![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15274 closed defect (can't reproduce)
Crash getting Residue::ss_id
| 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-14.5-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020136c240 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 107 in _make_ribbon_graphics
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600 in compute_ribbons
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1891 in _update_graphics_if_needed
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 54)
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{
"uptime" : 42000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 112800722,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 2318,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-05-22 16:08:36.0928 +0100",
"codeSigningMonitor" : 1,
"incident" : "79C7F36E-E3C9-4AAB-8D42-B33893BE19E8",
"pid" : 28943,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-22 13:38:17.3165 +0100",
"procStartAbsTime" : 797413723732,
"procExitAbsTime" : 1013863686628,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B1E171FE-81E3-50B3-B7C1-C759D109A6AD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1EFA766B-2BE5-950C-1611-B067EE858E49",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 17739,
"sleepWakeUUID" : "0A3FA40D-3704-40FB-8C7D-EA20B6D0B59D",
"sip" : "enabled",
"vmRegionInfo" : "0x210 is not in any region. Bytes before following region: 4311576048\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fd7000-100fdb000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000210","rawCodes":[1,528],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000210"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":28943},
"vmregioninfo" : "0x210 is not in any region. Bytes before following region: 4311576048\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fd7000-100fdb000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "b3b7d13ca6b84fdac12bff36e94b3357da8694ca",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64628732bf2f5257dedc8988",
"factorPackIds" : {
},
"deploymentId" : 240000001
},
{
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"factorPackIds" : {
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}
],
"experiments" : [
]
},
"reportNotes" : [
"PC register does not match crashing frame (0x0 vs 0x7FF8916AEA78)"
]
}
===== 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jurkevg/Desktop/new_refinement510/job237.cif-coot-6.pdb
> /Users/jurkevg/Desktop/new_refinement510/run_class001.mrc
Chain information for job237.cif-coot-6.pdb #1
---
Chain | Description
0 | No description available
0 | No description available
1 | No description available
1 v | No description available
2 w | No description available
2 8 | No description available
3 | No description available
3 4 7 d | No description available
4 | No description available
5 | No description available
5 | No description available
6 E j | No description available
6 | No description available
7 | No description available
8 | No description available
9 N | No description available
9 | No description available
A | No description available
A | No description available
B | No description available
B | No description available
C | No description available
C | No description available
D | No description available
D Z | No description available
E | No description available
F | No description available
F | No description available
G | No description available
G | No description available
H | No description available
H U | No description available
I | No description available
I p | No description available
J | No description available
J U | No description available
K | No description available
K O | No description available
L | No description available
L | No description available
M | No description available
M | No description available
N | No description available
O | No description available
P | No description available
P | No description available
Q x | No description available
Q | No description available
R | No description available
R | No description available
S | No description available
S | No description available
T | No description available
T | No description available
V | No description available
V | No description available
W | No description available
W | No description available
X | No description available
X | No description available
Y | No description available
Y | No description available
Z | No description available
a | No description available
a v | No description available
b | No description available
b | No description available
c | No description available
c | No description available
d | No description available
e | No description available
e t w | No description available
f | No description available
f | No description available
g j | No description available
g | No description available
h | No description available
h | No description available
i | No description available
i | No description available
k | No description available
k | No description available
l | No description available
l | No description available
m | No description available
m | No description available
n | No description available
n | No description available
o | No description available
o | No description available
p | No description available
q | No description available
q | No description available
r | No description available
r | No description available
s | No description available
s | No description available
t | No description available
u | No description available
u | No description available
x | No description available
y | No description available
y z | No description available
z | No description available
Opened run_class001.mrc as #2, grid size 360,360,360, pixel 1.08, shown at
level 0.0177, step 2, values float32
> set bgColor black
> set bgColor white
> hide #!2 models
> select /B
2455 atoms, 2693 bonds, 157 residues, 1 model selected
> show #!2 models
> fitmap #1 inMap #2
Fit molecule job237.cif-coot-6.pdb (#1) to map run_class001.mrc (#2) using
154602 atoms
average map value = 0.01908, steps = 40
shifted from previous position = 0.0128
rotated from previous position = 0.00435 degrees
atoms outside contour = 91145, contour level = 0.01766
Position of job237.cif-coot-6.pdb (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
1.00000000 0.00006479 -0.00003790 -0.01422802
-0.00006479 1.00000000 -0.00001090 0.02043640
0.00003790 0.00001090 1.00000000 -0.01779205
Axis 0.14368533 -0.49971549 -0.85418906
Axis point 338.09615643 226.13707807 0.00000000
Rotation angle (degrees) 0.00434592
Shift along axis 0.00294104
> select ~sel & ##selected
152147 atoms, 164402 bonds, 11132 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!2 models
Drag select of 1617 atoms, 269 bonds
Drag select of 1749 atoms, 289 bonds
> select clear
Drag select of 1749 atoms, 289 bonds
> delete atoms sel
> delete bonds sel
Drag select of 61 atoms, 52 bonds
> delete atoms sel
> delete bonds sel
Drag select of 19 atoms
> delete atoms sel
> delete bonds sel
Drag select of 135 atoms
> delete atoms sel
> delete bonds sel
Drag select of 45 atoms
> delete atoms sel
> delete bonds sel
> show #!2 models
> volume #2 level 0.007234
> open 5nwy
5nwy title:
2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex [more
info...]
