![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#14835 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-14.4-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" : 430000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1557841245,
"deployVersion" : 210,
"modelCode" : "iMac21,1",
"coalitionID" : 587,
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"train" : "macOS 14.4",
"build" : "23E214",
"releaseType" : "User"
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"captureTime" : "2024-03-22 18:43:46.2089 +0100",
"codeSigningMonitor" : 1,
"incident" : "72E9BEA8-3341-47F5-BC7F-AD8C05A8107F",
"pid" : 80624,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-21 18:50:06.0902 +0100",
"procStartAbsTime" : 8459529298240,
"procExitAbsTime" : 10524040666024,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C401F719-AD1B-57B5-9817-74A5703238AF",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"codeSigningValidationCategory" : 6,
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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 6N7X format mmcif fromDatabase pdb
6n7x title:
S. cerevisiae U1 snRNP [more info...]
Chain information for 6n7x #1
---
Chain | Description | UniProt
A | U1 small nuclear ribonucleoprotein 70 kDa homolog | RU17_YEAST 1-300
B | U1 small nuclear ribonucleoprotein C | RU1C_YEAST 1-231
C | U1 small nuclear ribonucleoprotein A | RU1A_YEAST 1-298
D | U1 small nuclear ribonucleoprotein component PRP42 | PRP42_YEAST 1-544
E | Pre-mRNA-processing factor 39 | PRP39_YEAST 26-629
F | Protein NAM8 | NAM8_YEAST 1-523
G | 56 kDa U1 small nuclear ribonucleoprotein component | SNU56_YEAST 1-492
H | U1 small nuclear ribonucleoprotein component SNU71 | SNU71_YEAST 1-620
K | Small nuclear ribonucleoprotein-associated protein B | RSMB_YEAST 1-196
L | Small nuclear ribonucleoprotein Sm D1 | SMD1_YEAST 1-146
M | Small nuclear ribonucleoprotein Sm D2 | SMD2_YEAST 1-110
N | Small nuclear ribonucleoprotein Sm D3 | SMD3_YEAST 1-101
O | Small nuclear ribonucleoprotein E | RUXE_YEAST 1-94
P | Small nuclear ribonucleoprotein F | RUXF_YEAST 1-86
Q | Small nuclear ribonucleoprotein G | RUXG_YEAST 1-77
R | U1 snRNA |
> hide #1/all atoms
> hide all atoms
> show 1/b s
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1/b surfaces
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A LEU 47
/A GLU 61
/A PRO 94
/A ASN 95
/A VAL 96
/A ASP 97
/A PRO 98
/A HIS 99
/A ILE 100
/A LYS 101
/A ASP 102
/A THR 103
/A ASP 104
/A PRO 105
/A TYR 106
/A ARG 107
/A THR 108
/A ILE 109
/A PHE 110
/A ILE 111
/A ARG 113
/A LEU 114
/A PRO 115
/A TYR 116
/A ASP 117
/A LEU 118
/A ASP 119
/A GLU 120
/A ILE 121
/A GLU 122
/A LEU 123
/A GLN 124
/A LYS 125
/A TYR 126
/A PHE 127
/A VAL 128
/A LYS 129
/A PHE 130
/A GLU 132
/A ILE 133
/A GLU 134
/A LYS 135
/A ILE 136
/A ARG 137
/A ILE 138
/A VAL 139
/A LYS 140
/A ASP 141
/A LYS 142
/A ILE 143
/A THR 144
/A GLN 145
/A LYS 146
/A SER 147
/A LYS 148
/A TYR 150
/A PHE 152
/A ILE 153
/A VAL 154
/A PHE 155
/A LYS 156
/A ASP 157
/A PRO 158
/A ILE 159
/A SER 160
/A SER 161
/A LYS 162
/A MET 163
/A PHE 165
/A LYS 166
/A GLU 167
/A ILE 168
/A VAL 170
/A HIS 171
/A ARG 172
/A ILE 174
/A GLN 175
/A ILE 176
/A LYS 177
/A ASP 178
/A ARG 179
/A ILE 180
/A CYS 181
/A ILE 182
/A VAL 183
/A ASP 184
/A ILE 185
/A GLU 186
/A ARG 187
/B ARG 21
/B LYS 48
/B LYS 58
/B CYS 77
/B MET 92
/B ASP 126
/B ASP 157
/B GLU 158
/B GLU 161
/B GLU 175
/B LYS 189
/C ASN 31
/C ASN 44
/C LYS 45
/C GLU 64
/C MET 73
/C GLN 76
/D LYS 205
/D LYS 231
/D MET 242
/D LYS 324
/D MET 336
/D LYS 343
