![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#17969 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-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 0x0000000204021f00 (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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PIL._webp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast (total: 57)
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{
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"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "MacBookPro17,1",
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"captureTime" : "2025-06-12 16:02:53.0001 +0100",
"codeSigningMonitor" : 1,
"incident" : "1518B29D-9913-47E6-91BE-693E533940F1",
"pid" : 96673,
"translated" : false,
"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2025-06-12 10:33:45.0563 +0100",
"procStartAbsTime" : 6587004975333,
"procExitAbsTime" : 7060954395495,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9C4F57C2-79B8-51E9-BC13-BF4E6573BE0E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B16EDD29-2A7F-435D-FF80-7678024D959D",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn","siriAssetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "30F6F5A7-5795-4001-B999-5FF3F36EB389",
"wakeTime" : 27016,
"sleepWakeUUID" : "E022DA39-CEFC-40B9-98DF-39DE8462E97A",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4299407000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10043c000-100440000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.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":96673},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4299407000\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10043c000-100440000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/gaurideak/Desktop/H2AZ-H2BV_Summary_Folder/Final_Structure/v28_for_thesis/TbH2AZ-H2BV_v29.2.pdb
TbH2AZ-H2BV_v29.2.pdb title:
The H2A.Z-H2B.V nucleosome core particle from trypanosoma brucei [more
info...]
Chain information for TbH2AZ-H2BV_v29.2.pdb #1
---
Chain | Description
A E | T. brucei Histone H3
B F | T. brucei Histone H4
C G | T. brucei Histone H2A.Z
D H | T. brucei Histone H2B.V
I | Widom 601 145 bp DNA (143-mer ordered and built)
J | Widom 601 145 bp DNA (143-mer ordered and built)
> open
> /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J381_007_volume_map_zflip.mrc
Opened cryosparc_P121_J381_007_volume_map_zflip.mrc as #2, grid size
304,304,304, pixel 0.829, shown at level 0.0171, step 2, values float32
> open
> /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J410_map_sharp_bfact80_zflip.mrc
Opened cryosparc_P121_J410_map_sharp_bfact80_zflip.mrc as #3, grid size
304,304,304, pixel 0.829, shown at level 0.0229, step 2, values float32
> open
> /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/J381_H2AZ_H2BV/zflip/cryosparc_P121_J408_map_sharp_deepemhance_zflip.mrc
Opened cryosparc_P121_J408_map_sharp_deepemhance_zflip.mrc as #4, grid size
304,304,304, pixel 0.829, shown at level 0.000929, step 2, values float32
> volume #2 level 0.03007
> volume #3 level 0.03474
> volume #4 level 0.03757
> hide atoms
> show cartoons
> volume #4 step 1
> volume #3 step 1
> volume #2 step 1
> transparency 50
> hide #!2 models
> hide #!3 models
> volume #4 level 0.0422
> hide #!4 models
> show #!3 models
> volume #3 level 0.05579
> hide #!3 models
> show #!2 models
> volume #2 level 0.02805
> ui tool show "Command Line Interface"
> color #1/A,E blue
> color #1/B,F green
> color #1/C,G #ee9b00
> color #1/D,H #f395ab
> color #1/I,J light grey
> set bgColor white
> undo
> color #1/I,J light grey
> graphics silhouettes true width 1.5
> graphics silhouettes true width 1
> lighting soft
> graphics silhouettes true width 1.5
> open
> /Users/gaurideak/Desktop/Computational/TbH2AZ-H2BV_Model_Building/TbH2AZ-H2BV_NCP_starting_model_truncated.pdb
