![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17718 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-14.6.1-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 0x00000001ec470f40 (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.pdb_lib._load_libs, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, 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.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, 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._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.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast (total: 125)
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{
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"procRole" : "Background",
"version" : 2,
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"captureTime" : "2025-05-17 16:07:38.1920 -0400",
"codeSigningMonitor" : 1,
"incident" : "C8C94F8D-FC94-4F97-9583-1160421A8C11",
"pid" : 84275,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-16 13:11:16.3726 -0400",
"procStartAbsTime" : 6312592699551,
"procExitAbsTime" : 6760709206897,
"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"},
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"crashReporterKey" : "7C2E0158-62F6-DBDC-2BC1-144DF5416C2D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "16C3A4FF-EDD6-4BC6-AD37-0E27460191DA",
"sip" : "enabled",
"vmRegionInfo" : "0x2e21258a3448 is not in any region. Bytes after previous region: 50238862275657 Bytes before following region: 54833217653688\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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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
> windowsize 720 720
> size stickRadius 0.2
Changed 0 bond radii
> open "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/emd_10480.map"
> name 6TEDmap
Opened 6TEDmap as #1, grid size 360,360,360, pixel 1.05, shown at level
0.0148, step 2, values float32
> surface dust #1 size 10.5
> volume #1 step 1
> volume #1 level 0.016
> open 6TED
6ted title:
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6
uncovers allosteric elongation activation by RTF1 [more info...]
Chain information for 6ted #2
---
Chain | Description | UniProt
A | DNA-directed RNA polymerase subunit | A0A480RVL6_PIG 1-1984
B | DNA-directed RNA polymerase subunit beta | I3LGP4_PIG -76-1174
C | RNA polymerase II subunit C | I3LCH3_PIG 1-275
D | RNA polymerase II subunit D | A0A287ADR4_PIG 1-142
E | RNA polymerase II subunit E | I3LSI7_PIG 1-210
F | RNA polymerase II subunit F | F1SKN8_PIG 1-127
G | RNA polymerase II subunit G | I3LJZ9_PIG 1-172
H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | I3LCB2_PIG 1-150
I | DNA-directed RNA polymerase II subunit RPB9 | RPB9_PIG 1-125
J | Uncharacterized protein | A0A287B432_PIG 1-67
K | Uncharacterized protein | F1RKE4_PIG 1-117
L | Uncharacterized protein | I3LN51_PIG 1-58
M | Transcription elongation factor SPT6 | SPT6H_HUMAN 1-1726
N | DNA (37-MER) |
P | RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3') |
Q | RNA polymerase-associated protein CTR9 homolog | CTR9_HUMAN 1-1173
R | RNA polymerase-associated protein RTF1 homolog | RTF1_HUMAN 1-710
T | Template DNA |
U | RNA polymerase-associated protein LEO1 | LEO1_HUMAN 1-673
V | RNA polymerase II-associated factor 1 homolog | PAF1_HUMAN 1-531
W | WD repeat-containing protein 61 | WDR61_HUMAN 1-305
X | Parafibromin | CDC73_HUMAN 1-531
Y | Transcription elongation factor SPT4 | SPT4H_HUMAN 1-117
Z | Transcription elongation factor SPT5 | SPT5H_HUMAN 1-1087
Non-standard residues in 6ted #2
---
MG — magnesium ion
ZN — zinc ion
> runscript "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/style_sheet.cxc"
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix default arrows false xsection oval width 3
> thickness 1.2
> nucleotides fill
> style stick
Changed 57142 atom styles
> graphics silhouettes width 3
> lighting depthCue false
> lighting soft
> lighting multiShadow 512
> graphics silhouettes true
> graphics bgColor white
> color /Y pale green
> color /Z forest green
> hide atoms
> show /Z:163-268 /Y cartoons
> color zone #1 near /Z:163-268 /Y distance 2.5
> view matrix camera
> 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11
> show /Z:163-268 /Y surfaces
> hide /Y,Z cartoons
> transparency /Y,Z 80
> transparency /Y,Z 90
> view matrix camera
> 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11
> volume #1 level 0.02275
> view matrix camera
