![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17877 closed defect (can't reproduce)
Crash opening mmCIF
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-140-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007f6b1e640640 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 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 0x00007f6b45aec640 (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 0x00007f6b462ed640 (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 0x00007f6b46aee640 (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 0x00007f6b472ef640 (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 0x00007f6b47af0640 (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 0x00007f6b482f1640 (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 0x00007f6b48af2640 (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 0x00007f6c076f5740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497 in remember_data_format
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526 in collated_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215 in provider_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132 in cmd_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 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/open_command/dialog.py", line 334 in _qt_safe
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, 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, psutil._psutil_linux, psutil._psutil_posix, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.mmcif.mmcif_write (total: 52)
===== 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: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Error in contacting registry: "org.freedesktop.DBus.Error.Spawn.ExecFailed"
"Failed to execute program org.a11y.atspi.Registry: Permission denied"
> open "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/Maps/cryosparc_P3_J39_006_volume_map_zflip.mrc"
Opened cryosparc_P3_J39_006_volume_map_zflip.mrc as #1, grid size 512,512,512,
pixel 0.73, shown at level 0.0452, step 2, values float32
> open 7K00 fromDatabase pdb format mmcif
Summary of feedback from opening 7K00 fetched from pdb
---
notes | Fetching compressed mmCIF 7k00 from http://files.rcsb.org/download/7k00.cif
Fetching CCD 4D4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/4D4/4D4.cif
Fetching CCD D2T from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/D2T/D2T.cif
Fetching CCD IAS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/IAS/IAS.cif
Fetching CCD MEQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/MEQ/MEQ.cif
Fetching CCD MS6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MS6/MS6.cif
Fetching CCD PAR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/PAR/PAR.cif
Fetching CCD SPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/SPD/SPD.cif
Fetching CCD SPM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/SPM/SPM.cif
7k00 title:
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]
Chain information for 7k00 #2
---
Chain | Description | UniProt
0 | 50S ribosomal protein L33 | D7Z9P0_ECOLX 1-55
1 | 50S ribosomal protein L34 | RL34_ECO45 1-46
2 | 50S ribosomal protein L35 | D7Z814_ECOLX 1-65
3 | 50S ribosomal protein L36 | A0A0E2L017_ECOU3 1-38
4 | 50S ribosomal protein L31 | D7ZFP6_ECOLX 1-70
5 | E-site tRNA |
A | 16S rRNA |
B | 30S ribosomal protein S2 | D7ZK99_ECOLX 1-241
