![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 22 months ago
#14406 closed defect (can't reproduce)
Crash in garbage collection during check_for_changes
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.7.2-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700015e05000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001194cf600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1558 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2225 in process_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 60)
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{
"uptime" : 99000,
"procLaunch" : "2024-01-19 02:03:35.3355 +1100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 4078,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"procStartAbsTime" : 91499352521132,
"coalitionID" : 16687,
"osVersion" : {
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"build" : "21G1974",
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"captureTime" : "2024-01-19 10:07:00.3929 +1100",
"incident" : "DCF433E2-A894-404E-A722-503758920C6C",
"bug_type" : "309",
"pid" : 29981,
"procExitAbsTime" : 99038989253844,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2D6DFDD4-45D7-5AD5-B81F-08355775273B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "50E56A3A-331C-058C-AAA9-6934D92089E1",
"wakeTime" : 5527,
"bridgeVersion" : {"build":"21P2057","train":"8.2"},
"sleepWakeUUID" : "90094FEF-92C4-4204-B6B6-039256652559",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487093591\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffecc000-7fffffecd000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487093591\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7fffffecc000-7fffffecd000 [ 4K] r-x\/r-x SM=ALI ",
"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" : 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"path" : "\/Applications\/ChimeraX-1.7.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=19.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=19.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1152K 9 \nActivity Tracing 256K 1 \nCG backing stores 4928K 16 \nCG image 788K 67 \nColorSync 232K 28 \nCoreAnimation 1788K 126 \nCoreGraphics 24K 5 \nCoreServices 624K 2 \nCoreUI image data 5404K 53 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 18.7G 1522 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 136K 34 \nStack 175.8M 35 \nStack Guard 56.0M 1 \nVM_ALLOCATE 298.3M 535 \nVM_ALLOCATE (reserved) 128.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 59.5M 696 \n__DATA_CONST 33.0M 352 \n__DATA_DIRTY 1662K 219 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 678.0M 160 \n__OBJC_RO 82.9M 1 \n__OBJC_RW 3200K 2 \n__TEXT 833.7M 696 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 529.4M 83 \nshared memory 3004K 32 \n=========== ======= ======= \nTOTAL 21.9G 4702 \nTOTAL, minus reserved VM space 21.4G 4702 \n",
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},
"trialInfo" : {
"rollouts" : [
{
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}
===== Log before crash start =====
Startup Messages
---
warnings | Could not find virtual screen for QCocoaScreen(0x6000000f0000, "HP
E243 (1)", QRect(3600,0 1920x1080), dpr=1, displayId=4128832, ) with displayId 4128832
Could not find virtual screen for QCocoaScreen(0x6000000f0000, "HP E243 (1)",
QRect(3600,0 1920x1080), dpr=1, displayId=4128832, )
with displayId 4128832
notes | Duplicate key in file '/Users/chua.n/.matplotlib/matplotlibrc', line 2
('backend: TkAgg')
Duplicate key in file '/Users/chua.n/.matplotlib/matplotlibrc', line 3
('backend: TkAgg')
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Could not find virtual screen for QCocoaScreen(0x6000000f0000, "HP E243 (1)",
QRect(3600,0 1920x1080), dpr=1, displayId=4128832, )
with displayId 4128832
[Repeated 1 time(s)]
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/RING CBL.pdb"
RING CBL.pdb title:
Structure of A CBL-UBCH7 complex: ring domain function In ubiquitin- protein
ligases [more info...]
Chain information for RING CBL.pdb #1
---
Chain | Description | UniProt
A | signal transduction protein CBL | CBL_HUMAN 47-434
Non-standard residues in RING CBL.pdb #1
---
ZN — zinc ion
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/RING RNF8.pdb"
RING RNF8.pdb title:
E3 ubiquitin-protein ligase RNF8 In complex with ubiquitin-conjugating enzyme
E2 N and polyubiquitin-B [more info...]
Chain information for RING RNF8.pdb #2
---
Chain | Description | UniProt
J | E3 ubiquitin-protein ligase RNF8 | RNF8_HUMAN 345-485
Non-standard residues in RING RNF8.pdb #2
---
ZN — zinc ion
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/RING RNF146.pdb"
RING RNF146.pdb title:
Crystal structure of RNF146(ring-wwe)/UBCH5A/iso-ADPR complex [more info...]
Chain information for RING RNF146.pdb #3
---
Chain | Description | UniProt
C | E3 ubiquitin-protein ligase RNF146 | RN146_MOUSE 30-183
Non-standard residues in RING RNF146.pdb #3
---
ZN — zinc ion
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/RING TRIM25.pdb"
RING TRIM25.pdb title:
Complex of TRIM25 ring with UBCH5-ub [more info...]
Chain information for RING TRIM25.pdb #4
---
Chain | Description | UniProt
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN 1-82
Non-standard residues in RING TRIM25.pdb #4
---
ZN — zinc ion
> set bgColor white
> ui tool show Matchmaker
> matchmaker #!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 100.4
RMSD between 33 pruned atom pairs is 1.067 angstroms; (across all 52 pairs:
3.035)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 87.2
RMSD between 30 pruned atom pairs is 1.001 angstroms; (across all 52 pairs:
6.654)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 100.3
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 53 pairs:
4.827)
> ui mousemode right "translate selected models"
> select add #1
421 atoms, 427 bonds, 8 pseudobonds, 57 residues, 2 models selected
> view matrix models #1,1,0,0,-1.2067,0,1,0,-28.126,0,0,1,5.4991
> select add #2
844 atoms, 854 bonds, 16 pseudobonds, 114 residues, 4 models selected
> select subtract #1
423 atoms, 427 bonds, 8 pseudobonds, 57 residues, 2 models selected
> view matrix models
> #2,-0.36977,-0.80996,0.45523,85.122,-0.090359,-0.45629,-0.88523,102.48,0.92472,-0.36846,0.095533,152.37
> view matrix models
> #2,-0.36977,-0.80996,0.45523,79.72,-0.090359,-0.45629,-0.88523,96.348,0.92472,-0.36846,0.095533,152.86
> select add #3
949 atoms, 871 bonds, 16 pseudobonds, 206 residues, 4 models selected
> select subtract #2
526 atoms, 444 bonds, 8 pseudobonds, 149 residues, 2 models selected
> view matrix models
> #3,-0.94699,-0.11173,0.3012,126.47,0.30615,-0.59797,0.74074,173.87,0.097345,0.79369,0.60048,74.495
> view matrix models
> #3,-0.94699,-0.11173,0.3012,161.48,0.30615,-0.59797,0.74074,185.7,0.097345,0.79369,0.60048,76.928
> select add #4
976 atoms, 905 bonds, 16 pseudobonds, 209 residues, 4 models selected
> view matrix models
> #3,-0.94699,-0.11173,0.3012,156.86,0.30615,-0.59797,0.74074,184.24,0.097345,0.79369,0.60048,76.587,#4,0.29514,-0.80352,0.51696,162.36,0.42065,-0.37652,-0.8254,250.8,0.85787,0.46107,0.22688,16.645
> select subtract #3
450 atoms, 461 bonds, 8 pseudobonds, 60 residues, 2 models selected
> view matrix models
> #4,0.29514,-0.80352,0.51696,146.11,0.42065,-0.37652,-0.8254,248.84,0.85787,0.46107,0.22688,14.805
> select add #3
976 atoms, 905 bonds, 16 pseudobonds, 209 residues, 4 models selected
> select subtract #4
526 atoms, 444 bonds, 8 pseudobonds, 149 residues, 2 models selected
> view matrix models
> #3,-0.94699,-0.11173,0.3012,152.22,0.30615,-0.59797,0.74074,175.69,0.097345,0.79369,0.60048,77.67
> view matrix models
> #3,-0.94699,-0.11173,0.3012,153.88,0.30615,-0.59797,0.74074,173.86,0.097345,0.79369,0.60048,78.268
> select add #1
947 atoms, 871 bonds, 16 pseudobonds, 206 residues, 4 models selected
> view matrix models
> #1,1,0,0,0.43396,0,1,0,-27.802,0,0,1,5.6594,#3,-0.94699,-0.11173,0.3012,155.53,0.30615,-0.59797,0.74074,174.18,0.097345,0.79369,0.60048,78.428
> select subtract #1
526 atoms, 444 bonds, 8 pseudobonds, 149 residues, 2 models selected
> view matrix models
> #3,-0.94699,-0.11173,0.3012,154.85,0.30615,-0.59797,0.74074,173.8,0.097345,0.79369,0.60048,78.414
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #1/A:380-434
419 atoms, 427 bonds, 55 residues, 1 model selected
> select #1/A:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:380
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #1/A:380-385
42 atoms, 41 bonds, 6 residues, 1 model selected
> select #1/A:380-385
42 atoms, 41 bonds, 6 residues, 1 model selected
> select #1/A:380-434
419 atoms, 427 bonds, 55 residues, 1 model selected
> select #1/A:430-434
41 atoms, 42 bonds, 5 residues, 1 model selected
> select #1/A:411-434
181 atoms, 185 bonds, 24 residues, 1 model selected
