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Opened 18 months ago
Closed 18 months ago
#15262 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-86-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007fcec720c740 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 956 in _atomspec_attr_filter
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1003 in _atomspec_filter_atom
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 921 in atomspec_filter
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 579 in _filter_parts
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 561 in find_selected_parts
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 572 in find_selected_parts
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 572 in find_selected_parts
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 637 in _add_model_parts
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 617 in find_matches
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1111 in evaluate
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 1309 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 901 in parse
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 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/preset_mgr/manager.py", line 99 in execute
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/preset_mgr/builtin.py", line 60 in run_preset
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/preset_mgr/__init__.py", line 55 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/preset_mgr/manager.py", line 71 in cb
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py", line 82 in run_preset
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py", line 61 in preset_cmd
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 1223 in
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif.mmcif_write, PIL._imagingmath, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 113)
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open ../../Building/CPC_combine_EMR.mrc
Opened CPC_combine_EMR.mrc as #1, grid size 360,360,360, pixel 2.64, shown at
level 4.71, step 2, values float32
> open crCPC_C1_emd25381_7sqc.cif
crCPC_C1_emd25381_7sqc.cif title:
Ciliary C1 central pair apparatus isolated from Chlamydomonas reinhardtii
[more info...]
Chain information for crCPC_C1_emd25381_7sqc.cif #2
---
Chain | Description | UniProt
0A 0B 0C 0D 0E 0F 0G 0H 0I 0J 0K 0L | Flagellar associated protein |
A8I439_CHLRE 1-93
1A 1B 1C 1D | FAP42 | A0A2K3D425_CHLRE 1-2540
1F 1G 1H 1I 1J 1K 1L 1M 1N 1O 1P 1Q 1R 1S 1T 1U 1V 1W 1X 1Y | FAP7 |
A8IVW2_CHLRE 1-507
2A 2B | FAP81 | A0A2K3DQM4_CHLRE 1-2215
2E 2F | FAP216 | A8JGM3_CHLRE 1-739
2H 2I | FAP297 | A0A2K3E6N2_CHLRE 1-945
2K 2L 2M 2N 2O 2P 2Q | FAP114 | Q45QX5_CHLRE 1-286
3A 3B 3C 3D | FAP305 | A0A2K3D8V0_CHLRE 1-427
3K 3L 3M 3N 3O 3P | FAP119 | Q45QX4_CHLRE 1-306
4A 4B 4C 4D 4E 4F 4G 4H 4I 4J 4K 4L | Calmodulin | A8IDP6_CHLRE 1-163
5A 5B 5C 5D | FAP101 | Q45QX3_CHLRE 1-835
6A 6B 6C 6D | FAP15 | Q9XGU3_CHLRE 1-304
7A 7B 7C 7D 7E 7F 7G 7H 7I 7J 7K 7L | FAP227 | Q45QX6_CHLRE 1-173
