![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16750 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001ed0ab840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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.map._map, chimerax.surface._surface, 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.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, 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.special._ellip_harm_2, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation (total: 104)
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 14359,
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"captureTime" : "2025-01-31 09:34:13.4373 +0100",
"codeSigningMonitor" : 1,
"incident" : "AC49B566-6DE4-4B8B-932E-4378DE940FD5",
"pid" : 44206,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-30 14:58:31.1696 +0100",
"procStartAbsTime" : 3260440607304,
"procExitAbsTime" : 3823883756196,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"278388F1-1642-52D1-860C-C5E998B9A4D6","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 24,
"sleepWakeUUID" : "5AB5FD25-3102-4124-82AA-AA9E8D997928",
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"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":44206},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4303961751\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100894000-100898000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
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
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Alphafold/AF-
> YNR021W-YeastCCDC47-model_v4.pdb" format pdb
AF-YNR021W-YeastCCDC47-model_v4.pdb title:
Alphafold monomer V2.0 prediction for UPF0674 endoplasmic reticulum membrane
protein YNR021W (P53723) [more info...]
Chain information for AF-YNR021W-YeastCCDC47-model_v4.pdb #1
---
Chain | Description | UniProt
A | UPF0674 endoplasmic reticulum membrane protein YNR021W | YN8B_YEAST 1-404
Computing secondary structure
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> open 7tm3 fromDatabase pdb format mmcif
Summary of feedback from opening 7tm3 fetched from pdb
---
warnings | Atom HO5' is not in the residue template for G /q:1
Atom HO5' is not in the residue template for G /u:1
Atom HO5' is not in the residue template for C /v:1
note | Fetching compressed mmCIF 7tm3 from http://files.rcsb.org/download/7tm3.cif
7tm3 title:
Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate
in complex with the multipass translocon [more info...]
Chain information for 7tm3 #2
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96
3 | Protein transport protein Sec61 gamma |
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224
7 | Nicalin | A0A8C0S144_CANLF -41-521
A | uL2 | G1TT27_RABIT 1-257
B | Nascent chain |
C | uL4 | G1SVW5_RABIT 1-425
D | uL18 | G1SYJ6_RABIT 1-297
E | eL6 | G1SKF7_RABIT 1-291
F | uL30 | G1TUB1_RABIT 1-247
G | eL8 | G1STW0_RABIT 1-319
H | uL6 | G1SWI6_RABIT 1-192
I | uL16 | B7NZQ2_RABIT 1-214
J | uL5 | G1TUB8_RABIT 1-178
K | 28S ribosomal RNA |
L | eL13 | G1TPV0_RABIT 1-211
M | eL14 | G1SZ12_RABIT 1-218
N | eL15 | G1T0C1_RABIT 1-204
O | uL13 |
P | uL22 | G1TVT6_RABIT 1-184
Q | eL18 |
R | eL19 | G1TJR3_RABIT 1-196
S | eL20 |
T | eL21 | G1SHQ2_RABIT 1-160
U | eL22 | G1TSG1_RABIT 1-128
V | uL14 | G1T6D1_RABIT 1-140
W | eL24 | G1SE28_RABIT 1-157
X | uL23 | G1SE76_RABIT 1-156
Y | uL24 | G1SQH0_RABIT 1-145
Z | eL27 | G1TXF6_RABIT 1-136
a | uL15 | G1SNY0_RABIT 1-148
b | eL29 | G1SGR6_RABIT 1-226
c | eL30 | G1TDL2_RABIT 1-115
d | eL31 | G1SHG0_RABIT 1-125
e | eL32 | G1U437_RABIT 1-135
f | eL33 | G1SF08_RABIT 1-110
g | eL34 | G1U945_RABIT 1-116
h | uL29 | G1SIT5_RABIT 1-123
i | eL36 | G1TTQ5_RABIT 1-105
j | eL37 | U3KPD5_RABIT 1-97
k | eL38 | G1U001_RABIT 1-70
l | eL39 | G1TTN1_RABIT 1-51
m | eL40 |
n | eL41 | A0A087WNH4_RABIT 1-25
o | eL42 | G1U344_RABIT 1-106
