![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9549 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I had opened 2 predicted structures differing at one amino acid, performed Matchmaker, selected the single amino acid that was different between them (S25/E25), then performed Contacts to see the differences in predicted contacts; I copied the information from the log and was processing it in a terminal window when I was notified ChimeraX quit in the background.
Fatal Python error: Segmentation fault
Current thread 0x000000010c0f6600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 514 in _cursor_position
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 472 in mouse_pause_tracking
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 140 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 56)
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{
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"procLaunch" : "2023-08-08 10:39:21.9832 +0900",
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "iMac17,1",
"procStartAbsTime" : 5864676814188598,
"coalitionID" : 349854,
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"build" : "21G646",
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"captureTime" : "2023-08-10 11:14:37.5470 +0900",
"incident" : "D345A94D-E04E-4B21-BEB5-46B91B4EAC90",
"bug_type" : "309",
"pid" : 47913,
"procExitAbsTime" : 6039593376928786,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B9141A2B-BB6A-AD8E-3FB5-46A0DD310398",
"sip" : "disabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487785815\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff75000-7ffffff76000 [ 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: 140737487785815\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff75000-7ffffff76000 [ 4K] r-x\/r-x SM=ALI ",
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"faultingThread" : 0,
"threads" : 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"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4425744384,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"sharedCache" : {
"base" : 140703328993280,
"size" : 19331678208,
"uuid" : "f2ce8b0d-f2e7-3c14-88fa-430ab7913380"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=11.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=11.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 4384K 8 \nCG image 340K 37 \nColorSync 232K 28 \nCoreAnimation 300K 26 \nCoreGraphics 16K 3 \nCoreServices 624K 2 \nCoreUI image data 5224K 43 \nFoundation 60K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 10.7G 1065 \nMALLOC guard page 48K 10 \nMALLOC_MEDIUM (reserved) 168.0M 3 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 171.7M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 296.1M 365 \n__CTF 756 1 \n__DATA 59.0M 687 \n__DATA_CONST 31.1M 342 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 677.3M 158 \n__TEXT 819.2M 684 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 498.4M 70 \nshared memory 3500K 27 \n=========== ======= ======= \nTOTAL 13.6G 3854 \nTOTAL, minus reserved VM space 13.3G 3854 \n",
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"queue" : "com.apple.main-thread"
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"trialInfo" : {
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===== Log before crash start =====
UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/pcarlton/My Drive
> (pmcarlton@gmail.com)/Carlton_Lab_Shared/AlphaFold/Pete/DSBzoo_relaxed/celeg-11c0d-DSB1_2_3_rank_1_model_1_relaxed.pdb"
> format pdb
Chain information for celeg-11c0d-DSB1_2_3_rank_1_model_1_relaxed.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
Drag select of 2 residues
> select up
3113 atoms, 3159 bonds, 213 residues, 1 model selected
> select clear
Drag select of 2 residues
Drag select of 3 residues
> select up
417 atoms, 425 bonds, 26 residues, 1 model selected
> select up
4408 atoms, 4452 bonds, 280 residues, 1 model selected
Alignment identifier is 1/B
> select clear
> select /B:196
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:196-280
1340 atoms, 1353 bonds, 85 residues, 1 model selected