> view matrix models #1,1,0,0,-0.52367,0,1,0,-31.611,0,0,1,6.0488
> select clear
> select #1/A:380-383
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #1/A:423-434
93 atoms, 95 bonds, 12 residues, 1 model selected
> select #1/A:419-434
125 atoms, 127 bonds, 16 residues, 1 model selected
> select #1/A:384-434
388 atoms, 396 bonds, 51 residues, 1 model selected
> select #1/A:384-430
354 atoms, 360 bonds, 47 residues, 1 model selected
> select #1/A:429
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:429-433
37 atoms, 37 bonds, 5 residues, 1 model selected
> select #1/A:434
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:428-434
56 atoms, 58 bonds, 7 residues, 1 model selected
> delete sel
> ui tool show "Show Sequence Viewer"
> sequence chain #2/J
Alignment identifier is 2/J
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #2/J:454
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/J:454
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/J:448
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/J:448-454
56 atoms, 56 bonds, 7 residues, 1 model selected
> select #2/J:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/J:440-448
68 atoms, 67 bonds, 9 residues, 1 model selected
> select clear
> select #2/J:401-451
389 atoms, 395 bonds, 51 residues, 1 model selected
> select #2/J:401-454
412 atoms, 418 bonds, 54 residues, 1 model selected
> select #2/J:452
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/J:452
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/J:449
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/J:449-454
49 atoms, 49 bonds, 6 residues, 1 model selected
> delete sel
> select #2/J:446-447
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/J:446-448
21 atoms, 20 bonds, 3 residues, 1 model selected
> delete sel
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #3/C:56-57
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/C:56-87
253 atoms, 258 bonds, 32 residues, 1 model selected
> select clear
> select #3/C:86
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/C:86-87
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/C:80-81
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/C:80-87
66 atoms, 67 bonds, 8 residues, 1 model selected
> delete sel
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #4/A:53-67
124 atoms, 126 bonds, 15 residues, 1 model selected
> select #4/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:65-67
24 atoms, 23 bonds, 3 residues, 1 model selected
> select clear
> select #4/A:55-67
107 atoms, 109 bonds, 13 residues, 1 model selected
> select #4/A:56-57
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #4/A:56-58
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #4/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:57
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4/A:57-67
95 atoms, 97 bonds, 11 residues, 1 model selected
> delete sel
> save "/Users/chua.n/Desktop/CBL RNF8 RNF146 TRIM25.cxs"
> color #1 #c3db4cff
> color #2 #9fef6aff
> color #3 #c3e528ff
> color #3 #52e58dff
> color #4 #eed433ff
> color #4 #8eee1cff
> color #4 #7cb454ff
> color #4 #75aa4fff
> hide #!1 models
> show #!1 models
> select add #1
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> select add #2
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> select add #3
1178 atoms, 1100 bonds, 24 pseudobonds, 239 residues, 6 models selected
> select add #4
1533 atoms, 1463 bonds, 32 pseudobonds, 288 residues, 8 models selected
> color sel byhetero
> select clear
> select #1/A:380-427
363 atoms, 368 bonds, 48 residues, 1 model selected
> select #1/A:380-381
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/A:380-427
363 atoms, 368 bonds, 48 residues, 1 model selected
> select #1/A:420
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:420
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/J:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/J:440-445
47 atoms, 46 bonds, 6 residues, 1 model selected
> select #2/J:435-436
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/J:435-442
60 atoms, 60 bonds, 8 residues, 1 model selected
> select #2/J:441
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/J:441
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3/C:63-79
135 atoms, 137 bonds, 17 residues, 1 model selected
> select #3/C:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/C:74
11 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.94699,-0.11173,0.3012,157.16,0.30615,-0.59797,0.74074,174.16,0.097345,0.79369,0.60048,78.88
> show sel atoms
> select add #3
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #4
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> select #4/A:54
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/A:54
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #4
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> select subtract #4
Nothing selected
> save "/Users/chua.n/Desktop/CBL RNF8 RNF146 TRIM25.cxs"
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/PHF7_PHD_02_160_207_unrelaxed_rank_1_model_4.pdb"
Chain information for PHF7_PHD_02_160_207_unrelaxed_rank_1_model_4.pdb #5
---
Chain | Description
A | No description available
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/RING PHD
> conflict/NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb"
Chain information for NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb #6
---
Chain | Description
A | No description available
> color #5 #fdd633ff
> color #6 #5bbfdbff
> color #5 #74aafeff
> ui tool show Matchmaker
> matchmaker #6 to #5
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 PHF7_PHD_02_160_207_unrelaxed_rank_1_model_4.pdb, chain A (#5) with
NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb, chain A (#6), sequence
alignment score = 97.7
RMSD between 34 pruned atom pairs is 0.731 angstroms; (across all 46 pairs:
2.542)
> ui tool show Matchmaker
> matchmaker #5#!4 to #6
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 NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb, chain A (#6) with
PHF7_PHD_02_160_207_unrelaxed_rank_1_model_4.pdb, chain A (#5), sequence
alignment score = 97.7
RMSD between 34 pruned atom pairs is 0.731 angstroms; (across all 46 pairs:
2.542)
Matchmaker NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb, chain A (#6) with
RING TRIM25.pdb, chain A (#4), sequence alignment score = 70.1
RMSD between 29 pruned atom pairs is 0.862 angstroms; (across all 41 pairs:
2.998)
> select add #6
394 atoms, 406 bonds, 51 residues, 1 model selected
> select add #5
774 atoms, 794 bonds, 99 residues, 2 models selected
> select add #4
1129 atoms, 1157 bonds, 8 pseudobonds, 148 residues, 4 models selected
> view matrix models
> #4,-0.48041,-0.72902,-0.48758,310.61,0.22853,-0.64079,0.73292,138.02,-0.84675,0.24067,0.47444,64.387,#5,1,3.7145e-16,1.158e-16,202.64,-3.7145e-16,1,-4.701e-17,174.7,-1.158e-16,4.701e-17,1,84.229,#6,0.91151,-0.2819,0.29948,202.45,0.17783,0.9267,0.33106,177.23,-0.37086,-0.24851,0.89482,81.787
> view matrix models
> #4,-0.48041,-0.72902,-0.48758,298.36,0.22853,-0.64079,0.73292,125.65,-0.84675,0.24067,0.47444,60.007,#5,1,3.7145e-16,1.158e-16,190.39,-3.7145e-16,1,-4.701e-17,162.33,-1.158e-16,4.701e-17,1,79.849,#6,0.91151,-0.2819,0.29948,190.21,0.17783,0.9267,0.33106,164.86,-0.37086,-0.24851,0.89482,77.408
> view matrix models
> #4,-0.48041,-0.72902,-0.48758,298.59,0.22853,-0.64079,0.73292,127.08,-0.84675,0.24067,0.47444,59.619,#5,1,3.7145e-16,1.158e-16,190.62,-3.7145e-16,1,-4.701e-17,163.76,-1.158e-16,4.701e-17,1,79.461,#6,0.91151,-0.2819,0.29948,190.44,0.17783,0.9267,0.33106,166.3,-0.37086,-0.24851,0.89482,77.02
> select clear
> select add #6
394 atoms, 406 bonds, 51 residues, 1 model selected
> select add #1
759 atoms, 774 bonds, 8 pseudobonds, 101 residues, 3 models selected
> select add #2
1112 atoms, 1130 bonds, 16 pseudobonds, 149 residues, 5 models selected
> select add #3
1572 atoms, 1506 bonds, 24 pseudobonds, 290 residues, 7 models selected
> select add #4
1927 atoms, 1869 bonds, 32 pseudobonds, 339 residues, 9 models selected
> select add #5
2307 atoms, 2257 bonds, 32 pseudobonds, 387 residues, 10 models selected
> ui tool show Matchmaker
> matchmaker #5-6#!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with
PHF7_PHD_02_160_207_unrelaxed_rank_1_model_4.pdb, chain A (#5), sequence
alignment score = 65.5
RMSD between 22 pruned atom pairs is 1.147 angstroms; (across all 39 pairs:
4.943)
Matchmaker RING CBL.pdb, chain A (#1) with
NFX1_PHD_01_358_408_unrelaxed_rank_1_model_4.pdb, chain A (#6), sequence
alignment score = 72.5
RMSD between 24 pruned atom pairs is 0.975 angstroms; (across all 39 pairs:
4.494)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 99.8
RMSD between 31 pruned atom pairs is 1.029 angstroms; (across all 44 pairs:
2.209)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 80.6
