![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17217 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-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00007ff846a2adc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, scipy._lib._ccallback_c, 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.optimize._minpack2, 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.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw (total: 113)
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{
"uptime" : 23000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 457,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-03-26 16:15:08.0233 +0100",
"codeSigningMonitor" : 0,
"incident" : "600105DB-40D4-4470-BE14-BA1DA680961D",
"pid" : 1101,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-26 09:01:55.5612 +0100",
"procStartAbsTime" : 941276316092,
"procExitAbsTime" : 23313469395745,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"29979687-E6C2-54B3-8B2E-4C12AE98305A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "ABCA9570-0C7A-12DD-5634-659ED5AEE61A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 13704,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "2A7E96BF-3EE7-45A1-BD33-766976D32FC6",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4487700120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b7ce000-10b7d2000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1101},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4487700120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b7ce000-10b7d2000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
warning | Registration file '/Users/lukaskruckemeyer/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/ChlH
> /Nostoc_ChlH_PPIX_Neurosnap-Boltz-1/output.cif"
Summary of feedback from opening
/Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/ChlH
/Nostoc_ChlH_PPIX_Neurosnap-Boltz-1/output.cif
---
warning | Atom O39 is not in the residue template for LIG /B:1
output.cif title:
. [more info...]
Chain information for output.cif #1
---
Chain | Description
A | .
Non-standard residues in output.cif #1
---
LIG — (LIG)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> color medium blue
> lighting flat
> color #1 #3a64d7ff
> select ::name="LIG"
42 atoms, 46 bonds, 1 residue, 1 model selected
> color sel orange
> ui mousemode right select
> select clear
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
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
> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3142_008_volume_map_sharp.mrc
Opened cryosparc_P7_J3142_008_volume_map_sharp.mrc as #2, grid size
440,440,440, pixel 0.68, shown at level 0.0158, step 2, values float32
> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3144_008_volume_map_sharp.mrc
Opened cryosparc_P7_J3144_008_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.68, shown at level 0.0165, step 2, values float32
> volume #2 step 1
> volume #3 step 1
> surface dust #2 size 6.8
> surface dust #3 size 6.8
> volume #2 level 0.09804
> volume #3 level 0.1116
> view #2 clip false
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.81989,0.40223,-0.40743,271.94,0.40583,0.91027,0.081981,-59.276,0.40384,-0.09813,-0.90955,247.28
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.81989,0.40223,-0.40743,300.75,0.40583,0.91027,0.081981,7.1751,0.40384,-0.09813,-0.90955,231.51
> volume flip #2
Opened cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip as #4, grid size
440,440,440, pixel 0.68, shown at step 1, values float32
> close #2
> select subtract #3
Nothing selected
> select add #4
2 models selected
> view matrix models #4,1,0,0,-40.725,0,1,0,5.26,0,0,1,10.228
> select subtract #4
Nothing selected
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.81989,0.40223,-0.40743,271.92,0.40583,0.91027,0.081981,-77.776,0.40384,-0.09813,-0.90955,257.09
> view matrix models
> #3,-0.81989,0.40223,-0.40743,232.84,0.40583,0.91027,0.081981,-54.341,0.40384,-0.09813,-0.90955,243.02
> view matrix models
> #3,-0.81989,0.40223,-0.40743,226.09,0.40583,0.91027,0.081981,-53.148,0.40384,-0.09813,-0.90955,242.88
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91121,0.15081,-0.38333,2.8257,-0.28049,0.90867,-0.30925,109.44,0.30169,0.38932,0.8703,-89.648
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91121,0.15081,-0.38333,0.2304,-0.28049,0.90867,-0.30925,101.38,0.30169,0.38932,0.8703,-84.426
> matchmaker #3 to #4
No 'to' model specified
> fitmap #3 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.2863, correlation about mean = 0.07494, overlap = 718.5
steps = 120, shift = 2.32, angle = 12.2 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.87724344 0.34026154 -0.33862373 9.17238215
-0.44705404 0.83605653 -0.31804428 132.72338424
0.17489034 0.43038536 0.88554040 -82.91424940
Axis 0.62288960 -0.42737828 -0.65525289
