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Opened 15 months ago
Closed 15 months ago
#15721 closed defect (duplicate)
Crash in garbage collection
| 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-12.6.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000002032df600 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2795 in _process_keyword_arguments
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2869 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 59)
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{
"uptime" : 1100000,
"procLaunch" : "2024-08-03 08:38:06.1953 +1000",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"procStartAbsTime" : 26803394811905,
"coalitionID" : 181771,
"osVersion" : {
"train" : "macOS 12.6.1",
"build" : "21G217",
"releaseType" : "User"
},
"captureTime" : "2024-08-03 09:48:39.5264 +1000",
"incident" : "E49A9421-10FF-4F27-80EB-309FD968C4C1",
"bug_type" : "309",
"pid" : 58786,
"procExitAbsTime" : 26904992602905,
"translated" : true,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3963FDE2-4226-5C97-BDB6-0409F41D3D50","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1B4A0CC3-B743-B7C2-04B9-60B5BB2A8FBE",
"wakeTime" : 9748,
"sleepWakeUUID" : "B1C12B96-C1FE-494C-BBB4-7038A2086096",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722651447127\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc8ba6c000-7ffc8c0a8000 [ 6384K] r-x\/r-x SM=COW ...t_id=9af643c7",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"ktriageinfo" : "VM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140722651447127\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc8ba6c000-7ffc8c0a8000 [ 6384K] r-x\/r-x SM=COW ...t_id=9af643c7",
"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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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/jill/Downloads/fold_ceres_mini_borg_114kb_res_21_09_03_r3_m2_mg_32_52_near_complete_132_6mer_model_0.cif
Chain information for
fold_ceres_mini_borg_114kb_res_21_09_03_r3_m2_mg_32_52_near_complete_132_6mer_model_0.cif
#1
---
Chain | Description
A B C D E F | .
> hide atoms
> show cartoons
> open 4KFT
Summary of feedback from opening 4KFT fetched from pdb
---
note | Fetching compressed mmCIF 4kft from
http://files.rcsb.org/download/4kft.cif
4kft title:
Structure of the genome packaging NTPase B204 from Sulfolobus turreted
icosahedral virus 2 in complex with ATP-gammaS [more info...]
Chain information for 4kft #2
---
Chain | Description | UniProt
A B C D | Genome packaging NTPase B204 | D5IEZ9_9VIRU 1-204
Non-standard residues in 4kft #2
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
CL — chloride ion
FLC — citrate anion
MG — magnesium ion
ZN — zinc ion
4kft mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> ui tool show Matchmaker
> matchmaker #1 to #2
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 4kft, chain C (#2) with
fold_ceres_mini_borg_114kb_res_21_09_03_r3_m2_mg_32_52_near_complete_132_6mer_model_0.cif,
chain A (#1), sequence alignment score = 273.8
RMSD between 124 pruned atom pairs is 1.069 angstroms; (across all 191 pairs:
2.779)
> hide #1 models
> show #1 models
> hide #!2 models
> view #1 clip false
> select #2/A
1665 atoms, 1639 bonds, 8 pseudobonds, 265 residues, 3 models selected
> hide #1 models
> show #!2 models
> save /Users/jill/Desktop/Ceres_mini-B_packing_ATPase.fa
No alignments open!
> save /Users/jill/Desktop/ceres_package_ATP.fa
No alignments open!
Alignment identifier is 2/A
> save /Users/jill/Documents/Borg_multi_copy_gene_AP2/Phage-virus-
> like/Ceres_packaging_ATPase.fa
> open /Users/jill/Downloads/ROSE_SR-VP_0-2_FINAL_179.pdb
ROSE_SR-VP_0-2_FINAL_179.pdb title:
Esmfold V1 prediction for input [more info...]
Chain information for ROSE_SR-VP_0-2_FINAL_179.pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #3 to #2
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 4kft, chain C (#2) with ROSE_SR-VP_0-2_FINAL_179.pdb, chain A (#3),
sequence alignment score = 60.9
RMSD between 5 pruned atom pairs is 1.287 angstroms; (across all 137 pairs:
16.681)
> select clear
> open
> /Users/jill/Downloads/SRVP18_trench_6_60cm_scaf_214_117_86_FINAL_1281.pdb
SRVP18_trench_6_60cm_scaf_214_117_86_FINAL_1281.pdb title:
Esmfold V1 prediction for input [more info...]
Chain information for SRVP18_trench_6_60cm_scaf_214_117_86_FINAL_1281.pdb #4
---
Chain | Description
A | No description available
> hide #3 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #4 to #2
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 4kft, chain C (#2) with
SRVP18_trench_6_60cm_scaf_214_117_86_FINAL_1281.pdb, chain A (#4), sequence
alignment score = 36.3
RMSD between 13 pruned atom pairs is 1.559 angstroms; (across all 90 pairs:
18.013)
> show #!2 models
> open 6R10
Summary of feedback from opening 6R10 fetched from pdb
---
note | Fetching compressed mmCIF 6r10 from
http://files.rcsb.org/download/6r10.cif
6r10 title:
Thermus thermophilus V/A-type ATPase/synthase, rotational state 1R [more
info...]