Chain information for 5nwy #3
---
Chain | Description | UniProt
0 | 16S rRNA |
1 | 30S ribosomal protein S2 | RS2_ECOLI 9-241
2 | 30S ribosomal protein S3 | RS3_ECOLI 1-233
3 | 30S ribosomal protein S4 | RS4_ECOLI 1-206
4 | 30S ribosomal protein S5 | RS5_ECOLI 1-166
5 | 30S ribosomal protein S6 | RS6_ECOLI 1-131
6 | 30S ribosomal protein S7 | RS7_ECOLI 1-156
7 | 30S ribosomal protein S8 | RS8_ECOLI 1-130
8 | 30S ribosomal protein S9 | RS9_ECOLI 1-130
9 | 30S ribosomal protein S10 | RS10_ECOLI 1-103
A | 30S ribosomal protein S11 | RS11_ECOLI 1-129
B | 30S ribosomal protein S12 | RS12_ECOLI 1-124
C | 30S ribosomal protein S13 | RS13_ECOLI 1-118
D | 30S ribosomal protein S14 | RS14_ECOLI 1-101
E | 30S ribosomal protein S15 | RS15_ECOLI 1-89
F | 30S ribosomal protein S16 | RS16_ECOLI 1-82
G | 30S ribosomal protein S17 | RS17_ECOLI 1-84
H | 30S ribosomal protein S18 | RS18_ECOLI 1-75
I | 30S ribosomal protein S19 | RS19_ECOLI 1-92
J | 30S ribosomal protein S20 | RS20_ECOLI 1-87
K | 30S ribosomal protein S21 | RS21_ECOLI 1-71
L | 50S ribosomal protein L31 | RL31_ECOLI 1-70
M | Gln-tRNA |
N | 23S rRNA |
O | 5S rRNA |
P | 50S ribosomal protein L2 | RL2_ECOLI 1-273
Q | 50S ribosomal protein L3 | RL3_ECOLI 1-209
R | 50S ribosomal protein L4 | RL4_ECOLI 1-201
S | 50S ribosomal protein L5 | RL5_ECOLI 1-179
T | 50S ribosomal protein L6 | RL6_ECOLI 1-177
U | 50S ribosomal protein L9 | RL9_ECOLI 1-149
V | 50S ribosomal protein L11 | RL11_ECOLI 1-142
W | 50S ribosomal protein L13 | RL13_ECOLI 1-142
X | 50S ribosomal protein L14 | RL14_ECOLI 1-123
Y | 50S ribosomal protein L15 | RL15_ECOLI 1-144
Z | 50S ribosomal protein L16 | RL16_ECOLI 1-136
a | 50S ribosomal protein L17 | RL17_ECOLI 1-127
b | 50S ribosomal protein L18 | RL18_ECOLI 1-117
c | 50S ribosomal protein L19 | RL19_ECOLI 1-115
d | 50S ribosomal protein L20 | RL20_ECOLI 1-118
e | 50S ribosomal protein L21 | RL21_ECOLI 1-103
f | 50S ribosomal protein L22 | RL22_ECOLI 1-110
g | 50S ribosomal protein L23 | RL23_ECOLI 1-100
h | 50S ribosomal protein L24 | RL24_ECOLI 1-104
i | 50S ribosomal protein L25 | RL25_ECOLI 1-94
j | 50S ribosomal protein L27 | RL27_ECOLI 1-85
k | 50S ribosomal protein L28 | RL28_ECOLI 1-78
l | 50S ribosomal protein L29 | RL29_ECOLI 1-63
m | 50S ribosomal protein L30 | RL30_ECOLI 1-59
n | 50S ribosomal protein L32 | RL32_ECOLI 1-57
o | 50S ribosomal protein L33 | RL33_ECOLI 1-55
p | 50S ribosomal protein L34 | RL34_ECOLI 1-46
q | 50S ribosomal protein L35 | RL35_ECOLI 1-65
r | 50S ribosomal protein L36 | RL36_ECOLI 1-38
s | VemP nascent chain | A0A0P7EF65_VIBAL 26-159
t | mRNA |
> select add #3
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 3 models
selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,164.56,0,1,0,210.06,0,0,1,-8.8218
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.47913,0.73235,-0.48383,450.71,0.84538,0.53334,-0.029886,119.38,0.23616,-0.42334,-0.87465,409.6
> view matrix models
> #3,-0.04494,0.34431,-0.93778,522.52,0.7493,0.63247,0.1963,74.736,0.6607,-0.69386,-0.28641,243.84
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.04494,0.34431,-0.93778,457.02,0.7493,0.63247,0.1963,-129.37,0.6607,-0.69386,-0.28641,296.78
> view matrix models
> #3,-0.04494,0.34431,-0.93778,328.81,0.7493,0.63247,0.1963,-82.983,0.6607,-0.69386,-0.28641,247.33
> fitmap #3 inMap #2
Fit molecule 5nwy (#3) to map run_class001.mrc (#2) using 144122 atoms
average map value = 0.01048, steps = 400
shifted from previous position = 28