Axis point 271.76070074 77.16439868 0.00000000
Rotation angle (degrees) 36.92523028
Shift along axis 3.32009168
> hide #!3 models
> hide #!4 models
> select subtract #3
Nothing selected
> show #!4 models
> volume #4 level 0.1121
> show #!3 models
> hide #!4 models
> volume flip #3
Opened cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip as #2, grid size
440,440,440, pixel 0.68, shown at step 1, values float32
> close #3
> show #!4 models
> fitmap #2 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.295, correlation about mean = 0.1092, overlap = 731.8
steps = 124, shift = 4.62, angle = 10.3 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.83637651 0.48870777 -0.24827209 -16.45094484
-0.54635926 0.77986309 -0.30545885 156.22040741
0.04433812 0.39112437 0.91926919 -60.52736312
Axis 0.54357354 -0.22833620 -0.80770687
Axis point 239.87809802 118.73060784 0.00000000
Rotation angle (degrees) 39.84733788
Shift along axis 4.27529386
> ui mousemode right "rotate selected models"
> select add #2
2 models selected
> view matrix models
> #2,-0.70817,-0.25695,0.65763,156.59,0.13971,0.86201,0.48725,-68.834,-0.69208,0.43693,-0.57456,269.74
> fitmap #2 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.2795, correlation about mean = 0.06207, overlap = 745.8
steps = 68, shift = 1.07, angle = 5.19 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.73606997 -0.23061148 0.63641130 199.83138753
0.09301636 0.89679966 0.43254864 -64.32156799
-0.67048412 0.37758273 -0.63865665 274.28912318
Axis -0.04079130 0.96987324 0.24017069
Axis point 153.57248499 0.00000000 105.23263123
Rotation angle (degrees) 137.64319495
Shift along axis -4.65894103
> view matrix models
> #2,-0.70315,-0.22165,0.67561,147.11,0.11442,0.90252,0.41517,-60.611,-0.70177,0.36923,-0.60925,286.2
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.70315,-0.22165,0.67561,142.38,0.11442,0.90252,0.41517,-65.138,-0.70177,0.36923,-0.60925,291.24
> fitmap #2 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.3138, correlation about mean = 0.02515, overlap = 931.1
steps = 244, shift = 4.81, angle = 15.2 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.80766532 -0.34336504 0.47935079 248.21616837
-0.08625325 0.87300833 0.48001752 -40.69123273
-0.58329847 0.34634794 -0.73471491 285.52213504
Axis -0.12135756 0.96477090 0.23342977
Axis point 166.06607561 0.00000000 109.12087265
Rotation angle (degrees) 146.58315099
Shift along axis -2.73126014
> fitmap #2 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.3138, correlation about mean = 0.02511, overlap = 931.1
steps = 48, shift = 0.00287, angle = 0.0102 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.80771457 -0.34332921 0.47929346 248.22781884
-0.08633861 0.87306561 0.47989800 -40.67100510
-0.58321763 0.34623907 -0.73483038 285.54515181
Axis -0.12136583 0.96478813 0.23335425
Axis point 166.06794169 0.00000000 109.13398180
Rotation angle (degrees) 146.58874104
Shift along axis -2.73210344
> view matrix models
> #2,-0.80771,-0.34333,0.47929,210.43,-0.086339,0.87307,0.4799,-38.913,-0.58322,0.34624,-0.73483,300.19
> fitmap #2 inMap #4
Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points
correlation = 0.8799, correlation about mean = 0.5716, overlap = 4218
steps = 164, shift = 2.26, angle = 22.4 degrees
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.84335283 -0.45720298 0.28234984 301.24773314
-0.38261248 0.87985278 0.28189850 30.82670487
-0.37731113 0.12970932 -0.91695790 318.08822868
Axis -0.22345081 0.96854311 0.10951704
Axis point 183.02742212 0.00000000 130.05866548
Rotation angle (degrees) 160.09004584
Shift along axis -2.62097611
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> select add #1
10488 atoms, 10708 bonds, 1329 residues, 1 model selected
Drag select of 5 atoms, 164 residues, 4 bonds
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,21.19,0,1,0,175.71,0,0,1,138.03
> view matrix models #1,1,0,0,109.02,0,1,0,144.01,0,0,1,153.56
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.25421,-0.92045,-0.2969,94.591,-0.83659,0.055246,0.54503,132.19,-0.48527,0.38693,-0.78409,152.9
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.25421,-0.92045,-0.2969,118.71,-0.83659,0.055246,0.54503,157.37,-0.48527,0.38693,-0.78409,166.83
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02819, steps = 144
shifted from previous position = 3.99
rotated from previous position = 7.05 degrees
atoms outside contour = 8990, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.18594866 -0.95673211 -0.22380072 156.79570665
-0.87065941 0.05487494 0.48881584 154.61045561
-0.45538476 0.28574885 -0.84319174 158.32977930
Axis -0.63496928 0.72413914 0.26914034
Axis point 154.15825218 0.00000000 39.78019363
Rotation angle (degrees) 170.79873409
Shift along axis 55.01195609
> view matrix models