RMSD between 31 pruned atom pairs is 1.040 angstroms; (across all 45 pairs:
2.328)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 87.8
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 42 pairs:
2.511)
> view matrix models
> #1,1,0,0,-11.787,0,1,0,-23.203,0,0,1,-5.7482,#2,-0.37072,-0.81383,0.44749,90.492,-0.092132,-0.44722,-0.88967,99.442,0.92416,-0.37105,0.090814,144.75,#3,-0.94827,-0.11143,0.29727,138.61,0.30226,-0.60326,0.73805,151.29,0.097093,0.78972,0.60574,71.79,#4,0.29514,-0.80352,0.51696,155.19,0.42065,-0.37652,-0.8254,229.06,0.85787,0.46107,0.22688,11.238,#5,0.23941,0.93685,-0.25495,165.77,0.47126,-0.34171,-0.81311,151.22,-0.84888,0.074519,-0.52331,96.03,#6,0.46372,0.8817,0.086951,168.73,0.62284,-0.25462,-0.73975,152.5,-0.6301,0.3972,-0.66724,97.849
> select subtract #1
1942 atoms, 1889 bonds, 24 pseudobonds, 337 residues, 8 models selected
> select subtract #2
1589 atoms, 1533 bonds, 16 pseudobonds, 289 residues, 6 models selected
> select subtract #5
1209 atoms, 1145 bonds, 16 pseudobonds, 241 residues, 5 models selected
> select add #5
1589 atoms, 1533 bonds, 16 pseudobonds, 289 residues, 6 models selected
> select subtract #6
1195 atoms, 1127 bonds, 16 pseudobonds, 238 residues, 5 models selected
> select subtract #4
840 atoms, 764 bonds, 8 pseudobonds, 189 residues, 3 models selected
> select subtract #5
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> select add #1
825 atoms, 744 bonds, 16 pseudobonds, 191 residues, 4 models selected
> select subtract #3
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> view matrix models #1,1,0,0,-34.967,0,1,0,-42.534,0,0,1,8.0303
> select clear
> select add #2
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,-0.37072,-0.81383,0.44749,76.884,-0.092132,-0.44722,-0.88967,104.17,0.92416,-0.37105,0.090814,134.25
> select add #1
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> view matrix models
> #1,1,0,0,-42.582,0,1,0,-40.918,0,0,1,2.9669,#2,-0.37072,-0.81383,0.44749,69.27,-0.092132,-0.44722,-0.88967,105.79,0.92416,-0.37105,0.090814,129.19
> select subtract #1
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,-0.37072,-0.81383,0.44749,77.877,-0.092132,-0.44722,-0.88967,100.71,0.92416,-0.37105,0.090814,137.47
> select subtract #2
Nothing selected
> select add #3
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> view matrix models
> #3,-0.94827,-0.11143,0.29727,141.73,0.30226,-0.60326,0.73805,176.88,0.097093,0.78972,0.60574,53.244
> select subtract #3
Nothing selected
> select add #4
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> view matrix models
> #4,0.29514,-0.80352,0.51696,147.36,0.42065,-0.37652,-0.8254,201.71,0.85787,0.46107,0.22688,28.822
> select subtract #4
Nothing selected
> select add #5
380 atoms, 388 bonds, 48 residues, 1 model selected
> view matrix models
> #5,0.23941,0.93685,-0.25495,173.81,0.47126,-0.34171,-0.81311,147.05,-0.84888,0.074519,-0.52331,103.31
> select subtract #5
Nothing selected
> select add #6
394 atoms, 406 bonds, 51 residues, 1 model selected
> view matrix models
> #6,0.46372,0.8817,0.086951,192.44,0.62284,-0.25462,-0.73975,174.37,-0.6301,0.3972,-0.66724,92.481
> select clear
> save "/Users/chua.n/Desktop/CBL RNF8 RNF146 TRIM25 PHF7 NFX1.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1,4
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:1,4,21
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #5/A:1,4,21,27
28 atoms, 25 bonds, 4 residues, 1 model selected
> select #5/A:1,4,21,27,45
34 atoms, 30 bonds, 5 residues, 1 model selected
> select #5/A:1,4,21,27,45,48
40 atoms, 35 bonds, 6 residues, 1 model selected
> select clear
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1,4
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:1,4-5
18 atoms, 16 bonds, 3 residues, 1 model selected
> select #5/A:1,4-6
27 atoms, 25 bonds, 4 residues, 1 model selected
> select clear
> select #5/A:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1,4
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:1,4,20
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #5/A:1,4,20,22
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #5/A:1,4,20-23
39 atoms, 36 bonds, 6 residues, 1 model selected
> select clear
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:1,4
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:1,4,20-21
24 atoms, 21 bonds, 4 residues, 1 model selected
> select #5/A:1,4,20-21,27
34 atoms, 31 bonds, 5 residues, 1 model selected
> select #5/A:1,4,20-21,27,30
40 atoms, 36 bonds, 6 residues, 1 model selected
> select #5/A:1,4,20-21,27,30,36
50 atoms, 46 bonds, 7 residues, 1 model selected
> select #5/A:1,4,20-21,27,30,36,45
56 atoms, 51 bonds, 8 residues, 1 model selected
> select #5/A:1,4,20-21,27,30,36,45,48
62 atoms, 56 bonds, 9 residues, 1 model selected
> select clear
> open /Users/chua.n/Downloads/AF-Q9BWX1-F1-model_v4.pdb
AF-Q9BWX1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for PHD finger protein 7 (Q9BWX1) [more
info...]
Chain information for AF-Q9BWX1-F1-model_v4.pdb #7
---
Chain | Description | UniProt
A | PHD finger protein 7 | PHF7_HUMAN 1-381
> select #7/A:1-381
3057 atoms, 3132 bonds, 381 residues, 1 model selected
> view matrix models #7,1,0,0,242.01,0,1,0,141.14,0,0,1,14.428
> view matrix models #7,1,0,0,277.82,0,1,0,151.12,0,0,1,30.143
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select #7/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:1-159
1277 atoms, 1303 bonds, 159 residues, 1 model selected
> select #7/A:157-158
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #7/A:1-158
1271 atoms, 1297 bonds, 158 residues, 1 model selected
> delete sel
> select #7/A:203-204
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #7/A:203-208
45 atoms, 45 bonds, 6 residues, 1 model selected
> view matrix models #7,1,0,0,257.83,0,1,0,110.78,0,0,1,64.66
> select #7/A:174-176,184-186,270-272,280-282
100 atoms, 99 bonds, 12 residues, 1 model selected
> select #7/A:216
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:216-381
1328 atoms, 1365 bonds, 166 residues, 1 model selected
> delete sel
> select add #7
458 atoms, 468 bonds, 57 residues, 1 model selected
> view matrix models #7,1,0,0,233.38,0,1,0,96.158,0,0,1,67.474
> select #7/A:204-205
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #7/A:204-209
44 atoms, 44 bonds, 6 residues, 1 model selected
> select #7/A:210
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #7/A:210-215
56 atoms, 57 bonds, 6 residues, 1 model selected
> select clear
> select #7/A:213-215
27 atoms, 28 bonds, 3 residues, 1 model selected
> delete sel
> rename #7 "PHF7 AF model"
> color #7 #993fffff
> select #7/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:160,163
12 atoms, 10 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Destroying pre-existing alignment with identifier 7/A
Alignment identifier is 7/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #7/A
431 atoms, 439 bonds, 54 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select #6/A:18
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:18-51
267 atoms, 276 bonds, 34 residues, 1 model selected
> select #6/A:42
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/A:42-49
61 atoms, 63 bonds, 8 residues, 1 model selected
> select #6/A:9
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:9-20
91 atoms, 93 bonds, 12 residues, 1 model selected
> select #6/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:1-7
50 atoms, 49 bonds, 7 residues, 1 model selected
> select #6/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:1,4
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #6/A:1,4,20
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #6/A:1,4,20,22
28 atoms, 25 bonds, 4 residues, 1 model selected
> select #6/A:1,4,20,22,25
38 atoms, 35 bonds, 5 residues, 1 model selected
> select #6/A:1,4,20,22,25,28
44 atoms, 40 bonds, 6 residues, 1 model selected
> select #6/A:1,4,17,20,22,25,28
50 atoms, 45 bonds, 7 residues, 1 model selected
> select #6/A:1,4,17,20,22,25,28,48
56 atoms, 50 bonds, 8 residues, 1 model selected
> select #6/A:1,4,17,20,22,25,28,48,51
62 atoms, 55 bonds, 9 residues, 1 model selected
> select #6/A:1,4,17,20,22,25,28,47-48,51
73 atoms, 66 bonds, 10 residues, 1 model selected
> select #6/A:37
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:37-40
25 atoms, 24 bonds, 4 residues, 1 model selected
> select #6/A:46
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #6/A:46-51
49 atoms, 51 bonds, 6 residues, 1 model selected
> select add #6
394 atoms, 406 bonds, 51 residues, 1 model selected
> select add #5
774 atoms, 794 bonds, 99 residues, 2 models selected
> delete sel
> open /Users/chua.n/Downloads/AF-Q12986-F1-model_v4.pdb
AF-Q12986-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for transcriptional repressor NF-X1 (Q12986)
[more info...]