p | eL43 | G1SY53_RABIT 1-92
q | P-site tRNA |
r | eL28 | G1U7L1_RABIT 1-137
u | 5S ribosomal RNA |
v | 5.8S ribosomal RNA |
w | uL3 | G1TL06_RABIT 2-403
Non-standard residues in 7tm3 #2
---
MG — magnesium ion
ZN — zinc ion
> hide surfaces
> select add #2
261738 atoms, 272680 bonds, 4073 pseudobonds, 12333 residues, 4 models
selected
> hide #1 models
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,91.078,0,1,0,144.55,0,0,1,13.92
> ui mousemode right select
Drag select of 7189 residues, 4 pseudobonds
> select up
207311 atoms, 217953 bonds, 4 pseudobonds, 8791 residues, 2 models selected
> select up
223410 atoms, 234211 bonds, 4 pseudobonds, 9768 residues, 2 models selected
> hide sel
> hide sel cartoons
Drag select of 170 residues
Drag select of 115 residues
> undo
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
Drag select of 80 residues
> select up
1771 atoms, 1783 bonds, 106 residues, 1 model selected
> select up
2045 atoms, 2061 bonds, 124 residues, 1 model selected
> hide sel cartoons
> select #2/H
3113 atoms, 3132 bonds, 190 residues, 1 model selected
> hide sel cartoons
> select #2/h
2145 atoms, 2153 bonds, 122 residues, 1 model selected
> hide sel cartoons
> select #2/l
927 atoms, 939 bonds, 50 residues, 1 model selected
> hide sel cartoons
> select #2/Y
2320 atoms, 2337 bonds, 134 residues, 1 model selected
> hide sel cartoons
> show #1 models
> select add #2
261738 atoms, 272680 bonds, 4073 pseudobonds, 12333 residues, 4 models
selected
> select add #1
265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected
> hide #!2 models
> show #!2 models
> select subtract #2
3324 atoms, 3394 bonds, 404 residues, 1 model selected
> select add #2.1
3324 atoms, 3394 bonds, 3775 pseudobonds, 404 residues, 2 models selected
> select add #2
265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected
> select subtract #2.1
265062 atoms, 276074 bonds, 298 pseudobonds, 12737 residues, 4 models selected
> select add #2
265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> select subtract #2
3324 atoms, 3394 bonds, 404 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,403.28,0,1,0,187.18,0,0,1,424.89
> view matrix models #1,1,0,0,394.53,0,1,0,185.82,0,0,1,419.48
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.56002,-0.33857,0.75614,393.16,0.82675,0.1694,-0.53646,192.2,0.053537,0.92557,0.37478,417.35
> view matrix models
> #1,0.26457,-0.23747,0.93467,392.84,0.93401,-0.17817,-0.30965,191.97,0.24006,0.95491,0.17466,417.65
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.26457,-0.23747,0.93467,403.29,0.93401,-0.17817,-0.30965,255.1,0.24006,0.95491,0.17466,469.12
> view matrix models
> #1,0.26457,-0.23747,0.93467,448.77,0.93401,-0.17817,-0.30965,264.22,0.24006,0.95491,0.17466,357.33
> view matrix models
> #1,0.26457,-0.23747,0.93467,483.59,0.93401,-0.17817,-0.30965,268.86,0.24006,0.95491,0.17466,303.25
> view matrix models
> #1,0.26457,-0.23747,0.93467,506.25,0.93401,-0.17817,-0.30965,360.23,0.24006,0.95491,0.17466,246.58
> view matrix models
> #1,0.26457,-0.23747,0.93467,496.04,0.93401,-0.17817,-0.30965,408.91,0.24006,0.95491,0.17466,279.83
> view matrix models
> #1,0.26457,-0.23747,0.93467,484.16,0.93401,-0.17817,-0.30965,401.09,0.24006,0.95491,0.17466,286.08
> mmaker #1 to #2/4
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7tm3, chain 4 (#2) with AF-YNR021W-YeastCCDC47-model_v4.pdb, chain
A (#1), sequence alignment score = 399.9
RMSD between 107 pruned atom pairs is 1.140 angstroms; (across all 318 pairs:
14.395)
> view matrix models
> #1,0.37726,0.42539,-0.82263,488.41,-0.11789,0.9031,0.41294,397.28,0.91857,-0.058808,0.39085,289.4
> color #1 #ff2600ff
> rainbow sel
> save /Users/annguyen/Desktop/image1.png supersample 3
> color #1 #ff9300ff
> set bgColor white
> set bgColor #ffffff00
> save /Users/annguyen/Desktop/image2.png supersample 3
> close session