C | 30S ribosomal protein S3 | RS3_ECO45 1-233
D | 30S ribosomal protein S4 | D7Z9H7_ECOLX 1-206
E | 30S ribosomal protein S5 | D7Z9H2_ECOLX 1-167
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135
G | 30S ribosomal protein S7 | A0A5Q2GFB5_ECOLX 1-179
H | 30S ribosomal protein S8 | D7Z9G9_ECOLX 1-130
I | 30S ribosomal protein S9 | D7ZES9_ECOLX 1-130
J | 30S ribosomal protein S10 | D7Z9F4_ECOLX 1-103
K | 30S ribosomal protein S11 | S1ELC2_ECOLX 1-129
L | 30S ribosomal protein S12 | I2UHF1_ECOLX 1-124
M | 30S ribosomal protein S13 | H4UQ02_ECOLX 1-118
N | 30S ribosomal protein S14 | D7Z9G8_ECOLX 1-101
O | 30S ribosomal protein S15 | D7ZEL4_ECOLX 1-89
P | 30S ribosomal protein S16 | RS16_ECO45 1-82
Q | 30S ribosomal protein S17 | D7Z9G4_ECOLX 1-84
R | 30S ribosomal protein S18 | A0A0E2KXL3_ECOU3 1-75
S | 30S ribosomal protein S19 | D7Z9F9_ECOLX 1-92
T | 30S ribosomal protein S20 | D7ZAS2_ECOLX 1-87
U | 30S ribosomal protein S21 | A0A0E2L2J1_ECOU3 1-71
X | mRNA |
Y | A-site tRNA-val |
Z | P-site tRNA-fMet |
a | 23S rRNA |
b | 5S rRNA |
c | 50S ribosomal protein L2 | RL2_ECOLI 1-273
d | 50S ribosomal protein L3 | I2X6U5_ECOLX 1-209
e | 50S ribosomal protein L4 | D7Z9F6_ECOLX 1-201
f | 50S ribosomal protein L5 | D7Z9G7_ECOLX 1-179
g | 50S ribosomal protein L6 | D7Z9H0_ECOLX 1-177
h | 50S ribosomal protein L9 | D7ZI15_ECOLX 1-149
i | 50S ribosomal protein L13 | D7ZET0_ECOLX 1-142
j | 50S ribosomal protein L14 | D7Z9G5_ECOLX 1-123
k | 50S ribosomal protein L15 | A0A037Y8L6_ECOLX 1-144
l | 50S ribosomal protein L16 | L4V2J8_ECOLX 1-136
m | 50S ribosomal protein L17 | D6I1Y5_ECOLX 1-127
n | 50S ribosomal protein L18 | D7Z9H1_ECOLX 1-117
o | 50S ribosomal protein L19 | D7ZKU3_ECOLX 1-115
p | 50S ribosomal protein L20 | RL20_ECO45 1-118
q | 50S ribosomal protein L21 | D7ZEN7_ECOLX 1-103
r | 50S ribosomal protein L22 | D7Z9G0_ECOLX 1-110
s | 50S ribosomal protein L23 | D7X2Z9_ECOLX 1-100
t | 50S ribosomal protein L24 | D7Z9G6_ECOLX 1-104
u | 50S ribosomal protein L25 | D7XH79_ECOLX 1-94
v | 50S ribosomal protein L27 | RL27_ECOLI 1-85
w | 50S ribosomal protein L28 | S0YB49_ECOLX 1-78
x | 50S ribosomal protein L29 | D7Z9G3_ECOLX 1-63
y | 50S ribosomal protein L30 | D7Z9H3_ECOLX 1-59
z | 50S ribosomal protein L32 | D7ZGG2_ECOLX 1-57
Non-standard residues in 7k00 #2
---
MG — magnesium ion
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
ZN — zinc ion
> select add #2
149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected
> ui mousemode right translate
> select subtract #2
Nothing selected
> select add #2
149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,109.68,0,1,0,106.25,0,0,1,53.654
> view matrix models #2,1,0,0,161.43,0,1,0,155.89,0,0,1,77.483
> view matrix models #2,1,0,0,220.87,0,1,0,39.108,0,0,1,151.08
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.23078,0.85678,-0.46115,377.58,-0.94536,-0.085271,0.31467,349.54,0.23028,0.50858,0.82965,48.836
> view matrix models
> #2,0.20028,0.84884,-0.48924,305.67,-0.97829,0.1461,-0.14701,401.64,-0.053308,0.50806,0.85967,94.984
> view matrix models
> #2,0.064369,0.99791,-0.0047735,210.65,-0.99132,0.064492,0.11454,368.89,0.11461,-0.002641,0.99341,131.89
> view matrix models
> #2,0.14528,0.74844,-0.64709,364.21,-0.98841,0.080743,-0.12852,411.88,-0.043942,0.65826,0.7515,86.563
> view matrix models