8A 8B 8C 8D | FAP105 | A8IKV8_CHLRE 1-287
9A 9B 9C 9D 9E 9F | PF6 | Q9ATK5_CHLRE 1-2301
A0 A1 A2 A3 A4 | FAP219 |
B0 B1 B2 | FAP99 | CFA99_CHLRE 1-795
C0 C1 C2 C3 C4 | CPC1 | Q6J4H1_CHLRE 1-1929
D0 D1 D2 D3 D4 D5 D6 D7 G0 G1 G2 G3 G4 G5 H0 H1 H2 H3 H4 H5 H6 H7 I0 I1 J0 J1
J2 J3 K0 K1 K2 K3 L0 L1 L2 L3 | PF16 | A0A2K3DEG1_CHLRE 1-512
E0 E1 E2 E3 | FAP108 | A0A2K3DQN7_CHLRE 1-446
F0 F1 F2 F3 | Hydin | A0A2K3E6E5_CHLRE 1-4929
M0 M1 | FAP221 | D4P3R6_CHLRE 1-971
N0 N1 N2 N3 | FAP194 | A0A2K3D452_CHLRE 1-571
NB ND NF NH NJ NL NN OD OF OH OJ OL ON OP PD PF PH PJ PL PN PP QD QF QH QJ QL
QN QP RD RF RH RJ RL RN RP SB SD SF SH SJ SL SN SP TB TD TF TH TJ TL TN TP UB
UD UF UH UJ UL UN UP VB VD VF VH VJ VL VN VP WB WD WF WH WJ WL WN XB XD XF XH
XJ XL XN YB YD YF YH YJ YL YN YP ZB ZD ZF ZH ZJ ZL ZN ZP | Tubulin alpha |
TBA1_CHLRE 1-451
NC NE NG NI NK NM NO OC OE OG OI OK OM OO OQ PC PE PG PI PK PM PO PQ QC QE QG
QI QK QM QO QQ RC RE RG RI RK RM RO SC SE SG SI SK SM SO TC TE TG TI TK TM TO
UC UE UG UI UK UM UO VC VE VG VI VK VM VO WA WC WE WG WI WK WM WO XA XC XE XG
XI XK XM XO YC YE YG YI YK YM YO ZC ZE ZG ZI ZK ZM ZO | Tubulin beta |
TBB_CHLRE 1-443
O0 O1 O2 | FAP74 | CFA74_CHLRE 1-1940
P0 P1 P2 P3 | FAP69 | A0A2K3DWV9_CHLRE 1-1102
Q0 Q1 | FAP54 | CFA54_CHLRE 3-3225
R0 R1 | FAP46 | CFA46_CHLRE 1-2784
S0 S1 S2 S3 | FAP275 | A8J870_CHLRE 1-168
S5 | Unknown protein |
T0 T1 T2 T3 | FAP47 | A0A2K3CP55_CHLRE 1-2939
U0 U1 | FAP279 | A0A2K3DN67_CHLRE 1-401
V0 V1 | FAP266 | A0A2K3CU78_CHLRE 1-761
W0 W1 | FAP76 | A0A2K3DDV4_CHLRE 1-1638
W3 W4 W5 W6 | Unknown protein |
W7 W9 | Unknown protein |
W8 | Unknown protein |
X0 X1 X2 X3 | FAP246 | A0A2K3CXT1_CHLRE 1-1138
Y0 Y1 Y2 Y3 Y4 Y5 Y6 Y7 | Phosphopyruvate hydratase | A8JH98_CHLRE 1-477
Z0 Z1 Z2 Z3 | Heat shock protein 70A | A8JEU4_CHLRE 1-651
Non-standard residues in crCPC_C1_emd25381_7sqc.cif #2
---
ADP — adenosine-5'-diphosphate
ANP — phosphoaminophosphonic acid-adenylate ester
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> show #!1 models
> ui mousemode right "rotate selected models"
> select add #2
1218816 atoms, 1238417 bonds, 1208 pseudobonds, 173186 residues, 3 models
selected
> volume #1 level 3.372
> view matrix models #2,1,0,0,24.154,0,1,0,18.69,0,0,1,-0.32704
> view matrix models
> #2,-0.15132,0.75775,0.63476,2.1978,0.7717,0.49185,-0.40318,23.304,-0.61772,0.42883,-0.65919,894.79
> view matrix models
> #2,-0.17221,0.78224,-0.59871,567.57,0.68408,0.53229,0.49869,-362.58,0.70878,-0.32369,-0.62678,525.46
> view matrix models
> #2,-0.34164,0.81349,0.47065,147.7,0.81717,0.50449,-0.2788,-60.15,-0.46423,0.28935,-0.83712,954.81
> view matrix models
> #2,-0.03149,0.76378,-0.64471,528.07,0.56049,0.54756,0.62131,-365.15,0.82757,-0.34179,-0.44533,392.24
> view matrix models
> #2,-0.65544,0.75191,-0.070951,569.05,0.72903,0.65443,0.20057,-293.37,0.19725,0.079739,-0.97711,780.15
> view matrix models
> #2,-0.25367,0.96728,0.0037192,261.7,0.94884,0.24808,0.19535,-244.37,0.18803,0.053082,-0.98073,796.19
> view matrix models
> #2,-0.26543,0.96413,0.0018098,269.4,0.94554,0.25995,0.19593,-247.5,0.18843,0.053718,-0.98062,795.71