> #1,-0.18595,-0.95673,-0.2238,113.35,-0.87066,0.054875,0.48882,162.7,-0.45538,0.28575,-0.84319,169.69
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02819, steps = 112
shifted from previous position = 4.09
rotated from previous position = 0.012 degrees
atoms outside contour = 8989, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.18581836 -0.95676976 -0.22374797 156.78949477
-0.87060741 0.05474602 0.48892291 154.60736644
-0.45553735 0.28564749 -0.84314366 158.31935263
Axis -0.63501506 0.72409025 0.26916385
Axis point 154.17103352 0.00000000 39.76072051
Rotation angle (degrees) 170.78987736
Shift along axis 54.99984198
> view matrix models
> #1,-0.18582,-0.95677,-0.22375,113.11,-0.87061,0.054746,0.48892,155.84,-0.45554,0.28565,-0.84314,161.54
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02526, steps = 80
shifted from previous position = 1.64
rotated from previous position = 2.34 degrees
atoms outside contour = 9095, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.22202901 -0.94576215 -0.23714357 153.75489113
-0.86861097 0.08136122 0.48876920 151.60021012
-0.44296512 0.31450645 -0.83956393 150.03868344
Axis -0.62124940 0.73375701 0.27504514
Axis point 147.50765612 0.00000000 37.52220316
Rotation angle (degrees) 171.93758020
Shift along axis 56.98499354
> view matrix models
> #1,-0.22203,-0.94576,-0.23714,113.14,-0.86861,0.081361,0.48877,156.52,-0.44297,0.31451,-0.83956,162.78
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02526, steps = 96
shifted from previous position = 2.54
rotated from previous position = 0.0138 degrees
atoms outside contour = 9094, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.22180819 -0.94579105 -0.23723491 153.75294201
-0.86867013 0.08113974 0.48870086 151.60592053
-0.44295973 0.31447674 -0.83957790 150.04121389
Axis -0.62134051 0.73368233 0.27503855
Axis point 147.52370869 0.00000000 37.52308817
Rotation angle (degrees) 171.94056900
Shift along axis 56.96477110
> view matrix models
> #1,-0.22181,-0.94579,-0.23723,114.12,-0.86867,0.08114,0.4887,157.39,-0.44296,0.31448,-0.83958,167.25
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02723, steps = 172
shifted from previous position = 5.24
rotated from previous position = 5.9 degrees
atoms outside contour = 9114, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.13490079 -0.97251154 -0.18979746 150.08247201
-0.87413881 0.02661192 0.48494653 152.76441055
-0.46656523 0.23132900 -0.85370005 158.95220827
Axis -0.65353310 0.71318767 0.25349129
Axis point 155.05911123 0.00000000 39.72525194
Rotation angle (degrees) 168.81160147
Shift along axis 51.15882932
> view matrix models
> #1,-0.1349,-0.97251,-0.1898,110.96,-0.87414,0.026612,0.48495,160.87,-0.46657,0.23133,-0.8537,170.03
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02941, steps = 112
shifted from previous position = 1.96
rotated from previous position = 7.93 degrees
atoms outside contour = 8981, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.08978721 -0.99333150 -0.07232408 153.55651177
-0.89661512 0.04900216 0.44009103 155.80500859
-0.43361225 0.10436141 -0.89503581 159.66080783
Axis -0.66799785 0.71885144 0.19243563
Axis point 162.66452536 0.00000000 42.95499378
Rotation angle (degrees) 165.44581769
Shift along axis 40.14966272
> view matrix models
> #1,-0.089787,-0.99333,-0.072324,113.87,-0.89662,0.049002,0.44009,162.98,-0.43361,0.10436,-0.89504,170.11
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02941, steps = 84
shifted from previous position = 2.19
rotated from previous position = 0.0101 degrees
atoms outside contour = 8983, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
-0.08988318 -0.99331555 -0.07242392 153.55896469
-0.89665845 0.04905614 0.43999673 155.80221831
-0.43350276 0.10448782 -0.89507410 159.66508838
Axis -0.66796981 0.71887738 0.19243611
Axis point 162.65002070 0.00000000 42.96852171
Rotation angle (degrees) 165.45497239
Shift along axis 40.15526578
> view matrix models
> #1,-0.089883,-0.99332,-0.072424,110.71,-0.89666,0.049056,0.44,157.69,-0.4335,0.10449,-0.89507,166.97
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.03285, steps = 100
shifted from previous position = 0.894
rotated from previous position = 9.21 degrees
atoms outside contour = 8864, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.02897633 -0.98821484 -0.15030569 152.29081384
-0.86617015 -0.09987528 0.48966743 151.80297446
-0.49890844 0.11600153 -0.85885622 156.24821762
Axis -0.71120291 0.66349993 0.23228916
Axis point 0.00000000 160.99919506 90.51598125
Rotation angle (degrees) 164.76967376
Shift along axis 28.70635991
> view matrix models
> #1,0.028976,-0.98821,-0.15031,115.89,-0.86617,-0.099875,0.48967,163.18,-0.49891,0.116,-0.85886,175.76
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.02737, steps = 136
shifted from previous position = 3.29
rotated from previous position = 1.9 degrees
