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Opened 18 months ago
Closed 18 months ago
#15095 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-26-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
crashed during saving chimera x session file, an empty (!) file named 6kwy.cxs.1658553.tmp was on the hard drive, but the session was lost.
Fatal Python error: Segmentation fault
Thread 0x00007e85637fe640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e8563fff640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e8580ff9640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/selectors.py", line 415 in select
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e85817fa640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e8581ffb640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e85827fc640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e8582ffd640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e85837fe640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e8583fff640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e85a4ff9640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007e85a57fa640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007e8684a83b80 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2000 in save_state
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1417 in take_snapshot
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 296 in process
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 273 in discovery
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 636 in save
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 912 in save
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/lib/ucsf-chimerax/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.pdb_lib._load_libs, chimerax.map._map, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 61)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
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 /home/raim/AF-P25786-F1-model_v4.pdb
AF-P25786-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786)
[more info...]
Chain information for AF-P25786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | proteasome subunit α type-1 | PSA1_HUMAN 1-263
> lighting soft
> lighting full
> lighting simple
> set bgColor white
> style sphere
Changed 2074 atom styles
> style ball
Changed 2074 atom styles
> select add #1
2074 atoms, 2115 bonds, 263 residues, 1 model selected
> select subtract #1
Nothing selected
> save /home/raim/test.cxs
> select ::name="LEU"
192 atoms, 170 bonds, 24 residues, 1 model selected
> save /home/raim/test.cxs
> open /home/raim/test.pdb
test.pdb title:
Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786)
[more info...]
Chain information for test.pdb #2
---
Chain | Description | UniProt
A | proteasome subunit α type-1 | PSA1_HUMAN 1-263
> hide #1 models
> select add #1
2074 atoms, 2115 bonds, 263 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
1052 atoms, 1051 bonds, 263 residues, 1 model selected
> select subtract #2
Nothing selected
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
Alignment identifier is 1
> select #1/A:93 #2/A:93
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/A:93-99 #2/A:93-99
90 atoms, 90 bonds, 14 residues, 2 models selected
Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [93-99] RMSD: 0.000
> select #1/A:158 #2/A:158
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/A:158-164 #2/A:158-164