> select /B:280
13 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:280
13 atoms, 12 bonds, 1 residue, 1 model selected
> select /B:196
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:196
12 atoms, 11 bonds, 1 residue, 1 model selected
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_915a4/SYP4around269_DSB1_915a4_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4around269_DSB1_915a4_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
> hide #1 models
> color #2 bypolymer
> color #2 bychain
Alignment identifier is 1/B
> select clear
> select #2/A:9
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
257 atoms, 258 bonds, 16 residues, 1 model selected
> select up
1769 atoms, 1784 bonds, 114 residues, 1 model selected
Alignment identifier is 2/A
> select clear
> select #2/A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_915a4/SYP4around269_DSB1_915a4_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
SYP4around269_DSB1_915a4_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
B | No description available
> select #2/A:4
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:4-35
518 atoms, 520 bonds, 32 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3/A to #2/A pairing ss
Parameters
---
Chain pairing | ss
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
SYP4around269_DSB1_915a4_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain A (#2) with
SYP4around269_DSB1_915a4_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#3), sequence alignment score = 540.9
RMSD between 14 pruned atom pairs is 1.100 angstroms; (across all 114 pairs:
21.573)
> select clear
> color #2-3 bychain
> select #3/B:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> select up
3022 atoms, 3094 bonds, 385 residues, 1 model selected
> select clear
Alignment identifier is 1
Alignment identifier is 1/B
Alignment identifier is 1/C
Alignment identifier is 2
> select #1/B:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1/B:1-198
3113 atoms, 3143 bonds, 198 residues, 1 model selected
> select #1/A:1 #2/B:1 #3/B:1
46 atoms, 43 bonds, 3 residues, 3 models selected
> select #1/A:1-279 #2/B:1-279 #3/B:1-279
10649 atoms, 10817 bonds, 837 residues, 3 models selected
1 [ID: 1] region 3 chains [1-279] RMSD: 67.500
> hide sel & #2-3 cartoons
> select clear
> matchmaker #3/B to #2/B pairing ss
Parameters
---
Chain pairing | ss
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
SYP4around269_DSB1_915a4_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2) with
SYP4around269_DSB1_915a4_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#3), sequence alignment score = 1876.8
RMSD between 11 pruned atom pairs is 1.348 angstroms; (across all 385 pairs:
39.821)
> select #2/B:358
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
290 atoms, 293 bonds, 17 residues, 1 model selected
> select add #2/B:333
314 atoms, 316 bonds, 18 residues, 1 model selected
> select up
500 atoms, 502 bonds, 30 residues, 1 model selected
> select add #2/B:343
524 atoms, 525 bonds, 31 residues, 1 model selected
> select up
565 atoms, 567 bonds, 33 residues, 1 model selected
> select add #2/B:320
589 atoms, 590 bonds, 34 residues, 1 model selected
> select up
795 atoms, 799 bonds, 45 residues, 1 model selected
> matchmaker #3/B to #2/B & sel pairing ss
Parameters
---
Chain pairing | ss
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
SYP4around269_DSB1_915a4_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2) with
SYP4around269_DSB1_915a4_unrelaxed_rank_002_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain B (#3), sequence alignment score = 238.4
RMSD between 35 pruned atom pairs is 0.831 angstroms; (across all 45 pairs:
1.745)
> select clear
Drag select of 26 residues
> select up
1832 atoms, 1856 bonds, 159 residues, 2 models selected
> select up
2661 atoms, 2691 bonds, 228 residues, 2 models selected
> rainbow sel
> select clear
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [13] RMSD: 5.006
> select #2/A:12 #3/A:12
35 atoms, 33 bonds, 2 residues, 2 models selected
> select #2/A:12 #3/A:12
