Crash in "build join peptide" (Residue::connects_to())

[chimerax-bug-report@…]

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.
{"app_name":"ChimeraX","timestamp":"2024-10-24 13:35:42.00 +0200","app_version":"1.7.1","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.4 (22F66)","roots_installed":0,"name":"ChimeraX","incident_id":"0578C160-E446-4DDF-99DD-044DC9DC05B0"}
{
  "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