> view matrix models
> #2,-0.48491,0.84557,0.22333,317.58,0.28982,-0.085575,0.95325,-150.49,0.82515,0.52696,-0.20356,-42.188
> view matrix models
> #2,-0.61451,0.72139,0.31932,382.23,0.77993,0.49465,0.38345,-341.71,0.11866,0.48468,-0.8666,615.79
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.61451,0.72139,0.31932,448.63,0.77993,0.49465,0.38345,-255.22,0.11866,0.48468,-0.8666,616.34
> view matrix models
> #2,-0.60665,0.79221,-0.066198,594.82,0.78816,0.61024,0.080031,-163.54,0.1038,-0.0036234,-0.99459,864.69
> view matrix models
> #2,-0.3683,0.92809,-0.054864,424.53,0.92447,0.37184,0.084234,-141.64,0.098577,-0.019697,-0.99493,873.36
> view matrix models
> #2,-0.3683,0.92809,-0.054864,455.37,0.92447,0.37184,0.084234,-87.276,0.098577,-0.019697,-0.99493,874.2
> view matrix models
> #2,-0.3683,0.92809,-0.054864,458.75,0.92447,0.37184,0.084234,-94.789,0.098577,-0.019697,-0.99493,754.07
> hide #!1 models
> select clear
Drag select of 113838 atoms, 209 pseudobonds
> select up
114713 atoms, 114503 bonds, 209 pseudobonds, 22673 residues, 2 models selected
> select up
117813 atoms, 117679 bonds, 209 pseudobonds, 23147 residues, 2 models selected
> select up
129631 atoms, 129706 bonds, 209 pseudobonds, 24765 residues, 2 models selected
> select up
134724 atoms, 134782 bonds, 209 pseudobonds, 25794 residues, 2 models selected
> select up
1218816 atoms, 1238417 bonds, 863 pseudobonds, 173186 residues, 2 models
selected
> select down
134724 atoms, 134782 bonds, 209 pseudobonds, 25794 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
Drag select of 145026 atoms, 158 pseudobonds
> select up
145586 atoms, 147607 bonds, 158 pseudobonds, 20807 residues, 2 models selected
> select up
147935 atoms, 150021 bonds, 158 pseudobonds, 21091 residues, 2 models selected
> select up
148508 atoms, 150612 bonds, 158 pseudobonds, 21165 residues, 2 models selected
> select up
148689 atoms, 150798 bonds, 158 pseudobonds, 21191 residues, 2 models selected
> select up
149255 atoms, 151365 bonds, 158 pseudobonds, 21266 residues, 2 models selected
> select up
155870 atoms, 158054 bonds, 158 pseudobonds, 22098 residues, 2 models selected
> select up
1084092 atoms, 1103635 bonds, 634 pseudobonds, 147392 residues, 2 models
selected
> select down
155870 atoms, 158054 bonds, 158 pseudobonds, 22098 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!1 models
> transparency 50
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule crCPC_C1_emd25381_7sqc.cif (#2) to map CPC_combine_EMR.mrc (#1)
using 928222 atoms
average map value = 2.471, steps = 124
shifted from previous position = 21.7
rotated from previous position = 7.28 degrees
atoms outside contour = 634054, contour level = 3.3719
Position of crCPC_C1_emd25381_7sqc.cif (#2) relative to CPC_combine_EMR.mrc
(#1) coordinates:
Matrix rotation and translation
-0.32217833 0.94632372 -0.02593542 403.22459267
0.94652561 0.32151196 -0.02682133 -46.86063944
-0.01704312 -0.03318980 -0.99930377 816.00680516
Axis -0.58215798 -0.81286623 0.01845484
