![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17117 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00000001f01f0840 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 640000,
"procRole" : "Background",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 4311,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-03-18 12:50:04.9464 +0000",
"codeSigningMonitor" : 1,
"incident" : "0C180477-2E2C-49D6-9E56-31735D108B85",
"pid" : 5986,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-17 15:17:37.4035 +0000",
"procStartAbsTime" : 14887294212809,
"procExitAbsTime" : 15388352198080,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"EEB06612-DA1C-576B-9EBE-0E8AF5F97D19","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B9F21D8A-9717-0200-DDC0-1DF3192EE17C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "560C9CEB-AC8D-4ED1-A5C6-B99B9BC36898",
"wakeTime" : 2,
"sleepWakeUUID" : "CBDB2DEC-8EB1-4447-92CC-7962D4A3C6C0",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4301881320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100698000-10069c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5986},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4301881320\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100698000-10069c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
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0.74,0.74,0.74, shown at level 0.0446, step 1, values float32
Log from Tue Feb 18 11:20:33 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/sxfp8838/Downloads/Map_model_Ub5_27Nov2024 copy.cxs" format
> session
Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
0.74,0.74,0.74, shown at level 0.0446, step 1, values float32
Log from Wed Nov 27 09:59:35 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Ub_states_movie.cxs"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
shown at level 0.0301, step 1, values float32
Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
0.74, shown at level 0.0641, step 1, values float32
Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
512,512,512, pixel 0.74, shown at level 0.113, step 1, values float32
Log from Fri Nov 22 14:40:20 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_localref.cxs"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
shown at level 0.0301, step 1, values float32
Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
0.74, shown at level 0.0641, step 1, values float32
Log from Thu Oct 31 16:48:37 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/zbxg977/Desktop/BRISC_Ub5_colouredbychain.cxs
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Log from Tue Oct 8 13:02:45 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured_v4.cxs"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened cryosparc_P64_J40_020_volume_map (1).mrc as #6, grid size 512,512,512,
pixel 0.74, shown at level 0.154, step 1, values float32
Log from Wed Oct 2 15:29:10 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured_v2.cxs"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Log from Tue Oct 1 13:16:34 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured.cxs"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
shown at level 0.04, step 1, values float32
Log from Wed Sep 4 11:11:03 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
> coot-48.pdb
Chain information for P64_J12_model-coot-48.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L Q | No description available
M | No description available
O | No description available
W | No description available
X | No description available
Y | No description available
> open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC
> processing/P64_W1_J12/Deepemhancer/P64_J12_deepemhancer.mrc"
Opened P64_J12_deepemhancer.mrc as #2, grid size 512,512,512, pixel 0.74,
shown at level 0.00279, step 2, values float32
> set bgColor white
> lighting soft
> volume #2 step 1
> hide atoms
> show cartoons
> dssp
> volume #2 level 0.02757
> surface dust #2 size 7.4
> hide #!2 models
> colour #1/B,G,X,M #0096FF
> colour #1/A,F,J,W #00F900
> colour #1/H,Y,D,I #9437FF
> colour #1/L,O,Q #FF9300
> colour #1/E,K,N,P #EF4E5D
> show #!2 models
> ui tool show "Surface Color"
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.44
> color zone #2 near #1 distance 4.54
> color zone #2 near #1 distance 4.64
> color zone #2 near #1 distance 4.74
> color zone #2 near #1 distance 4.84
> hide #!1 models
> color zone #2 near #1 distance 4.94
> color zone #2 near #1 distance 5.04
> color zone #2 near #1 distance 5.14
> color zone #2 near #1 distance 5.24
> color zone #2 near #1 distance 5.34
> color zone #2 near #1 distance 5.44
> color zone #2 near #1 distance 5.54
> color zone #2 near #1 distance 5.64
> color zone #2 near #1 distance 5.74
> volume #2 level 0.03
> volume #2 level 0.035
> save "/Users/zbxg977/Desktop/BRISC_project/Main
> figures/Map_model_coloured.cxs" includeMaps true
> volume #2 level 0.04
> save /Users/zbxg977/Desktop/image2.png supersample 3
> save /Users/zbxg977/Desktop/image3.png supersample 3
> save /Users/zbxg977/Desktop/image4.png supersample 3
> open 1ubq
1ubq title:
Structure of ubiquitin refined At 1.8 angstroms resolution [more info...]
Chain information for 1ubq #3
---
Chain | Description | UniProt
A | UBIQUITIN | UBIQ_HUMAN 1-76
> select add #3
660 atoms, 608 bonds, 134 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,22.142,0,1,0,146.55,0,0,1,177.99
> view matrix models #3,1,0,0,85.901,0,1,0,77.699,0,0,1,152.28
> view matrix models #3,1,0,0,106,0,1,0,120.98,0,0,1,189.39
> view matrix models #3,1,0,0,108.09,0,1,0,99.383,0,0,1,182.46
> close #3
> show #!1 models
> hide #!2 models
> select #1/O
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> show sel atoms
> save /Users/zbxg977/4Ub.pdb selectedOnly true relModel #2
> open /Users/zbxg977/Desktop/4Ub.pdb
Summary of feedback from opening /Users/zbxg977/Desktop/4Ub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU E 104
SER E 106 1 3
Start residue of secondary structure not found: HELIX 2 2 ALA E 120 VAL E 132
1 13
Start residue of secondary structure not found: HELIX 3 3 ARG E 133 HIS E 136
1 4
Start residue of secondary structure not found: HELIX 4 4 PRO E 163 SER E 168
1 6
Start residue of secondary structure not found: HELIX 5 5 GLU E 184 LYS E 193
1 10
230 messages similar to the above omitted
Chain information for 4Ub.pdb #3
---
Chain | Description
O | No description available
> hide #!1 models
> select add #1
45135 atoms, 45847 bonds, 43 pseudobonds, 4183 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!2 models
> select add #3
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> view matrix models #3,1,0,0,-45.77,0,1,0,-55.623,0,0,1,60.278
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.64657,0.76019,0.063756,122.26,-0.11869,-0.1828,0.97596,39.647,0.75356,0.62346,0.20842,-81.893
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.64657,0.76019,0.063756,133.01,-0.11869,-0.1828,0.97596,51.544,0.75356,0.62346,0.20842,-92.026
> volume #2 level 0.02
> view matrix models
> #3,-0.64657,0.76019,0.063756,131.7,-0.11869,-0.1828,0.97596,48.688,0.75356,0.62346,0.20842,-91.418
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.92486,0.37158,0.081038,254.86,-0.0046565,-0.22413,0.97455,34.504,0.38029,0.90094,0.20902,-70.711
> view matrix models