> open /Users/annguyen/Downloads/cryosparc_P4_J457_class_01_final_volume.mrc
Opened cryosparc_P4_J457_class_01_final_volume.mrc as #1, grid size
192,192,192, pixel 2.18, shown at level 1.33, step 1, values float32
> volume #1 level 0.3098
> save /Users/annguyen/Desktop/image3.png supersample 3
> open /Users/annguyen/Downloads/cryosparc_P4_J457_class_00_final_volume.mrc
Opened cryosparc_P4_J457_class_00_final_volume.mrc as #2, grid size
192,192,192, pixel 2.18, shown at level 0.858, step 1, values float32
> volume #2 level 0.3912
> save /Users/annguyen/Desktop/image4.png supersample 3
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/10-01-25-Fit map of ChaeRibo-Sec72 local refinement.cxs" format
> session
Opened cryosparc_P4_J32_010_volume_map.mrc as #2, grid size 450,450,450, pixel
0.97, shown at level 0.286, step 1, values float32
Opened cryosparc_P4_J429_class_01_final_volume.mrc as #14, grid size
192,192,192, pixel 2.02, shown at level 0.465, step 1, values float32
Opened cryosparc_P4_J431_003_volume_map.mrc z flip as #16, grid size
400,400,400, pixel 0.97, shown at level 0.162, step 1, values float32
Opened cryosparc_P4_J430_004_volume_map_sharp.mrc z flip as #17, grid size
400,400,400, pixel 0.97, shown at level 0.351, step 1, values float32
Opened cryosparc_P4_J436_003_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32
Opened cryosparc_P4_J436_003_volume_map.mrc z flip as #5, grid size
400,400,400, pixel 0.97, shown at level 0.126, step 1, values float32
Opened cryosparc_P4_J437_003_volume_map.mrc as #6, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32
Opened cryosparc_P4_J437_003_volume_map.mrc z flip as #12, grid size
400,400,400, pixel 0.97, shown at level 0.0853, step 1, values float32
Opened cryosparc_P4_J439_003_volume_map.mrc as #13, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32
Opened cryosparc_P4_J439_003_volume_map.mrc z flip as #18, grid size
400,400,400, pixel 0.97, shown at level 0.228, step 1, values float32
Opened 241024_P4_J458_004_volume_map.mrc as #19, grid size 400,400,400, pixel
0.97, shown at level 0.0325, step 1, values float32
Opened emd_12977 map of 7old.map as #20, grid size 486,486,486, pixel 1.1,
shown at level 2.25, step 1, values float32
Opened cryosparc_P4_J508_007_volume_map.mrc as #21, grid size 432,432,432,
pixel 0.97, shown at level 0.107, step 1, values float32
Opened cryosparc_P4_J513_005_volume_map.mrc as #22, grid size 432,432,432,
pixel 0.97, shown at level 0.0523, step 1, values float32
Opened cryosparc_P4_J458_004_1 to 60 uM.mrc as #23, grid size 400,400,400,
pixel 0.97, shown at level 0.0277, step 1, values float32
Opened cryosparc_P4_J459_004_1 to 60 uM.mrc z flip as #25, grid size
400,400,400, pixel 0.97, shown at level 0.0372, step 1, values float32
opened ChimeraX session
> hide #!20 models
> hide #!22 models
> hide #!8 models
> open /Users/annguyen/Downloads/cryosparc_P4_J470_004_volume_map.mrc
Opened cryosparc_P4_J470_004_volume_map.mrc as #24, grid size 432,432,432,
pixel 0.97, shown at level 0.643, step 2, values float32
> volume #24 level 0.6425
> volume #24 step 1
> volume #24 level 0.2073
> ui tool show "Side View"
> ui tool show EMalign
> show #!23 models
> hide #!23 models
> show #!20 models
Aligning the volumes using EMalign took 66.59 seconds
Rotation:
[[0.224 0.542 0.810],
[-0.974 0.144 0.173]
[-0.023 -0.828 0.560]]
Translation:
[-22.500, -68.625, -24.750]
Reflection:
1
Applying 'Fit in Map' to perform additional refinement:
Fit map cryosparc_P4_J470_004_volume_map.mrc in map emd_12977 map of 7old.map
using 3779673 points
correlation = 0.2031, correlation about mean = 0.01422, overlap = 6.094e+05
steps = 524, shift = 57.7, angle = 21.2 degrees
Position of cryosparc_P4_J470_004_volume_map.mrc (#24) relative to emd_12977
map of 7old.map (#20) coordinates:
Matrix rotation and translation
0.88423432 -0.42930989 -0.18390931 224.94048323