75 atoms, 73 bonds, 14 residues, 2 models selected
Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [158-164] RMSD: 0.000
> select add #1
2102 atoms, 2142 bonds, 270 residues, 2 models selected
> select subtract #1
28 atoms, 27 bonds, 7 residues, 1 model selected
> select #1/A:188 #2/A:188
11 atoms, 9 bonds, 2 residues, 2 models selected
> select #1/A:188-194 #2/A:188-194
82 atoms, 81 bonds, 14 residues, 2 models selected
Proteasome Subunit Α Type-1 [ID: 1] region 2 chains [188-194] RMSD: 0.000
> style sel & #2 sphere
Changed 28 atom styles
> style sel & #2 ball
Changed 28 atom styles
> rainbow sel & #2
> coulombic sel & #2
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
test.pdb #2/A MET 1
test.pdb #2/A PHE 2
test.pdb #2/A ARG 3
test.pdb #2/A ASN 4
test.pdb #2/A GLN 5
test.pdb #2/A TYR 6
test.pdb #2/A ASP 7
test.pdb #2/A ASN 8
test.pdb #2/A ASP 9
test.pdb #2/A VAL 10
test.pdb #2/A THR 11
test.pdb #2/A VAL 12
test.pdb #2/A TRP 13
test.pdb #2/A SER 14
test.pdb #2/A PRO 15
test.pdb #2/A GLN 16
test.pdb #2/A ARG 18
test.pdb #2/A ILE 19
test.pdb #2/A HIS 20
test.pdb #2/A GLN 21
test.pdb #2/A ILE 22
test.pdb #2/A GLU 23
test.pdb #2/A TYR 24
test.pdb #2/A ALA 25
test.pdb #2/A MET 26
test.pdb #2/A GLU 27
test.pdb #2/A ALA 28
test.pdb #2/A VAL 29
test.pdb #2/A LYS 30
test.pdb #2/A GLN 31
test.pdb #2/A SER 33
test.pdb #2/A ALA 34
test.pdb #2/A THR 35
test.pdb #2/A VAL 36
test.pdb #2/A LEU 38
test.pdb #2/A LYS 39
test.pdb #2/A SER 40
test.pdb #2/A LYS 41
test.pdb #2/A THR 42
test.pdb #2/A HIS 43
test.pdb #2/A ALA 44
test.pdb #2/A VAL 45
test.pdb #2/A LEU 46
test.pdb #2/A VAL 47
test.pdb #2/A ALA 48
test.pdb #2/A LEU 49
test.pdb #2/A LYS 50
test.pdb #2/A ARG 51
test.pdb #2/A ALA 52
test.pdb #2/A GLN 53
test.pdb #2/A SER 54
test.pdb #2/A GLU 55
test.pdb #2/A LEU 56
test.pdb #2/A ALA 57
test.pdb #2/A ALA 58
test.pdb #2/A HIS 59
test.pdb #2/A GLN 60
test.pdb #2/A LYS 61
test.pdb #2/A LYS 62
test.pdb #2/A ILE 63
test.pdb #2/A LEU 64
test.pdb #2/A HIS 65
test.pdb #2/A VAL 66
test.pdb #2/A ASP 67
test.pdb #2/A ASN 68
test.pdb #2/A HIS 69
test.pdb #2/A ILE 70
test.pdb #2/A ILE 72
test.pdb #2/A SER 73
test.pdb #2/A ILE 74
test.pdb #2/A ALA 75
test.pdb #2/A LEU 77
test.pdb #2/A THR 78
test.pdb #2/A ALA 79
test.pdb #2/A ASP 80
test.pdb #2/A ALA 81
test.pdb #2/A ARG 82
test.pdb #2/A LEU 83
test.pdb #2/A LEU 84
test.pdb #2/A CYS 85
test.pdb #2/A ASN 86
test.pdb #2/A PHE 87
test.pdb #2/A MET 88
test.pdb #2/A ARG 89
test.pdb #2/A GLN 90
test.pdb #2/A GLU 91
test.pdb #2/A CYS 92
test.pdb #2/A LEU 93
test.pdb #2/A ASP 94
test.pdb #2/A SER 95
test.pdb #2/A ARG 96
test.pdb #2/A PHE 97
test.pdb #2/A VAL 98
test.pdb #2/A PHE 99
test.pdb #2/A ASP 100
test.pdb #2/A ARG 101
test.pdb #2/A PRO 102
test.pdb #2/A LEU 103
test.pdb #2/A PRO 104
test.pdb #2/A VAL 105
test.pdb #2/A SER 106
test.pdb #2/A ARG 107
test.pdb #2/A LEU 108
test.pdb #2/A VAL 109
test.pdb #2/A SER 110
test.pdb #2/A LEU 111
test.pdb #2/A ILE 112
test.pdb #2/A SER 114
test.pdb #2/A LYS 115
test.pdb #2/A THR 116
test.pdb #2/A GLN 117
test.pdb #2/A ILE 118
test.pdb #2/A PRO 119
test.pdb #2/A THR 120
test.pdb #2/A GLN 121
test.pdb #2/A ARG 122
test.pdb #2/A TYR 123
test.pdb #2/A ARG 125
test.pdb #2/A ARG 126
test.pdb #2/A PRO 127
test.pdb #2/A TYR 128
test.pdb #2/A VAL 130
test.pdb #2/A LEU 132
test.pdb #2/A LEU 133
test.pdb #2/A ILE 134
test.pdb #2/A ALA 135
test.pdb #2/A TYR 137
test.pdb #2/A ASP 138
test.pdb #2/A ASP 139
test.pdb #2/A MET 140
test.pdb #2/A PRO 142