/D GLU 346
/D GLU 360
/D GLU 369
/D LYS 370
/D GLU 380
/D ASP 383
/D ASP 384
/D LYS 395
/D ARG 406
/D LYS 418
/D GLU 419
/D LYS 426
/D CYS 430
/D LYS 431
/D LYS 434
/D LYS 450
/D GLU 454
/D GLU 457
/D CYS 483
/D LYS 497
/D ARG 498
/D LYS 511
/D ASP 534
/D LEU 536
/D MET 539
/E LEU 44
/E ARG 45
/E LEU 47
/E ASP 48
/E THR 49
/E GLN 50
/E PHE 51
/E LEU 52
/E GLN 53
/E ASP 54
/E ASN 55
/E THR 56
/E LEU 58
/E VAL 59
/E GLN 60
/E TYR 62
/E ARG 63
/E LEU 65
/E ASP 66
/E TRP 67
/E SER 68
/E ASP 69
/E ILE 70
/E SER 71
/E SER 72
/E LEU 73
/E THR 74
/E GLN 75
/E MET 76
/E VAL 77
/E ASP 78
/E VAL 79
/E ILE 80
/E GLU 81
/E GLN 82
/E THR 83
/E VAL 84
/E VAL 85
/E LYS 86
/E TYR 87
/E ASN 89
/E PRO 90
/E ASN 91
/E ASP 92
/E SER 93
/E ILE 94
/E LYS 95
/E LEU 96
/E LEU 98
/E GLU 99
/E THR 100
/E ILE 101
/E LEU 102
/E TRP 103
/E GLN 104
/E ILE 105
/E LEU 106
/E ARG 107
/E LYS 108
/E TYR 109
/E PRO 110
/E LEU 111
/E LEU 112
/E PHE 113
/E PHE 115
/E TRP 116
/E LYS 117
/E ARG 118
/E PHE 119
/E THR 121
/E ILE 122
/E GLU 123
/E TYR 124
/E GLN 125
/E LEU 126
/E PHE 127
/E LEU 129
/E LYS 130
/E LYS 131
/E SER 132
/E ILE 133
/E VAL 135
/E LEU 136
/E THR 138
/E SER 139
/E VAL 140
/E LYS 141
/E TRP 142
/E PHE 143
/E PRO 144
/E THR 145
/E SER 146
/E LEU 147
/E GLU 148
/E LEU 149
/E TRP 150
/E CYS 151
/E ASP 152
/E TYR 153
/E LEU 154
/E ASN 155
/E VAL 156
/E LEU 157
/E CYS 158
/E VAL 159
/E ASN 160
/E ASN 161
/E PRO 162
/E ASN 163
/E GLU 164
/E THR 165
/E ASP 166
/E PHE 167
/E ILE 168
/E ARG 169
/E ASN 170
/E ASN 171
/E PHE 172
/E GLU 173
/E ILE 174
/E LYS 176
/E ASP 177
/E LEU 178
/E ILE 179
/E LYS 181
/E GLN 182
/E PHE 183
/E LEU 184
/E SER 185
/E HIS 186
/E PRO 187
/E PHE 188
/E TRP 189
/E ASP 190
/E LYS 191
/E PHE 192
/E ILE 193
/E GLU 194
/E PHE 195
/E GLU 196
/E VAL 197
/E GLN 199
/E LYS 200
/E ASN 201
/E TRP 202
/E HIS 203
/E ASN 204
/E VAL 205
/E GLN 206
/E ARG 207
/E ILE 208
/E TYR 209
/E GLU 210
/E TYR 211
/E ILE 212
/E ILE 213
/E GLU 214
/E VAL 215
/E PRO 216
/E LEU 217
/E HIS 218
/E GLN 219
/E TYR 220
/E ARG 222
/E PHE 223
/E PHE 224
/E THR 225
/E SER 226
/E TYR 227
/E LYS 228
/E LYS 229
/E PHE 230
/E LEU 231
/E ASN 232
/E GLU 233
/E LYS 234
/E ASN 235
/E LEU 236
/E LYS 237
/E THR 238
/E THR 239
/E ARG 240
/E ASN 241
/E ILE 242
/E ASP 243
/E ILE 244
/E VAL 245
/E LEU 246
/E ARG 247
/E LYS 248
/E THR 249
/E GLN 250
/E THR 251
/E THR 252
/E VAL 253
/E ASN 254
/E GLU 255
/E ILE 256
/E TRP 257
/E GLN 258
/E PHE 259
/E GLU 260
/E SER 261
/E LYS 262
/E ILE 263
/E LYS 264
/E GLN 265
/E PRO 266
/E PHE 267
/E PHE 268
/E ASN 269
/E LEU 270
/E GLN 272
/E VAL 273
/E LEU 274
/E ASN 275
/E ASP 276
/E ASP 277
/E LEU 278
/E GLU 279
/E ASN 280
/E TRP 281
/E SER 282
/E ARG 283
/E TYR 284
/E LEU 285
/E GLU 290
/E MET 294
/E MET 295
/E LYS 298
/E LYS 302
/E LYS 303
/E LYS 316
/E ASN 318
/E LYS 326
/E LEU 328
/E ARG 329
/E ASP 331
/E ARG 334
/E LYS 339
/E ARG 341
/E LEU 346
/E PHE 347
/E HIS 379
/E LYS 401
/E TYR 410
/E ASN 413
/E LYS 418
/E LYS 428
/E ASN 429
/E LYS 446
/E GLN 450
/E LEU 457
/E LYS 460
/E ASN 461
/E LYS 465
/E GLU 478
/E LYS 479
/E LYS 486
/E GLU 493
/E THR 502
/E GLU 526
/E ASP 536
/E GLU 567
/E GLU 570
/E GLN 613
/E GLU 627
/F ASN 289
/F HIS 290
/F MET 291
/F LYS 343
/F ASP 357
/F GLN 493
/G LYS 49
/G THR 57
/G LYS 58
/G ASN 60
/G ASP 78
/G ASP 83
/G GLU 84
/G MET 86
/G GLU 88
/G LYS 91
/G GLN 103
/G ASN 121
/G GLU 145
/G ARG 150
/G LYS 153
/K ASP 99
/K LYS 131
/K LYS 132
/L LYS 2
/L ARG 51
/M ARG 15
/M GLU 17
/M GLU 19
/M GLU 20
/M GLU 22
/M GLU 23
/M GLU 25
/M LYS 27
/M ASP 36
/M GLU 74
/M LYS 80
/M THR 107