Chain information for TbH2AZ-H2BV_NCP_starting_model_truncated.pdb #5
---
Chain | Description
A E | No description available
B F | No description available
C G | No description available
D H | No description available
I | No description available
J | No description available
> hide atoms
> show cartoons
> color #5 light green
> show atoms
> style stick
Changed 23929 atom styles
> volume #2 level 0.02453
> volume #2 level 0.0356
> volume #2 level 0.02906
> volume #2 level 0.02503
> volume #2 level 0.021
> color #2 #F8DD9A
> color #1 orange
> color #1 blue
> color #5 light grey
> color #1 cornflower blue
> transparency 0.5
> transparency 50
> transparency 90
> transparency 70
> volume #2 level 0.03762
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Surface Zone"
> ui mousemode right select
> select #1/C:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/C:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/C:160
7 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 1/C
> select #1/C:161
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/C:161-170
87 atoms, 88 bonds, 10 residues, 1 model selected
> surface zone #2 nearAtoms #1 distance 4.97
> surface zone #2 nearAtoms sel distance 4.97
> show #!2 models
> hide all atoms
> hide all cartoons
> show sel atoms
> select #1/C:160-170
94 atoms, 96 bonds, 11 residues, 1 model selected
> show sel atoms
> select #1/C:159-170
101 atoms, 103 bonds, 12 residues, 1 model selected
> show sel atoms
> surface zone #2 nearAtoms sel distance 4.81
> surface zone #2 nearAtoms sel distance 2.58
> volume #2 level 0.03033
> surface zone #2 nearAtoms sel distance 2.93
> select clear
> select #5/c
872 atoms, 881 bonds, 112 residues, 1 model selected
Alignment identifier is 5/C
> select #5/C:160
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:160-173
119 atoms, 121 bonds, 14 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 119 atom styles
> color sel byhetero
> color #5 coral
> select clear
> hide #5 models
> hide #1 models
> show #5 models
> select #5/C:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
No atoms selected for zoning
> show #1 models
No atoms selected for zoning
> select #1/C:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:159-170
101 atoms, 103 bonds, 12 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2.44
> volume #2 level 0.03033
> surface zone #2 nearAtoms sel distance 2.93
> surface zone #2 nearAtoms sel distance 2.85
> surface zone #2 nearAtoms sel distance 2.93
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #5 models
> select clear
> show #1 cartoons
> color #1 light grey
> select #5/C:159-160
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/C:159-173
126 atoms, 128 bonds, 15 residues, 1 model selected
> color sel blue
> select #1/C:159
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/C:159-170
101 atoms, 103 bonds, 12 residues, 1 model selected
> color sel blue
> color sel #ee9b00
> select clear
> show #5 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #5 models
> select #1/D:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/D:132
14 atoms, 12 bonds, 2 residues, 1 model selected
Alignment identifier is 1/D
> select #1/D:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:115-137
171 atoms, 172 bonds, 23 residues, 1 model selected
> select #1/D:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:115-137
171 atoms, 172 bonds, 23 residues, 1 model selected
> select #1/D:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:115-136
166 atoms, 167 bonds, 22 residues, 1 model selected
> select #1/D:115-116
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/D:115-135
157 atoms, 158 bonds, 21 residues, 1 model selected
> show sel atoms
> surface zone #2 nearAtoms sel distance 2.93
> select #1/D:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:111-134
179 atoms, 182 bonds, 24 residues, 1 model selected