rotated from previous position = 33.3 degrees
atoms outside contour = 55738, contour level = 0.0072342
Position of 5nwy (#3) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.16033562 -0.20553834 -0.96542554 464.62242576
0.77688636 0.57706496 -0.25188015 -13.82880156
0.60888428 -0.79041130 0.06715587 196.73999303
Axis -0.27870544 -0.81475086 0.50843319
Axis point 137.59641012 0.00000000 310.63287393
Rotation angle (degrees) 104.95482594
Shift along axis -18.19662742
> select up
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 3 models
selected
> select up
144568 atoms, 157124 bonds, 4785 pseudobonds, 10406 residues, 6 models
selected
> select up
144568 atoms, 157124 bonds, 4785 pseudobonds, 10406 residues, 6 models
selected
> select subtract #1
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 5 models
selected
> select subtract #2
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 3 models
selected
> select subtract #3
Nothing selected
> vop add #1-3
Opened run_class001.mrc resampled as #4, grid size 360,360,360, pixel 1.08,
shown at step 1, values float32
> hide #!1 models
> hide #!3 models
> close #3
> undo
Undo failed, probably because structures have been modified.
> close #4
> open 5nwy
5nwy title:
2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complex [more
info...]
Chain information for 5nwy #3
---
Chain | Description | UniProt
0 | 16S rRNA |
1 | 30S ribosomal protein S2 | RS2_ECOLI 9-241
2 | 30S ribosomal protein S3 | RS3_ECOLI 1-233
3 | 30S ribosomal protein S4 | RS4_ECOLI 1-206
4 | 30S ribosomal protein S5 | RS5_ECOLI 1-166
5 | 30S ribosomal protein S6 | RS6_ECOLI 1-131
6 | 30S ribosomal protein S7 | RS7_ECOLI 1-156
7 | 30S ribosomal protein S8 | RS8_ECOLI 1-130
8 | 30S ribosomal protein S9 | RS9_ECOLI 1-130
9 | 30S ribosomal protein S10 | RS10_ECOLI 1-103
A | 30S ribosomal protein S11 | RS11_ECOLI 1-129
B | 30S ribosomal protein S12 | RS12_ECOLI 1-124
C | 30S ribosomal protein S13 | RS13_ECOLI 1-118
D | 30S ribosomal protein S14 | RS14_ECOLI 1-101
E | 30S ribosomal protein S15 | RS15_ECOLI 1-89
F | 30S ribosomal protein S16 | RS16_ECOLI 1-82
G | 30S ribosomal protein S17 | RS17_ECOLI 1-84
H | 30S ribosomal protein S18 | RS18_ECOLI 1-75
I | 30S ribosomal protein S19 | RS19_ECOLI 1-92
J | 30S ribosomal protein S20 | RS20_ECOLI 1-87
K | 30S ribosomal protein S21 | RS21_ECOLI 1-71
L | 50S ribosomal protein L31 | RL31_ECOLI 1-70
M | Gln-tRNA |
N | 23S rRNA |
O | 5S rRNA |
P | 50S ribosomal protein L2 | RL2_ECOLI 1-273
Q | 50S ribosomal protein L3 | RL3_ECOLI 1-209
R | 50S ribosomal protein L4 | RL4_ECOLI 1-201
S | 50S ribosomal protein L5 | RL5_ECOLI 1-179
T | 50S ribosomal protein L6 | RL6_ECOLI 1-177
U | 50S ribosomal protein L9 | RL9_ECOLI 1-149
V | 50S ribosomal protein L11 | RL11_ECOLI 1-142
W | 50S ribosomal protein L13 | RL13_ECOLI 1-142
X | 50S ribosomal protein L14 | RL14_ECOLI 1-123
Y | 50S ribosomal protein L15 | RL15_ECOLI 1-144
Z | 50S ribosomal protein L16 | RL16_ECOLI 1-136
a | 50S ribosomal protein L17 | RL17_ECOLI 1-127
b | 50S ribosomal protein L18 | RL18_ECOLI 1-117
c | 50S ribosomal protein L19 | RL19_ECOLI 1-115
d | 50S ribosomal protein L20 | RL20_ECOLI 1-118
e | 50S ribosomal protein L21 | RL21_ECOLI 1-103
f | 50S ribosomal protein L22 | RL22_ECOLI 1-110
g | 50S ribosomal protein L23 | RL23_ECOLI 1-100
h | 50S ribosomal protein L24 | RL24_ECOLI 1-104
i | 50S ribosomal protein L25 | RL25_ECOLI 1-94
j | 50S ribosomal protein L27 | RL27_ECOLI 1-85