/N GLU 13
/N GLU 37
/N MET 40
/N ARG 65
/N MET 92
/O LEU 21
/O PHE 32
/O GLU 33
/O ARG 38
/O LYS 42
/O ILE 43
/O ASP 47
/O GLU 48
/O ILE 54
/O ASP 55
/O GLU 56
/O GLU 59
/O LEU 77
/O ILE 80
/O ASP 85
/P LEU 22
/P GLU 37
/P ASP 46
/P GLU 55
/P GLU 57
/P GLU 58
/P VAL 60
/P THR 67
/P GLU 70
/P ASN 77
/P GLU 83
/Q LYS 8
/Q LYS 9
/Q ASN 37
/Q ASP 41
/Q ASP 42
/Q MET 44
/Q GLU 49
/Q ARG 64
/Q SER 70
/Q ASP 75
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6n7x_A SES surface #1.4: minimum, -14.72, mean 0.27,
maximum 15.37
Coulombic values for 6n7x_B SES surface #1.3: minimum, -9.00, mean 2.69,
maximum 16.63
Coulombic values for 6n7x_C SES surface #1.5: minimum, -17.08, mean 3.32,
maximum 17.72
Coulombic values for 6n7x_D SES surface #1.6: minimum, -19.52, mean -1.04,
maximum 17.71
Coulombic values for 6n7x_E SES surface #1.7: minimum, -19.94, mean -2.21,
maximum 15.25
Coulombic values for 6n7x_F SES surface #1.8: minimum, -16.69, mean -0.76,
maximum 9.37
Coulombic values for 6n7x_G SES surface #1.9: minimum, -22.70, mean 0.24,
maximum 14.59
Coulombic values for 6n7x_H SES surface #1.10: minimum, -10.32, mean 0.68,
maximum 13.32
Coulombic values for 6n7x_K SES surface #1.11: minimum, -9.28, mean 3.32,
maximum 17.63
Coulombic values for 6n7x_L SES surface #1.12: minimum, -10.66, mean 0.77,
maximum 11.56
Coulombic values for 6n7x_M SES surface #1.13: minimum, -6.70, mean 2.73,
maximum 12.22
Coulombic values for 6n7x_N SES surface #1.14: minimum, -12.07, mean 0.35,
maximum 10.54
Coulombic values for 6n7x_O SES surface #1.15: minimum, -5.88, mean 0.36,
maximum 8.63
Coulombic values for 6n7x_P SES surface #1.16: minimum, -4.44, mean 3.87,
maximum 15.40
Coulombic values for 6n7x_Q SES surface #1.17: minimum, -10.57, mean -1.31,
maximum 7.74
Coulombic values for 6n7x_R SES surface #1.18: minimum, -53.65, mean -28.70,
maximum -7.54
To also show corresponding color key, enter the above coulombic command and
add key true
> hide all surfaces
> show #1/b surfaces
> open "/Users/meliopou/Desktop/AF
> models/U1C_78b4d/U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb"
Chain information for
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2
---
Chain | Description
A | No description available
> ui mousemode right "translate selected models"
> select add #2
1524 atoms, 1553 bonds, 194 residues, 1 model selected
> view matrix models #2,1,0,0,218.71,0,1,0,133.36,0,0,1,57.713
> view matrix models #2,1,0,0,233.24,0,1,0,147.94,0,0,1,148.82
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb_A SES surface
#2.1: minimum, -15.08, mean 1.14, maximum 18.75
To also show corresponding color key, enter the above coulombic command and
add key true
> open "/Users/meliopou/Desktop/AF
> models/U1C_78b4d/U1C_78b4d_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb"
Chain information for
U1C_78b4d_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
> select subtract #2
1 model selected
> select add #3
1524 atoms, 1553 bonds, 194 residues, 1 model selected
> view matrix models #3,1,0,0,168.2,0,1,0,218.98,0,0,1,120.28
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
U1C_78b4d_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000.pdb_A SES surface
#3.1: minimum, -14.54, mean 1.19, maximum 17.08
To also show corresponding color key, enter the above coulombic command and
add key true
> open "/Users/meliopou/Desktop/AF
> models/U1C_78b4d/U1C_78b4d_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb"
Chain information for
U1C_78b4d_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb #4
---
Chain | Description