> #2,0.11091,0.98079,-0.16049,235.06,-0.99284,0.11657,0.026272,376.55,0.044475,0.15642,0.98669,116.97
> view matrix models
> #2,-0.25375,0.95973,-0.12053,297.85,-0.88203,-0.28073,-0.37844,506.17,-0.39704,0.010285,0.91775,237.45
> view matrix models
> #2,-0.525,0.77296,-0.35625,426.54,-0.81133,-0.58097,-0.064881,488.06,-0.25712,0.25497,0.93214,164.51
> view matrix models
> #2,-0.54801,0.76431,-0.33986,429.19,-0.80241,-0.59511,-0.04448,485.11,-0.23625,0.24833,0.93942,160.52
> view matrix models
> #2,-0.48043,0.85012,-0.21558,377.42,-0.85028,-0.51174,-0.12311,493.68,-0.21498,0.12416,0.9687,173.68
> view matrix models
> #2,-0.24985,0.92494,-0.28646,335.22,-0.96698,-0.22298,0.12341,415.18,0.050275,0.30783,0.95011,95.291
> view matrix models
> #2,-0.17851,0.93055,-0.3197,327.52,-0.97377,-0.12048,0.19302,384.41,0.1411,0.34577,0.92765,76.079
> view matrix models
> #2,-0.0022917,0.94206,-0.33545,296.25,-0.99969,-0.010535,-0.022755,410.36,-0.024971,0.33529,0.94178,105.62
> view matrix models
> #2,0.0011763,0.99477,-0.10214,241.39,-0.99958,0.0041399,0.028808,397.8,0.02908,0.10207,0.99435,128.23
> view matrix models
> #2,-0.13059,0.98897,-0.069903,260.35,-0.98191,-0.13877,-0.12887,450.79,-0.13714,0.051809,0.9892,168.74
> view matrix models
> #2,-0.28546,0.94531,-0.15781,313.4,-0.95514,-0.29415,-0.034311,456.16,-0.078854,0.14093,0.98687,142.29
> view matrix models
> #2,-0.40759,0.84383,-0.34903,390.79,-0.90925,-0.41038,0.069634,449.1,-0.084479,0.34574,0.93452,115.97
> view matrix models
> #2,-0.20846,0.86818,-0.45034,369.35,-0.97311,-0.13796,0.18447,389.12,0.098026,0.47668,0.87359,70.406
> view matrix models
> #2,-0.30324,0.85882,-0.41289,381.21,-0.95291,-0.27182,0.13445,419.41,0.0032404,0.43421,0.9008,90.26
> view matrix models
> #2,-0.11822,0.94789,-0.29584,308.79,-0.98341,-0.15304,-0.097356,447.64,-0.13756,0.27943,0.95026,134.75
> view matrix models
> #2,-0.12969,0.94713,-0.29346,310.57,-0.98032,-0.1669,-0.10544,451.15,-0.14884,0.27401,0.95014,137.82
> view matrix models
> #2,-0.0952,0.94889,-0.30089,305.37,-0.98883,-0.12495,-0.081192,440.42,-0.11464,0.2898,0.9502,128.68
> view matrix models
> #2,0.24884,-0.94567,0.20924,490.54,-0.95644,-0.20587,0.20698,394.15,-0.15266,-0.25163,-0.95571,598.85
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.24884,-0.94567,0.20924,314.42,-0.95644,-0.20587,0.20698,355.79,-0.15266,-0.25163,-0.95571,397.08
> view matrix models
> #2,0.24884,-0.94567,0.20924,284.71,-0.95644,-0.20587,0.20698,349.86,-0.15266,-0.25163,-0.95571,438.26
> fitmap #2 inMap #1
Fit molecule 7k00 (#2) to map cryosparc_P3_J39_006_volume_map_zflip.mrc (#1)
using 149338 atoms
average map value = 0.05051, steps = 532
shifted from previous position = 25.4
rotated from previous position = 32.3 degrees
atoms outside contour = 77113, contour level = 0.04516
Position of 7k00 (#2) relative to cryosparc_P3_J39_006_volume_map_zflip.mrc
(#1) coordinates:
Matrix rotation and translation
0.35111942 -0.65926722 0.66489238 122.77763530
-0.93285364 -0.18516416 0.30902801 322.30256688
-0.08061780 -0.72875301 -0.68001456 437.94171451
Axis -0.79416282 0.57050230 -0.20936224
Axis point -0.00000000 307.52343415 126.61757717
Rotation angle (degrees) 139.20303362
Shift along axis -5.31953528
> volume style mesh
> style #2 stick
Changed 149338 atom styles
> view matrix models
> #2,0.35112,-0.65927,0.66489,124.3,-0.93285,-0.18516,0.30903,339.36,-0.080618,-0.72875,-0.68001,446.31
