![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16178 closed defect (can't reproduce)
Crash in "build join peptide" (Residue::connects_to())
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-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.
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{
"uptime" : 150000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 30823,
"osVersion" : {
"train" : "macOS 13.4",
"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2024-10-24 13:35:29.8449 +0200",
"incident" : "0578C160-E446-4DDF-99DD-044DC9DC05B0",
"pid" : 132,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-24 12:40:36.9876 +0200",
"procStartAbsTime" : 3577471606439,
"procExitAbsTime" : 3656496223566,
"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":"8B16F2CA-1535-5FB5-98AB-D37A08467174","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A0A9E16B-7E59-F68B-AD30-EF50843866FB",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 4509,
"sleepWakeUUID" : "F0231BA2-7523-4DAD-A277-6FAFC1223F7B",
"sip" : "enabled",
"vmRegionInfo" : "0x3c3e7669643f is not in any region. Bytes after previous region: 65757935920192 Bytes before following region: 39314144009153\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x69643c3e7669643f","rawCodes":[1,7594261110625756223],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x69643c3e7669643f -> 0x00003c3e7669643f (possible pointer authentication failure)"},
"vmregioninfo" : "0x3c3e7669643f is not in any region. Bytes after previous region: 65757935920192 Bytes before following region: 39314144009153\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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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
> ui windowfill toggle
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_0.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_1.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_2.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_3.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_4.cif
Chain information for fold_bsest_model_0.cif #1
---
Chain | Description
A | .
Chain information for fold_bsest_model_1.cif #2
---
Chain | Description
A | .
Chain information for fold_bsest_model_2.cif #3
---
Chain | Description
A | .
Chain information for fold_bsest_model_3.cif #4
---
Chain | Description
A | .
Chain information for fold_bsest_model_4.cif #5
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_1.cif,
chain A (#2), sequence alignment score = 2491.7
RMSD between 482 pruned atom pairs is 0.164 angstroms; (across all 483 pairs:
0.232)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_2.cif,
chain A (#3), sequence alignment score = 2494.7
RMSD between 481 pruned atom pairs is 0.170 angstroms; (across all 483 pairs:
0.282)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_3.cif,
chain A (#4), sequence alignment score = 2478.5
RMSD between 479 pruned atom pairs is 0.158 angstroms; (across all 483 pairs:
0.404)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_4.cif,
chain A (#5), sequence alignment score = 2488.1
RMSD between 480 pruned atom pairs is 0.238 angstroms; (across all 483 pairs:
0.353)
> select add #4
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> hide #1 models
> hide #2 models
> hide #3 models
> hide #5 models
> select add #1
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> select subtract #4
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select add #2
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> select add #4
11247 atoms, 11559 bonds, 1449 residues, 3 models selected
> select subtract #4
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> select add #3
11247 atoms, 11559 bonds, 1449 residues, 3 models selected
> select add #5
14996 atoms, 15412 bonds, 1932 residues, 4 models selected
> delete atoms #4
> delete bonds #4
> close
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_3.cif
Chain information for fold_bsest_model_3.cif #1
---
Chain | Description
A | .
> close session
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_0.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_1.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_2.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_3.cif
> /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_4.cif
Chain information for fold_bsest_model_0.cif #1
---
Chain | Description
A | .
Chain information for fold_bsest_model_1.cif #2
---
Chain | Description
A | .
Chain information for fold_bsest_model_2.cif #3
---
Chain | Description
A | .
Chain information for fold_bsest_model_3.cif #4
---
Chain | Description
A | .
Chain information for fold_bsest_model_4.cif #5
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #2-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_1.cif,
chain A (#2), sequence alignment score = 2491.7
RMSD between 482 pruned atom pairs is 0.164 angstroms; (across all 483 pairs:
0.232)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_2.cif,
chain A (#3), sequence alignment score = 2494.7
RMSD between 481 pruned atom pairs is 0.170 angstroms; (across all 483 pairs:
0.282)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_3.cif,
chain A (#4), sequence alignment score = 2478.5
RMSD between 479 pruned atom pairs is 0.158 angstroms; (across all 483 pairs:
0.404)
Matchmaker fold_bsest_model_0.cif, chain A (#1) with fold_bsest_model_4.cif,
chain A (#5), sequence alignment score = 2488.1
RMSD between 480 pruned atom pairs is 0.238 angstroms; (across all 483 pairs:
0.353)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> select #1/A#2/A#3/A#4/A#5/A
18745 atoms, 19265 bonds, 2415 residues, 5 models selected
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> select subtract #1
14996 atoms, 15412 bonds, 1932 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> color blue
> open /Users/zalaperko/Downloads/fold_bsest/fold_bsest_model_0.cif
Chain information for fold_bsest_model_0.cif #2
---
Chain | Description
A | .