35 atoms, 33 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [12] RMSD: 8.601
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [13] RMSD: 5.006
> select #2/A:15 #3/A:15
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #2/A:14-15 #3/A:14-15
58 atoms, 58 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [14-15] RMSD: 4.154
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [13] RMSD: 5.006
> select #2/A:14-15 #3/A:14-15
58 atoms, 58 bonds, 4 residues, 2 models selected
> select #2/A:14-15 #3/A:14-15
58 atoms, 58 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [14-15] RMSD: 4.154
> select #2/A:12-13 #3/A:12-13
52 atoms, 50 bonds, 4 residues, 2 models selected
> select #2/A:12-13 #3/A:12-13
52 atoms, 50 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [12-13] RMSD: 7.037
> select #2/A:14-15 #3/A:14-15
58 atoms, 58 bonds, 4 residues, 2 models selected
> select #2/A:14-15 #3/A:14-15
58 atoms, 58 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [14-15] RMSD: 4.154
> select #2/A:56 #3/A:56
24 atoms, 22 bonds, 2 residues, 2 models selected
> select #2/A:56-57 #3/A:56-57
45 atoms, 45 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [56-57] RMSD: 23.719
> select #2/A:14 #3/A:14
31 atoms, 31 bonds, 2 residues, 2 models selected
> select #2/A:14 #3/A:14
31 atoms, 31 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [14] RMSD: 5.729
> view sel
> cofr sel
> select ~sel & ##selected
11614 atoms, 11788 bonds, 996 residues, 2 models selected
> select ~sel & ##selected
31 atoms, 31 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [13] RMSD: 5.006
> select #2/A:12 #3/A:12
35 atoms, 33 bonds, 2 residues, 2 models selected
> select #2/A:12 #3/A:12
35 atoms, 33 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [12] RMSD: 8.601
> select #2/A:11 #3/A:11
20 atoms, 18 bonds, 2 residues, 2 models selected
> select #2/A:11-12 #3/A:11-12
55 atoms, 53 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [11-12] RMSD: 9.540
> select #2/A:18-19 #3/A:18-19
42 atoms, 40 bonds, 4 residues, 2 models selected
> select #2/A:18-19 #3/A:18-19
42 atoms, 40 bonds, 4 residues, 2 models selected
2 [ID: 2] region 2 chains [18-19] RMSD: 8.301
> select #2/A:16 #3/A:16
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #2/A:16 #3/A:16
27 atoms, 25 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [16] RMSD: 3.260
> select #2/A:15 #3/A:15
27 atoms, 25 bonds, 2 residues, 2 models selected
> select #2/A:15 #3/A:15
27 atoms, 25 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [15] RMSD: 1.302
> select #2/A:14 #3/A:14
31 atoms, 31 bonds, 2 residues, 2 models selected
> select #2/A:14 #3/A:14
31 atoms, 31 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [14] RMSD: 5.729
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #2/A:13 #3/A:13
17 atoms, 15 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [13] RMSD: 5.006
> select clear
> view
> close
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_3_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_2_seed_000.pdb
#3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb
#4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui mousemode right "translate selected models"
Drag select of 3 residues
> view matrix models #1,1,0,0,59.946,0,1,0,-25.982,0,0,1,-81.352
Drag select of 9 residues
> view matrix models #2,1,0,0,3.3686,0,1,0,-50.205,0,0,1,-68.221
Drag select of 4 residues
> view matrix models #5,1,0,0,54.595,0,1,0,40.738,0,0,1,10.002
Drag select of 5 residues
> view matrix models #3,1,0,0,-38.597,0,1,0,15.219,0,0,1,50.408
Drag select of 1 residues
> view matrix models #4,1,0,0,-34.148,0,1,0,-35.806,0,0,1,-19.739
> select clear
> color bychain
> select clear
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #1/A:13 #2/A:13 #3/A:13 #4/A:13 #5/A:13
35 atoms, 30 bonds, 5 residues, 5 models selected
> select #1/A:13 #2/A:13 #3/A:13 #4/A:13 #5/A:13
35 atoms, 30 bonds, 5 residues, 5 models selected
1 [ID: 1] region 5 chains [13] RMSD: 127.657
> style sel sphere
Changed 35 atom styles
> show sel atoms
> color sel red
> select clear
> close
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b/SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true select true
