5 models
> show #!17 models
> hide #!16 models
> show #1 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #1 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!6 models
> hide #!17 models
> show #15 models
> hide #!3 models
> show #!16 models
> hide #15 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!16 models
> show #!3 models
> show #1 models
> hide #1 models
> show #7 models
> hide #7 models
> hide #!6 models
> show #1 models
> hide #!3 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> hide #1 models
> show #7 models
> show #1 models
> hide #7 models
> show #7 models
> hide #1 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> view matrix models
> #16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786
> hide #8 models
> show #12 models
> hide #12 models
> show #9 models
> show #10 models
> hide #9 models
> show #!3 models
> hide #10 models
> select #3/A:104
11 atoms, 11 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show sel atoms
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #1 models
> view matrix models
> #3,0.23414,-0.80222,0.54921,11.186,0.21867,-0.50698,-0.83376,-19.133,0.94729,0.31531,0.056721,3.3647
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> open 2Bzs fromDatabase pdb format mmcif
Summary of feedback from opening 2Bzs fetched from pdb
---
notes | Fetching compressed mmCIF 2bzs from http://files.rcsb.org/download/2bzs.cif
Fetching CCD CB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/CB1/CB1.cif
2bzs title:
Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed
by the crystal structure of their complex. [more info...]
Chain information for 2bzs #19
---
Chain | Description | UniProt
A B | NRH DEHYDROGENASE [QUINONE] 2 | NQO2_HUMAN 1-230
Non-standard residues in 2bzs #19
---
CB1 — 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954; Tretazicar)
FAD — flavin-adenine dinucleotide
ZN — zinc ion
> hide #!3 models
> color #!19 bychain
> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159
> show #!3 models
> hide #!3 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #!19 to #3 & sel
Computing secondary structure
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2bzs, chain B
(#19), sequence alignment score = 223.4
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 198 pairs:
5.647)
> show #!3 models
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #1 models
> hide #!19 models
> select #3/A
1646 atoms, 1685 bonds, 208 residues, 1 model selected
> matchmaker #1 to #3 & sel
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)
> show #!19 models
> hide #1 models
> show #1 models
> hide #!3 models
> hide #!19 models
> show #!19 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #4 models
> hide #4 models
> show #1 models
> select #19/B
2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected
> color sel bychain
> select clear
> hide #1 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #4 models
> hide #!19 models
> show #!19 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #1 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select clear
> open 2VPw fromDatabase pdb format mmcif
Summary of feedback from opening 2VPw fetched from pdb
---
notes | Fetching compressed mmCIF 2vpw from http://files.rcsb.org/download/2vpw.cif
Fetching CCD MGD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MGD/MGD.cif
Fetching CCD MO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MO/MO.cif
Fetching CCD MQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/MQ7/MQ7.cif
2vpw title:
Polysulfide reductase with bound menaquinone [more info...]
Chain information for 2vpw #20
---
Chain | Description | UniProt
A E | THIOSULFATE REDUCTASE | Q72LA4_THET2 1-765
B F | NRFC PROTEIN | Q72LA5_THET2 1-195
C G | HYPOTHETICAL MEMBRANE SPANNING PROTEIN | Q72LA6_THET2 0-252 1-253
Non-standard residues in 2vpw #20
---
MGD —
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)
MO — molybdenum atom
MQ7 — menaquinone-7
SF4 — iron/sulfur cluster
> hide #!19 models
> hide #1 models
> hide #!20 surfaces
[Repeated 1 time(s)]
> hide #!20 atoms
> show #!20 cartoons
> matchmaker #!20 to #3 & sel
No 'to' model specified
> matchmaker #!20 to #3
Computing secondary structure
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2vpw, chain E
(#20), sequence alignment score = 78
RMSD between 8 pruned atom pairs is 1.398 angstroms; (across all 148 pairs:
20.313)
> show #!3 models
> hide #!3 models
> select /A
51617 atoms, 51746 bonds, 16 pseudobonds, 7421 residues, 24 models selected
> rainbow sel & #!20
> select ::name="MQ7"
30 atoms, 32 bonds, 2 residues, 1 model selected
> show sel surfaces
> open 7NZ1 fromDatabase pdb format mmcif
Summary of feedback from opening 7NZ1 fetched from pdb
---
notes | Fetching compressed mmCIF 7nz1 from http://files.rcsb.org/download/7nz1.cif
Fetching CCD CSX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CSX/CSX.cif
7nz1 title:
Respiratory complex I from Escherichia coli - focused refinement of
cytoplasmic arm [more info...]