> 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11
> volume #1 level 0.025
> volume #1 level 0.026
> save "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/6TEDNGN.png"
> format png width 1440 height 1440 supersample 4 transparentBackground true
> volume #1 level 0.02
> save "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/6TEDNGN.png"
> format png width 1440 height 1440 supersample 4 transparentBackground true
> show /Y,Z cartoons
> open "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Figures/IWS1
> interactions/cryosparc_P146_J525_007_volume_map.mrc" name J525
Opened J525 as #3, grid size 460,460,460, pixel 1.19, shown at level 0.014,
step 2, values float32
> surface dust #3 size 11.9
> volume #3 step 1
> volume #3 level 0.05
> hide #!1 models
> hide #!2 models
> open "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Structures/Revision 1
> modeling intermediates/250509_model_it062.pdb" name EC
Chain information for EC #4
---
Chain | Description
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
a | No description available
b | No description available
c g | No description available
d h | No description available
e | No description available
f | No description available
i | No description available
l | No description available
> runscript "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/style_sheet.cxc"
> cartoon style nucleic xsection oval width 2.5 thickness 2.5
> cartoon style protein modeHelix default arrows false xsection oval width 3
> thickness 1.2
> nucleotides fill
> style stick
Changed 201822 atom styles
> graphics silhouettes width 3
> lighting depthCue false
> lighting soft
> lighting multiShadow 512
> graphics silhouettes true
> graphics bgColor white
> runscript "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/naming.cxc"
> name PolII ##name="EC"/A-L
> name SPT6 ##name="EC"/M
> name ELOF1 ##name="EC"/O
> name CTR9 ##name="EC"/Q
> name RTF1 ##name="EC"/R
> name TFIIS ##name="EC"/S
> name LEO1 ##name="EC"/U
> name PAF1 ##name="EC"/V
> name WDR61 ##name="EC"/W
> name CDC73 ##name="EC"/X
> name SPT4 ##name="EC"/Y
> name SPT5 ##name="EC"/Z
> name IWS1 ##name="EC"/i
> name H2A ##name="EC"/c,g
> name H2B ##name="EC"/d,h
> name H3 ##name="EC"/a,e
> name H4 ##name="EC"/b,f
> name LEDGF ##name="EC"/l
> name Nucleic-acids ##name="EC"/T,N,P
> name template ##name="EC"/T
> name nontemplate ##name="EC"/N
> name RNA ##name="EC"/P
> runscript "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Scripts/coloring.cxc"
> color PolII silver
> color ELOF1 cyan
> color SPT4 pale green
> color SPT5 forest green
> color SPT6 dark blue
> color RTF1 hot pink
> color CDC73 brown
> color PAF1 green yellow
> color LEO1 purple
> color CTR9 orange
> color WDR61 teal
> color TFIIS #ffc300
> color IWS1 pink
> color template navy
> color nontemplate light steel blue
> color RNA red
> color H2A yellow
> color H2B red
> color H3 dodger blue
> color H4 chartreuse
> color LEDGF orchid
> color Mg deeppink
> style Mg sphere
Changed 2 atom styles
> show Mg atoms
> size Mg atomRadius 1.5
Changed 2 atom radii
> hide atoms
> show ##name=EC/Z:163-268 ##name=EC/Y cartoons
> color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 2.5
> view matrix camera
> -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43
> volume #3 level 0.0695
> volume #3 level 0.07
> view matrix camera
> -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43
> hide cartoons
> color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 2.75
> color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3
> color #3 silver
> color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3
> save "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/NGNdensity.png"
> format png width 1440 height 1440 supersample 4 transparentBackground true
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> view matrix camera
> 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11
> show #2/B cartoons
> hide #2/B cartoons
> volume #1 level 0.02811
> close #3
> open "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/IWS1_classification_tree/cryosparc_P146_J154_007_volume_map.mrc"
Opened cryosparc_P146_J154_007_volume_map.mrc as #3, grid size 460,460,460,
pixel 1.19, shown at level 0.0136, step 2, values float32
> surface dust #3 size 11.9
> volume #3 step 1
> volume #3 level 0.07
> color #3 silver
> color zone #3 near #4/A,B,O,i,M #4/Z:163-268 #4/Y distance 3
> view matrix camera
> -0.87789,0.47882,0.0061785,314.26,-0.45091,-0.83094,0.32591,322.65,0.16118,0.28333,0.94538,506.43