> select #1/D:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:110-129
145 atoms, 147 bonds, 20 residues, 1 model selected
> select #1/D:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:110-130
157 atoms, 160 bonds, 21 residues, 1 model selected
> surface zone #2 nearAtoms sel distance 2.93
> show sel atoms
> select #1/D:112
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:112-132
154 atoms, 157 bonds, 21 residues, 1 model selected
> show sel atoms
> surface zone #2 nearAtoms sel distance 2.93
> hide all atoms
> hide all cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
> surface zone #2 nearAtoms sel distance 2.73
> surface zone #2 nearAtoms sel distance 2.58
> show #!3 models
> hide #!3 models
> color sel #f395ab
> select clear
> transparency 70
> transparency 50
> transparency 60
> volume #2 level 0.06
> volume #2 level 0.03039
> show #!3 models
> hide #!2 models
No atoms selected for zoning
> select #1/D:112
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:112-132
154 atoms, 157 bonds, 21 residues, 1 model selected
> surface zone #3 nearAtoms sel distance 4.97
> surface zone #3 nearAtoms sel distance 5.12
> surface zone #3 nearAtoms sel distance 2.27
> surface zone #3 nearAtoms sel distance 2.21
> surface zone #3 nearAtoms sel distance 2.46
> select clear
> volume #2 level 0.03039
> hide #!2 models
> volume #3 level 0.065
> volume #3 level 0.06267
> volume #3 level 0.04058
> volume #3 level 0.05686
> select #1/D:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:66-90
189 atoms, 191 bonds, 25 residues, 1 model selected
> select #1/D:65-66
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/D:65-90
198 atoms, 200 bonds, 26 residues, 1 model selected
> surface zone #3 nearAtoms sel distance 2.46
> show all atoms
> hide all atoms
> show sel atoms
> color sel #f395ab
> surface zone #3 nearAtoms sel distance 2.57
> surface zone #3 nearAtoms sel distance 2.03
> volume #3 level 0.06035
> color #3 #F8DD9A
> select clear
> volume #3 level 0.06965
> volume #3 level 0.0603
> volume #3 level 0.062
> transparency 70
> select #1/d:65-90
198 atoms, 200 bonds, 26 residues, 1 model selected
> select #1/D:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:65-89
193 atoms, 195 bonds, 25 residues, 1 model selected
> select #1/D:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:90
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/D:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/D:65
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> view name H2B
> save /users/gaurideak/desktop/Model/H2B_chain_D_aa_65-90.tiff
> select #1/C
836 atoms, 845 bonds, 108 residues, 1 model selected
Alignment identifier is 1/C
> select #1/C:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/C:97
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/C:97-124
194 atoms, 195 bonds, 28 residues, 1 model selected
> select #1/C:95-120
180 atoms, 181 bonds, 26 residues, 1 model selected
> select #1/C:100-125
187 atoms, 188 bonds, 26 residues, 1 model selected
> show sel atoms
> color sel #ee9b00
> hide #1/d atoms
> surface zone #3 nearAtoms sel distance 2.03
> view name H2A
> save /users/gaurideak/desktop/Model/H2A_chainC_aa_100-125.tiff
> select clear
> save /users/gaurideak/desktop/Model/H2A_chainC_aa_100-125.tiff
> select #1/A
764 atoms, 774 bonds, 96 residues, 1 model selected
Alignment identifier is 1/A
> select #1/A:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:64
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:83
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:83-110
205 atoms, 206 bonds, 28 residues, 1 model selected
> select #1/A:85-110
193 atoms, 194 bonds, 26 residues, 1 model selected
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> hide #1 atoms
> show sel atoms
> surface zone #3 nearAtoms sel distance 2.03
> view list
Named views: H2A, H2B
> view H2A
> color sel #5772C5