test.pdb #2/A HIS 143
test.pdb #2/A ILE 144
test.pdb #2/A PHE 145
test.pdb #2/A GLN 146
test.pdb #2/A THR 147
test.pdb #2/A CYS 148
test.pdb #2/A PRO 149
test.pdb #2/A SER 150
test.pdb #2/A ALA 151
test.pdb #2/A ASN 152
test.pdb #2/A TYR 153
test.pdb #2/A PHE 154
test.pdb #2/A ASP 155
test.pdb #2/A CYS 156
test.pdb #2/A ARG 157
test.pdb #2/A ALA 158
test.pdb #2/A MET 159
test.pdb #2/A SER 160
test.pdb #2/A ILE 161
test.pdb #2/A ALA 163
test.pdb #2/A ARG 164
test.pdb #2/A SER 165
test.pdb #2/A GLN 166
test.pdb #2/A SER 167
test.pdb #2/A ALA 168
test.pdb #2/A ARG 169
test.pdb #2/A THR 170
test.pdb #2/A TYR 171
test.pdb #2/A LEU 172
test.pdb #2/A GLU 173
test.pdb #2/A ARG 174
test.pdb #2/A HIS 175
test.pdb #2/A MET 176
test.pdb #2/A SER 177
test.pdb #2/A GLU 178
test.pdb #2/A PHE 179
test.pdb #2/A MET 180
test.pdb #2/A GLU 181
test.pdb #2/A CYS 182
test.pdb #2/A ASN 183
test.pdb #2/A LEU 184
test.pdb #2/A ASN 185
test.pdb #2/A GLU 186
test.pdb #2/A LEU 187
test.pdb #2/A VAL 188
test.pdb #2/A LYS 189
test.pdb #2/A HIS 190
test.pdb #2/A LEU 192
test.pdb #2/A ARG 193
test.pdb #2/A ALA 194
test.pdb #2/A LEU 195
test.pdb #2/A ARG 196
test.pdb #2/A GLU 197
test.pdb #2/A THR 198
test.pdb #2/A LEU 199
test.pdb #2/A PRO 200
test.pdb #2/A ALA 201
test.pdb #2/A GLU 202
test.pdb #2/A GLN 203
test.pdb #2/A ASP 204
test.pdb #2/A LEU 205
test.pdb #2/A THR 206
test.pdb #2/A THR 207
test.pdb #2/A LYS 208
test.pdb #2/A ASN 209
test.pdb #2/A VAL 210
test.pdb #2/A SER 211
test.pdb #2/A ILE 212
test.pdb #2/A ILE 214
test.pdb #2/A VAL 215
test.pdb #2/A LYS 217
test.pdb #2/A ASP 218
test.pdb #2/A LEU 219
test.pdb #2/A GLU 220
test.pdb #2/A PHE 221
test.pdb #2/A THR 222
test.pdb #2/A ILE 223
test.pdb #2/A TYR 224
test.pdb #2/A ASP 225
test.pdb #2/A ASP 226
test.pdb #2/A ASP 227
test.pdb #2/A ASP 228
test.pdb #2/A VAL 229
test.pdb #2/A SER 230
test.pdb #2/A PRO 231
test.pdb #2/A PHE 232
test.pdb #2/A LEU 233
test.pdb #2/A GLU 234
test.pdb #2/A LEU 236
test.pdb #2/A GLU 237
test.pdb #2/A GLU 238
test.pdb #2/A ARG 239
test.pdb #2/A PRO 240
test.pdb #2/A GLN 241
test.pdb #2/A ARG 242
test.pdb #2/A LYS 243
test.pdb #2/A ALA 244
test.pdb #2/A GLN 245
test.pdb #2/A PRO 246
test.pdb #2/A ALA 247
test.pdb #2/A GLN 248
test.pdb #2/A PRO 249
test.pdb #2/A ALA 250
test.pdb #2/A ASP 251
test.pdb #2/A GLU 252
test.pdb #2/A PRO 253
test.pdb #2/A ALA 254
test.pdb #2/A GLU 255
test.pdb #2/A LYS 256
test.pdb #2/A ALA 257
test.pdb #2/A ASP 258
test.pdb #2/A GLU 259
test.pdb #2/A PRO 260
test.pdb #2/A MET 261
test.pdb #2/A GLU 262
test.pdb #2/A HIS 263
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean
-12.72, maximum 4.89
To also show corresponding color key, enter the above coulombic command and
add key true
> style sel & #!2 sphere
Changed 28 atom styles
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 28 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select subtract #2.1
54 atoms, 54 bonds, 7 residues, 2 models selected
> select add #2.1
1106 atoms, 54 bonds, 270 residues, 2 models selected
> hide #2.1 models
> show #2.1 models
> select subtract #2.1
54 atoms, 54 bonds, 7 residues, 2 models selected
> select ::name="SER"
160 atoms, 128 bonds, 32 residues, 2 models selected
> coulombic sel & #!2
Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean
-12.72, maximum 4.89
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1/A#2/A
3126 atoms, 3166 bonds, 526 residues, 2 models selected
> coulombic sel & #!2