Axis point 217.01424709 0.00000000 407.97193962
Rotation angle (degrees) 179.68660687
Shift along axis -181.58970609
> hide #!1 models
> select add /NB
3374 atoms, 3446 bonds, 4 pseudobonds, 432 residues, 3 models selected
> select add
> /NB/ND/NF/NH/NJ/NL/NN/OD/OF/OH/OJ/OL/ON/OP/PD/PF/PH/PJ/PL/PN/PP/QD/QF/QH/QJ/QL/QN/QP/RD/RF/RH/RJ/RL/RN/RP/SB/SD/SF/SH/SJ/SL/SN/SP/TB/TD/TF/TH/TJ/TL/TN/TP/UB/UD/UF/UH/UJ/UL/UN/UP/VB/VD/VF/VH/VJ/VL/VN/VP/WB/WD/WF/WH/WJ/WL/WN/XB/XD/XF/XH/XJ/XL/XN/YB/YD/YF/YH/YJ/YL/YN/YP/ZB/ZD/ZF/ZH/ZJ/ZL/ZN/ZP
327994 atoms, 334998 bonds, 396 pseudobonds, 42004 residues, 3 models selected
> select add
> /NC/NE/NG/NI/NK/NM/NO/OC/OE/OG/OI/OK/OM/OO/OQ/PC/PE/PG/PI/PK/PM/PO/PQ/QC/QE/QG/QI/QK/QM/QO/QQ/RC/RE/RG/RI/RK/RM/RO/SC/SE/SG/SI/SK/SM/SO/TC/TE/TG/TI/TK/TM/TO/UC/UE/UG/UI/UK/UM/UO/VC/VE/VG/VI/VK/VM/VO/WA/WC/WE/WG/WI/WK/WM/WO/XA/XC/XE/XG/XI/XK/XM/XO/YC/YE/YG/YI/YK/YM/YO/ZC/ZE/ZG/ZI/ZK/ZM/ZO
652969 atoms, 667259 bonds, 399 pseudobonds, 83153 residues, 3 models selected
> select add /S0/S1/S2/S3
657708 atoms, 672104 bonds, 403 pseudobonds, 83774 residues, 3 models selected
> select add /8A/8B/8C/8D
663755 atoms, 678310 bonds, 403 pseudobonds, 84562 residues, 3 models selected
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif
> relModel #2
Cannot save
'/data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif':
[Errno 13] Permission denied:
'/data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif'
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif
> relModel #2
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.pdb
> selectedOnly true relModel #1
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif
> selectedOnly true
> select ~sel & ##selected
264467 atoms, 267271 bonds, 366 pseudobonds, 40732 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 657963 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> show #!1 models
> volume #1 level 4.21
> volume #1 step 1
> transparency 0
> color bypolymer
> fitmap #2 inMap #1
Fit molecule crCPC_C1_emd25381_7sqc.cif (#2) to map CPC_combine_EMR.mrc (#1)
using 663755 atoms
average map value = 2.801, steps = 64
shifted from previous position = 1.08
rotated from previous position = 0.0967 degrees
atoms outside contour = 529073, contour level = 4.2104
Position of crCPC_C1_emd25381_7sqc.cif (#2) relative to CPC_combine_EMR.mrc
(#1) coordinates:
Matrix rotation and translation
-0.32197338 0.94641578 -0.02510843 402.82819472
0.94661464 0.32136811 -0.02536389 -46.69422710
-0.01593575 -0.03193452 -0.99936294 815.70853799
Axis -0.58224566 -0.81282192 0.01762156
Axis point 216.71703212 0.00000000 407.86308897
Rotation angle (degrees) 179.67670761
Shift along axis -182.21681851
> transparency 50
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.cif
> save /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/7sqc_MIPs_fit.pdb
> relModel #1
> close #2
> volume #1 level 3.013
> open
> /data2/zhuyun/MouseSperm/CPC/Models/crCPC_ZR_NSMB2022/crCPC_C2_emd25361_7som.cif
crCPC_C2_emd25361_7som.cif title:
Ciliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
[more info...]