Chain information for 7nz1 #21
---
Chain | Description | UniProt
B | NADH-quinone oxidoreductase subunit B |
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180
Non-standard residues in 7nz1 #21
---
CA — calcium ion
FES — FE2/S2 (inorganic) cluster
FMN — flavin mononucleotide (riboflavin monophosphate)
SF4 — iron/sulfur cluster
> hide sel atoms
> show sel cartoons
> hide #!20 models
> show #!21 cartoons
> hide #!21 atoms
> view matrix models
> #20,-0.20963,0.97025,0.12114,-159.27,0.41872,0.20104,-0.88558,-19.075,-0.88359,-0.13493,-0.44841,140.58
> color #!21 bychain
> matchmaker #!21 to #1
Computing secondary structure
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 fold_azor_monomer_model_0.cif, chain A (#1) with 7nz1, chain G
(#21), sequence alignment score = 86.3
RMSD between 22 pruned atom pairs is 0.859 angstroms; (across all 180 pairs:
20.357)
> show #1 models
> select #21/G
7630 atoms, 7235 bonds, 24 pseudobonds, 1469 residues, 2 models selected
> rainbow sel
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!21 models
> show #!21 models
> hide #1 models
> matchmaker #!21 to #8
Computing secondary structure
[Repeated 1 time(s)] 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 fold_mqo_model_0.cif, chain A (#8) with 7nz1, chain G (#21),
sequence alignment score = 63.6
RMSD between 5 pruned atom pairs is 1.257 angstroms; (across all 362 pairs:
31.062)
> show #8 models
> hide #!21 models
> hide #8 models
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif
Chain information for fold_tcr_ankkflltv_model_0.cif #22
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_1.cif #23
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_2.cif #24
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_3.cif #25
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_ankkflltv_model_4.cif #26
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show Matchmaker
> matchmaker #23-26 to #22
Computing secondary structure
[Repeated 4 time(s)] 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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_1.cif, chain B (#23), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.184 angstroms; (across all 111 pairs:
0.184)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_2.cif, chain B (#24), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.232 angstroms; (across all 111 pairs:
0.232)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_3.cif, chain B (#25), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.364 angstroms; (across all 111 pairs:
0.364)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_4.cif, chain B (#26), sequence alignment score =
573.8
RMSD between 110 pruned atom pairs is 0.269 angstroms; (across all 111 pairs:
0.332)
> view matrix models
> #21,0.56571,0.78878,0.24042,-111.9,-0.81332,0.5818,0.0049461,-39.828,-0.13598,-0.19834,0.97066,-77.181
Drag select of 9 atoms, 113 residues, 8 bonds
> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif
Chain information for fold_tcr_demefteae_model_0.cif #27
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_1.cif #28
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_2.cif #29
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_3.cif #30
---
Chain | Description
A | .
B | .
C | .
Chain information for fold_tcr_demefteae_model_4.cif #31
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
[Repeated 4 time(s)]
> matchmaker #27-31 to #22
Computing secondary structure
[Repeated 5 time(s)] 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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_0.cif, chain B (#27), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.323 angstroms; (across all 111 pairs:
0.323)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_1.cif, chain B (#28), sequence alignment score =
570.2
RMSD between 111 pruned atom pairs is 0.204 angstroms; (across all 111 pairs:
0.204)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_2.cif, chain B (#29), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.345 angstroms; (across all 111 pairs:
0.345)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_3.cif, chain B (#30), sequence alignment score = 581
RMSD between 111 pruned atom pairs is 0.287 angstroms; (across all 111 pairs:
0.287)
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_4.cif, chain B (#31), sequence alignment score =
573.8
RMSD between 111 pruned atom pairs is 0.349 angstroms; (across all 111 pairs:
0.349)
> select clear
> delete atoms #22-31
> delete bonds #22-31
> show #!13 models
> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs
——— End of log from Wed Mar 11 15:25:43 2026 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15H00105LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 216 days, 2 hours, 57 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:
DELL U2718Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 33 hours ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 33 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that
may help you avoid this crash. The Qt window toolkit crashed due to a
display configuration change, typically when waking from sleep or when an
external display is disconnected or connected. This has only been seen on
Mac computers. We hope a newer version of Qt will fix it. We update
ChimeraX daily builds whenever a new Qt is released. You can check here
https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see
if it has been fixed in a newer ChimeraX."
We have not seen this crash in Qt 6.10 which is used by the ChimeraX daily
build so you may want to try that ChimeraX version.
Note:
See TracTickets
for help on using tickets.
Reported by Emily Tai