Coulombic values for test.pdb_A SES surface #2.1: minimum, -36.03, mean
-12.72, maximum 4.89
To also show corresponding color key, enter the above coulombic command and
add key true
Alignment identifier is 2
> select #1/A:97-98 #2/A:97-98
26 atoms, 25 bonds, 4 residues, 2 models selected
> select #1/A:97-104 #2/A:97-104
102 atoms, 104 bonds, 16 residues, 2 models selected
Proteasome Subunit Α Type-1 [ID: 2] region 2 chains [97-104] RMSD: 0.000
> rainbow sel & #!2
> hbonds sel & #!2 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: test.pdb #2/A PRO 253 N; test.pdb #2/A PRO 260 N; test.pdb #2/A
PRO 249 N; test.pdb #2/A PRO 15 N; test.pdb #2/A PRO 104 N; test.pdb #2/A PRO
142 N; test.pdb #2/A PRO 102 N; test.pdb #2/A PRO 200 N; test.pdb #2/A PRO 149
N; test.pdb #2/A PRO 119 N; test.pdb #2/A PRO 240 N; test.pdb #2/A PRO 231 N;
test.pdb #2/A PRO 246 N; test.pdb #2/A PRO 127 N
14 hydrogen bonds found
> color sel & #!2 bypolymer
> color sel & #!2 bychain
> style sel & #!2 sphere
Changed 32 atom styles
> style sel & #!2 ball
Changed 32 atom styles
> nucleotides sel & #!2 atoms
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> nucleotides sel & #!2 fill
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> hide #3 models
> hide #3 target m
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes true
> set bgColor black
> set bgColor gray
> ui tool show "Side View"
> ui mousemode right distance
> distance #2/A:173@CA #2/A:248@O
Distance between test.pdb #2/A GLU 173 CA and GLN 248 O: 33.403Å
> save /home/raim/test.cxs
QXcbConnection: XCB error: 3 (BadWindow), sequence: 30577, resource id:
23134165, major code: 40 (TranslateCoords), minor code: 0
> show sel & #!2 surfaces
> hide sel & #!2 surfaces
> show sel & #!2 surfaces
> hide sel & #!2 surfaces
> style sel & #!2 ball
Changed 32 atom styles
> style sel & #!2 sphere
Changed 32 atom styles
> style sel & #!2 sphere
Changed 32 atom styles
> style sel & #!2 ball
Changed 32 atom styles
> style sel & #!2 sphere
Changed 32 atom styles
> style sel & #!2 ball
Changed 32 atom styles
> nucleotides sel & #!2 fill
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> mlp sel & #!2
Map values for surface "test.pdb_A SES surface": minimum -27.35, mean -15.1,
maximum -2.702
To also show corresponding color key, enter the above mlp command and add key
true
> style sel & #!2 ball
Changed 32 atom styles
> hide sel & #!2 surfaces
> hide sel & #!2 atoms
> show sel & #!2 atoms
> show sel & #!2 cartoons
> nucleotides sel & #!2 atoms
> style nucleic & sel & #!2 stick
Changed 0 atom styles
> color sel & #!2 byhetero
> color sel & #!2 bychain
> ui tool show "AlphaFold Error Plot"
> open /home/raim/test2.pdb
test2.pdb title:
Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786)
[more info...]
Chain information for test2.pdb #5
---
Chain | Description | UniProt
A | proteasome subunit α type-1 | PSA1_HUMAN 1-263
> hide #4.1 models
> hide #!4 models
> hide #2.1 models
> hide #!2 models
> help help:devel
> open 2zcp
Summary of feedback from opening 2zcp fetched from pdb
---
warning | PDB entry 2ZCP has been replaced by 3W7F
notes | Fetching compressed mmCIF 2zcp from
http://files.rcsb.org/download/2zcp.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD FPS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/FPS/FPS.cif
2zcp title:
Crystal structure of the C(30) carotenoid dehydrosqualene synthase from
Staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...]