Chain information for crCPC_C2_emd25361_7som.cif #2
---
Chain | Description | UniProt
A B C | FAP147 | CFA20_CHLRE 1-190
A1 | FAP239 |
A2 A4 | FAP388 |
A3 | FAP424 |
AA AC AE AG AI AK BA BC BE BG BI BK CA CC CE CG CI CK DC DE DG DI DK EA EC EE
EG EI EK FA FC FE FG FI FK GC GE GG GI GK GM HC HE HG HI HK HM IC IE IG II IK
IM JC JE JG JI JK JM KC KE KG KI KK LC LE LG LI LK MC ME MG MI MK | Tubulin
beta | TBB_CHLRE 1-443
AB AD AF AH AJ AL BB BD BF BH BJ BL CB CD CF CH CJ DB DD DF DH DJ DL EB ED EF
EH EJ EL FB FD FF FH FJ FL GD GF GH GJ GL HD HF HH HJ HL ID IF IH IJ IL JB JD
JF JH JJ JL KB KD KF KH KJ KL LB LD LF LH LJ LL MB MD MF MH MJ ML | Tubulin
alpha | TBA1_CHLRE 1-451
D E bb | Flagellar associated protein | A0A2K3DLJ2_CHLRE 1-2257
F G H I | FAP196 | A0A2K3DKW3_CHLRE 1-1074
J K | FAP213 | A0A2K3DUG8_CHLRE 1-976
L M N O X Y | FAP225 | A0A2K3D8Z6_CHLRE 1-222
P Q R S Z aa cc | FAP178 | PF20_CHLRE 1-606
T U V W | Flagellar WD repeat-containing protein Pf20 | A8I439_CHLRE 1-93
a b c d | Cilia- and flagella-associated protein 20 | A0A2K3CQT7_CHLRE 1-618
e f g | Unknown protein | A8JB78_CHLRE 1-201
h i j | Unknown protein | A8HNF2_CHLRE 1-758
k l s | Unknown protein | A0A2K3DV98_CHLRE 1-528
m n o | FAP65 | A0A2K3CXB9_CHLRE 1-421
p q r | FAP70 | A8HZB8_CHLRE 1-89
Non-standard residues in crCPC_C2_emd25361_7som.cif #2
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
> select add #2
618760 atoms, 631042 bonds, 383 pseudobonds, 82655 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
618760 atoms, 631042 bonds, 383 pseudobonds, 82655 residues, 3 models selected
> view matrix models
> #2,0.60547,-0.79527,-0.030802,351.68,0.79583,0.60462,0.033007,-107.01,-0.0076256,-0.044498,0.99898,15.572
> view matrix models
> #2,0.60547,-0.79527,-0.030802,391.86,0.79583,0.60462,0.033007,-64.037,-0.0076256,-0.044498,0.99898,18.156
> view matrix models
> #2,0.60547,-0.79527,-0.030802,415.02,0.79583,0.60462,0.033007,-41.241,-0.0076256,-0.044498,0.99898,19.616
> view matrix models
> #2,0.60547,-0.79527,-0.030802,441.96,0.79583,0.60462,0.033007,14.792,-0.0076256,-0.044498,0.99898,21.744
> view matrix models
> #2,0.60547,-0.79527,-0.030802,351.71,0.79583,0.60462,0.033007,-42.931,-0.0076256,-0.044498,0.99898,23.012
> view matrix models
> #2,0.60547,-0.79527,-0.030802,386.21,0.79583,0.60462,0.033007,-28.571,-0.0076256,-0.044498,0.99898,23.224
> view matrix models
> #2,0.60547,-0.79527,-0.030802,387.1,0.79583,0.60462,0.033007,-20.275,-0.0076256,-0.044498,0.99898,139.88
> transparency 0
> transparency 50
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> view matrix models
> #2,0.48154,-0.87552,-0.039826,447.13,0.87632,0.4803,0.037055,-6.3857,-0.013314,-0.052743,0.99852,144
> view matrix models
> #2,0.48154,-0.87552,-0.039826,458.7,0.87632,0.4803,0.037055,-10.371,-0.013314,-0.052743,0.99852,144.62
> select subtract #2
Nothing selected
> select add #2
618760 atoms, 631042 bonds, 383 pseudobonds, 82655 residues, 3 models selected
> hide #!2 models
> show #!2 models
> view matrix models
> #2,0.24922,-0.96667,0.058711,512.42,-0.93906,-0.25604,-0.22938,787.06,0.23676,0.0020319,-0.97157,765.93