> reveal true
11 clashes
Drag select of 2 residues
> show sel atoms
> hide sel cartoons
> ui mousemode right "bond rotation"
> torsion /A:23@HB2,CB,CA,N 148.39
> undo
> torsion /A:23@OD1,CG,CB,CA -119.85
> undo
> torsion /A:24@H /A:24@N /A:23@C /A:23@CA 54.41
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> undo
No undo action is available
> undo
No undo action is available
> close
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_DSB1_2_cterms_bcf7b/SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
SYP4around269_DSB1_2_cterms_bcf7b_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true select true
> reveal true
2 clashes
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> close
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4around269_269D_DSB1_2_cterms_46cf1/SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
Chain information for
SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color bychain
> ui tool show Clashes
> clashes interModel false intraMol false ignoreHiddenModels true select true
> reveal true
No clashes
> ui tool show H-Bonds
> hbonds color #9c48ff radius 0.125 dashes 0 interModel false intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
28 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 12 NE /B LYS 28 O /A ARG 12 HE 3.658 2.666
/A ARG 12 NE /B SER 32 OG /A ARG 12 HE 2.891 2.176
/A ARG 12 NH2 /B SER 32 OG /A ARG 12 HH22 2.782 1.904
/A SER 18 OG /C SER 32 O /A SER 18 HG 2.670 1.787
/A ARG 103 NH2 /B GLN 84 OE1 /A ARG 103 HH21 3.078 2.211
/B ARG 24 NE /A LEU 16 O /B ARG 24 HE 2.807 1.869
/B ARG 24 NH1 /A ASP 20 OD2 /B ARG 24 HH12 2.715 1.975
/B TYR 26 OH /C LEU 13 O /B TYR 26 HH 2.702 1.747
/B ARG 29 NE /C ASP 11 OD1 /B ARG 29 HE 2.768 1.925
/B ARG 29 NE /C ASP 11 OD2 /B ARG 29 HE 3.254 2.303
/B ARG 29 NH2 /C ASP 11 OD1 /B ARG 29 HH21 2.715 1.796
/B LYS 35 NZ /C ALA 14 O /B LYS 35 HZ2 3.360 2.409
/B LYS 35 NZ /C ASP 15 OD2 /B LYS 35 HZ1 2.656 1.763
/B ARG 38 NH1 /C ASP 15 O /B ARG 38 HH11 2.949 2.045
/B ARG 38 NH2 /C ASP 15 O /B ARG 38 HH22 3.242 2.421
/B ARG 44 NH1 /C GLU 60 O /B ARG 44 HH12 2.732 1.809
/B ARG 48 NH1 /C GLU 60 OE1 /B ARG 48 HH11 2.713 1.729
/B LYS 61 NZ /C GLU 29 O /B LYS 61 HZ1 2.901 2.196
/C TYR 18 OH /B ASP 14 OD1 /C TYR 18 HH 2.724 1.815
/C ARG 21 NH1 /B GLU 46 OE1 /C ARG 21 HH11 2.840 1.921
/C LYS 22 NZ /B VAL 13 O /C LYS 22 HZ1 2.850 1.905
/C LYS 22 NZ /B ASP 14 OD1 /C LYS 22 HZ3 2.673 1.808
/C LYS 26 NZ /B ASP 18 OD1 /C LYS 26 HZ2 2.673 1.745
/C ASN 30 ND2 /A THR 22 OG1 /C ASN 30 HD21 2.973 2.033
/C SER 32 OG /A THR 22 OG1 /C SER 32 HG 2.738 1.779
/C THR 43 OG1 /A ASP 11 OD2 /C THR 43 HG1 2.760 1.891
/C ARG 70 NH1 /B LEU 50 O /C ARG 70 HH12 2.896 2.047
/C ARG 70 NH2 /B LEU 50 O /C ARG 70 HH21 2.732 1.798
28 hydrogen bonds found
> select clear
Drag select of 1 residues
> select up
1230 atoms, 1242 bonds, 80 residues, 1 model selected
> select up
1770 atoms, 1785 bonds, 114 residues, 1 model selected
> hbonds color #9c48ff radius 0.125 dashes 0 interModel false intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
28 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 12 NE /B LYS 28 O /A ARG 12 HE 3.658 2.666
/A ARG 12 NE /B SER 32 OG /A ARG 12 HE 2.891 2.176
/A ARG 12 NH2 /B SER 32 OG /A ARG 12 HH22 2.782 1.904
/A SER 18 OG /C SER 32 O /A SER 18 HG 2.670 1.787
/A ARG 103 NH2 /B GLN 84 OE1 /A ARG 103 HH21 3.078 2.211
/B ARG 24 NE /A LEU 16 O /B ARG 24 HE 2.807 1.869
/B ARG 24 NH1 /A ASP 20 OD2 /B ARG 24 HH12 2.715 1.975
/B TYR 26 OH /C LEU 13 O /B TYR 26 HH 2.702 1.747
/B ARG 29 NE /C ASP 11 OD1 /B ARG 29 HE 2.768 1.925
/B ARG 29 NE /C ASP 11 OD2 /B ARG 29 HE 3.254 2.303
/B ARG 29 NH2 /C ASP 11 OD1 /B ARG 29 HH21 2.715 1.796
/B LYS 35 NZ /C ALA 14 O /B LYS 35 HZ2 3.360 2.409
/B LYS 35 NZ /C ASP 15 OD2 /B LYS 35 HZ1 2.656 1.763
/B ARG 38 NH1 /C ASP 15 O /B ARG 38 HH11 2.949 2.045
/B ARG 38 NH2 /C ASP 15 O /B ARG 38 HH22 3.242 2.421
/B ARG 44 NH1 /C GLU 60 O /B ARG 44 HH12 2.732 1.809
/B ARG 48 NH1 /C GLU 60 OE1 /B ARG 48 HH11 2.713 1.729
/B LYS 61 NZ /C GLU 29 O /B LYS 61 HZ1 2.901 2.196