Chain information for 6r10 #5
---
Chain | Description | UniProt
A B C | V-type ATP synthase alpha chain | VATA_THET8 1-578
D E F | V-type ATP synthase beta chain | VATB_THET8 1-478
G | V-type ATP synthase subunit D | VATD_THET8 1-223
H | V-type ATP synthase subunit F | VATF_THET8 1-104
I K | V-type ATP synthase, subunit (VAPC-THERM) | Q5SIT5_THET8 1-120
J L | V-type ATP synthase subunit E | VATE_THET8 1-188
M | V-type ATP synthase subunit C | VATC_THET8 1-323
N | V-type ATP synthase subunit I | Q5SIT6_THET8 1-652
O P Q R S T U V W X Y Z | V-type ATP synthase, subunit K | Q5SIT7_THET8 -18-80
Non-standard residues in 6r10 #5
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> close #1,3-4#2
> hide atoms
> show cartoons
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/SKY_pdb/SRVP18_hole-7m-from-
> trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_639_SKY_Borg_SRVP18_hole-7m-from-
> trench_1_80cm_complete_SRVP18_hole-7m-from-
> trench_1_80cm___429525___429770___-1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_639_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___429525___429770___-1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#1
---
Chain | Description
A | No description available
> color #1 #d7bc09ff
> ui tool show Matchmaker
> matchmaker #1 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 6r10, chain O (#5) with SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_639_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___429525___429770___-1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#1), sequence alignment score = 220.2
RMSD between 71 pruned atom pairs is 0.757 angstroms; (across all 73 pairs:
0.916)
> close #5
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/SKY_pdb/SRVP18_hole-7m-from-
> trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_76_SKY_Borg_SRVP18_hole-7m-from-
> trench_1_80cm_complete_SRVP18_hole-7m-from-
> trench_1_80cm___33844___34023___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
Chain information for SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_76_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___33844___34023___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#2
---
Chain | Description
A | No description available
> hide #1 models
> view clip false
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/SKY_pdb/SRVP18_hole-7m-from-
> trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_124_SKY_Borg_SRVP18_hole-7m-from-
> trench_1_80cm_complete_SRVP18_hole-7m-from-
> trench_1_80cm___59168___59935___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_124_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___59168___59935___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
> close #1-2
> open 5cot
Summary of feedback from opening 5cot fetched from pdb
---
note | Fetching compressed mmCIF 5cot from
http://files.rcsb.org/download/5cot.cif
5cot title:
Structure and mechanism of a eukaryal nick-sealing RNA ligase [more info...]
Chain information for 5cot #1
---
Chain | Description | UniProt
A | Naegleria gruberi RNA ligase | D2W2Z5_NAEGR 1-339
Non-standard residues in 5cot #1
---
AMP — adenosine monophosphate
UNX — unknown atom or ion
> ui tool show Matchmaker
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5cot, chain A (#1) with SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_124_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___59168___59935___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#3), sequence alignment score = 165.7
RMSD between 75 pruned atom pairs is 1.028 angstroms; (across all 210 pairs:
13.944)
> view clip false
> hide #3 models
> rainbow #1
> hide #1 models
> show #1 models
> show #3 models
> color #1 #4472d7ff
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/SKY_pdb/SRVP18_hole-7m-from-
> trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_158_SKY_Borg_SRVP18_hole-7m-from-
> trench_1_80cm_complete_SRVP18_hole-7m-from-
> trench_1_80cm___88902___90731___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_158_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___88902___90731___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#2
---
Chain | Description
A | No description available
> close #1,3
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_158_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___88902___90731___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A
SES surface #2.1: minimum, -42.94, mean 0.28, maximum 15.43
To also show corresponding color key, enter the above coulombic command and
add key true
> hide surfaces
> open 1yvp
1yvp title:
Ro autoantigen complexed with RNAs [more info...]