> view matrix models
> #2,0.25272,-0.96681,-0.037524,545.94,-0.9653,-0.24931,-0.077685,737.84,0.065752,0.055854,-0.99627,804.44
> view matrix models
> #2,0.24616,-0.96633,-0.074965,560.93,-0.96809,-0.24888,0.029339,700.2,-0.047008,0.065351,-0.99675,831.88
> view matrix models
> #2,0.24616,-0.96633,-0.074965,551.52,-0.96809,-0.24888,0.029339,907.97,-0.047008,0.065351,-0.99675,826.13
> view matrix models
> #2,0.24616,-0.96633,-0.074965,544.46,-0.96809,-0.24888,0.029339,925.77,-0.047008,0.065351,-0.99675,826.86
> view matrix models
> #2,0.34005,-0.93729,-0.076564,511.39,-0.9389,-0.34298,0.028798,946.03,-0.053253,0.062093,-0.99665,829.45
> view matrix models
> #2,0.34256,-0.93936,-0.015994,489.68,-0.93924,-0.34281,0.017526,950.1,-0.021946,0.0090185,-0.99972,837.91
> view matrix models
> #2,0.34256,-0.93936,-0.015994,494.87,-0.93924,-0.34281,0.017526,948.15,-0.021946,0.0090185,-0.99972,828.66
> view matrix models
> #2,0.41506,-0.90967,-0.015205,466.46,-0.90943,-0.41531,0.021448,960.25,-0.025825,0.0049252,-0.99965,830.89
> view matrix models
> #2,0.58165,-0.81331,-0.014586,393.27,-0.81273,-0.5818,0.031254,980.25,-0.033905,-0.006325,-0.99941,836.28
> view matrix models
> #2,0.6239,-0.78136,-0.014747,372.61,-0.78069,-0.624,0.033952,983.23,-0.035732,-0.0096699,-0.99931,837.73
> view matrix models
> #2,0.44759,-0.89412,-0.014945,453.08,-0.89382,-0.44783,0.023271,965.07,-0.027499,0.0029426,-0.99962,831.91
> view matrix models
> #2,0.44759,-0.89412,-0.014945,448.63,-0.89382,-0.44783,0.023271,937.63,-0.027499,0.0029426,-0.99962,831.39
> hide #!2 models
> select subtract #2
Nothing selected
> hide #!1 models
> show #!2 models
Drag select of 29922 atoms, 30 pseudobonds
> select up
30132 atoms, 30046 bonds, 30 pseudobonds, 6116 residues, 2 models selected
> select up
31290 atoms, 31216 bonds, 30 pseudobonds, 6349 residues, 2 models selected
> select up
39445 atoms, 39476 bonds, 30 pseudobonds, 7692 residues, 2 models selected
> select up
39455 atoms, 39484 bonds, 30 pseudobonds, 7694 residues, 2 models selected
> select up
40645 atoms, 40674 bonds, 30 pseudobonds, 7934 residues, 2 models selected
> select up
40715 atoms, 40742 bonds, 30 pseudobonds, 7948 residues, 2 models selected
> select up
41305 atoms, 41332 bonds, 30 pseudobonds, 8068 residues, 2 models selected
> select up
41343 atoms, 41368 bonds, 30 pseudobonds, 8076 residues, 2 models selected
> select up
45669 atoms, 45694 bonds, 30 pseudobonds, 8954 residues, 2 models selected
> select up
47104 atoms, 47128 bonds, 30 pseudobonds, 9246 residues, 2 models selected
> select up
618760 atoms, 631042 bonds, 147 pseudobonds, 82655 residues, 2 models selected
> select down
47104 atoms, 47128 bonds, 30 pseudobonds, 9246 residues, 2 models selected
> color (#!2 & sel) red
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open ../../Building/CPC_combine_EMR.mrc
Opened CPC_combine_EMR.mrc as #1, grid size 360,360,360, pixel 2.64, shown at
level 4.71, step 2, values float32
> open crCPC_C2_emd25361_7som.cif
crCPC_C2_emd25361_7som.cif title:
Ciliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
[more info...]