> hide #!1 models
> hide #!2 models
> volume #3 level 0.06044
> volume #3 level 0.05
> save "/Users/dellasyau/Dropbox
> (HMS)/Syau_IWS1/Extended_Data_Figures/Interactions_Extended/NGNdensity.png"
> format png width 1440 height 1440 supersample 4 transparentBackground true
> mmaker #4/A to #2/A
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 6ted, chain A (#2) with EC, chain A (#4), sequence alignment score
= 6599.3
RMSD between 1363 pruned atom pairs is 0.496 angstroms; (across all 1393
pairs: 0.713)
> hide #!3 models
> show #!2 models
> show #!1 models
> show #4 cartoons
> view matrix camera
> 0.01311,-0.39465,0.91874,375.79,0.77299,-0.57883,-0.25967,96.813,0.63428,0.71358,0.29747,280.11
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> close #1-4
> open /Users/dellasyau/Downloads/cryosparc_P146_J685_007_volume_map.mrc
Opened cryosparc_P146_J685_007_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.72, shown at level 0.102, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J686_005_volume_map.mrc
Opened cryosparc_P146_J686_005_volume_map.mrc as #2, grid size 360,360,360,
pixel 1.72, shown at level 0.109, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J687_006_volume_map.mrc
Opened cryosparc_P146_J687_006_volume_map.mrc as #3, grid size 360,360,360,
pixel 1.72, shown at level 0.142, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #3 step 1
> hide #!2 models
> hide #!3 models
> volume #1 level 0.1771
> volume #1 level 0.2087
> volume #2 level 0.2054
> show #!3 models
> hide #!2 models
> volume #3 level 0.2778
> volume #3 level 0.2559
> volume #3 level 0.2075
> volume #2 level 0.228
> volume #1 level 0.1857
> close #1-3
> open /Users/dellasyau/Downloads/cryosparc_P146_J688_003_volume_map.mrc
Opened cryosparc_P146_J688_003_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.72, shown at level 0.0948, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J689_002_volume_map.mrc
Opened cryosparc_P146_J689_002_volume_map.mrc as #2, grid size 360,360,360,
pixel 1.72, shown at level 0.079, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J690_004_volume_map.mrc
Opened cryosparc_P146_J690_004_volume_map.mrc as #3, grid size 360,360,360,
pixel 1.72, shown at level 0.102, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J691_002_volume_map.mrc
Opened cryosparc_P146_J691_002_volume_map.mrc as #4, grid size 360,360,360,
pixel 1.72, shown at level 0.078, step 2, values float32
> volume step 1
> volume level 0.2
> volume #2 level 0.1121
> volume #3 level 0.182
> volume #3 level 0.2067
> volume #4 level 0.1365
> show #!2 models
> open "/Users/dellasyau/HMS Dropbox/Della Syau/Syau_IWS1/Structures/Revision
> 1 modeling intermediates/250509_model_it062.pdb"
Chain information for 250509_model_it062.pdb #5
---
Chain | Description
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
a | No description available
b | No description available
c g | No description available
d h | No description available
e | No description available
f | No description available
i | No description available
l | No description available
> hide atoms
> show cartoons
> show #!1 models
> hide #!2 models
> vop flip #2
Opened cryosparc_P146_J689_002_volume_map.mrc z flip as #6, grid size
360,360,360, pixel 1.72, shown at step 1, values float32
> vop flip #1
Opened cryosparc_P146_J688_003_volume_map.mrc z flip as #7, grid size
360,360,360, pixel 1.72, shown at step 1, values float32
> hide #!6 models
> ui mousemode right "rotate selected models"
> select add #5
144680 atoms, 146848 bonds, 67 pseudobonds, 9652 residues, 3 models selected
> view matrix models
> #5,0.94375,-0.33067,0.0014512,104.46,0.29593,0.84263,-0.44988,97.324,0.14754,0.425,0.89309,-123.16
> view matrix models
> #5,0.41477,-0.87257,0.25805,313.92,0.90802,0.41525,-0.055389,-56.191,-0.058825,0.25729,0.96454,-45.125
> view matrix models
> #5,-0.73785,-0.60384,-0.3016,696.79,0.66378,-0.73016,-0.16204,350.53,-0.12237,-0.31976,0.93956,136.26
> view matrix models
> #5,-0.79426,-0.53592,-0.28625,688.19,0.59084,-0.79111,-0.15829,384.78,-0.14163,-0.29485,0.94499,132.8
> view matrix models
> #5,-0.84,-0.4017,-0.36474,685.83,0.51314,-0.80659,-0.29343,447.92,-0.17632,-0.43364,0.88367,197.36
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.84,-0.4017,-0.36474,738.06,0.51314,-0.80659,-0.29343,424.09,-0.17632,-0.43364,0.88367,244.98
> view matrix models
> #5,-0.84,-0.4017,-0.36474,770.67,0.51314,-0.80659,-0.29343,466.28,-0.17632,-0.43364,0.88367,244.11
> view matrix models