Chain information for 1yvp #1
---
Chain | Description | UniProt
A B | 60-kDa SS-A/Ro ribonucleoprotein | RO60_XENLA 1-538
C E G H | Y RNA sequence, first strand |
D F | Y RNA sequence, second strand |
Non-standard residues in 1yvp #1
---
ACT — acetate ion
MG — magnesium ion
1yvp mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1yvp, chain B (#1) with SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_158_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___88902___90731___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#2), sequence alignment score = 477.2
RMSD between 165 pruned atom pairs is 1.150 angstroms; (across all 477 pairs:
7.798)
> hide #!2 models
> rainbow #!1
> show #!2 models
> open /Users/jill/Documents/Borg_multi_copy_gene_AP2/BLACK_pdb/BLACK-SR-
> VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_130_BLACK-SR-
> VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_SR-
> VP_26_10_2019_C_40cm___71449___73065___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for BLACK-SR-
VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_130_BLACK-SR-
VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_SR-
VP_26_10_2019_C_40cm___71449___73065___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #3#!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1yvp, chain B (#1) with BLACK-SR-
VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_130_BLACK-SR-
VP_26_10_2019_C_40cm_scaffold_23_FINAL_IR_SR-
VP_26_10_2019_C_40cm___71449___73065___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb,
chain A (#3), sequence alignment score = 539.7
RMSD between 160 pruned atom pairs is 1.161 angstroms; (across all 483 pairs:
7.253)
Matchmaker 1yvp, chain B (#1) with SRVP18_hole-7m-from-
trench_1_80cm_scaf_35_ext_315-rev_6-w_terminal_repeats_158_SKY_Borg_SRVP18_hole-7m-from-
trench_1_80cm_complete_SRVP18_hole-7m-from-
trench_1_80cm___88902___90731___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#2), sequence alignment score = 477.2
RMSD between 165 pruned atom pairs is 1.150 angstroms; (across all 477 pairs:
7.798)
> color #1 #456aefff
> color #2 #ece838ff
> close #1-2
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Amber/FINAL_Amber_1.2m-terminal-
> inv-repeats_43_Amber_Borg_SR-VP_9_9_2021_87_5B_1_2m_2_complete_SR-
> VP_9_9_2021_87_5B_1_2m_2___30280___31182___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
Chain information for FINAL_Amber_1.2m-terminal-inv-repeats_43_Amber_Borg_SR-
VP_9_9_2021_87_5B_1_2m_2_complete_SR-
VP_9_9_2021_87_5B_1_2m_2___30280___31182___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#1
---
Chain | Description
A | No description available
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Amber/FINAL_Amber_1.2m-terminal-
> inv-repeats_44_Amber_Borg_SR-VP_9_9_2021_87_5B_1_2m_2_complete_SR-
> VP_9_9_2021_87_5B_1_2m_2___31363___32739___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
Chain information for FINAL_Amber_1.2m-terminal-inv-repeats_44_Amber_Borg_SR-
VP_9_9_2021_87_5B_1_2m_2_complete_SR-
VP_9_9_2021_87_5B_1_2m_2___31363___32739___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#2
---
Chain | Description
A | No description available
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Amber/FINAL_Amber_1.2m-terminal-
> inv-repeats_45_Amber_Borg_SR-VP_9_9_2021_87_5B_1_2m_2_complete_SR-
> VP_9_9_2021_87_5B_1_2m_2___32982___33185___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
Chain information for FINAL_Amber_1.2m-terminal-inv-repeats_45_Amber_Borg_SR-
VP_9_9_2021_87_5B_1_2m_2_complete_SR-
VP_9_9_2021_87_5B_1_2m_2___32982___33185___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#4
---
Chain | Description
A | No description available
> open
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Amber/FINAL_Amber_1.2m-terminal-
> inv-repeats_46_Amber_Borg_SR-VP_9_9_2021_87_5B_1_2m_2_complete_SR-
> VP_9_9_2021_87_5B_1_2m_2___33208___34542___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for FINAL_Amber_1.2m-terminal-inv-repeats_46_Amber_Borg_SR-
VP_9_9_2021_87_5B_1_2m_2_complete_SR-
VP_9_9_2021_87_5B_1_2m_2___33208___34542___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#5
---
Chain | Description
A | No description available
> close #3
> hide #1 models
> hide #2 models
> hide #5 models
> close #4
> open 1eyk
Summary of feedback from opening 1eyk fetched from pdb
---
note | Fetching compressed mmCIF 1eyk from
http://files.rcsb.org/download/1eyk.cif
1eyk title:
Fructose-1,6-bisphosphatase complex with amp, zinc, fructose-6-phosphate and
phosphate (T-state) [more info...]
Chain information for 1eyk #3
---
Chain | Description | UniProt
A B | FRUCTOSE-1,6-BISPHOSPHATASE | F16P_PIG 1-337
Non-standard residues in 1eyk #3
---
AMP — adenosine monophosphate
F6P — 6-O-phosphono-beta-D-fructofuranose (FRUCTOSE-6-PHOSPHATE;
6-O-phosphono-beta-D-fructose; 6-O-phosphono-D-fructose; 6-O-phosphono-
fructose)
PO4 — phosphate ion
ZN — zinc ion
1eyk mmCIF Assemblies
---
1| author_and_software_defined_assembly
> show #5 models
> hide #5 models
> show #1 models
> view #5 clip false
No displayed objects specified.
> view
> ui tool show Matchmaker
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
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: MacBookPro18,2
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 10
L2 Cache: 20 MB
Memory: 64 GB
Software:
System Software Overview:
System Version: macOS 12.6.1 (21G217)
Kernel Version: Darwin 21.6.0
Time since boot: 39 days 13:25
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
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: 1.7.1
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: 2.6.1
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: 1.5.14
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: 1.0.4
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: 1.12.4
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: 1.33.3
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: 0.2.1
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: 4.47.2
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: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
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: 10.2.0
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: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
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: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 15 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 |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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