0.28488345 0.18374703 0.94078606 -126.92981832
-0.37009598 -0.88426806 0.28477871 557.64594680
Axis -0.92706142 0.09457609 0.36278436
Axis point 0.00000000 311.71591871 403.53963021
Rotation angle (degrees) 79.84102241
Shift along axis -18.23294052
\----------------------------------------------------------------------------------------
Stats before alignment:
correlation = 0.0756, correlation about mean = 0.0620, overlap = 551750.015
\----------------------------------------------------------------------------------------
Stats after alignning with EMalign:
correlation = 0.0880, correlation about mean = 0.0843, overlap = 460238.537
\----------------------------------------------------------------------------------------
Stats after refining with Fit in Map:
correlation = 0.1191, correlation about mean = 0.1156, overlap = 622991.638
\----------------------------------------------------------------------------------------
> hide #!20 models
> clip off
Aligning the volumes using EMalign took 44.26 seconds
Rotation:
[[0.414 -0.775 -0.478],
[0.902 0.279 0.329]
[-0.121 -0.568 0.814]]
Translation:
[56.250, 29.250, -60.750]
Reflection:
1
Applying 'Fit in Map' to perform additional refinement:
Fit map cryosparc_P4_J470_004_volume_map.mrc in map emd_12977 map of 7old.map
using 3779088 points
correlation = 0.2432, correlation about mean = 0.09047, overlap = 7.632e+05
steps = 516, shift = 33.2, angle = 14.5 degrees
Position of cryosparc_P4_J470_004_volume_map.mrc (#24) relative to emd_12977
map of 7old.map (#20) coordinates:
Matrix rotation and translation
0.95882622 -0.28389857 0.00733729 82.15337832
0.06446600 0.24274092 0.96794677 -101.80044306
-0.27657976 -0.92761976 0.25104816 544.04216957
Axis -0.97302763 0.14573962 0.17882166
Axis point 0.00000000 306.92126698 345.66523677
Rotation angle (degrees) 76.92021498
Shift along axis 2.51265733
\----------------------------------------------------------------------------------------
Stats before alignment:
correlation = 0.1191, correlation about mean = 0.1156, overlap = 622991.638
\----------------------------------------------------------------------------------------
Stats after alignning with EMalign:
correlation = 0.1204, correlation about mean = 0.1169, overlap = 629921.297
\----------------------------------------------------------------------------------------
Stats after refining with Fit in Map:
correlation = 0.1511, correlation about mean = 0.1477, overlap = 790859.233
\----------------------------------------------------------------------------------------
> show #!20 models
> color #24 #b2ffff93 models
> color #24 #b2ffff94 models
> volume #25 level 0.2488
> volume #25 level 0.3123
> hide #!25 models
> volume #25 level 0.4441
> hide #!25 models
> volume #25 level 0.5044
> hide #!20 models
> hide #!25 models
> volume #24 level 0.4157
> color #24 #b2ffffff models
> volume #24 level 0.4494
> volume #24 level 0.5086
> show #!1 models
> select add #24
2 models selected
> view matrix models
> #24,0.81486,0.39076,0.42815,-505.06,-0.35236,0.9204,-0.16942,358.66,-0.46027,-0.012808,0.88769,38.433
> volume #2 level 0.05095
> hide #!2 models
> volume #1 level 0.3733
> hide #!1 models
> volume #24 level 0.4635
> volume #24 level 0.4607
> volume #24 level 0.4691
> volume #24 level 0.3931
> volume #24 level 0.3678
> volume #24 level 0.3565
> volume #24 level 0.2777
> volume #24 level 0.2327
> volume #24 level 0.2298
> volume #24 level 0.2045
> volume #24 level 0.2383
> volume #24 level 0.2862
> volume #24 level 0.289
> volume #24 level 0.3171
> volume #24 level 0.3199
> volume #24 level 0.3396
> volume #24 level 0.3537
> volume #24 level 0.3594
> volume #24 level 0.365
> volume #24 level 0.41
> volume #24 level 0.4128
> volume #24 level 0.4241
> volume #24 level 0.4382
> volume #24 level 0.4438
> volume #24 level 0.4607
> volume #24 level 0.4663
> volume #24 level 0.4832