Chain information for 2zcp #6
---
Chain | Description | UniProt
A B | Dehydrosqualene synthase | A9JQL9_STAAU 1-287
Non-standard residues in 2zcp #6
---
FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen
thiodiphosphate (farnesyl thiopyrophosphate)
MG — magnesium ion
2zcp mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
Drag select of 13 residues
> delete /b
> surface :fps sharpBoundaries false
> surface :fps sharpBoundaries falsesurface protein sharp false
Invalid "sharpBoundaries" argument: Expected true or false (or 1 or 0)
> surface :fps sharpBoundaries false
> contactArea #1.3 with #1.2 distance 3 slab -.1,0 color tan
Unknown command: measure contactArea #1.3 with #1.2 distance 3 slab -.1,0
color tan
Downloading file set_radius_to_bfactor.py
> open /home/raim/Downloads/set_radius_to_bfactor.py
executed set_radius_to_bfactor.py
> select #2-36
4721 atoms, 4596 bonds, 33 pseudobonds, 989 residues, 8 models selected
> select #2-36
4721 atoms, 4596 bonds, 33 pseudobonds, 989 residues, 8 models selected
> open /home/raim/Downloads/set_radius_to_bfactor.py
executed set_radius_to_bfactor.py
> save /home/raim/Downloads/test.png width 1014 height 717 supersample 3
> close session
> open 121p
Summary of feedback from opening 121p fetched from pdb
---
note | Fetching compressed mmCIF 121p from
http://files.rcsb.org/download/121p.cif
121p title:
Struktur und guanosintriphosphat-hydrolysemechanismus des C-terminal
verkuerzten menschlichen krebsproteins P21-H-ras [more info...]
Chain information for 121p #1
---
Chain | Description | UniProt
A | H-RAS P21 PROTEIN | RASH_HUMAN 1-166
Non-standard residues in 121p #1
---
GCP — phosphomethylphosphonic acid guanylate ester
MG — magnesium ion
121p mmCIF Assemblies
---
1| author_defined_assembly
> hide solvent
> style ligand ball
Changed 32 atom styles
> style ligand ball
Changed 32 atom styles
> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln
Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https
---
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
Downloaded 121p-consurf.aln to /home/raim/Downloads/121p-consurf.aln
Alignment identifier is 121p-consurf.aln
Associated 121p chain A to Input_pdb_SEQRES_A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln
Opened 150 sequences from 121p-consurf.aln
> color byattribute seq_conservation
1550 atoms, 363 residues, atom seq_conservation range -1.47 to 2.83
> open 1avo
Summary of feedback from opening 1avo fetched from pdb
---
note | Fetching compressed mmCIF 1avo from
http://files.rcsb.org/download/1avo.cif
1avo title:
Proteasome activator reg(α) [more info...]
Chain information for 1avo #2
---
Chain | Description | UniProt
A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63
B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242
> open 1avo
1avo title:
Proteasome activator reg(α) [more info...]
Chain information for 1avo #3
---
Chain | Description | UniProt
A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63
B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242
> close session
> open 1avo
1avo title:
Proteasome activator reg(α) [more info...]
Chain information for 1avo #1
---
Chain | Description | UniProt
A C E G I K M | 11S REGULATOR | PSME1_HUMAN 4-63
B D F H J L N | 11S REGULATOR | PSME1_HUMAN 104-242
Alignment identifier is 1
Alignment identifier is 2
> close session
> open 6kwy
Summary of feedback from opening 6kwy fetched from pdb
---
note | Fetching compressed mmCIF 6kwy from
http://files.rcsb.org/download/6kwy.cif
6kwy title:
human PA200-20S complex [more info...]