Chain information for crCPC_C2_emd25361_7som.cif #2
---
Chain | Description | UniProt
A B C | FAP147 | CFA20_CHLRE 1-190
A1 | FAP239 |
A2 A4 | FAP388 |
A3 | FAP424 |
AA AC AE AG AI AK BA BC BE BG BI BK CA CC CE CG CI CK DC DE DG DI DK EA EC EE
EG EI EK FA FC FE FG FI FK GC GE GG GI GK GM HC HE HG HI HK HM IC IE IG II IK
IM JC JE JG JI JK JM KC KE KG KI KK LC LE LG LI LK MC ME MG MI MK | Tubulin
beta | TBB_CHLRE 1-443
AB AD AF AH AJ AL BB BD BF BH BJ BL CB CD CF CH CJ DB DD DF DH DJ DL EB ED EF
EH EJ EL FB FD FF FH FJ FL GD GF GH GJ GL HD HF HH HJ HL ID IF IH IJ IL JB JD
JF JH JJ JL KB KD KF KH KJ KL LB LD LF LH LJ LL MB MD MF MH MJ ML | Tubulin
alpha | TBA1_CHLRE 1-451
D E bb | Flagellar associated protein | A0A2K3DLJ2_CHLRE 1-2257
F G H I | FAP196 | A0A2K3DKW3_CHLRE 1-1074
J K | FAP213 | A0A2K3DUG8_CHLRE 1-976
L M N O X Y | FAP225 | A0A2K3D8Z6_CHLRE 1-222
P Q R S Z aa cc | FAP178 | PF20_CHLRE 1-606
T U V W | Flagellar WD repeat-containing protein Pf20 | A8I439_CHLRE 1-93
a b c d | Cilia- and flagella-associated protein 20 | A0A2K3CQT7_CHLRE 1-618
e f g | Unknown protein | A8JB78_CHLRE 1-201
h i j | Unknown protein | A8HNF2_CHLRE 1-758
k l s | Unknown protein | A0A2K3DV98_CHLRE 1-528
m n o | FAP65 | A0A2K3CXB9_CHLRE 1-421
p q r | FAP70 | A8HZB8_CHLRE 1-89
Non-standard residues in crCPC_C2_emd25361_7som.cif #2
---
GDP — guanosine-5'-diphosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
OpenGL version: 3.3.0 NVIDIA 550.67
OpenGL renderer: NVIDIA GeForce RTX 4090 D/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: X11DPi-N(T)
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
Cache Size: 14080 KB
Memory:
total used free shared buff/cache available
Mem: 141Gi 30Gi 8.8Gi 167Mi 101Gi 109Gi
Swap: 2.0Gi 940Mi 1.1Gi
Graphics:
03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
DeviceName: Aspeed Video 2500
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.6.0
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.5
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
pandas: 2.1.4
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydantic: 2.7.1
pydantic-core: 2.18.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
starfile: 0.5.2
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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