id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
15274	Crash getting Residue::ss_id	chimerax-bug-report@…	Eric Pettersen	"{{{
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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]
}
===== 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
}}}
"	defect	closed	normal		Core		can't reproduce		Tom Goddard				all	ChimeraX