Chain information for 6kwy #1
---
Chain | Description | UniProt
A O | Proteasome subunit alpha type-2 | PSA2_HUMAN 0-233
B P | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261
C Q | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248
D R | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241
E S | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263
F T | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254
G U | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246
H V | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234
I W | Proteasome subunit beta type-3 | PSB3_HUMAN 0-204
J X | Proteasome subunit beta type-2 | PSB2_HUMAN 1-201
K Y | Proteasome subunit beta type-5 | PSB5_HUMAN -58-204
L Z | Proteasome subunit beta type-1 | PSB1_HUMAN -27-213
M a | Proteasome subunit beta type-4 | PSB4_HUMAN -44-219
N b | Proteasome subunit beta type-6 | PSB6_HUMAN -33-205
c | Proteasome activator complex subunit 4 | PSME4_HUMAN 1-1843
Non-standard residues in 6kwy #1
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
K0W —
[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy-
cyclohexyl] phosphono hydrogen phosphate
> hide cartoons
> show cartoons
> hide surfaces
> color byhetero
> color bychain
> color bypolymer
> hide surfaces
> select /E/S
3737 atoms, 3807 bonds, 478 residues, 1 model selected
> show sel cartoons
> show sel atoms
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> rainbow sel
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/E GLN 53
/E SER 54
/E GLU 55
/E LYS 208
/S PHE 2
/S ARG 3
/S GLN 53
/S ASP 218
/S GLU 238
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6kwy_E SES surface #1.2: minimum, -15.15, mean -0.41,
maximum 12.39
Coulombic values for 6kwy_S SES surface #1.3: minimum, -12.87, mean -0.28,
maximum 11.57
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color sel bychain
> mlp sel
Map values for surface "6kwy_E SES surface": minimum -29.14, mean -4.827,
maximum 22.49
Map values for surface "6kwy_S SES surface": minimum -28.74, mean -4.883,
maximum 22.05
To also show corresponding color key, enter the above mlp command and add key
true
> select
62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> show sel cartoons
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 62346 atom styles
> hide sel surfaces
> hide sel atoms
> select clear
> select /E/S
3737 atoms, 3807 bonds, 478 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
Alignment identifier is 1
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> select /E,S:166
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /E,S:166-171
100 atoms, 100 bonds, 12 residues, 1 model selected
> show sel surfaces
> select clear
> select /E,S:52
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E,S:52-69
273 atoms, 277 bonds, 36 residues, 1 model selected
> select /E,S:160-161
28 atoms, 26 bonds, 4 residues, 1 model selected
> select /E,S:156-161
88 atoms, 86 bonds, 12 residues, 1 model selected
> select /E,S:204
16 atoms, 14 bonds, 2 residues, 1 model selected
> select /E,S:204-213
140 atoms, 138 bonds, 20 residues, 1 model selected
> select /E,S:222
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /E,S:222-224
54 atoms, 54 bonds, 6 residues, 1 model selected
> select /E,S:69
20 atoms, 20 bonds, 2 residues, 1 model selected
> select /E,S:69-79
146 atoms, 146 bonds, 22 residues, 1 model selected
> coulombic sel
Coulombic values for 6kwy_E SES surface #1.2: minimum, -15.15, mean -0.41,
maximum 12.39
Coulombic values for 6kwy_S SES surface #1.3: minimum, -12.87, mean -0.28,
maximum 11.57
To also show corresponding color key, enter the above coulombic command and
add key true
> select /E:1-2/S:2
24 atoms, 23 bonds, 3 residues, 1 model selected
> select /E:1-17/S:2-17
268 atoms, 275 bonds, 33 residues, 1 model selected
Alignment identifier is 2
> select /E,S:11
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /E,S:11-13
56 atoms, 58 bonds, 6 residues, 1 model selected
> select
62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected
> color sel bypolymer
> color sel bychain
> color (#!1 & sel) hot pink
> color (#!1 & sel) light gray
> select clear
> select /E,S:11
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /E,S:11-13
56 atoms, 58 bonds, 6 residues, 1 model selected
> color (#!1 & sel) red
> show sel surfaces
> select /E,S:52
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E,S:52-54
31 atoms, 29 bonds, 6 residues, 1 model selected
> color (#!1 & sel) yellow
> show sel surfaces
> style sel ball
Changed 31 atom styles
> style sel sphere
Changed 31 atom styles
> style sel sphere
Changed 31 atom styles
> style sel stick
Changed 31 atom styles
> style sel ball
Changed 31 atom styles
> style sel sphere
Changed 31 atom styles
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 31 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> undo
> select
62346 atoms, 63535 bonds, 5 pseudobonds, 7970 residues, 2 models selected
> hide sel surfaces
> select /E,S:11
14 atoms, 12 bonds, 2 residues, 1 model selected
> select /E,S:11-13
56 atoms, 58 bonds, 6 residues, 1 model selected
> color (#!1 & sel) purple
> show sel surfaces
> select /E,S:52
10 atoms, 8 bonds, 2 residues, 1 model selected
> select /E,S:52-54
31 atoms, 29 bonds, 6 residues, 1 model selected
> show sel surfaces
> select /E,S:141
8 atoms, 6 bonds, 2 residues, 1 model selected
> select /E,S:141-143
42 atoms, 44 bonds, 6 residues, 1 model selected
> color (#!1 & sel) blue
> show sel surfaces
> save /home/raim/data/mistrans/figures/saap_3d/test.png width 987 height 1035
> supersample 3
> save /home/raim/data/mistrans/figures/saap_3d/6kwy_psma1.png width 987
> height 1035 supersample 3
> close session
> open /home/raim/test.pdb format pdb
test.pdb title:
Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786)
[more info...]