/C TYR 18 OH /B ASP 14 OD1 /C TYR 18 HH 2.724 1.815
/C ARG 21 NH1 /B GLU 46 OE1 /C ARG 21 HH11 2.840 1.921
/C LYS 22 NZ /B VAL 13 O /C LYS 22 HZ1 2.850 1.905
/C LYS 22 NZ /B ASP 14 OD1 /C LYS 22 HZ3 2.673 1.808
/C LYS 26 NZ /B ASP 18 OD1 /C LYS 26 HZ2 2.673 1.745
/C ASN 30 ND2 /A THR 22 OG1 /C ASN 30 HD21 2.973 2.033
/C SER 32 OG /A THR 22 OG1 /C SER 32 HG 2.738 1.779
/C THR 43 OG1 /A ASP 11 OD2 /C THR 43 HG1 2.760 1.891
/C ARG 70 NH1 /B LEU 50 O /C ARG 70 HH12 2.896 2.047
/C ARG 70 NH2 /B LEU 50 O /C ARG 70 HH21 2.732 1.798
28 hydrogen bonds found
> color sel red
> select clear
> hide atoms
> close #1.2
> close #1.1
> select clear
> color bychain
Drag select of 2 residues
> select up
1230 atoms, 1242 bonds, 80 residues, 1 model selected
> select up
1770 atoms, 1785 bonds, 114 residues, 1 model selected
> hbonds sel color #9c48ff radius 0.125 dashes 0 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 12 NE /B LYS 28 O /A ARG 12 HE 3.658 2.666
/A ARG 12 NE /B SER 32 OG /A ARG 12 HE 2.891 2.176
/A ARG 12 NH2 /B SER 32 OG /A ARG 12 HH22 2.782 1.904
/A SER 18 OG /C SER 32 O /A SER 18 HG 2.670 1.787
/A ARG 103 NH2 /B GLN 84 OE1 /A ARG 103 HH21 3.078 2.211
/B ARG 24 NE /A LEU 16 O /B ARG 24 HE 2.807 1.869
/B ARG 24 NH1 /A ASP 20 OD2 /B ARG 24 HH12 2.715 1.975
/C ASN 30 ND2 /A THR 22 OG1 /C ASN 30 HD21 2.973 2.033
/C SER 32 OG /A THR 22 OG1 /C SER 32 HG 2.738 1.779
/C THR 43 OG1 /A ASP 11 OD2 /C THR 43 HG1 2.760 1.891
10 hydrogen bonds found
> select /A:28
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 3 residues, 1 model selected
> select up
1770 atoms, 1785 bonds, 114 residues, 1 model selected
Drag select of 5 atoms, 4 residues, 4 bonds
> select subtract /A:103
1701 atoms, 1760 bonds, 110 residues, 1 model selected
> select subtract /A:105
1689 atoms, 1747 bonds, 109 residues, 1 model selected
Drag select of 7 residues
Drag select of 2 residues
Drag select of 61 residues
> hbonds sel color #9c48ff radius 0.125 dashes 0 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/A ARG 12 NE /B LYS 28 O /A ARG 12 HE 3.658 2.666
/A ARG 12 NE /B SER 32 OG /A ARG 12 HE 2.891 2.176
/A ARG 12 NH2 /B SER 32 OG /A ARG 12 HH22 2.782 1.904
/A SER 18 OG /C SER 32 O /A SER 18 HG 2.670 1.787
/B ARG 24 NE /A LEU 16 O /B ARG 24 HE 2.807 1.869
/B ARG 24 NH1 /A ASP 20 OD2 /B ARG 24 HH12 2.715 1.975
/C ASN 30 ND2 /A THR 22 OG1 /C ASN 30 HD21 2.973 2.033
/C SER 32 OG /A THR 22 OG1 /C SER 32 HG 2.738 1.779
/C THR 43 OG1 /A ASP 11 OD2 /C THR 43 HG1 2.760 1.891
9 hydrogen bonds found
> select clear
Drag select of 31 atoms, 12 residues, 29 bonds
> hide sel atoms
> select clear
> set bgColor white
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
> select /A:13
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:13
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:12
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:12
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:11
12 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
Drag select of 4 residues
> select up
1230 atoms, 1242 bonds, 80 residues, 1 model selected
> select up
1770 atoms, 1785 bonds, 114 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb_A
SES surface #1.2: minimum, -13.56, mean -2.09, maximum 8.35
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb_A
SES surface #1.2: minimum, -13.56, mean -2.09, maximum 8.35
Coulombic values for
SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb_B
SES surface #1.3: minimum, -12.78, mean 1.23, maximum 14.30
Coulombic values for
SYP4around269_269D_DSB1_2_cterms_46cf1_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb_C
SES surface #1.4: minimum, -16.85, mean -4.10, maximum 8.93
To also show corresponding color key, enter the above coulombic command and
add key true
> select /C:85
13 atoms, 12 bonds, 1 residue, 1 model selected
> select /C
1342 atoms, 1355 bonds, 85 residues, 1 model selected
> transparency sel 90
> select /A:4-22,27-34
432 atoms, 432 bonds, 27 residues, 1 model selected
> select clear
> select ~sel & ##selected
Nothing selected
> transparency 90
> transparency 0
> select /A:114
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A