> hide #2 models
> show #2 models
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #2
Nothing selected
> ui mousemode right "translate selected models"
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> view matrix models #2,1,0,0,27.183,0,1,0,1.1584,0,0,1,-59.484
> ui mousemode right select
Drag select of 32 residues
Drag select of 25 residues
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
Drag select of 11 residues
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
Drag select of 22 residues
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.9934,0.030965,0.11048,26.82,-0.036007,0.99838,0.043943,1.0171,-0.10894,-0.047631,0.99291,-59.451
> view matrix models
> #2,0.42636,0.73387,0.52882,25.22,0.34513,-0.67237,0.65483,-0.34353,0.83612,-0.096684,-0.53996,-54.502
> view matrix models
> #2,0.34215,0.86016,0.37822,25.653,0.47496,-0.50563,0.72024,-0.60195,0.81077,-0.066794,-0.58155,-54.38
> view matrix models
> #2,-0.3848,0.88883,0.24883,26.019,0.67858,0.089683,0.72903,-0.82155,0.62567,0.44938,-0.63765,-54.386
> view matrix models
> #2,-0.8286,-0.42937,-0.35926,28.381,-0.55281,0.72891,0.40385,-0.064547,0.088465,0.53323,-0.84133,-53.793
> view matrix models
> #2,-0.45452,-0.74877,0.48245,25.826,-0.88376,0.31144,-0.34925,2.46,0.11126,-0.58511,-0.80328,-53.534
> view matrix models
> #2,-0.88501,0.43646,-0.16206,27.456,0.19579,0.03308,-0.98009,4.6192,-0.42241,-0.89912,-0.11473,-55.648
> view matrix models
> #2,-0.45914,0.58968,-0.66443,29.027,0.54931,-0.39935,-0.73401,3.9997,-0.69817,-0.70199,-0.14056,-55.647
> view matrix models
> #2,-0.63815,0.38785,-0.66508,29.088,0.3213,-0.65087,-0.68785,3.9264,-0.69966,-0.65265,0.29074,-57.038
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.63815,0.38785,-0.66508,-28.157,0.3213,-0.65087,-0.68785,-131.76,-0.69966,-0.65265,0.29074,-18.263
> select add #1
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> select subtract #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> view matrix models #1,1,0,0,0.096939,0,1,0,-0.90979,0,0,1,-34.979
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.30052,-0.65198,0.69614,-1.9356,0.75857,0.60582,0.23991,-1.5021,-0.57815,0.45597,0.67663,-34.133
> view matrix models
> #1,0.85377,0.0046926,0.52063,-1.571,-0.22372,0.90625,0.3587,-2.0323,-0.47013,-0.42272,0.77478,-34.142
> view matrix models
> #1,0.49497,-0.44328,0.74733,-2.1596,0.79799,0.57224,-0.18909,-0.12174,-0.34383,0.68995,0.63698,-34.074
> open
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_3.cif
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_2.cif
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_1.cif
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_0.cif
> /Users/zalaperko/Downloads/fold_l1_sso10a_l2_dimer/fold_l1_sso10a_l2_dimer_model_4.cif
Chain information for fold_l1_sso10a_l2_dimer_model_3.cif #3
---
Chain | Description
A B | .
Chain information for fold_l1_sso10a_l2_dimer_model_2.cif #4
---
Chain | Description
A B | .
Chain information for fold_l1_sso10a_l2_dimer_model_1.cif #5
---
Chain | Description
A B | .
Chain information for fold_l1_sso10a_l2_dimer_model_0.cif #6
---
Chain | Description
A B | .
Chain information for fold_l1_sso10a_l2_dimer_model_4.cif #7
---
Chain | Description
A B | .
> ui tool show Matchmaker
> matchmaker #3-5,7 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_l1_sso10a_l2_dimer_model_0.cif, chain A (#6) with
fold_l1_sso10a_l2_dimer_model_3.cif, chain A (#3), sequence alignment score =
271.2
RMSD between 37 pruned atom pairs is 0.535 angstroms; (across all 57 pairs:
10.838)
Matchmaker fold_l1_sso10a_l2_dimer_model_0.cif, chain A (#6) with
fold_l1_sso10a_l2_dimer_model_2.cif, chain A (#4), sequence alignment score =
261.6
RMSD between 35 pruned atom pairs is 0.592 angstroms; (across all 57 pairs:
10.264)
Matchmaker fold_l1_sso10a_l2_dimer_model_0.cif, chain A (#6) with
fold_l1_sso10a_l2_dimer_model_1.cif, chain A (#5), sequence alignment score =
279
RMSD between 29 pruned atom pairs is 0.458 angstroms; (across all 57 pairs:
15.263)
Matchmaker fold_l1_sso10a_l2_dimer_model_0.cif, chain A (#6) with
fold_l1_sso10a_l2_dimer_model_4.cif, chain A (#7), sequence alignment score =
277.8
RMSD between 42 pruned atom pairs is 0.570 angstroms; (across all 57 pairs:
4.126)
> view matrix models
> #1,0.69339,-0.36419,0.62175,-1.7763,0.69856,0.55136,-0.45609,0.73107,-0.17671,0.75058,0.63672,-34.085
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.69339,-0.36419,0.62175,-38.528,0.69856,0.55136,-0.45609,25.212,-0.17671,0.75058,0.63672,-80.299
> hide #4 models
> show #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #3 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #3 models
> hide #4 models