Chain information for AF-Q12986-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | transcriptional repressor NF-X1 | NFX1_HUMAN 1-1120
> select add #5
8645 atoms, 8847 bonds, 1120 residues, 1 model selected
> view matrix models #5,1,0,0,115.05,0,1,0,33.753,0,0,1,-55.828
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
Could not find virtual screen for QCocoaScreen(0x6000000e5a20, "HP E243 (2)",
QRect(1680,0 1920x1080), dpr=1, displayId=4128833, )
with displayId 4128833
> select clear
> select #5/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-349
2739 atoms, 2805 bonds, 349 residues, 1 model selected
> delete sel
> select #5/A:394
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:394-896
3782 atoms, 3875 bonds, 503 residues, 1 model selected
> select #5/A:399
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:399-945
4119 atoms, 4214 bonds, 547 residues, 1 model selected
> delete sel
> select clear
> select #5/A:946-1120
1395 atoms, 1423 bonds, 175 residues, 1 model selected
> delete sel
> ui tool show Matchmaker
> matchmaker #7#!2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with PHF7 AF model, chain A (#7),
sequence alignment score = 13
RMSD between 26 pruned atom pairs is 1.181 angstroms; (across all 45 pairs:
4.815)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 99.8
RMSD between 31 pruned atom pairs is 1.029 angstroms; (across all 44 pairs:
2.209)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 80.6
RMSD between 31 pruned atom pairs is 1.040 angstroms; (across all 45 pairs:
2.328)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 87.8
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 42 pairs:
2.511)
Matchmaker RING CBL.pdb, chain A (#1) with AF-Q12986-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 52.8
RMSD between 20 pruned atom pairs is 0.797 angstroms; (across all 35 pairs:
4.475)
> select add #1
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> view matrix models #1,1,0,0,-64.586,0,1,0,-73.095,0,0,1,16.293
> select add #2
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> view matrix models
> #1,1,0,0,-67.125,0,1,0,-76.71,0,0,1,14.886,#2,-0.37072,-0.81383,0.44749,57.159,-0.092132,-0.44722,-0.88967,78.112,0.92416,-0.37105,0.090814,152.06
> select subtract #1
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,-0.37072,-0.81383,0.44749,51.007,-0.092132,-0.44722,-0.88967,69.216,0.92416,-0.37105,0.090814,152.73
> select add #3
813 atoms, 732 bonds, 16 pseudobonds, 189 residues, 4 models selected
> select subtract #2
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> view matrix models
> #3,-0.94827,-0.11143,0.29727,116.79,0.30226,-0.60326,0.73805,147.06,0.097093,0.78972,0.60574,64.062
> select add #4
815 atoms, 739 bonds, 16 pseudobonds, 190 residues, 4 models selected
> select subtract #3
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> view matrix models
> #4,0.29514,-0.80352,0.51696,108.21,0.42065,-0.37652,-0.8254,186.93,0.85787,0.46107,0.22688,52.801
> select subtract #4
Nothing selected
> select add #5
392 atoms, 402 bonds, 49 residues, 1 model selected
> view matrix models
> #5,0.89016,-0.20682,-0.406,140.36,-0.44456,-0.58956,-0.67437,130.64,-0.099887,0.78079,-0.61675,106.36
> select subtract #5
Nothing selected
> select add #7
431 atoms, 439 bonds, 54 residues, 1 model selected
> view matrix models
> #7,-0.093966,-0.83237,0.5462,168.64,0.49004,-0.51624,-0.7024,165.59,0.86662,0.20166,0.4564,106.77
> select clear
> select add #5
392 atoms, 402 bonds, 49 residues, 1 model selected
> select #5/A:350
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:350-354
40 atoms, 39 bonds, 5 residues, 1 model selected
> delete sel
> select add #5
352 atoms, 362 bonds, 44 residues, 1 model selected
> select #5/A:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:362
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:362
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:362
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:361-362
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/A:358,361-362
18 atoms, 16 bonds, 3 residues, 1 model selected
> select clear
> select #5/A:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:358,361
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:358,361,374
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #5/A:358,361,374,377
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #5/A:358,361,374,377,382
34 atoms, 30 bonds, 5 residues, 1 model selected
> select #5/A:358,361,374,377,382,385
40 atoms, 35 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> view matrix models
> #5,0.89016,-0.20682,-0.406,136.97,-0.44456,-0.58956,-0.67437,119.87,-0.099887,0.78079,-0.61675,105.07
> undo
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A
Alignment identifier is 7/A
> select clear
> select #7/A
431 atoms, 439 bonds, 54 residues, 1 model selected
> view matrix models
> #7,-0.093966,-0.83237,0.5462,167.62,0.49004,-0.51624,-0.7024,163.58,0.86662,0.20166,0.4564,114.39
> view matrix models
> #7,-0.093966,-0.83237,0.5462,169.7,0.49004,-0.51624,-0.7024,166.95,0.86662,0.20166,0.4564,109.55
> select clear
> select #7/A:159-160
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #7/A
431 atoms, 439 bonds, 54 residues, 1 model selected
> select #7/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:160
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A:160,163
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #7/A:160,163,180
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #7/A:160,163,180,186
28 atoms, 25 bonds, 4 residues, 1 model selected
> select #7/A:160,163,180,186,189
34 atoms, 30 bonds, 5 residues, 1 model selected
> select #7/A:160,163,180,186,189,204
40 atoms, 35 bonds, 6 residues, 1 model selected
> select #7/A:160,163,180,186,189,204,207
46 atoms, 40 bonds, 7 residues, 1 model selected
> show sel atoms
> color sel byhetero
> view matrix models
> #7,-0.093966,-0.83237,0.5462,172.11,0.49004,-0.51624,-0.7024,171.38,0.86662,0.20166,0.4564,107.89
> view matrix models
> #7,-0.093966,-0.83237,0.5462,170.24,0.49004,-0.51624,-0.7024,167.96,0.86662,0.20166,0.4564,109.13
> select clear
> select add #5
352 atoms, 362 bonds, 44 residues, 1 model selected
> delete sel
> open /Users/chua.n/Downloads/AF-A0JLR2-F1-model_v4.pdb
AF-A0JLR2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for NFX1 protein (A0JLR2) [more info...]
Chain information for AF-A0JLR2-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | NFX1 protein | A0JLR2_HUMAN 1-681
> hide #5 models
> select add #5
5214 atoms, 5336 bonds, 681 residues, 1 model selected
> hide #!1 models
> hide #!2 models
> select subtract #5
Nothing selected
> select add #5
5214 atoms, 5336 bonds, 681 residues, 1 model selected
> show #5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:1
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:1-319
2499 atoms, 2558 bonds, 319 residues, 1 model selected
> delete sel
> select #5/A:635-681
354 atoms, 366 bonds, 47 residues, 1 model selected
> select #5/A:438-681
1853 atoms, 1895 bonds, 244 residues, 1 model selected
> delete sel
> select add #5
862 atoms, 881 bonds, 118 residues, 1 model selected
> delete sel
> open /Users/chua.n/Downloads/AF-A0JLR2-F1-model_v4.pdb
AF-A0JLR2-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for NFX1 protein (A0JLR2) [more info...]