> #5,-0.84,-0.4017,-0.36474,758.23,0.51314,-0.80659,-0.29343,470.63,-0.17632,-0.43364,0.88367,222.8
> fitmap #5 inMap #7
Fit molecule 250509_model_it062.pdb (#5) to map
cryosparc_P146_J688_003_volume_map.mrc z flip (#7) using 144680 atoms
average map value = 0.2114, steps = 196
shifted from previous position = 11.9
rotated from previous position = 21.7 degrees
atoms outside contour = 75738, contour level = 0.2
Position of 250509_model_it062.pdb (#5) relative to
cryosparc_P146_J688_003_volume_map.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.96811951 -0.18441872 -0.16951205 671.63770620
0.24826891 -0.79634080 -0.55154681 614.09702817
-0.03327381 -0.57604780 0.81673850 251.83379040
Axis -0.05393246 -0.29989243 0.95244728
Axis point 305.49792027 387.33310436 0.00000000
Rotation angle (degrees) 166.87094482
Shift along axis 19.47228748
> select subtract #5
Nothing selected
> ui mousemode right translate
> volume #6 color #ffffb2b0
> vop flip #4
Opened cryosparc_P146_J691_002_volume_map.mrc z flip as #8, grid size
360,360,360, pixel 1.72, shown at step 1, values float32
> volume #6 color #ffffb2
> volume #6 level 0.1346
> volume #8 level 0.1141
> volume #8 level 0.1533
> open 6s01
6s01 title:
Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome [more
info...]
Chain information for 6s01 #9
---
Chain | Description | UniProt
A E | Histone H3 | A0A310TTQ1_XENLA 1-135
B F | Histone H4 | H4_XENLA 1-102
C G | Histone H2A | Q6AZJ8_XENLA 1-129
D H | Histone H2B 1.1 | H2B11_XENLA 1-122
I | Wisdom 601 DNA (165-MER) |
J | Wisdom 601 DNA (165-MER) |
K | PC4 and SFRS1-interacting protein | PSIP1_HUMAN 1-530
> mmaker #9/A to #5/a
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 250509_model_it062.pdb, chain a (#5) with 6s01, chain A (#9),
sequence alignment score = 486.4
RMSD between 97 pruned atom pairs is 0.111 angstroms; (across all 97 pairs:
0.111)
> hide atoms
> show cartoons
> select add #9
12959 atoms, 13814 bonds, 351 pseudobonds, 1153 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.31482,0.76562,0.56099,136.88,-0.39512,0.64311,-0.65596,322.33,-0.863,-0.015154,0.50498,462.16
> view matrix models
> #9,-0.053111,0.85546,0.51514,180.06,-0.52896,0.41345,-0.74113,382.23,-0.84699,-0.31185,0.43054,509.6
> view matrix models
> #9,-0.28695,0.89323,0.34613,227.84,-0.7913,-0.017375,-0.61118,459.41,-0.53991,-0.44927,0.7118,451.24
> view matrix models
> #9,-0.34821,0.8712,0.34606,239.07,-0.71158,-0.0053326,-0.70258,458.62,-0.61025,-0.49089,0.62179,477.74
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.34821,0.8712,0.34606,240.7,-0.71158,-0.0053326,-0.70258,432.09,-0.61025,-0.49089,0.62179,455.62
> view matrix models
> #9,-0.34821,0.8712,0.34606,241.63,-0.71158,-0.0053326,-0.70258,427.75,-0.61025,-0.49089,0.62179,453.6
> volume #8 level 0.1664
> open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map.mrc
Opened cryosparc_P146_J589_006_volume_map.mrc as #10, grid size 460,460,460,
pixel 1.19, shown at level 0.0198, step 2, values float32
> close #9
> close #7-8,10
> close #4-6
> close #1-3
> open "/Users/dellasyau/Dropbox (HMS)/Syau_IWS1/Structures/Revision 1
> modeling intermediates/250509_model_it062.pdb" format pdb
Chain information for 250509_model_it062.pdb #1
---
Chain | Description
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
a | No description available
b | No description available
c g | No description available
d h | No description available
e | No description available
f | No description available
i | No description available
l | No description available
> open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map_sharp.mrc
Opened cryosparc_P146_J589_006_volume_map_sharp.mrc as #2, grid size
460,460,460, pixel 1.19, shown at level 0.0674, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J589_006_volume_map.mrc
Opened cryosparc_P146_J589_006_volume_map.mrc as #3, grid size 460,460,460,
pixel 1.19, shown at level 0.0198, step 2, values float32
> hide atoms
> show cartoons
> volume step 1
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> surface dust #2 size 11.9
> surface dust #3 size 11.9
> volume #3 level 0.3
> volume #3 level 0.1
> hide #!1 models
> show #!1 models
> open /Users/dellasyau/Downloads/cryosparc_P146_J670_004_volume_map_sharp.mrc
Opened cryosparc_P146_J670_004_volume_map_sharp.mrc as #4, grid size
460,460,460, pixel 1.19, shown at level 0.0446, step 2, values float32
> open /Users/dellasyau/Downloads/cryosparc_P146_J670_004_volume_map.mrc