atoms outside contour = 9130, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.01334314 -0.99204106 -0.12520583 153.85365063
-0.87387827 -0.07242560 0.48071955 156.58648538
-0.48596164 0.10300035 -0.86788951 164.24666864
Axis -0.70533494 0.67365830 0.22065158
Axis point 0.00000000 166.93460678 93.21399045
Rotation angle (degrees) 164.46905700
Shift along axis 33.20871686
> view matrix models
> #1,0.013343,-0.99204,-0.12521,107.86,-0.87388,-0.072426,0.48072,153.89,-0.48596,0.103,-0.86789,165.41
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.03413, steps = 180
shifted from previous position = 4
rotated from previous position = 9.53 degrees
atoms outside contour = 8705, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.16362504 -0.96780624 -0.19125356 151.13600788
-0.86379252 -0.23419786 0.44610967 151.79460746
-0.47653889 0.09220868 -0.87430443 154.69072662
Axis -0.75892627 0.61178280 0.22305318
Axis point 0.00000000 148.64095788 88.33728425
Rotation angle (degrees) 166.51687288
Shift along axis 12.66850183
> hide #!2 models
> color #4 #b2b2b27e models
> color #4 #b2b2b280 models
> view #4 clip false
> view matrix models
> #1,0.16363,-0.96781,-0.19125,109.24,-0.86379,-0.2342,0.44611,158.08,-0.47654,0.092209,-0.8743,164.78
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.03674, steps = 144
shifted from previous position = 2.11
rotated from previous position = 8.52 degrees
atoms outside contour = 8707, contour level = 0.11213
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.23610261 -0.96966647 -0.06326528 149.17646777
-0.87188706 -0.24013981 0.42678544 152.62195743
-0.42903205 -0.04560498 -0.90213729 156.49401629
Axis -0.78030569 0.60418221 0.16151433
Axis point 0.00000000 149.58775587 78.59419460
Rotation angle (degrees) 162.38041224
Shift along axis 1.08425099
> volume #4 level 0.1309
> volume #4 level 0.1544
> view matrix models
> #1,0.2361,-0.96967,-0.063265,140.87,-0.87189,-0.24014,0.42679,146.5,-0.42903,-0.045605,-0.90214,185.27
> view matrix models
> #1,0.2361,-0.96967,-0.063265,121.67,-0.87189,-0.24014,0.42679,172.34,-0.42903,-0.045605,-0.90214,182.5
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.01981, steps = 160
shifted from previous position = 4.3
rotated from previous position = 9.4 degrees
atoms outside contour = 9845, contour level = 0.15443
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.22182187 -0.97446967 0.03469746 158.45108148
-0.93056349 -0.20092926 0.30607028 166.05675350
-0.29128447 -0.10018127 -0.95137641 170.81146053
Axis -0.77719325 0.62363074 0.08399620
Axis point 0.00000000 161.25202690 79.48097211
Rotation angle (degrees) 164.84933588
Shift along axis -5.24150106
> view matrix models
> #1,0.22182,-0.97447,0.034697,113.73,-0.93056,-0.20093,0.30607,158.59,-0.29128,-0.10018,-0.95138,170.61
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 180
shifted from previous position = 8.56
rotated from previous position = 18.7 degrees
atoms outside contour = 7148, contour level = 0.15443
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.34157459 -0.91285471 -0.22365840 150.42082873
-0.91383675 -0.37818340 0.14791791 157.89255807
-0.21961145 0.15386226 -0.96337802 154.95048317
Axis 0.81901540 -0.55758946 -0.13530621
Axis point 0.00000000 129.97610643 90.08411631
Rotation angle (degrees) 179.79207512
Shift along axis 14.19198575
> volume #4 level 0.09334
> surface dust #4 size 6.8
> hide #1 models
> show #1 models
> show #!2 models
> hide #!4 models
> volume #2 level 0.09
> volume #2 level 0.12
> volume #4 level 0.12
> hide #1 models
> show #!4 models
> hide #!2 models
> show #1 models
> view matrix models
> #1,0.34157,-0.91285,-0.22366,109.7,-0.91384,-0.37818,0.14792,163.18,-0.21961,0.15386,-0.96338,165.15
> ui mousemode right select
> select clear
> hide #1 models
> select clear
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> select clear
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
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
nucleotides tube/slab shape box
> hide #!4 models
> hide #1 models
> open
> "/Users/lukaskruckemeyer/Downloads/cryosparc_P125_J409_class_00_final_volume
> (1).mrc"
Opened cryosparc_P125_J409_class_00_final_volume (1).mrc as #3, grid size
140,140,140, pixel 3.12, shown at level 0.732, step 1, values float32
> volume #3 level 0.7634
> volume #3 color #78ff78
> volume #3 color #44ff7b
> volume #3 color #2ba14d
> volume #3 color #9899a1
> volume #3 color #9899a1a5
> volume #3 color #9899a1a6
> view #4 clip false
No displayed objects specified.
> view #4 clip false
No displayed objects specified.
> view #3 clip false
> open
> /Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/FeCh/fold_2024_09_10_13_07_fech_dim_2chlorophyll/fold_2024_09_10_13_07_fech_dim_2chlorophyll_model_0.cif
Chain information for fold_2024_09_10_13_07_fech_dim_2chlorophyll_model_0.cif
#5
---
Chain | Description
A B | .