> select clear
No atoms selected for zoning
> select #1/A:85-110
193 atoms, 194 bonds, 26 residues, 1 model selected
> surface zone #3 nearAtoms sel distance 2.24
> surface zone #3 nearAtoms sel distance 2.06
> surface zone #3 nearAtoms sel distance 2.12
> surface zone #3 nearAtoms sel distance 1.98
> surface zone #3 nearAtoms sel distance 2.09
> select clear
> view name H3
> save /users/gaurideak/desktop/Model/H3_chainA_aa_85-110.tiff
> select #1/B
600 atoms, 605 bonds, 76 residues, 1 model selected
Alignment identifier is 1/B
> select #1/B:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:24
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:48-49
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #1/B:48-73
210 atoms, 213 bonds, 26 residues, 1 model selected
> select #1/B:45-70
199 atoms, 201 bonds, 26 residues, 1 model selected
> hide all atoms
> show sel atoms
> surface zone #3 nearAtoms sel distance 2.09
> color sel green
> select clear
> view name H4
> save /users/gaurideak/desktop/Model/H4_chainB_aa_45-70.tiff
> hide all atoms
> show #1 atoms
> select #1/i,j
5863 atoms, 6576 bonds, 286 residues, 1 model selected
Alignment identifier is 1/I
Alignment identifier is 1/J
> select clear
> select #1/I:68-69
39 atoms, 42 bonds, 2 residues, 1 model selected
> select #1/I:39-69
634 atoms, 710 bonds, 31 residues, 1 model selected
> select #1/i:45-70
535 atoms, 599 bonds, 26 residues, 1 model selected
> select #1/i:50-70
431 atoms, 482 bonds, 21 residues, 1 model selected
> select #1/i:50-60
224 atoms, 250 bonds, 11 residues, 1 model selected
> select #1/i:45-60
328 atoms, 367 bonds, 16 residues, 1 model selected
> select #1/i:50-60
224 atoms, 250 bonds, 11 residues, 1 model selected
> select #1/J:-50@P
1 atom, 1 residue, 1 model selected
> select #1/J:-50@P
1 atom, 1 residue, 1 model selected
> select #1/j:50-60
227 atoms, 254 bonds, 11 residues, 1 model selected
> select #1/j:-50- -60
Expected an objects specifier or a keyword
> select #1/j:-50
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/J:-50
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/J:-50--28
471 atoms, 527 bonds, 23 residues, 1 model selected
> select #1/J:-50
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/J:-64--50
306 atoms, 342 bonds, 15 residues, 1 model selected
> select #1/J:-60--50
227 atoms, 254 bonds, 11 residues, 1 model selected
> select #1/I:50-60 /J:-60--50
451 atoms, 504 bonds, 22 residues, 1 model selected
> surface zone #3 nearAtoms sel distance 2.09
> hide all atoms
> show sel atoms
> surface zone #3 nearAtoms sel distance 2.06
> surface zone #3 nearAtoms sel distance 3.29
> volume #3 level 0.04223
> surface zone #3 nearAtoms sel distance 3.07
> surface zone #3 nearAtoms sel distance 4.52
> volume #3 level 0.04921
> select clear
> volume #!3 style mesh
> transparency #3.1 0
> volume #!3 style surface
> transparency #3.1 50
> surface unzone #3
> hide all atoms
> show #1 cartoons
> color #3 #F8DD9A
> ui tool show "Side View"
> volume #3 level 0.062
> volume #2 level 0.04107
> hide #!2 models
> volume #3 level 0.05502
> volume #3 level 0.05037
> volume #3 level 0.04456
> show #!2 models
> hide #!3 models
> volume #2 level 0.04508
> hide #!2 models
> show #!2 models
> ui tool show "Color Zone"
> ui tool show "Surface Zone"
> surface unzone #2
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color #1/A,E blue
> color #1/B,F green
> color #1/C,G #ee9b00
> color #9/D,H #f395ab
> color #9/I,J light grey
> color #1/A,E #5772C5 #1/B,F green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/C,G #ee9b00
> color #1/D,H #f395ab
> color #1/I,J light grey
> color #1/a,e #5772C5
> select clear
> color zone #2 near #1 distance 4.97
> volume #2 level 0.0319
> volume #2 level 0.0323
> hide #!2 models
> show #!2 models
> volume #2 level 0.0279
> volume #2 level 0.03549
> volume #2 level 0.0279
> color #2 light grey