Chain information for AF-A0JLR2-F1-model_v4.pdb #5
---
Chain | Description | UniProt
A | NFX1 protein | A0JLR2_HUMAN 1-681
> select add #5
5214 atoms, 5336 bonds, 681 residues, 1 model selected
> view matrix models #5,1,0,0,66.427,0,1,0,86.988,0,0,1,50.835
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:681
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:504-681
1360 atoms, 1392 bonds, 178 residues, 1 model selected
> delete sel
> select #5/A:1
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:1-374
2909 atoms, 2981 bonds, 374 residues, 1 model selected
> select #5/A:62-112
386 atoms, 396 bonds, 51 residues, 1 model selected
> select #5/A:62-329
2114 atoms, 2169 bonds, 268 residues, 1 model selected
> select #5/A:1-2
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #5/A:1-170
1321 atoms, 1353 bonds, 170 residues, 1 model selected
> delete sel
> select clear
> select #5/A:171-216
363 atoms, 366 bonds, 46 residues, 1 model selected
> delete sel
> select clear
> select #5/A:337-503
1226 atoms, 1252 bonds, 167 residues, 1 model selected
> select clear
> select #5/A:367-503
1010 atoms, 1027 bonds, 137 residues, 1 model selected
> delete sel
> select clear
> select #5/A:217-342
987 atoms, 1014 bonds, 126 residues, 1 model selected
> select #5/A:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:217-236
158 atoms, 159 bonds, 20 residues, 1 model selected
> delete sel
> select #5/A:237
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:237-243
60 atoms, 60 bonds, 7 residues, 1 model selected
> view matrix models #5,1,0,0,85.972,0,1,0,142.34,0,0,1,54.152
> select #5/A:279-280
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/A:279-292
100 atoms, 102 bonds, 14 residues, 1 model selected
> select #5/A:293-294
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/A:293-299
52 atoms, 52 bonds, 7 residues, 1 model selected
> select #5/A:314
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:314-366
402 atoms, 415 bonds, 53 residues, 1 model selected
> delete sel
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> matchmaker #5 to #7
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 PHF7 AF model, chain A (#7) with AF-A0JLR2-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 41.1
RMSD between 37 pruned atom pairs is 0.871 angstroms; (across all 52 pairs:
2.894)
> select add #5
600 atoms, 618 bonds, 77 residues, 1 model selected
> view matrix models
> #5,-0.40425,-0.32812,-0.85377,163.11,0.54151,0.66641,-0.51251,163.62,0.73712,-0.66951,-0.091711,143.57
> select #5/A:237
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:237-240
37 atoms, 37 bonds, 4 residues, 1 model selected
> delete sel
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242-243,245
20 atoms, 18 bonds, 3 residues, 1 model selected
> select clear
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242,245
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/A:242,245,263
22 atoms, 20 bonds, 3 residues, 1 model selected
> select #5/A:242,245,263,266
32 atoms, 30 bonds, 4 residues, 1 model selected
> select clear
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:242,245
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:261
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:261
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:261,266
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/A:258,261,266
22 atoms, 20 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #5/A:269
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:269
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:283
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/A:283-289
54 atoms, 55 bonds, 7 residues, 1 model selected
> select #5/A:267
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:267-270
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #5/A:268
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:268
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:269
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:269
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:289
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:289
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:289,292
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> select #5/A:301
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:301-310
77 atoms, 78 bonds, 10 residues, 1 model selected
> select clear
> select #5/A:301-313
101 atoms, 103 bonds, 13 residues, 1 model selected
> delete sel
> ui tool show Matchmaker
> matchmaker #5,7#!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with AF-A0JLR2-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 19.4
RMSD between 27 pruned atom pairs is 1.058 angstroms; (across all 47 pairs:
5.348)
Matchmaker RING CBL.pdb, chain A (#1) with PHF7 AF model, chain A (#7),
sequence alignment score = 13
RMSD between 26 pruned atom pairs is 1.181 angstroms; (across all 45 pairs:
4.815)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 99.8
RMSD between 31 pruned atom pairs is 1.029 angstroms; (across all 44 pairs:
2.209)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 80.6
RMSD between 31 pruned atom pairs is 1.040 angstroms; (across all 45 pairs:
2.328)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 87.8
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 42 pairs:
2.511)
> show #!1 models
> show #!2 models
> select add #1
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> view matrix models #1,1,0,0,-84.46,0,1,0,-93.358,0,0,1,6.2547
> select add #2
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> view matrix models
> #1,1,0,0,-88.169,0,1,0,-96.999,0,0,1,4.0101,#2,-0.37072,-0.81383,0.44749,31.446,-0.092132,-0.44722,-0.88967,42.295,0.92416,-0.37105,0.090814,163.14
> select clear
> select add #2
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,-0.37072,-0.81383,0.44749,36.947,-0.092132,-0.44722,-0.88967,44.271,0.92416,-0.37105,0.090814,149.2
> select add #4
708 atoms, 719 bonds, 16 pseudobonds, 97 residues, 4 models selected
> select add #3
1168 atoms, 1095 bonds, 24 pseudobonds, 238 residues, 6 models selected
> select subtract #3
708 atoms, 719 bonds, 16 pseudobonds, 97 residues, 4 models selected
> select subtract #2
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> select add #3
815 atoms, 739 bonds, 16 pseudobonds, 190 residues, 4 models selected
> select subtract #4
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> view matrix models
> #3,-0.94827,-0.11143,0.29727,109.72,0.30226,-0.60326,0.73805,116.57,0.097093,0.78972,0.60574,72.185
> select add #4
815 atoms, 739 bonds, 16 pseudobonds, 190 residues, 4 models selected
> select subtract #3
355 atoms, 363 bonds, 8 pseudobonds, 49 residues, 2 models selected
> view matrix models
> #4,0.29514,-0.80352,0.51696,79.273,0.42065,-0.37652,-0.8254,160.26,0.85787,0.46107,0.22688,44.159
> select subtract #4
Nothing selected
> select add #5
462 atoms, 476 bonds, 60 residues, 1 model selected
> view matrix models
> #5,-0.28122,-0.37882,-0.88171,141.13,0.59329,0.65353,-0.47001,130.06,0.75427,-0.65528,0.040966,154.15
> select add #7
893 atoms, 915 bonds, 114 residues, 2 models selected
> select subtract #5
431 atoms, 439 bonds, 54 residues, 1 model selected
> view matrix models
> #7,-0.093966,-0.83237,0.5462,151.12,0.49004,-0.51624,-0.7024,125.98,0.86662,0.20166,0.4564,119.12
> select subtract #7
Nothing selected
> select add #5
462 atoms, 476 bonds, 60 residues, 1 model selected
> view matrix models
> #5,-0.28122,-0.37882,-0.88171,142.51,0.59329,0.65353,-0.47001,129.62,0.75427,-0.65528,0.040966,145.94
> select subtract #5
Nothing selected
> select add #7
431 atoms, 439 bonds, 54 residues, 1 model selected
> view matrix models
> #7,-0.093966,-0.83237,0.5462,156.84,0.49004,-0.51624,-0.7024,130.8,0.86662,0.20166,0.4564,118.54
> select subtract #7
Nothing selected
> select add #3
460 atoms, 376 bonds, 8 pseudobonds, 141 residues, 2 models selected
> view matrix models
> #3,-0.94827,-0.11143,0.29727,114.52,0.30226,-0.60326,0.73805,120.51,0.097093,0.78972,0.60574,71.237
> select subtract #3
Nothing selected
> select add #2
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,-0.37072,-0.81383,0.44749,38.408,-0.092132,-0.44722,-0.88967,45.526,0.92416,-0.37105,0.090814,149.18
> select clear
> select #5/A:245
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:244-245
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:244
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #7/A
431 atoms, 439 bonds, 54 residues, 1 model selected
> select #7/A:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/J
Alignment identifier is 2/J
> sequence chain #3/C
Alignment identifier is 3/C
> sequence chain #4/A
Alignment identifier is 4/A