> color #5 #57fd61ff
> color #5 #42c04aff
> view #5 clip false
> select add #5
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,103.87,0,1,0,261.6,0,0,1,289.26
> view matrix models #5,1,0,0,214.22,0,1,0,230.81,0,0,1,309.84
> view #5 clip false
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.55061,0.68349,-0.47924,214.83,-0.60357,-0.070618,-0.79417,237.14,-0.57665,0.72654,0.37365,311.04
> view matrix models
> #5,0.57054,0.69546,-0.43683,214.69,-0.57861,-0.037082,-0.81476,236.88,-0.58283,0.71761,0.38124,311.1
> view matrix models
> #5,0.63211,0.62128,-0.46309,214.51,-0.63523,0.073234,-0.76884,236.94,-0.44375,0.78016,0.44095,310.1
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.63211,0.62128,-0.46309,211.2,-0.63523,0.073234,-0.76884,228.16,-0.44375,0.78016,0.44095,312.94
> view matrix models
> #5,0.63211,0.62128,-0.46309,214.6,-0.63523,0.073234,-0.76884,225.4,-0.44375,0.78016,0.44095,303.83
> view matrix models
> #5,0.63211,0.62128,-0.46309,217.15,-0.63523,0.073234,-0.76884,226.09,-0.44375,0.78016,0.44095,301.5
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.59334,0.7434,-0.30871,217.12,-0.46969,0.0082807,-0.88279,225.19,-0.65372,0.66879,0.35408,303.07
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.59334,0.7434,-0.30871,217.72,-0.46969,0.0082807,-0.88279,223.25,-0.65372,0.66879,0.35408,298.32
> ui mousemode right select
> select clear
> view #5 clip false
> select clear
> select add #3
2 models selected
> select add #5
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected
> select clear
> select add #5
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected
> select add #3
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-1.4264,0,1,0,7.3595,0,0,1,26.278,#5,0.59334,0.7434,-0.30871,216.3,-0.46969,0.0082807,-0.88279,230.6,-0.65372,0.66879,0.35408,324.6
> ui mousemode right rotate
> ui mousemode right select
> select clear
> color #3 #9899a15b models
> color #3 #bcbdc55b models
> color #3 #bcbdc55c models
> hide #!5 models
> show #!5 models
> hide #!5 models
> open
> /Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/FeCh/fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla/fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif
Chain information for
fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif #6
---
Chain | Description
A B C D | .
> select add #6
12672 atoms, 13032 bonds, 16 pseudobonds, 1552 residues, 2 models selected
> view #6 clip false
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,184.35,0,1,0,270.73,0,0,1,323.94
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.64496,0.74122,0.18604,180.16,0.22232,-0.050929,0.97364,271.11,0.73116,0.66932,-0.13194,326.01
> view #6 clip false
> fitmap #6 inMap #3
Fit molecule fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif (#6)
to map cryosparc_P125_J409_class_00_final_volume (1).mrc (#3) using 12672
atoms
average map value = 0.754, steps = 140
shifted from previous position = 53.2
rotated from previous position = 35.6 degrees
atoms outside contour = 6268, contour level = 0.7634
Position of fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif (#6)
relative to cryosparc_P125_J409_class_00_final_volume (1).mrc (#3)
coordinates:
Matrix rotation and translation
-0.64383139 0.37053803 0.66946450 216.74374107
0.54253430 -0.39590511 0.74088844 223.67438389
0.53957176 0.84021468 0.05386655 302.95226335
Axis 0.41853385 0.54733279 0.72474563
Axis point 21.43629069 -1.09450152 -0.00000000
Rotation angle (degrees) 173.18524080
Shift along axis 432.70224723
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select clear
> volume #3 level 0.7033
> select clear
> view #3 clip false
> surface dust #3 size 31.2
> color #6 #8fdb8fff
> color #6 #91db8eff
> color #6 #a1f39eff
> select clear
> show #!5 models
> hide #!6 models
> color #5 #378f43ff
> hide #!5 models
> show #!6 models
> select clear
> show #!5 models
> hide #!6 models
> save /Users/lukaskruckemeyer/Desktop/image1.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/lukaskruckemeyer/Desktop/image2.png supersample 3
> hide #!6 models
> show #!6 models
> show #!5 models
> select add #3
2 models selected
> select add #5
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected
> select add #6
19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 6 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-0.39312,0,1,0,7.9458,0,0,1,26.354,#5,0.59334,0.7434,-0.30871,217.33,-0.46969,0.0082807,-0.88279,231.19,-0.65372,0.66879,0.35408,324.68,#6,-0.64383,0.37054,0.66946,216.35,0.54253,-0.39591,0.74089,231.62,0.53957,0.84021,0.053867,329.31
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79418,0.41093,0.44768,-152.37,0.25463,0.44388,-0.85915,278.82,-0.55177,0.79631,0.24788,159.15,#5,-0.014454,0.8932,-0.44942,245.83,0.50424,-0.38162,-0.77467,177.05,-0.86344,-0.23781,-0.44487,290.74,#6,-0.046813,0.50773,0.86024,247.31,-0.3867,-0.80325,0.45305,173.02,0.92102,-0.31144,0.23394,292.77
> ui mousemode right select
> select clear
> hide #!5 models
> select clear
> show #!5 models
> select add #5
6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected
> select add #6
19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 4 models selected
> select add #3