> color zone #2 near #1 distance 4.97
> hide #1 models
> turn y -60
> turn y -30
> transparency #2.1 50
> show #1 models
> hide #1 models
> transparency #2.1 0
> save /users/gaurideak/desktop/map_coloured_by_histone.tiff
> transparency #2.1 50
> show #1 models
> save /users/gaurideak/desktop/map_with_model.tiff
> turn y -90
> save /users/gaurideak/desktop/map_with_model_90.tiff
> turn y 90
> turn y -90
> view name front
> hide #1 models
> show #1 models
> hide #!2 models
> save /users/gaurideak/desktop/model_alone.tiff
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #3 level 0.03717
> hide #!3 models
> select #1/J:-46
19 atoms, 20 bonds, 1 residue, 1 model selected
> select add #1/J:-33
40 atoms, 43 bonds, 2 residues, 1 model selected
Alignment identifier is 1/J
> select #1/J:-45
21 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/J:-45--29
352 atoms, 395 bonds, 17 residues, 1 model selected
> select #1/J:-45--30
333 atoms, 374 bonds, 16 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select #1/I:45
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/J:-45--30 /I:30-45
656 atoms, 734 bonds, 32 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #1 distance 4.97
> show #!3 models
> surface zone #3 nearAtoms #1 distance 4.97
> surface zone #3 nearAtoms sel distance 4.97
> hide all cartoons
> surface zone #3 nearAtoms sel distance 4.65
> surface zone #3 nearAtoms sel distance 2.93
> select clear
No atoms selected for zoning
> select #1/J:-45--30 /I:30-45
656 atoms, 734 bonds, 32 residues, 1 model selected
> surface zone #3 nearAtoms sel distance 2.67
> surface zone #3 nearAtoms sel distance 2.52
> surface zone #3 nearAtoms sel distance 2.7
> surface zone #3 nearAtoms sel distance 2.49
> surface zone #3 nearAtoms sel distance 2.55
> hide #!3 models
> show #!3 models
> volume #3 level 0.04944
> select clear
> save /users/gaurideak/desktop/DNA_bases_30-45.tiff
> transparency 70
> transparency 60
> transparency 70
> save /users/gaurideak/desktop/DNA.tiff
> hide #!3 models
> hide all atoms
> show #1 cartoons
> open 8com
8com title:
Structure of the Nucleosome Core Particle from Trypanosoma brucei [more
info...]
Chain information for 8com #6
---
Chain | Description | UniProt
A E | Histone H3, putative | Q4GYX7_TRYB2 1-132
B F | Histone H4 | Q57Z31_TRYB2 1-99
C G | Histone H2A | Q57YA3_TRYB2 1-133
D H | Histone H2B | Q389T1_TRYB2 1-111
I | Widom 601 145 bp DNA (127-mer ordered and built) |
J | Widom 601 145 bp DNA (127-mer ordered and built) |
> mmaker #6 to #1
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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 8com, chain J (#6),
sequence alignment score = 789.4
RMSD between 90 pruned atom pairs is 1.164 angstroms; (across all 127 pairs:
1.881)
> hide all atoms
> show #8 cartoons
> show #6 cartoons
> color #6 light pink
> color #6 grey
> ui tool show Clashes
> select #1/c
836 atoms, 845 bonds, 108 residues, 1 model selected
> select #1/g
833 atoms, 842 bonds, 108 residues, 1 model selected
> select #1/c
836 atoms, 845 bonds, 108 residues, 1 model selected
> select clear
> select #6/J:55
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/J:55
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:55
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/J:56
19 atoms, 20 bonds, 1 residue, 1 model selected
> select #1/J:56
19 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> select #1/c
836 atoms, 845 bonds, 108 residues, 1 model selected
> select #1/c #8/d
836 atoms, 845 bonds, 108 residues, 1 model selected
> select #1/c #8/d
836 atoms, 845 bonds, 108 residues, 1 model selected
> select #1/c #8/d
836 atoms, 845 bonds, 108 residues, 1 model selected
> select #1/c #6/d
1567 atoms, 1583 bonds, 201 residues, 2 models selected
> clashes sel restrict both ignoreHiddenModels true reveal true
83 clashes
> clashes sel saveFile /Users/gaurideak/Desktop/H2AZ-H2B_clashes restrict both