> #3,-0.99669,0.0074678,0.080982,336.17,0.077958,-0.19583,0.97753,12.84,0.023158,0.98061,0.1946,-14.243
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
atoms
average map value = 0.02144, steps = 152
shifted from previous position = 3.73
rotated from previous position = 9.35 degrees
atoms outside contour = 820, contour level = 0.02
Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98830394 -0.01606640 0.15164823 329.56486754
0.14821753 -0.33513041 0.93044031 28.20456991
0.03587311 0.94203475 0.33359202 -29.19789796
Axis 0.05759369 0.57509586 0.81605620
Axis point 165.14304010 34.55878631 0.00000000
Rotation angle (degrees) 174.22298154
Shift along axis 11.37406101
> hide #!2 models
> show #!1 models
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.9883,-0.016066,0.15165,335.85,0.14822,-0.33513,0.93044,32.137,0.035873,0.94203,0.33359,-27.52
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.78284,-0.58586,-0.20959,455.92,-0.24052,-0.025733,0.9703,44.024,-0.57386,0.81,-0.12077,183.11
> view matrix models
> #3,-0.80058,-0.5206,0.29672,371.17,0.27623,0.11879,0.95372,-80.16,-0.53176,0.84549,0.048707,142.93
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.87819,-0.058049,0.47478,273.77,0.44528,0.26324,0.85582,-124.88,-0.17466,0.96298,-0.20532,90.305
> fitmap #3 inMap #2
Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
atoms
average map value = 0.02942, steps = 84
shifted from previous position = 2.76
rotated from previous position = 7.03 degrees
atoms outside contour = 753, contour level = 0.02
Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
coordinates:
Matrix rotation and translation
-0.86861384 0.06310794 0.49145435 247.47541190
0.48957680 0.26208308 0.83164116 -131.75136294
-0.07631871 0.96297967 -0.25854517 77.15930390
Axis 0.18187306 0.78623263 0.59055943
Axis point 149.05714988 0.00000000 58.37470019
Rotation angle (degrees) 158.83395882
Shift along axis -13.01095516
> volume #2 level 0.015
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.86861,0.063108,0.49145,245.67,0.48958,0.26208,0.83164,-132.49,-0.076319,0.96298,-0.25855,78.734
> fitmap #3 inMap #2
Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
atoms
average map value = 0.04094, steps = 272
shifted from previous position = 3.53
rotated from previous position = 24.2 degrees
atoms outside contour = 675, contour level = 0.015
Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
coordinates:
Matrix rotation and translation
-0.66115790 0.32526680 0.67607081 131.95953052
0.72210154 0.03138215 0.69107490 -114.53308250
0.20356717 0.94510141 -0.25562421 24.27981973
Axis 0.38068765 0.70810053 0.59470207
Axis point 100.89632926 0.00000000 43.47460178
Rotation angle (degrees) 160.51004202
Shift along axis -16.42631342
> hide #!2 models
> show #!2 models
> view matrix models
> #3,-0.66116,0.32527,0.67607,129.56,0.7221,0.031382,0.69107,-115.04,0.20357,0.9451,-0.25562,25.841
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.81701,0.17495,0.54944,206.56,0.56462,0.43612,0.70072,-160.98,-0.11703,0.88272,-0.4551,129.36
> hide #!2 models
> hide sel atoms
> show sel cartoons
> select subtract #3
Nothing selected
> hide atoms
> show #!2 models
> select add #3
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.81701,0.17495,0.54944,208.56,0.56462,0.43612,0.70072,-159.01,-0.11703,0.88272,-0.4551,130.17
> view matrix models
> #3,-0.81701,0.17495,0.54944,207.37,0.56462,0.43612,0.70072,-159.4,-0.11703,0.88272,-0.4551,131.11
> view matrix models
> #3,-0.81701,0.17495,0.54944,206.51,0.56462,0.43612,0.70072,-159.88,-0.11703,0.88272,-0.4551,131.78
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.93722,0.21306,0.27609,263.78,0.3343,0.3234,0.88524,-122.21,0.099324,0.92196,-0.37432,70.546
> show #!2 models
> view matrix models
> #3,-0.9119,0.33361,0.23904,242.14,0.32086,0.21634,0.92209,-105.33,0.2559,0.91755,-0.30432,30.568
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.9119,0.33361,0.23904,241.56,0.32086,0.21634,0.92209,-103.63,0.2559,0.91755,-0.30432,28.63
> view matrix models
> #3,-0.9119,0.33361,0.23904,242.51,0.32086,0.21634,0.92209,-102.98,0.2559,0.91755,-0.30432,29.306
> view matrix models
> #3,-0.9119,0.33361,0.23904,242.12,0.32086,0.21634,0.92209,-103.19,0.2559,0.91755,-0.30432,29.625
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.87355,0.41506,0.25422,217.34,0.3549,0.18575,0.91626,-103.23,0.33309,0.89063,-0.30957,20.475
> fitmap #3 inMap #2
Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
atoms
average map value = 0.04273, steps = 188
shifted from previous position = 6.11
rotated from previous position = 27.6 degrees
atoms outside contour = 691, contour level = 0.015
Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
coordinates:
Matrix rotation and translation
-0.68181384 0.30235068 0.66611857 146.23416859
0.68338301 -0.06162106 0.72745481 -90.64295049
0.26099339 0.95120287 -0.16460723 3.10516441
Axis 0.37323744 0.67579529 0.63560565
Axis point 98.83947470 0.00000000 27.38301406
Rotation angle (degrees) 162.55803812
Shift along axis -4.70235247
> undo
> hide #!2 models
> view matrix models
> #3,-0.71118,0.70096,-0.053665,179.29,0.064186,0.14076,0.98796,-49.463,0.70007,0.69917,-0.1451,-39.754
> view matrix models
> #3,-0.70029,0.71301,-0.034876,172.12,0.066121,0.11343,0.99134,-45.286,0.71079,0.69192,-0.12658,-43.266
> view matrix models
> #3,-0.52247,0.83371,0.17875,83.286,-0.01801,-0.22038,0.97525,35.207,0.85247,0.50632,0.13015,-74.88
> view matrix models
> #3,-0.93075,-0.10152,-0.35128,415.05,-0.13281,0.98894,0.066087,-29.866,0.34068,0.10816,-0.93394,257.72
> view matrix models
> #3,-0.64634,0.57103,0.50613,106.67,0.56883,-0.081552,0.8184,-80.391,0.50861,0.81687,-0.27211,-5.4368
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.64634,0.57103,0.50613,107.8,0.56883,-0.081552,0.8184,-80.999,0.50861,0.81687,-0.27211,-7.3342
> view matrix models
> #3,-0.64634,0.57103,0.50613,108.34,0.56883,-0.081552,0.8184,-80.397,0.50861,0.81687,-0.27211,-7.3389
> fitmap #3 inMap #2
Fit molecule 4Ub.pdb (#3) to map P64_J12_deepemhancer.mrc (#2) using 1034
atoms
average map value = 0.04552, steps = 96
shifted from previous position = 1.7
rotated from previous position = 22.8 degrees
atoms outside contour = 528, contour level = 0.015
Position of 4Ub.pdb (#3) relative to P64_J12_deepemhancer.mrc (#2)
coordinates:
Matrix rotation and translation
-0.60159277 0.47587877 0.64158049 97.54037792
0.45805470 -0.45249689 0.76513558 15.82248234
0.65442496 0.75417900 0.05424035 -70.47054678
Axis -0.44628855 -0.52318661 -0.72601811
Axis point 70.49501793 32.89156096 0.00000000
Rotation angle (degrees) 179.29666393
Shift along axis -0.64637166
> hide #!2 models
> show #!2 models
> hide #!2 models
> select subtract #3
Nothing selected
> select add #3
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> show sel atoms
> save /Users/zbxg977/Desktop/4Ub.pdb models #3 selectedOnly true relModel #2
> close #3
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
> coot-49.pdb
Chain information for P64_J12_model-coot-49.pdb #3
---
Chain | Description
A | No description available
B | No description available
D | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L Q | No description available
M | No description available
O R | No description available
W | No description available
X | No description available
Y | No description available
> hide #!1 models
> hide #!3 atoms
> show #!3 cartoons
> dssp
> colour #3/B,G,X,M #0096FF