19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.81484,0.35706,0.45666,-147.53,0.28997,0.43107,-0.85446,272.63,-0.50194,0.82867,0.24771,141.21,#5,0.017241,0.91413,-0.40506,245.83,0.52816,-0.35231,-0.77261,177.09,-0.84897,-0.20062,-0.48888,290.82,#6,-0.084501,0.54426,0.83465,247.3,-0.41387,-0.78114,0.46747,173.04,0.90641,-0.30593,0.29126,292.82
> view matrix models
> #3,0.80497,0.39352,0.44403,-149.08,0.2417,0.46597,-0.85115,275.26,-0.54185,0.79247,0.27998,148.18,#5,0.0025192,0.89864,-0.43868,246.5,0.48096,-0.3857,-0.78735,178,-0.87674,-0.209,-0.43318,290.65,#6,-0.065182,0.51555,0.85437,247.94,-0.36207,-0.81007,0.46119,174.02,0.92987,-0.27928,0.23947,292.81
> select subtract #3
19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 4 models selected
> select subtract #5
12672 atoms, 13032 bonds, 16 pseudobonds, 1552 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #!5 models
> hide #!6 models
> show #!5 models
> save /Users/lukaskruckemeyer/Desktop/image3.png supersample 3
> show #!6 models
> hide #!5 models
> save /Users/lukaskruckemeyer/Desktop/image4.png supersample 3
> hide #!6 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #1 models
> show #!4 models
> show #!6 models
> show #!5 models
> delete #5
> delete #6
> hide #!3 models
> show #!3 models
> close #3
> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3164_007_volume_map_sharp.mrc
Opened cryosparc_P7_J3164_007_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.68, shown at level 0.0173, step 2, values float32
> volume #3 level 0.01093
> volume #3 step 1
> volume #3 level 0.12
> volume flip #3
Opened cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip as #5, grid size
440,440,440, pixel 0.68, shown at step 1, values float32
> close #3
> hide #!2 models
> hide #1 models
> select add #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-10.375,0,1,0,-4.9797,0,0,1,20.481
> view matrix models #5,1,0,0,-30.581,0,1,0,15.507,0,0,1,22.982
> select up
10488 atoms, 10708 bonds, 1329 residues, 7 models selected
> fitmap #5 inMap #4
Fit map cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 100332 points
correlation = 0.3006, correlation about mean = 0.07433, overlap = 757.6
steps = 152, shift = 5.27, angle = 6.03 degrees
Position of cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99468960 -0.06119212 -0.08275334 27.34927905
0.06293562 0.99784380 0.01862438 0.40014333
0.08143524 -0.02373361 0.99639601 3.90233440
Axis -0.20156818 -0.78132096 0.59068420
Axis point -59.03960295 0.00000000 325.70546604
Rotation angle (degrees) 6.03126561
Shift along axis -3.52033741
> view matrix models
> #1,0.34157,-0.91285,-0.22366,140.34,-0.91384,-0.37818,0.14792,250.8,-0.21961,0.15386,-0.96338,243.54,#4,1,0,0,-10.084,0,1,0,92.88,0,0,1,88.615,#2,-0.84335,-0.4572,0.28235,291.16,-0.38261,0.87985,0.2819,123.71,-0.37731,0.12971,-0.91696,406.7,#5,0.99469,-0.061192,-0.082753,17.265,0.062936,0.99784,0.018624,93.281,0.081435,-0.023734,0.9964,92.517
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select subtract #2
10488 atoms, 10708 bonds, 1329 residues, 5 models selected
> select subtract #1
4 models selected
> select subtract #4
2 models selected
> select subtract #5
Nothing selected
> select add #5
2 models selected
> view matrix models
> #5,0.99469,-0.061192,-0.082753,12.666,0.062936,0.99784,0.018624,80.163,0.081435,-0.023734,0.9964,80.867
> fitmap #5 inMap #4
Fit map cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 100332 points
correlation = 0.99, correlation about mean = 0.9371, overlap = 5773
steps = 84, shift = 1.16, angle = 5.95 degrees
Position of cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.99999762 -0.00217361 0.00020144 0.38027762
0.00217323 0.99999597 0.00182782 -0.58813910
-0.00020541 -0.00182738 0.99999831 0.30024801
Axis -0.64194425 0.07145441 0.76341459
Axis point 269.04956351 157.84447119 0.00000000
Rotation angle (degrees) 0.16311971
Shift along axis -0.05692846
> select subtract #5
Nothing selected
> view #5 clip false
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> surface dust #4 size 6.8
> surface dust #5 size 6.8
> surface dust #4 size 6.8
> surface dust #5 size 6.8
> surface dust #4 size 6.8
> surface dust #5 size 6.8
> show #1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #5 #ffb2b281 models
> color #5 #ffb2b282 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> hide #1 models
> show #1 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> volume #4 level 0.0571
> volume #4 level 0.07887
> volume #4 level 0.07162
> volume #4 level 0.05226
> volume #4 level 0.05
> volume #4 level 0.06
> show #!5 models
> hide #!4 models
> volume #5 level 0.06
> show #!4 models
> hide #!4 models
> volume #5 level 0.04634
> view
> ui tool show "Side View"
> view #1 clip false
> volume #5 level 0.05545
> volume #5 level 0.07366
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> volume #5 level 0.1351
> volume #5 level 0.07366
> hide #!5 models
> show #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show Matchmaker
> ui tool show "Segment Map"
> toolshed show
> ui tool show "Fit in Map"
> hide #!4 models
> show #!4 models
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1328
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1151-1328
1430 atoms, 1455 bonds, 178 residues, 1 model selected