Opened cryosparc_P146_J670_004_volume_map.mrc as #5, grid size 460,460,460,
pixel 1.19, shown at level 0.0185, step 2, values float32
> volume step 1
> surface dust #3 size 11.9
> surface dust #4 size 11.9
> surface dust #5 size 11.9
> volume #5 level 0.1
> volume #3 level 0.04843
> volume #3 level 0.04029
> volume #3 level 0.04843
> hide #!1 models
> ui tool show "Side View"
> show #!1 models
> volume #3 level 0.03215
> volume #3 level 0.02265
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Side View"
> volume #3 level 0.03215
> volume #3 level 0.03622
> volume #3 level 0.04436
> volume #3 level 0.03758
> volume #3 level 0.04708
> volume #3 level 0.09864
> volume #3 level 0.04708
> volume #3 level 0.0475
> volume #5 level 0.475
> volume #5 level 0.0475
> volume #2 level 0.07845
> volume #2 level 0.1079
> volume #2 level 0.06003
> volume #2 level 0.04528
> close #2-3
> show #!4 models
> volume #4 level 0.07
> volume #5 level 0.07
> hide #!5 models
> fitmap #1 inMap #4
Fit molecule 250509_model_it062.pdb (#1) to map
cryosparc_P146_J670_004_volume_map_sharp.mrc (#4) using 144680 atoms
average map value = 0.06737, steps = 84
shifted from previous position = 0.615
rotated from previous position = 0.61 degrees
atoms outside contour = 103215, contour level = 0.07
Position of 250509_model_it062.pdb (#1) relative to
cryosparc_P146_J670_004_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
0.99994636 0.00550710 0.00877235 -4.38159006
-0.00548537 0.99998183 -0.00249942 2.38927378
-0.00878595 0.00245117 0.99995840 2.03757886
Axis 0.23243578 0.82438184 -0.51610870
Axis point 223.65792196 0.00000000 498.18540782
Rotation angle (degrees) 0.61017583
Shift along axis -0.10037659
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 250509_model_it062.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G | No description available
1.2/H | No description available
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/O | No description available
1.2/P | No description available
1.2/Q | No description available
1.2/R | No description available
1.2/S | No description available
1.2/T | No description available
1.2/U | No description available
1.2/V | No description available
1.2/W | No description available
1.2/X | No description available
1.2/Y | No description available
1.2/Z | No description available
1.2/a | No description available
1.2/b | No description available
1.2/c 1.2/g | No description available
1.2/d 1.2/h | No description available
1.2/e | No description available
1.2/f | No description available
1.2/i | No description available
1.2/l | No description available
> clipper associate #4 toModel #1
Opened cryosparc_P146_J670_004_volume_map_sharp.mrc as #1.1.1.1, grid size
460,460,460, pixel 1.19, shown at step 1, values float32
> select /A:10
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde stepto /A:10
> isolde stepto prev
> isolde stepto next
> select /A:1
Nothing selected
> select /A:9
Nothing selected
> volume #5 level 0.06368
> volume #1.1.1.1 level 0.06591
> select clear
> select up
10 atoms, 9 bonds, 1 residue, 2 models selected
> select up
158 atoms, 158 bonds, 10 residues, 2 models selected
> isolde sim start /A:10-19
ISOLDE: started sim
> isolde stepto /A:14
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:29
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:42
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:48
ISOLDE: started sim
> select clear
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:57
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:65
ISOLDE: started sim
> isolde stepto next
> isolde stepto /A:69
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:74
ISOLDE: started sim
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:80
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:90
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:97
ISOLDE: started sim
> isolde stepto next
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
> isolde sim start /A:113
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/dellasyau/HMS Dropbox/Della Syau/Syau_IWS1/Structures/Revision
> 1 modeling intermediates/250517_model_it063.pdb"
===== 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
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
Model Number: Z15H00105LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 12 days, 57 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2723QE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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