> colour #3/A,F,J,W #00F900
> colour #3/H,Y,D,I #9437FF
> colour #3/L,O,Q,R #FF9300
> colour #3/E,K,N,P #EF4E5D
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near #3 distance 5.74
> hide #!3 models
> volume #2 level 0.035
> hide #!2 models
> show #!3 models
> select #3/O,L,Q
2220 atoms, 2238 bonds, 228 residues, 1 model selected
> show sel atoms
> save /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/Ub3.pdb models
> #3 selectedOnly true relModel #2
> open /Users/zbxg977/Desktop/Ub3.pdb
Summary of feedback from opening /Users/zbxg977/Desktop/Ub3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU E 104
SER E 106 1 3
Start residue of secondary structure not found: HELIX 2 2 ALA E 120 VAL E 132
1 13
Start residue of secondary structure not found: HELIX 3 3 ARG E 133 HIS E 136
1 4
Start residue of secondary structure not found: HELIX 4 4 PRO E 163 SER E 168
1 6
Start residue of secondary structure not found: HELIX 5 5 GLU E 184 LYS E 193
1 10
221 messages similar to the above omitted
Chain information for Ub3.pdb #4
---
Chain | Description
L Q | No description available
O | No description available
> ui tool show Matchmaker
> matchmaker #4 to #3/R pairing bs
Parameters
---
Chain pairing | bs
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 P64_J12_model-coot-49.pdb, chain R (#3) with Ub3.pdb, chain O (#4),
sequence alignment score = 374
RMSD between 76 pruned atom pairs is 0.000 angstroms; (across all 76 pairs:
0.000)
> select add #3
46169 atoms, 46887 bonds, 43 pseudobonds, 4259 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
46169 atoms, 46887 bonds, 43 pseudobonds, 4259 residues, 2 models selected
> hide sel atoms
> select subtract #3
Nothing selected
> show #!2 models
> color #2 #b2b2b2dd models
> select add #4
2220 atoms, 2238 bonds, 228 residues, 1 model selected
> lighting simple
> view matrix models
> #4,-0.60159,0.47588,0.64158,93.534,0.45806,-0.45249,0.76514,14.188,0.65442,0.75418,0.054236,-72.225
> view matrix models
> #4,-0.60159,0.47588,0.64158,92.645,0.45806,-0.45249,0.76514,15.149,0.65442,0.75418,0.054236,-71.708
> view matrix models
> #4,-0.60159,0.47588,0.64158,93.136,0.45806,-0.45249,0.76514,15.699,0.65442,0.75418,0.054236,-73.795
> view matrix models
> #4,-0.60159,0.47588,0.64158,94.386,0.45806,-0.45249,0.76514,15.328,0.65442,0.75418,0.054236,-74.44
> hide #!2 models
> select subtract #4
Nothing selected
> select #4/L,Q
1186 atoms, 1198 bonds, 152 residues, 1 model selected
> show sel atoms
> save /Users/zbxg977/Desktop/Ub5_6.pdb models #4 selectedOnly true relModel
> #2
> close #4
> close #1
> close #3
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_46/P64_J12_model-
> coot-50.pdb
Chain information for P64_J12_model-coot-50.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L Q S T | No description available
M | No description available
O R | No description available
W | No description available
X | No description available
Y | No description available
> hide atoms
> show cartoons
> colour #1/B,G,X,M #0096FF
> colour #1/A,F,J,W #00F900
> colour #1/H,Y,D,I #9437FF
> colour #1/L,O,Q,R,S,T #FF9300
> colour #1/E,K,N,P #EF4E5D
> dssp
> show #!2 models
> color zone #2 near #1 distance 5.74
> lighting soft
> hide #!1 models
> volume #2 level 0.04
> ui tool show "Map Eraser"
> select add #3
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,251.41,0,1,0,177.58,0,0,1,180.61
> view matrix models #3,1,0,0,255.51,0,1,0,182.96,0,0,1,177.37
> view matrix models #3,1,0,0,256.04,0,1,0,181.46,0,0,1,179.8
> volume erase #2 center 256.04,181.46,179.8 radius 13.074
Opened P64_J12_deepemhancer.mrc copy as #4, grid size 512,512,512, pixel 0.74,
shown at step 1, values float32
> color #4 #b2b2b2ff models
> view matrix models #3,1,0,0,246.66,0,1,0,183.58,0,0,1,182.44
> volume erase #4 center 246.66,183.58,182.44 radius 12.882
> surface dust #4 size 7.4
> view matrix models #3,1,0,0,287.73,0,1,0,151.7,0,0,1,186.47
> view matrix models #3,1,0,0,131.22,0,1,0,184.9,0,0,1,227.76
> view matrix models #3,1,0,0,128.37,0,1,0,188.93,0,0,1,233.07
> volume erase #4 center 128.37,188.93,233.07 radius 12.882
> view matrix models #3,1,0,0,130.5,0,1,0,187.1,0,0,1,229.29
> volume erase #4 center 130.5,187.1,229.29 radius 12.882
> color zone #4 near #1 distance 4.44
> view matrix models #3,1,0,0,157.62,0,1,0,181.5,0,0,1,79.409
> view matrix models #3,1,0,0,162,0,1,0,207.4,0,0,1,79.905
> view matrix models #3,1,0,0,195.48,0,1,0,203.89,0,0,1,88.793
> volume erase #4 center 195.48,203.89,88.793 radius 12.882
> color zone #4 near #1 distance 4.28
> color zone #4 near #1 distance 9.51
[Repeated 1 time(s)]
> view matrix models #3,1,0,0,118.5,0,1,0,217.26,0,0,1,155.6
> view matrix models #3,1,0,0,119.32,0,1,0,224.9,0,0,1,156.18
> view matrix models #3,1,0,0,120.41,0,1,0,224.7,0,0,1,154.87
> volume erase #4 center 120.41,224.7,154.87 radius 12.882
> view matrix models #3,1,0,0,132.73,0,1,0,234.58,0,0,1,160.81
> view matrix models #3,1,0,0,132.69,0,1,0,234.45,0,0,1,160.79
> view matrix models #3,1,0,0,132.7,0,1,0,233.37,0,0,1,158.05
> volume erase #4 center 132.7,233.37,158.05 radius 12.882
> view matrix models #3,1,0,0,199.12,0,1,0,91.549,0,0,1,168.91
> view matrix models #3,1,0,0,225.06,0,1,0,103.46,0,0,1,184.2
> view matrix models #3,1,0,0,225.89,0,1,0,100,0,0,1,191.46
> view matrix models #3,1,0,0,225.33,0,1,0,99.137,0,0,1,194.08
> view matrix models #3,1,0,0,225.33,0,1,0,97.404,0,0,1,193.65
> volume erase #4 center 225.33,97.404,193.65 radius 12.882
> view matrix models #3,1,0,0,224.86,0,1,0,149.52,0,0,1,283.13
> view matrix models #3,1,0,0,211.04,0,1,0,137.18,0,0,1,287.39
> view matrix models #3,1,0,0,209.5,0,1,0,136.2,0,0,1,276.75
> view matrix models #3,1,0,0,211.99,0,1,0,133.21,0,0,1,273.61
> volume erase #4 center 211.99,133.21,273.61 radius 12.882
> view matrix models #3,1,0,0,204.87,0,1,0,143.03,0,0,1,282
> volume erase #4 center 204.87,143.03,282 radius 12.882
> view matrix models #3,1,0,0,225.79,0,1,0,222.83,0,0,1,236.03
> view matrix models #3,1,0,0,206.22,0,1,0,265.74,0,0,1,169.52
> view matrix models #3,1,0,0,206.01,0,1,0,267.32,0,0,1,166.4
> volume erase #4 center 206.01,267.32,166.4 radius 12.882
> view matrix models #3,1,0,0,211.1,0,1,0,201.51,0,0,1,232.99
> view matrix models #3,1,0,0,249.46,0,1,0,178.84,0,0,1,255.3
> view matrix models #3,1,0,0,252.28,0,1,0,177.38,0,0,1,211.75
> color zone #4 near #1 distance 9.66
> color zone #4 near #1 distance 21.47
> hide #3 models
> select subtract #3
Nothing selected
> save "/Users/zbxg977/Desktop/BRISC_project/Main
> figures/Map_model_coloured.cxs" includeMaps true
——— End of log from Wed Sep 4 11:11:03 2024 ———
opened ChimeraX session
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
> coot-51_modified.pdb
Chain information for P64_J12_model-coot-51_modified.pdb #3
---
Chain | Description
A | No description available
B | No description available
D | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
L Q S T | No description available
M | No description available
O R | No description available
W | No description available
X | No description available
Y | No description available
> show #!1 models
> hide #!4 models
> select add #3
63902 atoms, 64635 bonds, 43 pseudobonds, 4411 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #3
Nothing selected
> dssp
> color #3 by #1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #3 bychain #1