Average map value = 0.1115 for 10488 atoms, 4968 outside contour
> fitmap #1 inMap #4
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 136
shifted from previous position = 0.0256
rotated from previous position = 0.0176 degrees
atoms outside contour = 4966, contour level = 0.06
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:
Matrix rotation and translation
0.34150799 -0.91287025 -0.22369666 150.42327919
-0.91392282 -0.37808190 0.14764535 157.90211567
-0.21935671 0.15401942 -0.96341094 154.94639770
Axis 0.81899497 -0.55763467 -0.13524357
Axis point 0.00000000 129.97458321 90.09013044
Rotation angle (degrees) 179.77703866
Shift along axis 14.18871147
> select /A:1328
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1251-1328
649 atoms, 659 bonds, 78 residues, 1 model selected
Average map value = 0.1115 for 10488 atoms, 4966 outside contour
> fitmap #1 inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 64
shifted from previous position = 0.0103
rotated from previous position = 0.0183 degrees
atoms outside contour = 4973, contour level = 0.06
> ui mousemode right select
> select clear
> select /A:1328
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1051-1328
2219 atoms, 2256 bonds, 278 residues, 1 model selected
Drag select of 16 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip
> select /A:1328
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1051-1328
2219 atoms, 2256 bonds, 278 residues, 1 model selected
Average map value = 0.1115 for 10488 atoms, 4973 outside contour
> fitmap #1 inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 64
shifted from previous position = 0.00694
rotated from previous position = 0.0124 degrees
atoms outside contour = 4968, contour level = 0.06
> fitmap #1 inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 96
shifted from previous position = 0.00591
rotated from previous position = 0.00366 degrees
atoms outside contour = 4967, contour level = 0.06
> fitmap #1 inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms
average map value = 0.1115, steps = 96
shifted from previous position = 0.00039
rotated from previous position = 0.00827 degrees
atoms outside contour = 4967, contour level = 0.06
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 2219 atoms
average map value = 0.2104, steps = 68
shifted from previous position = 0.307
rotated from previous position = 0.632 degrees
atoms outside contour = 449, contour level = 0.06
Drag select of 7 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip
> select /A:1328
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1201-1328
1053 atoms, 1071 bonds, 128 residues, 1 model selected
Average map value = 0.2322 for 1053 atoms, 212 outside contour
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1053 atoms
average map value = 0.2338, steps = 68
shifted from previous position = 0.0763
rotated from previous position = 0.931 degrees
atoms outside contour = 203, contour level = 0.06
> select /A:1200
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:1051-1200
1166 atoms, 1184 bonds, 150 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1166 atoms
average map value = 0.1914, steps = 48
shifted from previous position = 0.0954
rotated from previous position = 0.44 degrees
atoms outside contour = 231, contour level = 0.06
> select /A:1050
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:901-1050
1146 atoms, 1168 bonds, 150 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1146 atoms
average map value = 0.1611, steps = 48
shifted from previous position = 0.137
rotated from previous position = 0.874 degrees
atoms outside contour = 290, contour level = 0.06
> select /A:900
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:751-900
1177 atoms, 1194 bonds, 150 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1177 atoms
average map value = 0.1445, steps = 48
shifted from previous position = 0.0994
rotated from previous position = 1.55 degrees
atoms outside contour = 353, contour level = 0.06
> select /A:750
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:601-750
1171 atoms, 1195 bonds, 150 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1171 atoms
average map value = 0.1441, steps = 64
shifted from previous position = 0.467
rotated from previous position = 1.4 degrees
atoms outside contour = 368, contour level = 0.06
> select /A:600
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:451-600
1184 atoms, 1219 bonds, 150 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1184 atoms
average map value = 0.1402, steps = 60
shifted from previous position = 1.57
rotated from previous position = 5.19 degrees
atoms outside contour = 367, contour level = 0.06
> select /A:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:251-450
1548 atoms, 1582 bonds, 200 residues, 1 model selected
> fitmap sel inMap #4 moveWholeMolecules false
Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1548 atoms
average map value = 0.06931, steps = 64
shifted from previous position = 1.68
rotated from previous position = 5.79 degrees
atoms outside contour = 839, contour level = 0.06
> select clear
> hide #1 models
> show #1 models
> volume #4 level 0.06726
> volume #4 level 0.08
> hide #1 models
> hide #!4 models
> show #1 models
> show #!4 models