> select clear
> select #1/A:380-427
363 atoms, 368 bonds, 48 residues, 1 model selected
> select #1/A:383
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/J:400-412
106 atoms, 107 bonds, 13 residues, 1 model selected
> select #2/J:400-445
351 atoms, 356 bonds, 46 residues, 1 model selected
> select #2/J:405
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/J:405
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/C:34
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:34-79
353 atoms, 362 bonds, 46 residues, 1 model selected
> select #3/C:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/C:38
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/C:43-44
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/C:43-79
288 atoms, 296 bonds, 37 residues, 1 model selected
> select clear
> select #4/A:10-56
353 atoms, 363 bonds, 47 residues, 1 model selected
> select #4/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/chua.n/Desktop/image1.png supersample 3
> save "/Users/chua.n/Desktop/CBL RNF8 RNF146 TRIM25 PHF7 NFX1.cxs"
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/PHD/G2E3
> Q7L622 PHD3.pdb"
Chain information for G2E3 Q7L622 PHD3.pdb #6
---
Chain | Description
A | No description available
> select add #6
455 atoms, 467 bonds, 57 residues, 1 model selected
> view matrix models #6,1,0,0,100.73,0,1,0,99.075,0,0,1,52.932
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> view matrix models #6,1,0,0,125.64,0,1,0,146.71,0,0,1,173.86
> view matrix models #6,1,0,0,122.95,0,1,0,140.9,0,0,1,157.59
> view matrix models #6,1,0,0,122.72,0,1,0,139.28,0,0,1,150.75
> color #6 #dba345ff
> select #6/A:143
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:143
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:144-145
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A:144-145
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #6/A:142-144,150-151,159-161,169-171
102 atoms, 104 bonds, 11 residues, 1 model selected
> select #6/A:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:144,146-147
20 atoms, 18 bonds, 3 residues, 1 model selected
> select #6/A:144,146-147,171
30 atoms, 28 bonds, 4 residues, 1 model selected
> select #6/A:144,146-147,171,189
36 atoms, 33 bonds, 5 residues, 1 model selected
> select #6/A:144,146-147,171,189,192-193
50 atoms, 46 bonds, 7 residues, 1 model selected
> select #6/A:144,146-147,171,189,192-194
58 atoms, 54 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #6/A:194-195
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:193-195
22 atoms, 21 bonds, 3 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.57585,0.75512,-0.31335,90.496,-0.62956,-0.65409,-0.41931,120.46,-0.52159,-0.044193,0.85205,139.19
> view matrix models
> #6,-0.30596,0.3797,-0.87305,90.001,-0.89405,0.20059,0.40056,124.24,0.32722,0.9031,0.2781,152.01
> view matrix models
> #6,-0.021257,-0.3984,-0.91697,93.838,-0.71529,0.64685,-0.26446,122.38,0.6985,0.65028,-0.29872,153.53
> view matrix models
> #6,0.56357,-0.062456,0.8237,121.67,0.81842,-0.093154,-0.56702,148.18,0.11215,0.99369,-0.0013842,145.43
> view matrix models
> #6,0.80664,-0.30762,0.50468,123.07,0.54805,0.069608,-0.83354,140.76,0.22129,0.94896,0.22474,149.54
> view matrix models
> #6,-0.29242,0.081961,0.95277,106.45,0.94891,0.14841,0.27846,158.84,-0.11858,0.98552,-0.12117,139.84
> view matrix models
> #6,-0.32075,0.027396,0.94677,105.76,0.92231,0.23652,0.30562,158.72,-0.21555,0.97124,-0.10113,138.11
> view matrix models
> #6,0.35383,-0.037746,0.93455,118.65,0.92471,-0.13592,-0.35559,152.11,0.14045,0.99,-0.013189,145.86
> view matrix models
> #6,0.35383,-0.037746,0.93455,116.72,0.92471,-0.13592,-0.35559,149.51,0.14045,0.99,-0.013189,142.62
> view matrix models
> #6,0.4332,0.1953,0.87989,118.15,0.84183,-0.43643,-0.31759,147.75,0.32198,0.87829,-0.35347,142.85
> view matrix models
> #6,0.12033,0.69332,0.71051,111.35,0.82022,-0.47263,0.32228,153.12,0.55925,0.544,-0.62555,144.42
> select #6/A:174
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:174-189
126 atoms, 128 bonds, 16 residues, 1 model selected
> select clear
> select #6/A:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:140-144
36 atoms, 36 bonds, 5 residues, 1 model selected
> select #6/A:140-142
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #6/A:140-142
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #6/A:143-144
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:140-144
36 atoms, 36 bonds, 5 residues, 1 model selected
> select clear
> select #6/A:157-158
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #6/A:157-165
72 atoms, 73 bonds, 9 residues, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164,171
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/A:165-166
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A:165-166
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:164-165
12 atoms, 11 bonds, 2 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> show sel atoms
> select #6/A:171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:171-174
35 atoms, 35 bonds, 4 residues, 1 model selected
> select #6/A:174-175
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:174-175
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:174
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:174
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/A:161
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:161-167
53 atoms, 53 bonds, 7 residues, 1 model selected
> color sel byhetero
> select clear
> select #6/A
455 atoms, 467 bonds, 57 residues, 1 model selected
> color sel byhetero
> ui tool show Matchmaker
> select ~sel
2426 atoms, 2378 bonds, 32 pseudobonds, 402 residues, 10 models selected
> select ~sel
455 atoms, 467 bonds, 57 residues, 1 model selected
> select ~sel
2426 atoms, 2378 bonds, 32 pseudobonds, 402 residues, 10 models selected
> matchmaker #5-7#!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with AF-A0JLR2-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 19.4
RMSD between 27 pruned atom pairs is 1.058 angstroms; (across all 47 pairs:
5.348)
Matchmaker RING CBL.pdb, chain A (#1) with G2E3 Q7L622 PHD3.pdb, chain A (#6),
sequence alignment score = 47.7
RMSD between 20 pruned atom pairs is 1.126 angstroms; (across all 44 pairs:
4.151)
Matchmaker RING CBL.pdb, chain A (#1) with PHF7 AF model, chain A (#7),
sequence alignment score = 13
RMSD between 26 pruned atom pairs is 1.181 angstroms; (across all 45 pairs:
4.815)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 99.8
RMSD between 31 pruned atom pairs is 1.029 angstroms; (across all 44 pairs:
2.209)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 80.6
RMSD between 31 pruned atom pairs is 1.040 angstroms; (across all 45 pairs:
2.328)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 87.8
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 42 pairs:
2.511)
> view matrix models
> #1,0.58588,0.34639,0.73264,-149.56,-0.51674,0.8561,0.0084583,23.273,-0.62428,-0.38354,0.68056,220.88,#2,0.42797,-0.90356,0.020531,63.106,0.12051,0.034536,-0.99211,76.691,0.89572,0.42707,0.12367,212.42,#3,-0.37973,0.30433,0.87361,55.802,0.7496,-0.45219,0.48335,95.601,0.54214,0.8384,-0.056411,112.84,#4,0.94714,-0.26339,0.18318,48.09,0.21487,0.096772,-0.97184,153.09,0.23825,0.95982,0.14825,31.454,#7,0.74961,-0.51874,0.41108,99.887,0.47541,-0.010128,-0.87971,78.738,0.4605,0.85487,0.23902,99.999,#5,0.59336,-0.47565,-0.64937,131.75,0.65961,0.74969,0.053585,90.636,0.46134,-0.46013,0.75858,97.209
> view matrix models
> #1,0.277,-0.69224,0.66639,97.075,-0.90445,-0.42199,-0.062405,327.03,0.32441,-0.58543,-0.74299,234.65,#2,0.57694,-0.16311,0.80033,140.8,0.31651,0.94795,-0.034965,173.38,-0.75297,0.27348,0.59854,84.207,#3,-0.40721,0.913,-0.024899,69.613,0.72405,0.30608,-0.61812,112.53,-0.55672,-0.26973,-0.78569,123.67,#4,0.36224,0.34532,0.86576,-19.978,-0.49799,0.85686,-0.13341,68.501,-0.7879,-0.38281,0.48236,128.51,#7,0.21226,0.26118,0.94167,93.019,-0.17589,0.9581,-0.22609,70.151,-0.96125,-0.11764,0.2493,116.71,#5,0.014046,-0.99401,0.10842,95.896,-0.043087,0.10773,0.99325,46.499,-0.99897,-0.018622,-0.041316,92.272
> ui tool show "Render by Attribute"
> view matrix models
> #1,0.1654,-0.89315,0.41824,179.08,-0.98532,-0.16782,0.031285,287.53,0.042246,-0.41728,-0.9078,274.68,#2,0.4075,0.10964,0.9066,149.4,0.40965,0.86533,-0.28878,170.88,-0.81617,0.48907,0.3077,91.2,#3,-0.3862,0.85067,-0.35667,80.536,0.88666,0.23574,-0.39782,112.48,-0.25433,-0.46988,-0.8453,137.83,#4,0.031909,0.39623,0.9176,-11.502,-0.33456,0.86934,-0.36375,81.202,-0.94183,-0.29539,0.1603,161.05,#7,-0.090764,0.40775,0.90857,92.225,0.037462,0.91309,-0.40603,70.316,-0.99517,-0.0028168,-0.098151,115.97,#5,-0.26094,-0.92042,0.29109,83.684,0.20112,0.24309,0.94892,53.196,-0.94417,0.30616,0.12169,87.706