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide #!1 models
> colour #3/B,G,X,M #0096FF
> colour #3/A,F,J,W #00F900
> colour #3/H,Y,D,I #9437FF
> colour #3/L,O,Q,R,S,T #FF9300
> colour #3/E,K,N,P #EF4E5D
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured_v2.cxs" includeMaps true
——— End of log from Tue Oct 1 13:16:34 2024 ———
opened ChimeraX session
> open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
Chain information for penta_Ub_merged.pdb #5
---
Chain | Description
A B C L | No description available
O | No description available
> select add #5
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> color sel orange
> ui mousemode right select
> select clear
> ui tool show Matchmaker
> matchmaker #5 to #3
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 P64_J12_model-coot-51_modified.pdb, chain Q (#3) with
penta_Ub_merged.pdb, chain A (#5), sequence alignment score = 381.3
RMSD between 76 pruned atom pairs is 0.252 angstroms; (across all 76 pairs:
0.252)
> undo
[Repeated 3 time(s)]
> select subtract #5
Nothing selected
> hide #5 models
> show #5 models
> close #5
> open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
Chain information for penta_Ub_merged.pdb #5
---
Chain | Description
A B C L | No description available
O | No description available
> hide #5#!3 atoms
> show #5#!3 cartoons
> ui tool show Matchmaker
> matchmaker #5 to #3/O pairing bs
Parameters
---
Chain pairing | bs
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 P64_J12_model-coot-51_modified.pdb, chain O (#3) with
penta_Ub_merged.pdb, chain O (#5), sequence alignment score = 374
RMSD between 76 pruned atom pairs is 0.115 angstroms; (across all 76 pairs:
0.115)
> show #!4 models
> open "/Users/zbxg977/Desktop/cryosparc_P64_J40_020_volume_map (1).mrc"
Opened cryosparc_P64_J40_020_volume_map (1).mrc as #6, grid size 512,512,512,
pixel 0.74, shown at level 0.00718, step 2, values float32
> volume #6 step 1
> volume #6 level 0.1541
> ui tool show "Fit in Map"
> fitmap #6 inMap #4
Fit map cryosparc_P64_J40_020_volume_map (1).mrc in map
P64_J12_deepemhancer.mrc copy using 129829 points
correlation = 0.5054, correlation about mean = 0.1598, overlap = 3273
steps = 68, shift = 1.22, angle = 0.929 degrees
Position of cryosparc_P64_J40_020_volume_map (1).mrc (#6) relative to
P64_J12_deepemhancer.mrc copy (#4) coordinates:
Matrix rotation and translation
0.99997912 -0.00487300 -0.00424498 0.66325650
0.00493555 0.99987753 0.01485147 -2.81150978
0.00417209 -0.01487211 0.99988070 2.51382637
Axis -0.91705127 -0.25968865 0.30261984
Axis point 0.00000000 149.66536670 175.10960512
Rotation angle (degrees) 0.92857977
Shift along axis 0.88261072
> fitmap #5 inMap #6
Fit molecule penta_Ub_merged.pdb (#5) to map cryosparc_P64_J40_020_volume_map
(1).mrc (#6) using 3424 atoms
average map value = 0.1626, steps = 124
shifted from previous position = 5.16
rotated from previous position = 14.8 degrees
atoms outside contour = 1623, contour level = 0.15407
Position of penta_Ub_merged.pdb (#5) relative to
cryosparc_P64_J40_020_volume_map (1).mrc (#6) coordinates:
Matrix rotation and translation
0.99999913 0.00110329 0.00072892 -0.22178002
-0.00110201 0.99999785 -0.00175506 0.47587376
-0.00073085 0.00175425 0.99999819 -0.26439380
Axis 0.79861150 0.33219833 -0.50186048
Axis point 0.00000000 118.45743317 249.48623484
Rotation angle (degrees) 0.12588650
Shift along axis 0.11365719
> hide #!6 models
> hide #!4 models
> select #5/O
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> hide sel cartoons
> select clear
> select #3/L,Q
2394 atoms, 2406 bonds, 152 residues, 1 model selected
> hide sel cartoons
> select clear
> select #5/A:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 9 atom styles
> select clear
> select #5
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> color sel orange
> select #5:63
47 atoms, 42 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 47 atom styles
> select up
464 atoms, 461 bonds, 45 residues, 1 model selected
> select up
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> select up
114681 atoms, 116174 bonds, 9202 residues, 9 models selected
> select up
114681 atoms, 116174 bonds, 9202 residues, 9 models selected
> select down
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> select down
464 atoms, 461 bonds, 45 residues, 1 model selected
> select down
47 atoms, 42 bonds, 5 residues, 1 model selected
> select down
47 atoms, 42 bonds, 5 residues, 1 model selected
> select clear
> select #5/O
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> hide sel atoms
> select clear
> color #3,5 byhetero
> select #3/O
1070 atoms, 1076 bonds, 76 residues, 1 model selected
> select #3/O:63
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> select clear
> delete H
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured_v3.cxs" includeMaps true
> ui tool show "Side View"
> cartoon style width 1
> cartoon style width 1.5
> select add #5
2929 atoms, 2959 bonds, 380 residues, 1 model selected
> show sel surfaces
> select clear
> lighting soft
> select #5/O
539 atoms, 545 bonds, 76 residues, 1 model selected
> hide sel surfaces
> select #3/O
539 atoms, 545 bonds, 76 residues, 1 model selected
> show sel surfaces
> select clear
> save /Users/zbxg977/Desktop/image1.png supersample 3
> cartoon style thickness 1
> cartoon style thickness 0.8
> cartoon style thickness 0.7
> cartoon style width 2 0.7
Expected a keyword
> cartoon style width 2
> lighting soft
> lighting full
> lighting simple
> lighting soft
> save /Users/zbxg977/Desktop/image2.png supersample 3
> select add #5
2929 atoms, 2959 bonds, 380 residues, 1 model selected
> hide sel surfaces
> select #3/O
539 atoms, 545 bonds, 76 residues, 1 model selected
> hide sel surfaces
> select clear
> save /Users/zbxg977/Desktop/image3.png supersample 3
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
> coot-52.pdb
Summary of feedback from opening
/Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
coot-52.pdb
---
warnings | Start residue of secondary structure not found: HELIX 46 46 ILE L
23 GLU L 34 1 12
Start residue of secondary structure not found: HELIX 47 47 PRO L 38 GLN L 40
5 3
Start residue of secondary structure not found: HELIX 48 48 SER L 57 TYR L 59
5 3
Start residue of secondary structure not found: HELIX 49 49 ILE Q 23 GLU Q 34
1 12
Start residue of secondary structure not found: HELIX 50 50 PRO Q 38 GLN Q 40
5 3
9 messages similar to the above omitted
Chain information for P64_J12_model-coot-52.pdb #7
---
Chain | Description
A | No description available
B | No description available
D | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
M | No description available
O R | No description available
S T | No description available
W | No description available
X | No description available
Y | No description available
> select add #7
61508 atoms, 62229 bonds, 43 pseudobonds, 4259 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!5 models
> select add #7
61508 atoms, 62229 bonds, 43 pseudobonds, 4259 residues, 2 models selected
> show sel atoms
> close #7
> show #!6 models
> hide #!6 models
> show #!5 models
> open /Users/zbxg977/Desktop/penta_Ub.pdb
Summary of feedback from opening /Users/zbxg977/Desktop/penta_Ub.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 23
LYS A 33 1 11
Start residue of secondary structure not found: HELIX 2 2 PRO A 38 GLN A 40 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 57 TYR A 59 1