> undo
> select subtract #2
Nothing selected
> color #1 #99c1f1ff models
> color #2 #9a9996ff
> open "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/coot/70S_6ORE_fitted_J39.cif-
> coot-0.cif"
Summary of feedback from opening
/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/coot/70S_6ORE_fitted_J39.cif-
coot-0.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 7032
Unknown polymer entity '6' on line 7254
Unknown polymer entity '7' on line 7286
Unknown polymer entity '8' on line 9369
Unknown polymer entity '9' on line 10935
Unknown polymer entity '10' on line 12487
50 messages similar to the above omitted
Unable to fetch template for '---': will connect using distance criteria
Unable to fetch template for 'Che': will connect using distance criteria
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 70S_6ORE_fitted_J39.cif-coot-0.cif #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> undo
> hide #3 models
> open "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/ChimeraX/J39/70S_6ORE_fitted_J39.cif"
Chain information for 70S_6ORE_fitted_J39.cif #4
---
Chain | Description
1 | 23S ribosomal RNA
2 | 16S ribosomal RNA
3 | 5S ribosomal RNA
4 | RNA (5'-R(P*UP*UP*CP*UP*UP*CP*UP*AP*A)-3')
5 | P-tRNA
A | FME-PHE-PHE
B | 50S ribosomal protein L2
C | 50S ribosomal protein L3
D | 50S ribosomal protein L4
E | 50S ribosomal protein L5
F | 50S ribosomal protein L6
G | 50S ribosomal protein L9
J | 50S ribosomal protein L13
K | 50S ribosomal protein L14
L | 50S ribosomal protein L15
M | 50S ribosomal protein L16
N | 50S ribosomal protein L17
O | 50S ribosomal protein L18
P | 50S ribosomal protein L19
Q | 50S ribosomal protein L20
R | 50S ribosomal protein L21
S | 50S ribosomal protein L22
T | 50S ribosomal protein L23
U | 50S ribosomal protein L24
V | 50S ribosomal protein L25
W | 50S ribosomal protein L27
X | 50S ribosomal protein L28
Y | 50S ribosomal protein L29
Z | 50S ribosomal protein L30
a | 50S ribosomal protein L31
b | 50S ribosomal protein L32
c | 50S ribosomal protein L33
d | 50S ribosomal protein L34
e | 50S ribosomal protein L35
f | 50S ribosomal protein L36
g | 30S ribosomal protein S2
h | 30S ribosomal protein S3
i | 30S ribosomal protein S4
j | 30S ribosomal protein S5
k | 30S ribosomal protein S6
l | 30S ribosomal protein S7
m | 30S ribosomal protein S8
n | 30S ribosomal protein S9
o | 30S ribosomal protein S10
p | 30S ribosomal protein S11
q | 30S ribosomal protein S12
r | 30S ribosomal protein S13
s | 30S ribosomal protein S14
t | 30S ribosomal protein S15
u | 30S ribosomal protein S16
v | 30S ribosomal protein S17
w | 30S ribosomal protein S18
x | 30S ribosomal protein S19
y | 30S ribosomal protein S20
z | 30S ribosomal protein S21
> close #3
> rainbow residues
> select add #2
149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected
> view matrix models
> #2,0.35112,-0.65927,0.66489,231.99,-0.93285,-0.18516,0.30903,367.63,-0.080618,-0.72875,-0.68001,627.51
> volume style sphere
Invalid "style" argument: Should be one of 'image', 'mesh', 'solid', or
'surface'
> volume style surface
> style #2 sphere
Changed 149338 atom styles
> view matrix models
> #2,0.35112,-0.65927,0.66489,107.07,-0.93285,-0.18516,0.30903,321.45,-0.080618,-0.72875,-0.68001,449.62
> view matrix models
> #2,0.35112,-0.65927,0.66489,103.92,-0.93285,-0.18516,0.30903,324.68,-0.080618,-0.72875,-0.68001,446.77