> ui tool show Matchmaker
> matchmaker #5-7#!2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with AF-A0JLR2-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 19.4
RMSD between 27 pruned atom pairs is 1.058 angstroms; (across all 47 pairs:
5.348)
Matchmaker RING CBL.pdb, chain A (#1) with G2E3 Q7L622 PHD3.pdb, chain A (#6),
sequence alignment score = 47.7
RMSD between 20 pruned atom pairs is 1.126 angstroms; (across all 44 pairs:
4.151)
Matchmaker RING CBL.pdb, chain A (#1) with PHF7 AF model, chain A (#7),
sequence alignment score = 13
RMSD between 26 pruned atom pairs is 1.181 angstroms; (across all 45 pairs:
4.815)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF8.pdb, chain J (#2),
sequence alignment score = 99.8
RMSD between 31 pruned atom pairs is 1.029 angstroms; (across all 44 pairs:
2.209)
Matchmaker RING CBL.pdb, chain A (#1) with RING RNF146.pdb, chain C (#3),
sequence alignment score = 80.6
RMSD between 31 pruned atom pairs is 1.040 angstroms; (across all 45 pairs:
2.328)
Matchmaker RING CBL.pdb, chain A (#1) with RING TRIM25.pdb, chain A (#4),
sequence alignment score = 87.8
RMSD between 29 pruned atom pairs is 0.866 angstroms; (across all 42 pairs:
2.511)
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.1654,-0.89315,0.41824,200.86,-0.98532,-0.16782,0.031285,314.4,0.042246,-0.41728,-0.9078,268.48,#2,0.4075,0.10964,0.9066,171.18,0.40965,0.86533,-0.28878,197.75,-0.81617,0.48907,0.3077,84.998,#3,-0.3862,0.85067,-0.35667,102.31,0.88666,0.23574,-0.39782,139.35,-0.25433,-0.46988,-0.8453,131.63,#4,0.031909,0.39623,0.9176,10.27,-0.33456,0.86934,-0.36375,108.07,-0.94183,-0.29539,0.1603,154.85,#7,-0.090764,0.40775,0.90857,114,0.037462,0.91309,-0.40603,97.187,-0.99517,-0.0028168,-0.098151,109.77,#5,-0.26094,-0.92042,0.29109,105.46,0.20112,0.24309,0.94892,80.067,-0.94417,0.30616,0.12169,81.504
> select subtract #1
2061 atoms, 2010 bonds, 24 pseudobonds, 352 residues, 8 models selected
> select subtract #2
1708 atoms, 1654 bonds, 16 pseudobonds, 304 residues, 6 models selected
> select subtract #3
1248 atoms, 1278 bonds, 8 pseudobonds, 163 residues, 4 models selected
> select subtract #5
786 atoms, 802 bonds, 8 pseudobonds, 103 residues, 3 models selected
> select subtract #4
431 atoms, 439 bonds, 54 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #1
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,166.68,-0.98532,-0.16782,0.031285,299.85,0.042246,-0.41728,-0.9078,259.29
> select add #2
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> select subtract #1
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> view matrix models
> #2,0.4075,0.10964,0.9066,157.4,0.40965,0.86533,-0.28878,203.57,-0.81617,0.48907,0.3077,72.514
> view matrix models
> #2,0.4075,0.10964,0.9066,155.87,0.40965,0.86533,-0.28878,205.42,-0.81617,0.48907,0.3077,72.058
> select add #1
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,162.29,-0.98532,-0.16782,0.031285,308.66,0.042246,-0.41728,-0.9078,254,#2,0.4075,0.10964,0.9066,151.49,0.40965,0.86533,-0.28878,214.23,-0.81617,0.48907,0.3077,66.768
> select subtract #1
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
353 atoms, 356 bonds, 8 pseudobonds, 48 residues, 2 models selected
> select add #1
718 atoms, 724 bonds, 16 pseudobonds, 98 residues, 4 models selected
> select add #5
1180 atoms, 1200 bonds, 16 pseudobonds, 158 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #5-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RING CBL.pdb, chain A (#1) with AF-A0JLR2-F1-model_v4.pdb, chain A
(#5), sequence alignment score = 19.4
RMSD between 27 pruned atom pairs is 1.058 angstroms; (across all 47 pairs:
5.348)
Matchmaker RING CBL.pdb, chain A (#1) with G2E3 Q7L622 PHD3.pdb, chain A (#6),
sequence alignment score = 47.7
RMSD between 20 pruned atom pairs is 1.126 angstroms; (across all 44 pairs:
4.151)
> view matrix models
> #1,0.1654,-0.89315,0.41824,168.41,-0.98532,-0.16782,0.031285,323.2,0.042246,-0.41728,-0.9078,248.01,#2,0.4075,0.10964,0.9066,157.61,0.40965,0.86533,-0.28878,228.77,-0.81617,0.48907,0.3077,60.779,#5,-0.26094,-0.92042,0.29109,73.016,0.20112,0.24309,0.94892,88.873,-0.94417,0.30616,0.12169,61.041
> undo
> select subtract #1
815 atoms, 832 bonds, 8 pseudobonds, 108 residues, 3 models selected
> select subtract #2
462 atoms, 476 bonds, 60 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
462 atoms, 476 bonds, 60 residues, 1 model selected
> select add #6
917 atoms, 943 bonds, 117 residues, 2 models selected
> select add #7
1348 atoms, 1382 bonds, 171 residues, 3 models selected
> select subtract #7
917 atoms, 943 bonds, 117 residues, 2 models selected
> select add #1
1282 atoms, 1311 bonds, 8 pseudobonds, 167 residues, 4 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,149.55,-0.98532,-0.16782,0.031285,292.25,0.042246,-0.41728,-0.9078,257.7,#5,-0.26094,-0.92042,0.29109,54.147,0.20112,0.24309,0.94892,57.922,-0.94417,0.30616,0.12169,70.727,#6,-0.61675,0.78339,-0.076961,56.715,-0.11315,-0.18499,-0.9762,78.116,-0.77898,-0.59337,0.20273,81.936
> view matrix models
> #1,0.1654,-0.89315,0.41824,149.42,-0.98532,-0.16782,0.031285,307.99,0.042246,-0.41728,-0.9078,246.7,#5,-0.26094,-0.92042,0.29109,54.024,0.20112,0.24309,0.94892,73.661,-0.94417,0.30616,0.12169,59.728,#6,-0.61675,0.78339,-0.076961,56.593,-0.11315,-0.18499,-0.9762,93.856,-0.77898,-0.59337,0.20273,70.937
> view matrix models
> #1,0.1654,-0.89315,0.41824,147.15,-0.98532,-0.16782,0.031285,310.85,0.042246,-0.41728,-0.9078,242.58,#5,-0.26094,-0.92042,0.29109,51.749,0.20112,0.24309,0.94892,76.515,-0.94417,0.30616,0.12169,55.611,#6,-0.61675,0.78339,-0.076961,54.318,-0.11315,-0.18499,-0.9762,96.709,-0.77898,-0.59337,0.20273,66.82
> view matrix models
> #1,0.1654,-0.89315,0.41824,145.45,-0.98532,-0.16782,0.031285,310.88,0.042246,-0.41728,-0.9078,240.97,#5,-0.26094,-0.92042,0.29109,50.055,0.20112,0.24309,0.94892,76.544,-0.94417,0.30616,0.12169,53.994,#6,-0.61675,0.78339,-0.076961,52.624,-0.11315,-0.18499,-0.9762,96.738,-0.77898,-0.59337,0.20273,65.203
> select subtract #1
917 atoms, 943 bonds, 117 residues, 2 models selected
> select add #1
1282 atoms, 1311 bonds, 8 pseudobonds, 167 residues, 4 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,138.76,-0.98532,-0.16782,0.031285,300.45,0.042246,-0.41728,-0.9078,243.47,#5,-0.26094,-0.92042,0.29109,43.357,0.20112,0.24309,0.94892,66.116,-0.94417,0.30616,0.12169,56.501,#6,-0.61675,0.78339,-0.076961,45.926,-0.11315,-0.18499,-0.9762,86.31,-0.77898,-0.59337,0.20273,67.71
> select subtract #5
820 atoms, 835 bonds, 8 pseudobonds, 107 residues, 3 models selected
> select subtract #6
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
365 atoms, 368 bonds, 8 pseudobonds, 50 residues, 2 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,152.88,-0.98532,-0.16782,0.031285,324.99,0.042246,-0.41728,-0.9078,233.65
> select subtract #1
Nothing selected
> select add #5
462 atoms, 476 bonds, 60 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
462 atoms, 476 bonds, 60 residues, 1 model selected
> view matrix models
> #5,-0.26094,-0.92042,0.29109,21.71,0.20112,0.24309,0.94892,43.371,-0.94417,0.30616,0.12169,45.156
> view matrix models
> #5,-0.26094,-0.92042,0.29109,37.968,0.20112,0.24309,0.94892,66.416,-0.94417,0.30616,0.12169,43.094
> select subtract #5
Nothing selected
> select add #6
455 atoms, 467 bonds, 57 residues, 1 model selected
> view matrix models
> #6,-0.61675,0.78339,-0.076961,19.676,-0.11315,-0.18499,-0.9762,58.767,-0.77898,-0.59337,0.20273,53.886
> view matrix models
> #6,-0.61675,0.78339,-0.076961,17.254,-0.11315,-0.18499,-0.9762,54.442,-0.77898,-0.59337,0.20273,55.774
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!4 models
> hide #5 models
> show #5 models
> hide #7 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> select add #1
820 atoms, 835 bonds, 8 pseudobonds, 107 residues, 3 models selected
> select add #5
1282 atoms, 1311 bonds, 8 pseudobonds, 167 residues, 4 models selected
> view matrix models
> #1,0.1654,-0.89315,0.41824,163.95,-0.98532,-0.16782,0.031285,353.15,0.042246,-0.41728,-0.9078,250.84,#5,-0.26094,-0.92042,0.29109,49.044,0.20112,0.24309,0.94892,94.58,-0.94417,0.30616,0.12169,60.282,#6,-0.61675,0.78339,-0.076961,28.33,-0.11315,-0.18499,-0.9762,82.607,-0.77898,-0.59337,0.20273,72.961
> select clear
> save /Users/chua.n/Desktop/image2.png supersample 3
> hide #!1 models
> hide #5 models
> hide #6 models
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/PHD/DPF1
> AF-Q92782-F1-model_v4.pdb"
DPF1 AF-Q92782-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for zinc finger protein neuro-D4 (Q92782)
[more info...]