3
Start residue of secondary structure not found: SHEET 1 1 1 GLN A 2 THR A 7 0
Start residue of secondary structure not found: SHEET 2 2 1 THR A 12 GLU A 16
0
7 messages similar to the above omitted
Chain information for penta_Ub.pdb
---
Chain | Description
7.1/A 7.2/A 7.3/A 7.4/A 7.6/L | No description available
7.5/O | No description available
> close #7
> open /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
> coot-52.pdb
Chain information for P64_J12_model-coot-52.pdb #7
---
Chain | Description
A B C L S T | No description available
E K N P | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
M | No description available
O R | No description available
Q | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
> hide #!5 models
> hide #!3 models
> select add #7
63898 atoms, 64643 bonds, 43 pseudobonds, 4563 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> dssp
> save /Users/zbxg977/Desktop/BRISC_project/Phenix/PDBTools_55/P64_J12_model-
> coot-52.pdb models #7
> colour #7/B,G,X,M #0096FF
> colour #7/A,F,J,W #00F900
> colour #7/H,Y,D,I #9437FF
> colour #7/L,O,Q,R,S,T #FF9300
> colour #7/E,K,N,P #EF4E5D
> colour #7/G,X,M,U #0096FF
> colour #7/Q,F,J,W #00F900
> colour #7/H,Y,D,I,V #9437FF
> colour #7/L,O,R,S,T,C,B,A #FF9300
> colour #7/E,K,N,P #EF4E5D
> cartoon style width 1
> cartoon style width 2
> cartoon style width 1.5
> cartoon style width 2
> open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
Chain information for penta_Ub_merged.pdb #8
---
Chain | Description
A B C L | No description available
O | No description available
> select add #8
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #8 to #7/S pairing bs
Parameters
---
Chain pairing | bs
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 P64_J12_model-coot-52.pdb, chain S (#7) with penta_Ub_merged.pdb,
chain L (#8), sequence alignment score = 373.5
RMSD between 76 pruned atom pairs is 0.190 angstroms; (across all 76 pairs:
0.190)
> select clear
> select #8/O
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #7/S,T
2394 atoms, 2406 bonds, 152 residues, 1 model selected
> hide sel cartoons
> color #8 #ff9300ff
> select clear
> save /Users/zbxg977/Desktop/image4.png supersample 3
> hide #8 models
> show #8 models
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_model_coloured_v4.cxs" includeMaps true
——— End of log from Wed Oct 2 15:29:10 2024 ———
opened ChimeraX session
> lighting simple
> hide #8 models
> show #8 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> close #1
> show #!2 models
> hide #!2 models
> close #3
> show #!4 models
> hide #!4 models
> close #4
> show #!5 models
> hide #!5 models
> close #5
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> hide #8 models
> show #8 models
> save /Users/zbxg977/Desktop/BRISC_Ub5_colouredbychain.cxs includeMaps true
——— End of log from Tue Oct 8 13:02:45 2024 ———
opened ChimeraX session
> open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
> Ub5/P64_W2_J50/P64_W2_J50_tightTarget.mrc"
Opened P64_W2_J50_tightTarget.mrc as #1, grid size 512,512,512, pixel 0.74,
shown at level 9.17e-05, step 2, values float32
> hide #8 models
> hide #!7 models
> show #!2 models
> volume #1 step 1
> volume #1 level 0.03755
> volume #1 level 0.04504
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map P64_W2_J50_tightTarget.mrc in map P64_J12_deepemhancer.mrc using
199202 points
correlation = 0.5686, correlation about mean = 0.3003, overlap = 8709
steps = 48, shift = 0.318, angle = 0.391 degrees
Position of P64_W2_J50_tightTarget.mrc (#1) relative to
P64_J12_deepemhancer.mrc (#2) coordinates:
Matrix rotation and translation
0.99997687 -0.00507535 -0.00452680 1.41739114
0.00507771 0.99998698 0.00051083 -1.00298621
0.00452415 -0.00053381 0.99998962 -0.85475381
Axis -0.07657733 -0.66347764 0.74426698
Axis point 208.59266405 277.12373612 0.00000000
Rotation angle (degrees) 0.39080851
Shift along axis -0.07924613
[deleted to fit within ticket limits]
> crossfade
> color #3/V #C0C0C0
> color #3/I dimgrey
> wait 50
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> wait 100
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> roll x 1 90
> wait 100
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> roll y 1 90
> wait 100
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> wait 50
> crossfade
> color #3/Q dimgray
> color #3/Z #C0C0C0
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I #9437FF
> wait 50
> wait 50
> crossfade
> color #3/V #C0C0C0
> color #3/I dimgrey
> wait 50
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> Movie record
Unknown command: Movie record
> roll y 1 360
> wait 390
> roll x -1 90
> wait 100
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> roll x 1 90
> wait 100
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> roll y 1 90
> wait 100
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> wait 50
> crossfade
> color #3/Q dimgray
> color #3/Z #C0C0C0
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I #9437FF
> wait 50
> wait 50
> crossfade
> color #3/V #C0C0C0
> color #3/I dimgrey
> wait 50
> wait 100
> movie encode
No frames have been recorded
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> Movie start
Unknown command: Movie start
> roll y 1 360
> wait 390
> roll x -1 90
> wait 100
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> roll x 1 90
> wait 100
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> roll y 1 90
> wait 100
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> wait 50
> crossfade
> color #3/Q dimgray
> color #3/Z #C0C0C0
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I #9437FF
> wait 50
> wait 50
> crossfade
> color #3/V #C0C0C0
> color #3/I dimgrey
> wait 50
> wait 100
> movie encode
No frames have been recorded
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> movie record
> roll y 1 360
> wait 390
> roll x -1 90
> wait 100
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> roll x 1 90
> wait 100
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> roll y 1 90
> wait 100
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> wait 50
> crossfade
> color #3/Q dimgray
> color #3/Z #C0C0C0
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I #9437FF
> wait 50
> wait 50
> crossfade
> color #3/V #C0C0C0
> color #3/I dimgrey
> wait 50
> wait 100
> movie encode
Movie saved to /Users/zbxg977/Desktop/movie.mp4
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Ub_states_movie.cxs" includeMaps true
——— End of log from Fri Nov 22 14:40:20 2024 ———
opened ChimeraX session
> close #7
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #1-2
> close #4-5
> hide #!8 models
> show #!8 models
> hide #6 models
> show #6 models
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> show sel cartoons
> hide #6 models
> select subtract #3
22 models selected
> show #6 models
> hide #6 models
> hide #!8 models
> show #!8 models
> select #8/L,T
584 atoms, 590 bonds, 76 residues, 1 model selected
> select #8/L,C
1186 atoms, 1198 bonds, 152 residues, 1 model selected
> hide sel cartoons
> select add #8
3424 atoms, 3454 bonds, 380 residues, 3 models selected
> select subtract #8
5 models selected
> open "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
> Ub5/Composite_map_v1.mrc"
Opened Composite_map_v1.mrc as #1, grid size 881,854,755, pixel
0.74,0.74,0.74, shown at step 1, values float32