k | 50S ribosomal protein L28 | RL28_ECOLI 1-78
l | 50S ribosomal protein L29 | RL29_ECOLI 1-63
m | 50S ribosomal protein L30 | RL30_ECOLI 1-59
n | 50S ribosomal protein L32 | RL32_ECOLI 1-57
o | 50S ribosomal protein L33 | RL33_ECOLI 1-55
p | 50S ribosomal protein L34 | RL34_ECOLI 1-46
q | 50S ribosomal protein L35 | RL35_ECOLI 1-65
r | 50S ribosomal protein L36 | RL36_ECOLI 1-38
s | VemP nascent chain | A0A0P7EF65_VIBAL 26-159
t | mRNA |
> show #!2 models
> select add #3
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 3 models
selected
> view matrix models #3,1,0,0,90.949,0,1,0,200.48,0,0,1,-72.571
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.8558,0.4984,0.13861,368.01,0.37594,0.78324,-0.49518,262.95,-0.35536,-0.37166,-0.85766,458.88
> view matrix models
> #3,0.12085,0.13373,-0.98362,460.63,0.65221,0.7363,0.18023,70.755,0.74834,-0.66331,0.0017661,95.539
> view matrix models
> #3,0.19258,0.12082,-0.97382,445.61,0.75876,0.61096,0.22585,60.759,0.62225,-0.78239,0.025989,138.39
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.19258,0.12082,-0.97382,412.98,0.75876,0.61096,0.22585,-89.744,0.62225,-0.78239,0.025989,188.24
> view matrix models
> #3,0.19258,0.12082,-0.97382,323.68,0.75876,0.61096,0.22585,-101.8,0.62225,-0.78239,0.025989,210.29
> fitmap #3 inMap #2
Fit molecule 5nwy (#3) to map run_class001.mrc (#2) using 144122 atoms
average map value = 0.01048, steps = 328
shifted from previous position = 17.8
rotated from previous position = 27.8 degrees
atoms outside contour = 55722, contour level = 0.0072342
Position of 5nwy (#3) relative to run_class001.mrc (#2) coordinates:
Matrix rotation and translation
-0.16031973 -0.20556860 -0.96542174 464.63223399
0.77689549 0.57705060 -0.25188490 -13.82418230
0.60887682 -0.79041391 0.06719273 196.72476056
Axis -0.27870286 -0.81474071 0.50845088
Axis point 137.60202784 0.00000000 310.63701831
Rotation angle (degrees) 104.95368761
Shift along axis -18.20632979
> select subtract #3
Nothing selected
> color #3 darkgrey
> select #3/g
738 atoms, 744 bonds, 93 residues, 1 model selected
> color sel light sea green
> select #3/h
779 atoms, 787 bonds, 102 residues, 1 model selected
> color sel purple
> select #3/l
508 atoms, 509 bonds, 63 residues, 1 model selected
> color sel blue
> ui tool show "Color Zone"
> color zone #2 near #1 distance 6.48
> color zone #2 near #3 distance 6.48
> color zone #2 near #1 distance 6.48
> select add #3
144122 atoms, 156663 bonds, 4785 pseudobonds, 10351 residues, 3 models
selected
> hide #!3 models
> select subtract #3
Nothing selected
> hide #!1 models
> volume #2 level 0.01083
> color zone #2 near #1 distance 4.95
> color zone #2 near #1 distance 3.17
> volume #2 level 0.005373
> volume #2 level 0.005124
> show #!3 models
> hide #!2 models
> show #!2 models
> color zone #2 near #3 distance 3.17
> hide #!2 models
> show #!2 models
> hide #!3 models
> color zone #2 near #3 distance 2.94
> color zone #2 near #3 distance 3.48
> color zone #2 near #3 distance 3.29
> color zone #2 near #3 distance 4.19
> color zone #2 near #3 distance 4.27
> color zone #2 near #3 distance 4.43
> volume #2 level 0.005869
> color zone #2 near #3 distance 4.5
> color zone #2 near #3 distance 4
> color zone #2 near #3 distance 4.6
> color zone #2 near #3 distance 4.11
> color zone #2 near #3 distance 5.43
> surface dust #2 size 10.8
> volume #2 level 0.003387
> lighting full
> ui mousemode right "map eraser"
> volume erase #2 center 193.32,193.32,193.32 radius 185.84 outside true