> fitmap #2 inMap #1
Fit molecule 7k00 (#2) to map cryosparc_P3_J39_006_volume_map_zflip.mrc (#1)
using 149338 atoms
average map value = 0.05052, steps = 200
shifted from previous position = 21
rotated from previous position = 0.00242 degrees
atoms outside contour = 77150, contour level = 0.04516
Position of 7k00 (#2) relative to cryosparc_P3_J39_006_volume_map_zflip.mrc
(#1) coordinates:
Matrix rotation and translation
0.35108491 -0.65928749 0.66489050 122.78112027
-0.93286497 -0.18513106 0.30901363 322.29382184
-0.08063694 -0.72874308 -0.68002293 437.93903183
Axis -0.79415110 0.57052046 -0.20935722
Axis point -0.00000000 307.52219543 126.61800637
Rotation angle (degrees) 139.20346262
Shift along axis -5.31723987
> volume style mesh
> style #2 stick
Changed 149338 atom styles
> style #3 stick
Changed 0 atom styles
> style #4 stick
Changed 144774 atom styles
> view matrix models
> #2,0.35108,-0.65929,0.66489,116.63,-0.93286,-0.18513,0.30901,314.28,-0.080637,-0.72874,-0.68002,455.93
> undo
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> select subtract #2
Nothing selected
> save "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/ChimeraX/J39/70S_7K00_fitted.cif"
> models #2 relModel #1
> close #4
> color #2 white
> color blue #2/5
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color blue #2 chain 5
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/5 blue
> color #1/5 yellow
> color #2/Z red
> color #2/5 green
> color #2/Y orange
> color #2/X purple
> save /homes/zu49odeb/Desktop/image1.png supersample 3
> save /homes/zu49odeb/Desktop/image2.png supersample 3
> save "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/Images/7K001.png" width 1266
> height 898 supersample 3
> save "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/Images/7K002.png" width 1266
> height 898 supersample 3
> hide #!2 models
> open "/homes/zu49odeb/ZE/AG_Straeter/stpublic/People/Paula
> Schliebe/CryoEM/Auswertung/2412_Ecoli_D4K/coot/Peptid_7K00/70S_7K00_fitted+peptid-
> coot-1.cif"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Error in contacting registry: "org.freedesktop.DBus.Error.Spawn.ExecFailed"
"Failed to execute program org.a11y.atspi.Registry: Permission denied"
OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_AU.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:0
Manufacturer: HP
Model: HP ProDesk 600 G3 MT
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 7.6Gi 1.4Gi 4.8Gi 392Mi 1.4Gi 5.6Gi
Swap: 2.0Gi 841Mi 1.2Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company HD Graphics 530 [103c:829d]
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (3)
comment:1 by , 5 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening mmCIF |
comment:2 by , 5 months ago
comment:3 by , 5 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Unable to fix without the mmCIF file that triggers the bug. Please update to ChimeraX 1.10 when it comes out in a week or so.
Note:
See TracTickets
for help on using tickets.
Hello, can you share the mmCIF that didn't work with me? If you want to keep it private, email it to me at gregc@…. Otherwise, you could attach it to your response to this ticket. There is a chance that the bug is already fixed in the 1.10 release candidate, but if not, I'd to sneak in a fix before the final 1.10 release.