> volume #24 level 0.4945
> volume #24 level 0.4973
> show #!7 models
> view matrix models
> #24,0.81486,0.39076,0.42815,-566.23,-0.35236,0.9204,-0.16942,342.63,-0.46027,-0.012808,0.88769,14.796
> view matrix models
> #24,0.81486,0.39076,0.42815,-268.56,-0.35236,0.9204,-0.16942,-79.513,-0.46027,-0.012808,0.88769,80.645
> view matrix models
> #24,0.81486,0.39076,0.42815,-305.94,-0.35236,0.9204,-0.16942,-70.442,-0.46027,-0.012808,0.88769,68.055
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.2131,0.20263,-0.95579,406.52,-0.075588,0.97191,0.2229,-268.19,0.9741,0.11975,-0.19179,-20.854
> view matrix models
> #24,-0.96541,-0.26056,-0.0091224,433.93,-0.22953,0.8328,0.50374,-277.62,-0.12366,0.48841,-0.86381,373.54
> view matrix models
> #24,-0.99084,0.13161,0.030162,338.08,0.111,0.66681,0.73692,-395.16,0.076877,0.73352,-0.67531,209.86
> view matrix models
> #24,-0.98485,0.16651,0.048353,323.14,0.15176,0.69297,0.70481,-402.47,0.083848,0.70148,-0.70774,224.92
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.98485,0.16651,0.048353,365.7,0.15176,0.69297,0.70481,-213.67,0.083848,0.70148,-0.70774,359.72
> view matrix models
> #24,-0.98485,0.16651,0.048353,422.13,0.15176,0.69297,0.70481,-162.82,0.083848,0.70148,-0.70774,259.43
> fitmap #7 inMap #24
Fit molecule 7old (#7) to map cryosparc_P4_J470_004_volume_map.mrc (#24) using
214209 atoms
average map value = 0.255, steps = 272
shifted from previous position = 32.6
rotated from previous position = 12.8 degrees
atoms outside contour = 166436, contour level = 0.4973
Position of 7old (#7) relative to cryosparc_P4_J470_004_volume_map.mrc (#24)
coordinates:
Matrix rotation and translation
-0.99195802 -0.08597927 0.09288084 537.06027100
-0.10979205 0.94963433 -0.29349676 135.06712643
-0.06296820 -0.30133404 -0.95143723 646.59826071
Axis -0.04964939 0.98730837 -0.15085465
Axis point 284.89643728 0.00000000 322.85872966
Rotation angle (degrees) 175.47315242
Shift along axis 9.14583899
> color #24 #b2ffffcf models
> color #24 #b2ffffff models
> view matrix models
> #24,-0.98485,0.16651,0.048353,299.66,0.15176,0.69297,0.70481,-284,0.083848,0.70148,-0.70774,156.33
> view matrix models
> #24,-0.98485,0.16651,0.048353,386.04,0.15176,0.69297,0.70481,-144.87,0.083848,0.70148,-0.70774,261.84
> color #24 #b2ffffd3 models
> view matrix models
> #24,-0.98485,0.16651,0.048353,417.11,0.15176,0.69297,0.70481,-156.27,0.083848,0.70148,-0.70774,232.68
> volume flip #24 axis z
Opened cryosparc_P4_J470_004_volume_map.mrc z flip as #26, grid size
432,432,432, pixel 1.24, shown at step 1, values float32
> volume #24 color #b2ffff
> view matrix models
> #24,-0.98485,0.16651,0.048353,472.39,0.15176,0.69297,0.70481,-155.59,0.083848,0.70148,-0.70774,202
> hide #!26 models
> show #!26 models
> hide #!24 models
> select subtract #24
Nothing selected
> select add #26
2 models selected
> color #26 #b2ffffff models
> view matrix models
> #26,-0.98485,0.16651,0.048353,336.66,0.15176,0.69297,0.70481,-97.35,0.083848,0.70148,-0.70774,209.36
> view matrix models
> #26,-0.98485,0.16651,0.048353,175.16,0.15176,0.69297,0.70481,20.1,0.083848,0.70148,-0.70774,148.72
> view matrix models
> #26,-0.98485,0.16651,0.048353,171.21,0.15176,0.69297,0.70481,47.196,0.083848,0.70148,-0.70774,131.73
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.51227,-0.2572,-0.81941,91.979,-0.74447,0.34271,-0.57299,670.99,0.42819,0.90355,-0.015918,-172.36
> view matrix models
> #26,-0.12566,-0.077561,-0.98904,256.86,-0.77327,0.63221,0.048665,460.39,0.6215,0.77091,-0.13942,-161.72
> close #26
> show #!24 models
> ui mousemode right "translate selected models"
> select add #24
2 models selected
> view matrix models
> #24,-0.98485,0.16651,0.048353,464.88,0.15176,0.69297,0.70481,-108.42,0.083848,0.70148,-0.70774,232.32
> color #24 #b2ffffd7 models
> color #24 #b2ffffd6 models