> ignoreHiddenModels true reveal true
83 clashes
> select #1/c:75 #6/d:92
13 atoms, 11 bonds, 2 residues, 2 models selected
> select #1/c:92 #6/d:75
20 atoms, 18 bonds, 19 pseudobonds, 2 residues, 3 models selected
> style sel stick
Changed 20 atom styles
> hide #7 models
> select add #7
20 atoms, 18 bonds, 83 pseudobonds, 2 residues, 3 models selected
> select clear
> hide all atoms
> hide #!6 models
> show #!6 models
> hide #!6 models
> select #1/C:156
4 atoms, 3 bonds, 1 residue, 1 model selected
Alignment identifier is 1/C
> select #1/C:156
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/C:156-170
116 atoms, 118 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select #1/E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
Alignment identifier is 1/E
> select #1/E:53
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/E:35-53
173 atoms, 176 bonds, 19 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 173 atom styles
> style sel stick
Changed 173 atom styles
> color sel byhetero
> select clear
> select #1/J:70
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/I:-67
42 atoms, 45 bonds, 2 residues, 1 model selected
> show sel atoms
> select #1/J:69
19 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/I:-67
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #1/I:-68
21 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/E:42
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/E:35-36
20 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/E:35-42
74 atoms, 76 bonds, 8 residues, 1 model selected
> hide sel atoms
> select #1/E:46
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1/E:43
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #1/E:50
27 atoms, 24 bonds, 3 residues, 1 model selected
> select add #1/E:53
38 atoms, 34 bonds, 4 residues, 1 model selected
> hide sel atoms
> select clear
> select #1/C:158
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1/C:159
14 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> hide #1/i,j atoms
> select clear
> open 9B3P
Summary of feedback from opening 9B3P fetched from pdb
---
note | Fetching compressed mmCIF 9b3p from http://files.rcsb.org/download/9b3p.cif
9b3p title:
The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome [more
info...]
Chain information for 9b3p #8
---
Chain | Description | UniProt
A E | Histone H3.3 | H33_HUMAN 0-135
B F | Histone H4 | H4_XENLA 0-102
C G | Histone H2A.Z | H2AZ_MOUSE 0-127
D H | Histone H2B 1.1 | H2B11_XENLA 0-125
I | DNA (128-MER) |
J | DNA (128-MER) |
> mmaker #8 to #1
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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 9b3p, chain J (#8),
sequence alignment score = 761.6
RMSD between 111 pruned atom pairs is 1.256 angstroms; (across all 128 pairs:
1.552)
> mmaker #8/c to #1/xc
No 'to' model specified
> mmaker #8/c to #1/c
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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 9b3p, chain C (#8),
sequence alignment score = 373.4
RMSD between 93 pruned atom pairs is 0.894 angstroms; (across all 98 pairs:
1.056)
> hide #8 atoms
> show #8 cartoons
> ui tool show "Side View"
> color #8/A,E cornflower blue
> color #8/B,F medium sea green
> color #8/C,G khaki
> color #8/D,H light pink
> color #8/I,J light grey
> show #!6 models
> mmaker #8 to #6
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 8com, chain J (#6) with 9b3p, chain J (#8), sequence alignment
score = 752
RMSD between 65 pruned atom pairs is 1.285 angstroms; (across all 120 pairs:
2.074)
> hide #!8 models
> show #!8 models
> hide #!6 models
> color #8/c,g wheat
> open 7xd1
Summary of feedback from opening 7xd1 fetched from pdb
---
note | Fetching compressed mmCIF 7xd1 from http://files.rcsb.org/download/7xd1.cif
7xd1 title:
cryo-EM structure of unmodified nucleosome [more info...]