1770 atoms, 1785 bonds, 114 residues, 1 model selected
> transparency sel 90
> select /B:90
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /B
1465 atoms, 1478 bonds, 90 residues, 1 model selected
> transparency sel 90
> select clear
> hide surfaces
> select /C:12
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
60 atoms, 59 bonds, 4 residues, 2 models selected
> select up
1342 atoms, 1355 bonds, 85 residues, 2 models selected
> ui tool show Contacts
[deleted to fit within ticket limits]
> select clear
> select #2/A:9
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
188 atoms, 187 bonds, 12 residues, 1 model selected
> select add #2/A:25
199 atoms, 197 bonds, 13 residues, 1 model selected
> select up
302 atoms, 301 bonds, 19 residues, 1 model selected
> select add #2/A:45
316 atoms, 314 bonds, 20 residues, 1 model selected
> select up
487 atoms, 485 bonds, 31 residues, 1 model selected
> close #2.1
> hide sel atoms
> select clear
> hide #2 atoms
> ui tool show Contacts
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
No atoms match given atom specifier
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
No atoms match given atom specifier
> select clear
> ui tool show H-Bonds
Drag select of 5 residues
> select up
482 atoms, 487 bonds, 32 residues, 1 model selected
> select up
1261 atoms, 1269 bonds, 81 residues, 1 model selected
> select up
4937 atoms, 4977 bonds, 311 residues, 1 model selected
> select down
1261 atoms, 1269 bonds, 81 residues, 1 model selected
> hbonds sel color #9c48ff radius 0.125 dashes 0 interModel false intraMol
> false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 NE SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HE 2.832 1.859
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 NH1 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A ASP 32 OD2 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HH11 2.694 1.895
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 2 NZ SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A GLU 6 OE1 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 2 HZ3 2.788 1.784
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C CYS 19 SG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A ASN 7 O no hydrogen 3.784 N/A
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 22 NZ SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A GLY 12 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 22 HZ2 3.365 2.674
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 26 NZ SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A LEU 14 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C LYS 26 HZ1 2.510 1.782
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C ASN 30 ND2 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A LEU 16 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C ASN 30 HD22 3.319 2.497
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C ASN 30 ND2 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A ASP 17 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C ASN 30 HD21 2.836 2.009
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C SER 32 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A GLU 18 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/C SER 32 HG 2.768 1.821
9 hydrogen bonds found
> select clear
> select #2/A:2-13,24-30,38-49
487 atoms, 485 bonds, 31 residues, 1 model selected
> select #2/A:6
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:6-32
423 atoms, 424 bonds, 27 residues, 1 model selected
> select clear
> select #2/A:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:25
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> color sel byhetero
> select clear
> select #2/A:7
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2/A:7
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2/A:11
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/C:63
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:25@OG
1 atom, 1 residue, 1 model selected
> view sel
> select #2/A:25@HG
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #2/A:25@HG P 4 geometry tetrahedral name P1 connectBack false