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.98485,0.16651,0.048353,466.82,0.15176,0.69297,0.70481,-146.01,0.083848,0.70148,-0.70774,226.3
> view matrix models
> #24,-0.98485,0.16651,0.048353,421.12,0.15176,0.69297,0.70481,-111.7,0.083848,0.70148,-0.70774,205.63
> view matrix models
> #24,-0.98485,0.16651,0.048353,418.89,0.15176,0.69297,0.70481,-165.44,0.083848,0.70148,-0.70774,234.98
> volume #24 level 0.6606
> fitmap #7 inMap #24
Fit molecule 7old (#7) to map cryosparc_P4_J470_004_volume_map.mrc (#24) using
214209 atoms
average map value = 0.2548, steps = 160
shifted from previous position = 26.5
rotated from previous position = 3.67 degrees
atoms outside contour = 187584, contour level = 0.66059
Position of 7old (#7) relative to cryosparc_P4_J470_004_volume_map.mrc (#24)
coordinates:
Matrix rotation and translation
-0.98776464 -0.07472793 0.13688219 522.41411799
-0.11720443 0.93473165 -0.33546964 153.16751387
-0.10287916 -0.34740824 -0.93205332 667.73111883
Axis -0.04897138 0.98348548 -0.17423582
Axis point 285.83482002 0.00000000 331.17234155
Rotation angle (degrees) 172.99859438
Shift along axis 8.71200957
> view matrix models
> #24,-0.98485,0.16651,0.048353,400.13,0.15176,0.69297,0.70481,-163.68,0.083848,0.70148,-0.70774,205.82
> hide #!24 models
> select subtract #24
Nothing selected
> hide #!7 models
> show #!24 models
> color #24 #b2ffffff models
> volume #24 level 0.4523
> volume #24 level 0.3059
> close #24
> open "/Volumes/TOSHIBA EXT/CryoSparc
> /cryosparc_P4_J470_004_volume_map_sharp.mrc-2.download/"
'/Volumes/TOSHIBA EXT/CryoSparc
/cryosparc_P4_J470_004_volume_map_sharp.mrc-2.download/' has no suffix
> show #!22 models
> hide #!22 models
> show #!21 models
> hide #!21 models
> close session
> open "/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J520_mask.mrc"
Opened cryosparc_P4_J520_mask.mrc as #1, grid size 432,432,432, pixel 0.97,
shown at level 0.922, step 2, values float32
> open "/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J470_004_volume_map
> (1).mrc"
Opened cryosparc_P4_J470_004_volume_map (1).mrc as #2, grid size 432,432,432,
pixel 0.97, shown at level 0.643, step 2, values float32
> volume #1 color #b2b2b2bc
> volume #1 color #b2b2b2bd
> volume #2 step 1
> volume #2 level 0.4234
> volume #2 level 0.1376
> ui tool show "Side View"
> volume #2 level 0.1618
> volume #2 level 0.1296
> save /Users/annguyen/Desktop/image5.png supersample 3
> save /Users/annguyen/Desktop/image6.png supersample 3
> close session
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/13-02-25 fit TPR domian in map of RiboSec72.cxs"
Opened cryosparc_P26_J18_003_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.245, step 1, values float32
Opened cryosparc_P26_J18_003_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.34, shown at level 1.28, step 2, values float32
Opened cryosparc_P4_J508_007_volume_map.mrc as #15, grid size 432,432,432,
pixel 0.97, shown at level 0.469, step 1, values float32
Opened cryosparc_P4_J532_002_with particle substraction center.mrc as #16,
grid size 432,432,432, pixel 0.97, shown at level 0.0316, step 1, values
float32
Opened cryosparc_P4_J521_005_wo particle substraction side.mrc as #17, grid
size 432,432,432, pixel 0.97, shown at level 0.111, step 1, values float32
Opened cryosparc_P4_J527_005_wo particle substrction center.mrc as #18, grid
size 432,432,432, pixel 0.97, shown at level 0.111, step 1, values float32
Opened cryosparc_P4_J531_002_with particle substraction side.mrc as #19, grid
size 432,432,432, pixel 0.97, shown at level 0.05, step 1, values float32
opened ChimeraX session
> save /Users/annguyen/Desktop/image7.png supersample 3
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> save /Users/annguyen/Desktop/image8.png supersample 3
> hide #!16 models
> show #!17 models
> color #17 #919191d3 models
> color #17 #919191bd models
> volume #17 level 0.1193
> volume #17 level 0.1401