Chain information for 7xd1 #9
---
Chain | Description | UniProt
A E | Histone H3 | A0A6I9KHI6_CHRAS 37-134
B F | Histone H4 | A0A0P9AXL3_DROAN 22-101
C G | Histone H2A type 1-B/E | H2A1B_HUMAN 10-118
D H | Histone H2B type 1-K | H2B1K_HUMAN 31-124
I | DNA (147-MER) |
J | DNA (147-MER) |
> mmaker #3 to #1
No molecules/chains to match specified
> mmaker #9 to #1
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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 7xd1, chain J (#9),
sequence alignment score = 778.5
RMSD between 111 pruned atom pairs is 1.120 angstroms; (across all 143 pairs:
1.646)
> mmaker #9/c to #1/c
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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 7xd1, chain C (#9),
sequence alignment score = 321.7
RMSD between 97 pruned atom pairs is 0.729 angstroms; (across all 106 pairs:
1.536)
> hide all atoms
> show #9 cartoons
> hide #1,8,9/d,h,b,f cartoons
> hide #1,8,9/d,h,b,f,g,a cartoons
> mmaker #8/c to #1/c
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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 9b3p, chain C (#8),
sequence alignment score = 373.4
RMSD between 93 pruned atom pairs is 0.894 angstroms; (across all 98 pairs:
1.056)
> color #9/i,j light grey
> color #9/c,g khaki
> hide #1,8,9/c,g cartoons
> hide #1,8,9/c,a cartoons
> hide #1,8,9/c,e cartoons
> show #1,8,9/g,a cartoons
> color #9/a,e cornflower blue
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #1 models
> show #1 models
> hide #!9 models
> close #5
> close #7
> show #!9 models
> hide #!9 models
> open 1f66
Summary of feedback from opening 1f66 fetched from pdb
---
notes | Fetching compressed mmCIF 1f66 from http://files.rcsb.org/download/1f66.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
1f66 title:
2.6 A crystal structure of A nucleosome core particle containing the variant
histone H2A.Z [more info...]
Chain information for 1f66 #5
---
Chain | Description | UniProt
A E | HISTONE H3 | Q7ZT64_9ZZZZ 400-535 600-635
B F | HISTONE H4 | H4_MOUSE 0-102 200-302
C G | HISTONE H2A.Z | H2AZ_HUMAN 801-927 1001-1127
D H | HISTONE H2B | H2B1_XENLA 1198-1322 1398-1522
I J | PALINDROMIC 146 BASE PAIR DNA FRAGMENT |
Non-standard residues in 1f66 #5
---
MN — manganese (II) ion
> show #!6 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> show #!5 models
> mmaker #5 to #9
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 7xd1, chain A (#9) with 1f66, chain A (#5), sequence alignment
score = 477.5
RMSD between 97 pruned atom pairs is 0.377 angstroms; (across all 98 pairs:
0.553)
> hide all atoms
> show all cartoons
> hide #!5 models
> show #!5 models
> hide #!5 models
> open 9k43
Summary of feedback from opening 9k43 fetched from pdb
---
note | Fetching compressed mmCIF 9k43 from http://files.rcsb.org/download/9k43.cif
9k43 title:
Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom
601 DNA (C2 symmetry) [more info...]
Chain information for 9k43 #7
---
Chain | Description | UniProt
A E | Histone H3.1 | H31_ARATH 0-135
B F | Histone H4 | H4_ARATH 0-102
C G | Probable histone H2A variant 3 | H2AV3_ARATH 0-133
D H | Histone H2B.1 | H2B1_ARATH 0-147
I | Widom 601 DNA (147-MER) |
J | Widom 601 DNA (147-MER) |
> mmaker #7 to #8
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 9b3p, chain J (#8) with 9k43, chain I (#7), sequence alignment
score = 803.2
RMSD between 120 pruned atom pairs is 1.046 angstroms; (across all 128 pairs:
1.179)
> hide #1#!7 atoms
> show #1#!7 cartoons
> select clear
> open 7m1x
Summary of feedback from opening 7m1x fetched from pdb
---
note | Fetching compressed mmCIF 7m1x from http://files.rcsb.org/download/7m1x.cif
7m1x title:
Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z [more
info...]