> select add #3
4547 atoms, 4653 bonds, 597 residues, 2 models selected
> color sel yellow
> select subtract #3
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> color sel medium blue
> select add #2
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> color sel blue
> select subtract #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #4
798 atoms, 800 bonds, 114 residues, 1 model selected
> show #4 models
> show #5 models
> show #6 models
> show #7 models
> select add #5
1596 atoms, 1600 bonds, 228 residues, 2 models selected
> select add #6
2394 atoms, 2400 bonds, 342 residues, 3 models selected
> select add #7
3192 atoms, 3200 bonds, 456 residues, 4 models selected
> delete atoms sel
> delete bonds sel
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B
Alignment identifier is 1
> select #3/A-B:1
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #3/A-B:1-12
108 atoms, 106 bonds, 24 residues, 1 model selected
> color sel light gray
> select #3/A-B:57
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/A-B:46-57
140 atoms, 140 bonds, 24 residues, 1 model selected
> color sel dim gray
> select add #3
798 atoms, 800 bonds, 114 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #1
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.079004,0.03972,0.99608,-39.897,0.94412,0.32372,0.061973,23.651,-0.31999,0.94532,-0.063076,-78.143
> view matrix models
> #1,0.47458,0.24994,0.84398,-39.455,0.78484,-0.55425,-0.27719,25.021,0.3985,0.79394,-0.4592,-76.793
> view matrix models
> #1,-0.34928,0.8473,-0.4001,-35.735,0.50973,0.5301,0.67762,21.597,0.78624,0.032743,-0.61705,-76.012
> view matrix models
> #1,-0.50435,-0.43084,-0.74834,-34.2,-0.79194,0.57621,0.202,23.031,0.34417,0.69452,-0.63181,-76.212
> view matrix models
> #1,0.71019,-0.53317,-0.45974,-35.023,-0.43437,-0.84576,0.30985,23.188,-0.55404,-0.02035,-0.83224,-75.376
> view matrix models
> #1,0.85478,-0.29411,-0.42761,-35.199,-0.11553,-0.91108,0.39571,22.952,-0.50597,-0.28884,-0.81275,-75.345
> select add #2
7498 atoms, 7706 bonds, 966 residues, 2 models selected
> select subtract #1
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> view matrix models
> #2,-0.46006,0.75523,-0.46688,-28.905,-0.38943,-0.64419,-0.6583,-131.89,-0.79793,-0.12104,0.59047,-19.404
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.46006,0.75523,-0.46688,-3.5088,-0.38943,-0.64419,-0.6583,-63.523,-0.79793,-0.12104,0.59047,51.201
> view matrix models
> #2,-0.46006,0.75523,-0.46688,-2.0772,-0.38943,-0.64419,-0.6583,-67.125,-0.79793,-0.12104,0.59047,51.744
> select subtract #2
Nothing selected
> select add #2
3749 atoms, 3853 bonds, 483 residues, 1 model selected
> view matrix models
> #2,-0.46006,0.75523,-0.46688,16.955,-0.38943,-0.64419,-0.6583,-63.997,-0.79793,-0.12104,0.59047,52.154
> view matrix models
> #2,-0.46006,0.75523,-0.46688,20.394,-0.38943,-0.64419,-0.6583,-61.019,-0.79793,-0.12104,0.59047,51.91
> view matrix models
> #2,-0.46006,0.75523,-0.46688,22.89,-0.38943,-0.64419,-0.6583,-55.531,-0.79793,-0.12104,0.59047,49.119
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.46402,-0.03079,0.88529,18.894,0.88401,-0.04777,-0.46502,-56.285,0.056608,0.99838,0.0050519,50.648
> view matrix models
> #2,0.39094,-0.33569,0.85702,19.084,0.91186,0.014612,-0.41023,-56.479,0.12519,0.94186,0.31182,49.694
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.39094,-0.33569,0.85702,44.99,0.91186,0.014612,-0.41023,-26.514,0.12519,0.94186,0.31182,67.021
> view matrix models
> #2,0.39094,-0.33569,0.85702,39.226,0.91186,0.014612,-0.41023,-20.09,0.12519,0.94186,0.31182,75.734
> ui mousemode right translate
> ui tool show "Build Structure"
> select clear
> select #3/B:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #2/A:483
14 atoms, 12 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
Remapping chain ID 'A' in fold_l1_sso10a_l2_dimer_model_3.cif #3 to 'C'
> select clear
> select #2/C:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1/A:483
14 atoms, 12 bonds, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
===== 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 - 83.1
OpenGL renderer: Apple M2
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 Air
Model Identifier: Mac14,2
Model Number: MLY13CR/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 9 days, 16 hours, 40 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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 , 13 months ago
| Component: | Unassigned → Structure Editing |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in "build join peptide" (Residue::connects_to()) |
comment:2 by , 13 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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