> volume #17 level 0.1027
> ui tool show "Hide Dust"
> surface dust #17 size 5.82
> color #17 #91919187 models
> color #17 #91919184 models
> color #17 #91919185 models
> clip off
> volume #17 level 0.1484
> volume #17 level 0.1941
> volume #17 level 0.02374
> show #!16 models
> hide #!17 models
> save /Users/annguyen/Desktop/image9.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/annguyen/Desktop/movie1.mp4
Movie saved to /Users/annguyen/Desktop/movie1.mp4
> save /Users/annguyen/Desktop/image10.png supersample 3
> hide #!16 models
> show #!17 models
> volume #17 level 0.06114
> volume #17 level 0.1276
> volume #17 level 0.1235
> volume #17 level 0.111
> show #!16 models
> hide #!17 models
> volume #16 level 0.111
> volume #16 level 0.03447
> volume #16 level 0.03141
> hide #!16 models
> show #!17 models
> save /Users/annguyen/Desktop/image7.png supersample 3
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!16 models
> save /Users/annguyen/Desktop/image8.png supersample 3
> hide #!16 models
> show #!15 models
> volume #15 level 0.09918
> color #15 #588b94ad models
> color #15 #588b949d models
> color #15 #588b9497 models
> color #15 #588b9496 models
> color #15 #ecefefff models
> color #15 #929292ff models
> color #15 darkgrey models
> color #15 #a9a9a9a8 models
> open "/Volumes/TOSHIBA EXT/CryoSparc /110125_P4_J470_004_volume_map.mrc"
Opened 110125_P4_J470_004_volume_map.mrc as #20, grid size 432,432,432, pixel
0.97, shown at level 0.643, step 2, values float32
> fitmap #20 to #15
Expected a keyword
> ui tool show "Fit in Map"
> volume #20 level 0.6425
> volume #20 step 1
> fitmap #20 inMap #15
Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 805166 points
correlation = 0.5839, correlation about mean = 0.02471, overlap = 1.385e+05
steps = 560, shift = 10.2, angle = 23.5 degrees
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:
Matrix rotation and translation
-0.98428643 -0.17517813 0.02220026 456.74807319
0.15184765 -0.90388049 -0.39992794 443.73306515
0.09012502 -0.39027259 0.91627768 73.49476206
Axis 0.02889570 -0.20327929 0.97869432
Axis point 208.26201902 249.13621015 0.00000000
Rotation angle (degrees) 170.38234946
Shift along axis -5.07478190
> ui tool show EMalign
Aligning the volumes using EMalign took 41.50 seconds
Rotation:
[[1.000 -0.003 0.021],
[0.003 1.000 -0.010]
[-0.021 0.010 1.000]]
Translation:
[0.000, 0.000, 0.000]
Reflection:
0
Applying 'Fit in Map' to perform additional refinement:
Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 805293 points
correlation = 0.6057, correlation about mean = 0.03729, overlap = 1.483e+05
steps = 168, shift = 6.46, angle = 7.44 degrees
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:
Matrix rotation and translation
-0.98360871 -0.17003199 0.06002529 445.08953919
0.11631208 -0.85266107 -0.50935313 464.32653872
0.13778756 -0.49402251 0.85846162 100.85272092
Axis 0.05159898 -0.26172802 0.96376138
Axis point 201.86600584 263.10761087 0.00000000
Rotation angle (degrees) 171.45677611
Shift along axis -1.36314246
\----------------------------------------------------------------------------------------
Stats before alignment:
correlation = 0.3252, correlation about mean = 0.3136, overlap = 366124.319
\----------------------------------------------------------------------------------------
Stats after alignning with EMalign:
correlation = 0.3253, correlation about mean = 0.3195, overlap = 366217.448
\----------------------------------------------------------------------------------------
Stats after refining with Fit in Map:
correlation = 0.3432, correlation about mean = 0.3375, overlap = 386350.541
\----------------------------------------------------------------------------------------
> select add #20
2 models selected
> view matrix models
> #20,0.97877,0.14201,-0.1478,146.08,-0.055502,0.87778,0.47583,-221.39,0.19731,-0.45753,0.86703,132.15