> resName PSE
> select #2/A:25@H11
1 atom, 1 residue, 1 model selected
> select #2/A:25@H13
1 atom, 1 residue, 1 model selected
> select add #2/A:25@H11
2 atoms, 1 residue, 1 model selected
> select add #2/A:25@H12
3 atoms, 1 residue, 1 model selected
> select clear
> select #2/A:25@H11
1 atom, 1 residue, 1 model selected
> build modify #2/A:25@H11 O 1 name O1 connectBack false
> select #2/A:25@H13
1 atom, 1 residue, 1 model selected
> build modify #2/A:25@H13 O 1 name O2 connectBack false
> select #2/A:25@H12
1 atom, 1 residue, 1 model selected
> build modify #2/A:25@H12 O 1 name O3 connectBack false
> select clear
> view
> select clear
> ui tool show Clashes
> select #2/A:41
16 atoms, 15 bonds, 1 residue, 1 model selected
> select up
185 atoms, 184 bonds, 12 residues, 1 model selected
> select up
1264 atoms, 1272 bonds, 81 residues, 1 model selected
> clashes interModel false intraMol false ignoreHiddenModels true select true
> reveal true
2 clashes
> select clear
Drag select of 2 residues
Drag select of 30 residues
> hide sel cartoons
Drag select of 29 residues
> hide sel cartoons
> select clear
Drag select of 121 atoms, 252 residues, 110 bonds, 11 pseudobonds
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PSE (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpcfbk0cu3/ante.in.mol2 -fi
mol2 -o
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpcfbk0cu3/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(PSE) ``
(PSE) `Welcome to antechamber 20.0: molecular input file processor.`
(PSE) ``
(PSE) `Info: Finished reading file
(/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpcfbk0cu3/ante.in.mol2);
atoms read (26), bonds read (25).`
(PSE) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PSE) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PSE) ``
(PSE) ``
(PSE) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PSE) `Info: Total number of electrons: 126; net charge: -2`
(PSE) ``
(PSE) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(PSE) ``
(PSE) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PSE) ``
(PSE) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PSE) ``
Charges for residue PSE determined
Coulombic values for
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_A
SES surface #2.2: minimum, -15.53, mean -1.40, maximum 8.05
Coulombic values for
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_B
SES surface #2.3: minimum, -19.93, mean 0.95, maximum 14.80
Coulombic values for
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_C
SES surface #2.4: minimum, -18.36, mean -3.85, maximum 13.97
Coulombic values for
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_D
SES surface #2.5: minimum, -16.63, mean -3.51, maximum 9.22
To also show corresponding color key, enter the above coulombic command and
add key true
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> transparency sel 90
> select clear
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
4 hydrogen bonds found
> select #2/A:25@CB
1 atom, 1 residue, 1 model selected
> select clear
> hide #!2 surfaces
> select clear
> close #4
> close #3
> select #2/A:23
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> ui mousemode right "bond rotation"
> torsion #2/A:25@P1,OG,CB,CA 52.15
> torsion #2/A:25@P1,OG,CB,CA -141.13
> select clear
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
Exactly one bond must be selected in graphics window
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 911, in
lambda trig_name, rotator, f=self._at_add_torsion: f(rotator)))
^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 515, in _at_add_torsion
self._at_update_torsion_value(rotater)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 706, in
_at_update_torsion_value
dial.setValue(10 * torsion_value)
TypeError: setValue(self, a0: int): argument 1 has unexpected type 'float'
Error processing trigger "created":
TypeError: setValue(self, a0: int): argument 1 has unexpected type 'float'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 706, in
_at_update_torsion_value
dial.setValue(10 * torsion_value)
See log for complete Python traceback.