> volume #1 level 0,0 level 0.01661,0.8 level 1.287,1
> volume #1 level 0,1 level 0.01661,0.8 level 1.287,1
> volume #1 region 0,0,0,880,853,754 step 4
[Repeated 1 time(s)]
> volume #1 step 1
> hide #!1 models
> show #!1 models
> volume #1 level 0,1 level 0,0 level 1.287,1
> volume #1 level 0,1 level 0,0 level 1.322,0
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume style surface
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> volume #1 orthoplanes xyz positionPlanes 440,427,377 style image region all
> mousemode rightMode "move planes"
> volume style surface
> volume #1 level 0.04462
> surface dust #1 size 7.4
> ui tool show "Side View"
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule P64_J12_model-coot-56.pdb (#3) to map Composite_map_v1.mrc (#1)
using 53424 atoms
average map value = 0.2036, steps = 252
shifted from previous position = 23.8
rotated from previous position = 6.84 degrees
atoms outside contour = 19147, contour level = 0.044618
Position of P64_J12_model-coot-56.pdb (#3) relative to Composite_map_v1.mrc
(#1) coordinates:
Matrix rotation and translation
0.99999824 -0.00034178 0.00184313 -0.29642060
0.00034053 0.99999971 0.00068229 -0.21302121
-0.00184336 -0.00068166 0.99999807 0.51592373
Axis -0.34188411 0.92404809 0.17102743
Axis point 280.38615462 0.00000000 162.43947673
Rotation angle (degrees) 0.11429067
Shift along axis -0.00726324
> fitmap #8 inMap #1
Fit molecule penta_Ub_merged.pdb (#8) to map Composite_map_v1.mrc (#1) using
3424 atoms
average map value = 0.144, steps = 232
shifted from previous position = 18.2
rotated from previous position = 20.5 degrees
atoms outside contour = 1522, contour level = 0.044618
Position of penta_Ub_merged.pdb (#8) relative to Composite_map_v1.mrc (#1)
coordinates:
Matrix rotation and translation
-0.65356489 0.44939063 0.60901642 118.65823822
0.44163674 -0.42703489 0.78904891 10.59241835
0.61466245 0.78465869 0.08062760 -72.88467696
Axis -0.41618722 -0.53523602 -0.73505823
Axis point 79.98021623 31.62011254 0.00000000
Rotation angle (degrees) 179.69780160
Shift along axis -1.47900474
> transparency 0
> transparency 50
> close #6
> transparency 0
> dssp
> volume showOutlineBox false
> hide #!1 models
> select #8/O
1034 atoms, 1040 bonds, 76 residues, 1 model selected
> hide sel cartoons
> select add #8
3424 atoms, 3454 bonds, 380 residues, 2 models selected
> select subtract #8
5 models selected
> save "/Users/zbxg977/Desktop/BRISC_project/CryoSPARC processing
> Ub5/Map_model_Ub5_27Nov2024.cxs" includeMaps true
——— End of log from Wed Nov 27 09:59:35 2024 ———
opened ChimeraX session
> save /Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/BRISC.cxs
——— End of log from Tue Feb 18 11:20:33 2025 ———
opened ChimeraX session
> select #3/N:309
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
45 atoms, 45 bonds, 3 residues, 2 models selected
> select up
3760 atoms, 3805 bonds, 237 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
3760 atoms, 3805 bonds, 237 residues, 23 models selected
> color (#!3 & sel) #ff8ad8ff
[Repeated 1 time(s)]
> color (#!3 & sel) #fc7d78ff
[Repeated 1 time(s)]
> select #3/A:281
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
42 atoms, 42 bonds, 5 residues, 2 models selected
> select up
1839 atoms, 1884 bonds, 231 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
1839 atoms, 1884 bonds, 231 residues, 23 models selected
> color (#!3 & sel) #fc7d78ff
> select #3/Z:383
20 atoms, 19 bonds, 1 residue, 1 model selected
> select up
351 atoms, 356 bonds, 22 residues, 2 models selected
> select up
3987 atoms, 4047 bonds, 251 residues, 2 models selected
> select up
4001 atoms, 4060 bonds, 253 residues, 2 models selected
> select up
4600 atoms, 4672 bonds, 314 residues, 2 models selected
> select up
4761 atoms, 4831 bonds, 330 residues, 2 models selected
> select up
4866 atoms, 4939 bonds, 340 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
4866 atoms, 4939 bonds, 340 residues, 23 models selected
> color (#!3 & sel) #9838ffff
> color (#!3 & sel) #9437ffff
[Repeated 1 time(s)]
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Q:88
Nothing selected
> select #3/Q:145
Nothing selected
> select #3/G:134
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
188 atoms, 187 bonds, 14 residues, 2 models selected
> select up
1601 atoms, 1620 bonds, 110 residues, 2 models selected
> select up
1640 atoms, 1657 bonds, 113 residues, 2 models selected
> select up
3743 atoms, 3777 bonds, 250 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 24 models selected
> select down
53424 atoms, 54081 bonds, 4083 residues, 23 models selected
> select down
3743 atoms, 3777 bonds, 250 residues, 23 models selected
> color (#!3 & sel) #28a3ffff
> color (#!3 & sel) #2bb3ffff
> color (#!3 & sel) #2799ffff
> color (#!3 & sel) #28a2ffff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #0433ffff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #76d6ffff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #005493ff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #125895ff
> color (#!3 & sel) #2591f6ff
> color (#!3 & sel) #0096ffff
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel stick
Changed 7 atom styles
> show sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> style sel ball
Changed 7 atom styles
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> ~hbonds
> style sel stick
Changed 7 atom styles
> hbonds sel reveal true
0 hydrogen bonds found
> ~hbonds
> select #3/B:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 96 bonds, 12 residues, 2 models selected
> select up
272 atoms, 272 bonds, 35 residues, 2 models selected
> select up
287 atoms, 287 bonds, 37 residues, 2 models selected
> select up
602 atoms, 606 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
602 atoms, 606 bonds, 76 residues, 23 models selected
> show sel atoms
> hide sel atoms
> style sel sphere
Changed 602 atom styles
> style sel sphere
Changed 602 atom styles
> show sel atoms
> style sel stick
Changed 602 atom styles
> hide sel atoms
> show sel surfaces
> select #3/O:69
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
85 atoms, 85 bonds, 5 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
1070 atoms, 1076 bonds, 76 residues, 23 models selected
> show sel surfaces
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel ball
Changed 7 atom styles
> color (#!3 & sel) blue
> select #3/F:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
639 atoms, 640 bonds, 47 residues, 2 models selected
> select up
1049 atoms, 1056 bonds, 80 residues, 2 models selected
> select up
1319 atoms, 1327 bonds, 98 residues, 2 models selected
> select up
2901 atoms, 2929 bonds, 195 residues, 2 models selected
> select up
2925 atoms, 2952 bonds, 197 residues, 2 models selected
> select up
3369 atoms, 3402 bonds, 229 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
3369 atoms, 3402 bonds, 229 residues, 23 models selected
> color (#!3 & sel) lime
> select #3/M:222
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
472 atoms, 473 bonds, 41 residues, 2 models selected
> select up
934 atoms, 941 bonds, 75 residues, 2 models selected
> select up
1124 atoms, 1132 bonds, 89 residues, 2 models selected
> select up
1888 atoms, 1907 bonds, 154 residues, 2 models selected
> select up
1906 atoms, 1924 bonds, 156 residues, 2 models selected
> select up