> view matrix models
> #20,0.97877,0.14201,-0.1478,215.81,-0.055502,0.87778,0.47583,-305.26,0.19731,-0.45753,0.86703,167.67
> volume #20 level 0.06958
> volume #20 level 0.1269
> view matrix models
> #20,0.97877,0.14201,-0.1478,200.08,-0.055502,0.87778,0.47583,-271.99,0.19731,-0.45753,0.86703,133.16
> ui mousemode right "move picked models"
> view matrix models
> #20,0.97877,0.14201,-0.1478,177.48,-0.055502,0.87778,0.47583,-246.68,0.19731,-0.45753,0.86703,60.84
> view matrix models
> #20,0.97877,0.14201,-0.1478,186.78,-0.055502,0.87778,0.47583,-228.7,0.19731,-0.45753,0.86703,119.27
> ui mousemode right "rotate selected models"
> view matrix models
> #20,-0.99567,0.086636,-0.033657,591.51,-0.090674,-0.98498,0.14697,238.86,-0.020419,0.14939,0.98857,12.321
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.99567,0.086636,-0.033657,532.39,-0.090674,-0.98498,0.14697,439.89,-0.020419,0.14939,0.98857,-40.753
> view matrix models
> #20,-0.99567,0.086636,-0.033657,411.69,-0.090674,-0.98498,0.14697,414.91,-0.020419,0.14939,0.98857,-31.323
Aligning the volumes using EMalign took 41.68 seconds
Rotation:
[[0.999 0.015 -0.035],
[-0.016 0.999 -0.030]
[0.034 0.031 0.999]]
Translation:
[0.000, 0.000, 0.000]
Reflection:
0
Applying 'Fit in Map' to perform additional refinement:
Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 4771418 points
correlation = 0.9808, correlation about mean = 0.9194, overlap = 9.601e+05
steps = 328, shift = 9.72, angle = 12.5 degrees
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:
Matrix rotation and translation
0.99913639 0.01530929 0.03862765 -11.46678109
-0.01606262 0.99968531 0.01926815 0.84750554
-0.03832051 -0.01987197 0.99906789 11.76656337
Axis -0.42611207 0.83772209 -0.34154091
Axis point 314.14671375 0.00000000 286.47758692
Rotation angle (degrees) 2.63235022
Shift along axis 1.57734513
\----------------------------------------------------------------------------------------
Stats before alignment:
correlation = 0.4967, correlation about mean = 0.4924, overlap = 559211.345
\----------------------------------------------------------------------------------------
Stats after alignning with EMalign:
correlation = 0.4552, correlation about mean = 0.4506, overlap = 512497.332
\----------------------------------------------------------------------------------------
Stats after refining with Fit in Map:
correlation = 0.9457, correlation about mean = 0.9456, overlap = 1064762.828
\----------------------------------------------------------------------------------------
> hide #!15 models
> color #20 #797979ff models
> color #20 #919191ff models
> color #20 #9191919c models
> color #20 #9191918c models
> volume #20 level 0.1139
> ui tool show "Hide Dust"
> surface dust #20 size 5.82
> save /Users/annguyen/Desktop/image9.png supersample 3
> select add #16
4 models selected
> select subtract #16
2 models selected
> select subtract #20
Nothing selected
> save /Users/annguyen/Desktop/image10.png supersample 3
===== 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
> open "/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J598_003_volume_map.mrc"
Opened cryosparc_P4_J598_003_volume_map.mrc as #1, grid size 432,432,432,
pixel 0.97, shown at level 0.641, step 2, values float32
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 7 days, 21 hours, 49 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
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: 2023.11.17
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-EMalign: 0.1.1
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-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
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
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 (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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