> ui tool show "Side View"
Drag select of 1 bonds, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip
> select #4
3 models selected
> select clear
> volume #4 level 0.04613
> volume #4 level 0.2856
> volume #4 level 0.04371
> view orient
> ui tool show "Side View"
> volume #4 level 0.08242
> hide #1 models
> select ::name="LIG"
42 atoms, 46 bonds, 1 residue, 1 model selected
> show #1 models
> select add #1
10488 atoms, 10708 bonds, 1329 residues, 1 model selected
> select subtract #1
Nothing selected
> hide cartoons
> show cartoons
> hide cartoons
> show cartoons
> volume #4 color #c6c6c600
> volume #4 color #c6c6c60d
> volume #4 color #c6c6c6f4
Drag select of 2 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip
Drag select of 1 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> color #4 #c6c6c6d3 models
> color #4 #c6c6c6d4 models
> volume #4 level 0.1308
> volume #4 level 0.08726
> volume #4 level 0.04371
> volume #4 level 0.1623
> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3155_005_volume_map_sharp.mrc
Opened cryosparc_P7_J3155_005_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.68, shown at level 0.0157, step 2, values float32
> hide #1 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!3 target m
> view #3 clip false
> volume #3 level 0.08175
> surface dust #3 size 6.8
> volume #3 level 0.1021
> volume #3 level 0.1038
> hide #!3 models
> show #1 models
> show #!4 models
> view #4 clip false
> volume #4 level 0.08
> volume #4 level 0.09
> ui mousemode right select
> select /A:577
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4
2 models selected
> select /A:578
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:577
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #4
2 models selected
> select #4
2 models selected
> select clear
> hide #!4 models
> select /A:589
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> select /A:1171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /A:1172
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:1171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /A:744
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:1172
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /A:588
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:588-589
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:1171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /A:744
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:1171
10 atoms, 10 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> show #!4 models
Drag select of 3 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip
> select #4
2 models selected
> select /A:1171
10 atoms, 10 bonds, 1 residue, 1 model selected
> select
> /A:7-10,32-48,61-65,67-79,91-104,118-123,131-135,140-152,156-165,167-173,176-193,197-212,215-220,249-258,264-267,280-284,289-300,316-322,353-363,378-383,390-397,400-403,425-443,446-448,462-464,473-487,498-506,526-532,536-541,581-586,594-606,621-623,636-641,655-664,684-699,705-718,732-734,737-756,773-783,788-790,795-803,807-815,819-843,852-860,866-873,881-899,903-912,928-930,942-944,948-968,983-988,992-1001,1021-1024,1037-1042,1044-1058,1064-1066,1068-1080,1084-1087,1103-1108,1115-1126,1142-1151,1173-1175,1178-1184,1208-1220,1223-1254,1259-1271,1273-1282,1284-1299,1307-1324
5576 atoms, 5600 bonds, 685 residues, 1 model selected
> select /A:1170
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:1170-1173
39 atoms, 41 bonds, 4 residues, 1 model selected
> volume #4 level 0.1088
> volume #4 level 0.0853
> select #4
2 models selected
> select clear
> volume #4 level 0.1095
> show atoms
> volume #4 level 0.08046
> select /A:1-2
19 atoms, 19 bonds, 2 residues, 1 model selected
> select /A:1-270
2172 atoms, 2218 bonds, 270 residues, 1 model selected
> select /A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:1-180
1431 atoms, 1454 bonds, 180 residues, 1 model selected
> select /A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:179-180
14 atoms, 13 bonds, 2 residues, 1 model selected
> select clear
> show #!5 models
> hide #!5 models
> view #3 clip false
No displayed objects specified.
> view #3 clip false
No displayed objects specified.
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> view #4 clip false
> show #!4 target m
> view #4 clip false
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #3
2 models selected
> view #4 clip false
> hide #!3 models
> hide #!4 models
> view #3 clip false
No displayed objects specified.
> show #!3 models
> hide #1 models
> view #3 clip false
> select clear
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #1 models
> view #1 clip false
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/lukaskruckemeyer/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 1 Tag, 1 Stunde und 43 Minuten
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
PA278CV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: M6LMQS089968
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
PA278CV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: M6LMQS089975
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 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 , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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