Chain information for 7m1x #10
---
Chain | Description | UniProt
A E | Histone H3 | A0A310TTQ1_XENLA 400-535 600-735
B F | Histone H4 | H4_XENLA 0-102 200-302
C G | Histone H2A.Z | H2AZ_MOUSE 800-927 1000-1127
D H | Histone H2B 1.1 | H2B11_XENLA 1197-1322 1397-1522
I | DNA (136-MER) |
J | DNA (136-MER) |
> mmaker #10 to #1
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 TbH2AZ-H2BV_v29.2.pdb, chain J (#1) with 7m1x, chain J (#10),
sequence alignment score = 768.5
RMSD between 121 pruned atom pairs is 1.070 angstroms; (across all 134 pairs:
1.440)
> hide #1#!7,10 atoms
> show #1#!7,10 cartoons
> mmaker #10/c to #1/c
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 TbH2AZ-H2BV_v29.2.pdb, chain C (#1) with 7m1x, chain C (#10),
sequence alignment score = 380
RMSD between 98 pruned atom pairs is 0.689 angstroms; (across all 103 pairs:
1.088)
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> open "/Users/gaurideak/Desktop/EM maps
> inventory/H2AZ_structures/emd_44148_9B3P_Hs.map"
Opened emd_44148_9B3P_Hs.map as #11, grid size 256,256,256, pixel 1.08, shown
at level 0.00622, step 1, values float32
> open "/Users/gaurideak/Desktop/EM maps
> inventory/H2AZ_structures/emd_62042_9K43_Arabidopsis.map"
Opened emd_62042_9K43_Arabidopsis.map as #12, grid size 256,256,256, pixel
1.07, shown at level 0.182, step 1, values float32
> open "/Users/gaurideak/Desktop/EM maps
> inventory/HsCanonical_structures/emd_33132_7XD1.map"
Opened emd_33132_7XD1.map as #13, grid size 256,256,256, pixel 1.07, shown at
level 0.00466, step 1, values float32
> open "/Users/gaurideak/Desktop/EM maps inventory/emd_16777_8COM.map"
Opened emd_16777_8COM.map as #14, grid size 316,316,316, pixel 0.829, shown at
level 0.197, step 2, values float32
> open "/Users/gaurideak/Desktop/EM maps
> inventory/H2AZ_structures/emd_23626_7M1X_mouse.map"
Opened emd_23626_7M1X_mouse.map as #15, grid size 200,200,200, pixel 1.1,
shown at level 0.026, step 1, values float32
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!7 models
> show #!11 models
> volume #11 level 0.0368
> volume #11 level 0.03841
> select add #11
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.86367,-0.11873,0.48987,194.5,-0.1366,-0.88036,-0.4542,351.78,0.48519,-0.4592,0.74413,37.746
> view matrix models
> #11,-0.75563,-0.090423,0.64873,154.04,-0.27764,-0.85283,-0.44226,364.75,0.59325,-0.5143,0.61932,48.826
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.75563,-0.090423,0.64873,155.53,-0.27764,-0.85283,-0.44226,344.47,0.59325,-0.5143,0.61932,27.703
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.75565,-0.35676,0.54928,207.71,-0.024752,-0.82248,-0.56826,324.33,0.65451,-0.443,0.61267,10.298
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.75565,-0.35676,0.54928,196.42,-0.024752,-0.82248,-0.56826,321.37,0.65451,-0.443,0.61267,12.291
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.88619,-0.30487,0.34888,234.11,0.034286,-0.79409,-0.60683,314.88,0.46204,-0.52581,0.71417,35.425
> view matrix models
> #11,-0.87856,-0.30998,0.36338,231.82,0.068426,-0.83463,-0.54655,307.8,0.4727,-0.45531,0.75448,18.261
> view matrix models
> #11,-0.87561,-0.3116,0.36908,230.86,0.08182,-0.84874,-0.52244,304.71,0.47605,-0.42725,0.76866,11.808
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.87561,-0.3116,0.36908,237.93,0.08182,-0.84874,-0.52244,303.87,0.47605,-0.42725,0.76866,11.859
> show #!2 models
===== 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 - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: MacBookPro17,1
Model Number: MYD92B/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 10 days, 53 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
PHL24E1N1300A:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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