Chain information for test.pdb #1
---
Chain | Description | UniProt
A | proteasome subunit α type-1 | PSA1_HUMAN 1-263
Alignment identifier is 1/A
> select /A:11-12
8 atoms, 7 bonds, 2 residues, 1 model selected
> select /A:11-13
12 atoms, 11 bonds, 3 residues, 1 model selected
> select /A:52
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:52-54
12 atoms, 11 bonds, 3 residues, 1 model selected
> select /A:11
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:11-13
12 atoms, 11 bonds, 3 residues, 1 model selected
> select /A:50-51
8 atoms, 7 bonds, 2 residues, 1 model selected
> select /A:50-53
16 atoms, 15 bonds, 4 residues, 1 model selected
> close session
> open /home/raim/AF-P25786-F1-model_v4.pdb format pdb
AF-P25786-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for proteasome subunit α type-1 (P25786)
[more info...]
Chain information for AF-P25786-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | proteasome subunit α type-1 | PSA1_HUMAN 1-263
> close session
> open 6kwy format mmcif fromDatabase pdb
6kwy title:
human PA200-20S complex [more info...]
Chain information for 6kwy #1
---
Chain | Description | UniProt
A O | Proteasome subunit alpha type-2 | PSA2_HUMAN 0-233
B P | Proteasome subunit alpha type-4 | PSA4_HUMAN 1-261
C Q | Proteasome subunit alpha type-7 | PSA7_HUMAN 1-248
D R | Proteasome subunit alpha type-5 | PSA5_HUMAN 1-241
E S | Proteasome subunit alpha type-1 | PSA1_HUMAN 1-263
F T | Proteasome subunit alpha type-3 | PSA3_HUMAN 0-254
G U | Proteasome subunit alpha type-6 | PSA6_HUMAN 1-246
H V | Proteasome subunit beta type-7 | PSB7_HUMAN -42-234
I W | Proteasome subunit beta type-3 | PSB3_HUMAN 0-204
J X | Proteasome subunit beta type-2 | PSB2_HUMAN 1-201
K Y | Proteasome subunit beta type-5 | PSB5_HUMAN -58-204
L Z | Proteasome subunit beta type-1 | PSB1_HUMAN -27-213
M a | Proteasome subunit beta type-4 | PSB4_HUMAN -44-219
N b | Proteasome subunit beta type-6 | PSB6_HUMAN -33-205
c | Proteasome activator complex subunit 4 | PSME4_HUMAN 1-1843
Non-standard residues in 6kwy #1
---
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
K0W —
[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy-
cyclohexyl] phosphono hydrogen phosphate
> save /home/raim/data/mistrans/figures/saap_3d/6kwy.cxs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
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: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2)
OpenGL vendor: Intel
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: OptiPlex 7040
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 19Gi 2.1Gi 3.9Gi 40Gi 38Gi
Swap: 2.0Gi 632Mi 1.4Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06)
DeviceName: Intel HD Graphics
Subsystem: Dell HD Graphics 530 [1028:06b9]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
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: 2023.11.17
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-LinuxSupport: 1.0.1
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
distro: 1.7.0
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: 23.2
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
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 , 18 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 , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Rainer,
--Eric