Opened run_class001.mrc copy as #5, grid size 360,360,360, pixel 1.08, shown
at step 1, values float32
> volume #5 level 0.005538
> volume #5 level 0.003953
> color zone #5 near #3 distance 6.48
> surface dust #5 size 10.8
> color zone #5 near #3 distance 5.74
> color zone #5 near #3 distance 4.77
> color zone #5 near #3 distance 4.19
> color zone #5 near #3 distance 5
> close #2
> color zone #5 near #3 distance 5.14
> color zone #5 near #3 distance 6.42
> color zone #5 near #3 distance 6.54
> color zone #5 near #3 distance 6.3
> color zone #5 near #3 distance 6.2
> color zone #5 near #3 distance 6.1
> color zone #5 near #3 distance 6
> color zone #5 near #3 distance 5.9
> color zone #5 near #3 distance 5.8
> color zone #5 near #3 distance 5.7
> color zone #5 near #3 distance 5.6
> close #5
> open
> /Users/jurkevg/Downloads/cryosparc_P421_J20_series_all_clusters/J20_cluster_000.mrc
Opened J20_cluster_000.mrc as #2, grid size 180,180,180, pixel 2.16, shown at
level 0.86, step 1, values float32
> open
> /Users/jurkevg/Downloads/cryosparc_P421_J20_series_all_clusters/J20_cluster_001.mrc
Opened J20_cluster_001.mrc as #4, grid size 180,180,180, pixel 2.16, shown at
level 1.02, step 1, values float32
> open
> /Users/jurkevg/Downloads/cryosparc_P421_J20_series_all_clusters/J20_cluster_002.mrc
Opened J20_cluster_002.mrc as #5, grid size 180,180,180, pixel 2.16, shown at
level 1.11, step 1, values float32
> hide #!5 models
> hide #!4 models
> volume #2 level 0.9675
> surface dust #2 size 21.6
> volume #2 level 0.8989
> lighting simple
> close #2
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> close #5
> open /Users/jurkevg/Desktop/new_refinement510/run_class001.mrc
Opened run_class001.mrc as #2, grid size 360,360,360, pixel 1.08, shown at
level 0.0177, step 2, values float32
> color #2 darkgrey models
> lighting full
> volume #2 level 0.01518
> show #!1 models
> ui mousemode right "translate selected models"
> show #!1 cartoons
===== 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
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: Mac
Model Identifier: Mac14,9
Model Number: MPHE3B/A
Chip: Unknown
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 1 day, 4 hours, 20 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
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: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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-Clipper: 0.22.4
ChimeraX-clix: 0.1.4
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
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-ISOLDE: 1.7.1
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
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: 1.5.13
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: 1.0.3
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: 1.12.3
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: 1.33.2
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: 0.2.0
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: 4.47.0
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: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
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: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.2.2
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash getting Residue::ss_id |
comment:2 by , 17 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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