A | No description available
> select subtract #3
1 model selected
> select add #4
1524 atoms, 1553 bonds, 194 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
U1C_78b4d_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000.pdb_A SES surface
#4.1: minimum, -15.68, mean 1.40, maximum 17.09
To also show corresponding color key, enter the above coulombic command and
add key true
> view matrix models #4,1,0,0,34.766,0,1,0,53.45,0,0,1,75.481
> show #1/R atoms
> hide #1/b surfaces
> show #1/b cartoons
> hide #2 surfaces
> mmaker #2:1-20 to #1/b:28-45
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 6n7x, chain B (#1) with
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 28.9
RMSD between 18 pruned atom pairs is 0.502 angstroms; (across all 18 pairs:
0.502)
> mmaker #2:1-20 to #1/b:28-45 showAlignment t
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 6n7x, chain B (#1) with
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 28.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6n7x #1/B,
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 18 pruned atom pairs is 0.502 angstroms; (across all 18 pairs:
0.502)
> show #2 surfaces
> hide #2 surfaces
> show #1/b surfaces
> hide #2/b surfaces
> hide #1/b surfaces
> show #2 surfaces
> select subtract #4
1 model selected
> select add #2
1524 atoms, 1553 bonds, 194 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.98027,0.14938,0.12945,220.66,-0.081611,-0.90233,0.42325,243.42,0.18003,0.40433,0.89672,188.42
> view matrix models
> #2,-0.67769,-0.60268,-0.42133,231.56,0.401,-0.78316,0.47525,241.93,-0.61639,0.15312,0.77241,191.66
> view matrix models
> #2,-0.022758,-0.84552,-0.53346,235.13,0.61554,-0.43231,0.65895,237.1,-0.78778,-0.31337,0.53029,198.11
> ui mousemode right "translate selected models"
> hide #2 surfaces
> mmaker #2:45-70 to #1/b:1-37
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 6n7x, chain B (#1) with
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb, chain A
(#2), sequence alignment score = 42.5
RMSD between 24 pruned atom pairs is 0.687 angstroms; (across all 26 pairs:
1.300)
> show #2 surfaces
> hide #2 surfaces
> hide #2:45-70 surfaces
> show #2:45-70 surfaces
> show #2 surfaces
> hide #1/R atoms
> show #1/R cartoons
> open
> /Users/meliopou/Desktop/Network/meliopou/af_output/u1c_znf/TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#5
---
Chain | Description
A | No description available
Associated
TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
chain A to U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 6n7x #1/B,
U1C_78b4d_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb #2/A,
TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#5/A
===== 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
> open
> /Users/meliopou/Desktop/Network/meliopou/af_output/u1c_znf/TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
Chain information for
TbU1C_ZnF_45_70_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb
#1
---
Chain | Description
A | No description available
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
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: iMac
Model Identifier: iMac21,1
Model Number: Z12X0018TFN/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4 (23E214)
Kernel Version: Darwin 23.4.0
Time since boot: 9 days, 20 hours, 12 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2723QE:
Resolution: 4608 x 2592
UI Looks like: 2304 x 1296 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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