> select clear
> hbonds #!2 reveal true
290 hydrogen bonds found
> ~hbonds
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> clashes sel interModel false intraMol false ignoreHiddenModels true select
> true reveal true
No clashes
> ui tool show Contacts
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
No atoms match given atom specifier
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
No atoms match given atom specifier
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
No atoms match given atom specifier
> select #2/A:25
14 atoms, 13 bonds, 1 residue, 1 model selected
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 6 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
2 contacts
atom1 atom2 overlap distance
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A PSE 25 O1 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B LYS 4 HD2 -0.038 2.538
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A PSE 25 O1 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B LYS 4 CD -0.303 3.503
2 contacts
> select clear
> close #1
> close
> open
> "/Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000
> (1).pdb"
Chain information for
SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000
(1).pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> color bychain
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
> close
> toolshed show
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4_region_DSB1233mer_S269Etestx_e627e_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 2/A
> select clear
> ui tool show Matchmaker
> close #2
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_testx_82e80/SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select clear
> ui tool show Matchmaker
> matchmaker #1/B to #2/B pairing ss
Parameters
---
Chain pairing | ss
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
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain B (#2) with
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#1), sequence alignment score = 434
RMSD between 41 pruned atom pairs is 0.528 angstroms; (across all 90 pairs:
13.596)
> select clear
> color bychain
Drag select of 3 residues
Drag select of 5 residues
> select up
975 atoms, 985 bonds, 65 residues, 2 models selected
> select up
2530 atoms, 2546 bonds, 162 residues, 2 models selected
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Alignment identifier is 2/A
> select clear
> select #1/A:30
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/A:30
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:30
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #1/A:30
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #2/A:30
26 atoms, 24 bonds, 2 residues, 2 models selected
> show sel atoms
> ui tool show Contacts
> contacts sel resSeparation 6 interModel false intraMol false
> ignoreHiddenModels true select true dashes 0 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 6 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
41 contacts
atom1 atom2 overlap distance
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 OE1 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HH12 0.325 1.755
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 OE1 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 CD 0.225 2.955
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HE 0.221 1.859
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CD SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HH12 0.201 2.499
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CD SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 CD 0.153 3.247
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CD SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HD2 0.147 2.553
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 HA 0.136 1.864
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 HA 0.050 2.450
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 HG2 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 NH1 0.013 2.612
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 OE1 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HD3 -0.001 2.481
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 CB -0.040 3.220
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 OE1 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 NH1 -0.054 2.759
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CG SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HH12 -0.074 2.774
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 29 CD -0.088 3.288
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 OE1 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HD2 -0.121 2.601
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CG SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 NH1 -0.123 3.448
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CD SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 NH1 -0.125 3.450
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 NE -0.127 2.832
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 HB2 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B PHE 22 HE2 -0.132 2.132
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HB3 -0.176 2.656
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 CA -0.185 2.885
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 HG2 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HH12 -0.188 2.188
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 29 HD3 -0.200 2.700
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CB SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B PHE 22 HE2 -0.203 2.903
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 CB SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B PHE 22 CE2 -0.234 3.634
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 C SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HE -0.271 2.971
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HB2 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B PHE 22 CE2 -0.273 2.973
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 CA -0.276 3.476
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 C SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B PHE 22 CE2 -0.278 3.678
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CG SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HD2 -0.291 2.991
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 CD -0.295 3.475
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 CD SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HD3 -0.300 3.000
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 CB SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 HA -0.303 3.003
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B PHE 22 CD2 -0.328 3.508
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/A GLU 30 HG2 SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #1/B ARG 29 HH11 -0.337 2.337
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HB3 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 CA -0.379 3.079
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 O SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 25 HB2 -0.382 2.862
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 CB SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 CA -0.383 3.783
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 29 CB -0.391 3.091
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 HB3 SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B TYR 26 N -0.395 3.020
SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/A SER 30 OG SYP4_region_DSB1233mer_testx_82e80_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #2/B ARG 29 HD2 -0.399 2.899
41 contacts
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/pcarlton/Library/CloudStorage/Dropbox/Downloads/SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
Chain information for
SYP4_region_DSB1233mer_S269Etestx_7e182_relaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select clear
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 32 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.33f12
Software:
System Software Overview:
System Version: macOS 12.6.6 (21G646)
Kernel Version: Darwin 21.6.0
Time since boot: 69 days 21:41
Graphics/Displays:
AMD Radeon R9 M380:
Chipset Model: AMD Radeon R9 M380
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 2 GB
Vendor: AMD (0x1002)
Device ID: 0x6640
Revision ID: 0x0080
ROM Revision: 113-C6005R-800
VBIOS Version: 113-C6005T-009
EFI Driver Version: 01.00.800
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
EV2736W:
Resolution: 1440 x 2560
UI Looks like: 1440 x 2560 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: 90
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46
ChimeraX-AtomicLibrary: 10.0.7
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: 2.10.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307112022
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1
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
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.30.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.8.1
prompt-toolkit: 3.0.39
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
pyparsing: 3.1.0
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Hi Peter,
--Eric