2009 atoms, 2030 bonds, 163 residues, 2 models selected
> select up
2382 atoms, 2408 bonds, 192 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
2382 atoms, 2408 bonds, 192 residues, 23 models selected
> color (#!3 & sel) lime
> select #3/Q:306
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
363 atoms, 366 bonds, 31 residues, 2 models selected
> select up
1386 atoms, 1399 bonds, 100 residues, 2 models selected
> select up
1538 atoms, 1556 bonds, 112 residues, 2 models selected
> select up
1838 atoms, 1861 bonds, 140 residues, 2 models selected
> select up
1869 atoms, 1891 bonds, 142 residues, 2 models selected
> select up
2009 atoms, 2033 bonds, 151 residues, 2 models selected
> select up
2045 atoms, 2068 bonds, 155 residues, 2 models selected
> select up
2420 atoms, 2446 bonds, 183 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
2420 atoms, 2446 bonds, 183 residues, 23 models selected
> color (#!3 & sel) #0096ffff
> select #3/I:122
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
320 atoms, 322 bonds, 19 residues, 2 models selected
> select up
4963 atoms, 5054 bonds, 383 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
4963 atoms, 5054 bonds, 383 residues, 23 models selected
> color (#!3 & sel) #9437ffff
> select #3/J:122
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
256 atoms, 258 bonds, 16 residues, 2 models selected
> select up
1430 atoms, 1454 bonds, 100 residues, 2 models selected
> select up
1465 atoms, 1487 bonds, 104 residues, 2 models selected
> select up
1838 atoms, 1864 bonds, 132 residues, 2 models selected
> select up
2185 atoms, 2211 bonds, 161 residues, 2 models selected
> select up
4726 atoms, 4795 bonds, 322 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
4726 atoms, 4795 bonds, 322 residues, 23 models selected
> color (#!3 & sel) #9437ffff
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> select #3/B:36@CD1
1 atom, 1 residue, 1 model selected
> select #3/J:298
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/Y:9
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
106 atoms, 106 bonds, 8 residues, 2 models selected
> select up
565 atoms, 568 bonds, 44 residues, 2 models selected
> select up
602 atoms, 604 bonds, 47 residues, 2 models selected
> select up
723 atoms, 727 bonds, 53 residues, 2 models selected
> select up
808 atoms, 812 bonds, 60 residues, 2 models selected
> select up
2035 atoms, 2062 bonds, 151 residues, 2 models selected
> select up
2247 atoms, 2275 bonds, 168 residues, 2 models selected
> select up
4056 atoms, 4129 bonds, 351 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
4056 atoms, 4129 bonds, 351 residues, 23 models selected
> color (#!3 & sel) #9437ffff
> select #3/U:137
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 14 residues, 2 models selected
> select up
631 atoms, 639 bonds, 46 residues, 2 models selected
> select up
943 atoms, 951 bonds, 69 residues, 2 models selected
> select up
1303 atoms, 1319 bonds, 94 residues, 2 models selected
> select up
1574 atoms, 1591 bonds, 114 residues, 2 models selected
> select up
2313 atoms, 2337 bonds, 178 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 24 models selected
> select up
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 24 models selected
> select down
43 pseudobonds, 23 models selected
> select #3/U:137
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
178 atoms, 180 bonds, 14 residues, 2 models selected
> select up
631 atoms, 639 bonds, 46 residues, 2 models selected
> select up
943 atoms, 951 bonds, 69 residues, 2 models selected
> select up
1303 atoms, 1319 bonds, 94 residues, 2 models selected
> select up
1574 atoms, 1591 bonds, 114 residues, 2 models selected
> select up
2313 atoms, 2337 bonds, 178 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
2313 atoms, 2337 bonds, 178 residues, 23 models selected
> color (#!3 & sel) lime
> select #3/V:262
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
329 atoms, 330 bonds, 22 residues, 2 models selected
> select up
1237 atoms, 1249 bonds, 91 residues, 2 models selected
> select up
1558 atoms, 1577 bonds, 116 residues, 2 models selected
> select up
1653 atoms, 1673 bonds, 124 residues, 2 models selected
> select up
1660 atoms, 1679 bonds, 125 residues, 2 models selected
> select up
1997 atoms, 2019 bonds, 152 residues, 2 models selected
> select up
1998 atoms, 2019 bonds, 153 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
1998 atoms, 2019 bonds, 153 residues, 23 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #0096ffff
> select #3/X:262
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
329 atoms, 330 bonds, 22 residues, 2 models selected
> select up
1411 atoms, 1424 bonds, 100 residues, 2 models selected
> select up
1657 atoms, 1671 bonds, 116 residues, 2 models selected
> select up
1715 atoms, 1730 bonds, 119 residues, 2 models selected
> select up
2709 atoms, 2735 bonds, 200 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
2709 atoms, 2735 bonds, 200 residues, 23 models selected
> color (#!3 & sel) #0096ffff
> select #3/W:237
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
605 atoms, 606 bonds, 44 residues, 2 models selected
> select up
787 atoms, 789 bonds, 57 residues, 2 models selected
> select up
794 atoms, 795 bonds, 58 residues, 2 models selected
> select up
927 atoms, 929 bonds, 68 residues, 2 models selected
> select up
1285 atoms, 1288 bonds, 92 residues, 2 models selected
> select up
2872 atoms, 2895 bonds, 189 residues, 2 models selected
> select up
2904 atoms, 2926 bonds, 191 residues, 2 models selected
> select up
3353 atoms, 3381 bonds, 223 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
3353 atoms, 3381 bonds, 223 residues, 23 models selected
> color (#!3 & sel) lime
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> select #3/G:88@CB
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) cyan
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> select #3/G:88@CB
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) #ff2600ff
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) #ff2600ff
> select #3/X:290
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/G:88@CA
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) #0096ffff
> select #3/G:88@CB
1 atom, 1 residue, 1 model selected
> color (#!3 & sel) #0096ffff
> select #3/G:129
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/G:88@CB
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> color bfactor sel
17 atoms, 1 residues, 1 surfaces, atom bfactor range 64.7 to 84.5
> color bfactor sel
17 atoms, 1 residues, 1 surfaces, atom bfactor range 64.7 to 84.5
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel ball
Changed 17 atom styles
> hide sel atoms
> show sel atoms
> lighting simple
> ui tool show "Side View"
[Repeated 2 time(s)]
> view
> color (#!3 & sel) red
> view sel
> view
> ui tool show "Side View"
> select #3/X:215
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of P64_J12_model-coot-56.pdb_O SES surface, 70 of 93436 triangles,
2 residues
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel atoms
> color (#!3 & sel) #0096ffff
> select #3/O:34@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
102 atoms, 103 bonds, 8 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
1070 atoms, 1076 bonds, 76 residues, 23 models selected
> select down