Chain information for DPF1 AF-Q92782-F1-model_v4.pdb #8
---
Chain | Description | UniProt
A | zinc finger protein neuro-D4 | DPF1_HUMAN 1-380
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/PHD/DPF2
> AF-Q92785-F1-model_v4.pdb"
DPF2 AF-Q92785-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for zinc finger protein ubi-D4 (Q92785)
[more info...]
Chain information for DPF2 AF-Q92785-F1-model_v4.pdb #9
---
Chain | Description | UniProt
A | zinc finger protein ubi-D4 | REQU_HUMAN 1-391
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/PHD/DPF3
> AF-Q92784-F1-model_v4.pdb"
DPF3 AF-Q92784-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for zinc finger protein DPF3 (Q92784) [more
info...]
Chain information for DPF3 AF-Q92784-F1-model_v4.pdb #10
---
Chain | Description | UniProt
A | zinc finger protein DPF3 | DPF3_HUMAN 1-378
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> sequence chain #10/A
Alignment identifier is 10/A
> sequence chain #9/A
Alignment identifier is 9/A
> select #8/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:1-219
1728 atoms, 1762 bonds, 219 residues, 1 model selected
> select #8/A:265
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:1-265
2090 atoms, 2136 bonds, 265 residues, 1 model selected
> delete sel
> select clear
> select #8/A:351
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:351-380
235 atoms, 242 bonds, 30 residues, 1 model selected
> delete sel
> select
> #10/A:8-37,59-61,91-93,117-122,133-149,210-221,300-308,314-316,328-330,361-376
830 atoms, 837 bonds, 102 residues, 1 model selected
> select #10/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1-308
2461 atoms, 2511 bonds, 308 residues, 1 model selected
> delete sel
> select #10/A:335-378
345 atoms, 357 bonds, 44 residues, 1 model selected
> select #10/A:378
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #10/A:345-378
258 atoms, 267 bonds, 34 residues, 1 model selected
> undo
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/C) Curation merge/C7) Key data/3_Figures (structure)/PHD/DPF1
> AF-Q92782-F1-model_v4.pdb"
DPF1 AF-Q92782-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for zinc finger protein neuro-D4 (Q92782)
[more info...]
Chain information for DPF1 AF-Q92782-F1-model_v4.pdb #11
---
Chain | Description | UniProt
A | zinc finger protein neuro-D4 | DPF1_HUMAN 1-380
> select clear
> select #8/A
642 atoms, 656 bonds, 85 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
642 atoms, 656 bonds, 85 residues, 1 model selected
> delete sel\
Missing or invalid "atoms" argument: only initial part "sel" of atom specifier
valid
> select subtract #8
Nothing selected
> select add #8
642 atoms, 656 bonds, 85 residues, 1 model selected
> delete sel
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A
Alignment identifier is 11/A
> select #11/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/A:1-303
2378 atoms, 2431 bonds, 303 residues, 1 model selected
> delete sel
> select #9/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:1-322
2549 atoms, 2604 bonds, 322 residues, 1 model selected
> delete sel
> select clear
> select #10/A
553 atoms, 569 bonds, 70 residues, 1 model selected
> select clear
> select #9/A
537 atoms, 547 bonds, 69 residues, 1 model selected
> select #11/A:336-380
355 atoms, 366 bonds, 45 residues, 1 model selected
> select #11/A
589 atoms, 604 bonds, 77 residues, 1 model selected
> color #9 #e11fffff
> color #9 #ff65eaff
> color #9 #a70fffff
> color #9 #fffb19ff
> color #10 #946e00ff
> color #11 #a78e55ff
> ui tool show Matchmaker
> matchmaker #10-11 to #9
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 DPF2 AF-Q92785-F1-model_v4.pdb, chain A (#9) with DPF3
AF-Q92784-F1-model_v4.pdb, chain A (#10), sequence alignment score = 1039.7
RMSD between 56 pruned atom pairs is 0.411 angstroms; (across all 67 pairs:
7.464)
Matchmaker DPF2 AF-Q92785-F1-model_v4.pdb, chain A (#9) with DPF1
AF-Q92782-F1-model_v4.pdb, chain A (#11), sequence alignment score = 787.2
RMSD between 56 pruned atom pairs is 0.317 angstroms; (across all 67 pairs:
4.299)
> view matrix models
> #11,0.889,-0.022869,0.45734,24.869,0.0054653,0.99921,0.039341,2.3869,-0.45788,-0.032474,0.88842,-9.916
> view matrix models
> #11,0.889,-0.022869,0.45734,42.878,0.0054653,0.99921,0.039341,7.5445,-0.45788,-0.032474,0.88842,-21.491
> select clear
> select #10/A:309-314
58 atoms, 60 bonds, 6 residues, 1 model selected
> select #10/A:313
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #10/A:313-378
509 atoms, 522 bonds, 66 residues, 1 model selected
> select add #10
553 atoms, 569 bonds, 70 residues, 1 model selected
> select add #11
1142 atoms, 1173 bonds, 147 residues, 2 models selected
> select subtract #10
589 atoms, 604 bonds, 77 residues, 1 model selected
> view matrix models
> #11,0.889,-0.022869,0.45734,44.011,0.0054653,0.99921,0.039341,11.558,-0.45788,-0.032474,0.88842,-18.605
> select subtract #11
Nothing selected
> select add #9
537 atoms, 547 bonds, 69 residues, 1 model selected
> view matrix models #9,1,0,0,8.6569,0,1,0,3.7453,0,0,1,-3.0647
> select subtract #9
Nothing selected
> select add #10
553 atoms, 569 bonds, 70 residues, 1 model selected
> view matrix models
> #10,0.85656,-0.40556,-0.31912,-10.743,0.41932,0.18652,0.88847,-9.3495,-0.3008,-0.89484,0.32983,10.218
> view matrix models
> #10,0.85656,-0.40556,-0.31912,-12.123,0.41932,0.18652,0.88847,-9.8594,-0.3008,-0.89484,0.32983,10.788
> color #11 #b69414ff
> color #11 #efc21aff
> color #6 #e388c9ff
> color #6 #e059e3ff
> color #6 #e38272ff
> color #6 #e32400ff
> color #7 #f178ffff
> select clear
> select add #9
537 atoms, 547 bonds, 69 residues, 1 model selected
> select add #10
1090 atoms, 1116 bonds, 139 residues, 2 models selected
> select add #11
1679 atoms, 1720 bonds, 216 residues, 3 models selected
===== Log before crash end =====
Log:
Startup Messages
---
notes | Duplicate key in file '/Users/chua.n/.matplotlib/matplotlibrc', line 2
('backend: TkAgg')
Duplicate key in file '/Users/chua.n/.matplotlib/matplotlibrc', line 3
('backend: TkAgg')
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/B5) PHD - Peter Mace, Cameron Reddington/06) Otago
> file_05-12-2022/STRONG RING (annotated by Otago
> group)/DPF1_PHD_01_274_328_unrelaxed_rank_1_model_4.pdb"
Chain information for DPF1_PHD_01_274_328_unrelaxed_rank_1_model_4.pdb #1
---
Chain | Description
A | No description available
> open "/Users/chua.n/Library/CloudStorage/OneDrive-
> wehi.edu.au/Postdoctoral/Experiments/C_E3 ubiquitin ligase project/1)
> Curation data/B5) PHD - Peter Mace, Cameron Reddington/06) Otago
> file_05-12-2022/STRONG RING (annotated by Otago
> group)/DPF2_PHD_01_273_329_unrelaxed_rank_1_model_4.pdb"
Chain information for DPF2_PHD_01_273_329_unrelaxed_rank_1_model_4.pdb #2
---
Chain | Description
A | No description available
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0)
OS Loader Version: 540.120.3~37
Software:
System Software Overview:
System Version: macOS 12.7.2 (21G1974)
Kernel Version: Darwin 21.6.0
Time since boot: 2 days 9:36
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2719DC:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: GRRXNS2
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection during check_for_changes |
comment:2 by , 22 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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