102 atoms, 103 bonds, 8 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> select #3/B:66@N
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
48 atoms, 48 bonds, 6 residues, 2 models selected
> select up
330 atoms, 334 bonds, 41 residues, 2 models selected
> select up
334 atoms, 337 bonds, 42 residues, 2 models selected
> select up
369 atoms, 372 bonds, 46 residues, 2 models selected
> select up
432 atoms, 434 bonds, 54 residues, 2 models selected
> select up
602 atoms, 606 bonds, 76 residues, 2 models selected
> select down
432 atoms, 434 bonds, 54 residues, 2 models selected
> hide sel surfaces
> select up
602 atoms, 606 bonds, 76 residues, 2 models selected
> hide sel surfaces
> select #3/Y:140
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/D:25
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 12 residues, 2 models selected
> select up
602 atoms, 608 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
602 atoms, 608 bonds, 76 residues, 23 models selected
> show sel surfaces
> ui tool show "Side View"
> select #3/D:8@CD2
1 atom, 1 residue, 1 model selected
> select #3/Y:140
20 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
[Repeated 2 time(s)]
> view
> color (#!3 & sel) red
> select #3/L:19
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
584 atoms, 590 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
584 atoms, 590 bonds, 76 residues, 23 models selected
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select #3/Y:71
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/Y:140
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel atoms
> color (#!3 & sel) #9437ffff
> select #3/D:16@N
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
39 atoms, 38 bonds, 5 residues, 2 models selected
> select up
602 atoms, 608 bonds, 76 residues, 2 models selected
> hide sel surfaces
> select #3/G:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/G:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/G:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> view
> select #3/f:33
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select #3/Q:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> view
> show sel atoms
> color (#!3 & sel) orange red
> color (#!3 & sel) red
> select #3/G:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> view sel
> show sel atoms
> color (#!3 & sel) red
> view
> select #3/Q:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color (#!3 & sel) #0096ffff
> hide sel atoms
> select #3/O:25
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
168 atoms, 167 bonds, 11 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
1070 atoms, 1076 bonds, 76 residues, 23 models selected
> show sel surfaces
> select #3/B:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 38 bonds, 5 residues, 2 models selected
> select up
233 atoms, 234 bonds, 30 residues, 2 models selected
> select up
268 atoms, 268 bonds, 34 residues, 2 models selected
> select up
272 atoms, 272 bonds, 35 residues, 2 models selected
> select up
287 atoms, 287 bonds, 37 residues, 2 models selected
> select up
602 atoms, 606 bonds, 76 residues, 2 models selected
> show sel surfaces
> select #3/L:14
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
37 atoms, 36 bonds, 5 residues, 2 models selected
> select up
584 atoms, 590 bonds, 76 residues, 2 models selected
> show sel surfaces
> select #3/A:161
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/G:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/L:20@N
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select up
44 atoms, 44 bonds, 6 residues, 2 models selected
> select up
584 atoms, 590 bonds, 76 residues, 2 models selected
> hide sel surfaces
> style sel ball
Changed 584 atom styles
> style sel ball
Changed 584 atom styles
> select clear
> style sel ball
Changed 0 atom styles
> style sel ball
Changed 0 atom styles
> style sel stick
Changed 0 atom styles
> style sel ball
Changed 0 atom styles
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/G:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/G:33
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide sel atoms
> color (#!3 & sel) #0096ffff
> select #3/G:88@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/B:49@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
93 atoms, 93 bonds, 12 residues, 2 models selected
> select up
330 atoms, 334 bonds, 41 residues, 2 models selected
> select up
334 atoms, 337 bonds, 42 residues, 2 models selected
> select up
369 atoms, 372 bonds, 46 residues, 2 models selected
> select up
432 atoms, 434 bonds, 54 residues, 2 models selected
> select up
602 atoms, 606 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
602 atoms, 606 bonds, 76 residues, 23 models selected
> hide sel surfaces
> select #3/O:45@CE1
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 20 bonds, 1 residue, 2 models selected
> select up
279 atoms, 280 bonds, 21 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> hide sel surfaces
> select #3/Y:263
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) red
> select #3/Y:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) red
> style sel ball
Changed 11 atom styles
> select #3/Y:263
20 atoms, 20 bonds, 1 residue, 1 model selected
> style sel ball
Changed 20 atom styles
> select #3/L:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
584 atoms, 590 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
584 atoms, 590 bonds, 76 residues, 23 models selected
> show sel surfaces
> select #3/O:20
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
65 atoms, 65 bonds, 6 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> show sel surfaces
> select #3/D:29
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 12 residues, 2 models selected
> select up
602 atoms, 608 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
602 atoms, 608 bonds, 76 residues, 23 models selected
> show sel surfaces
> select #3/F:133
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/Y:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> color (#!3 & sel) #9437ffff
> select #3/Y:263
20 atoms, 20 bonds, 1 residue, 1 model selected
> color (#!3 & sel) #9437ffff
> hide sel atoms
> select #3/D:58@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
26 atoms, 26 bonds, 3 residues, 2 models selected
> select up
602 atoms, 608 bonds, 76 residues, 2 models selected
> hide sel surfaces
> select #3/L:1@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
584 atoms, 590 bonds, 76 residues, 2 models selected
> select up
53424 atoms, 54081 bonds, 4083 residues, 2 models selected
> select down
584 atoms, 590 bonds, 76 residues, 23 models selected
> hide sel surfaces
> select #3/O:32@O
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
168 atoms, 167 bonds, 11 residues, 2 models selected
> select up
1070 atoms, 1076 bonds, 76 residues, 2 models selected
> hide sel surfaces
> save "/Users/sxfp8838/OneDrive - University of Leeds/BRISC/BRISC coloured
> .cxs"
——— End of log from Tue Feb 25 14:10:22 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33B/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 35 days, 3 hours, 46 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PL2783Q:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Platform: | → all |
| Project: | → ChimeraX |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | new → closed |
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