![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Last modified 7 months ago
#17117 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| 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-15.3.1-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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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/BRISC.cxs
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 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
> volume #1 level 0.1462
> hide #!1 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,177.62,0,1,0,221.79,0,0,1,116.11
> volume erase #2 center 177.62,221.79,116.11 radius 32.12
> view matrix models #3,1,0,0,188.72,0,1,0,194.5,0,0,1,112.11
> view matrix models #3,1,0,0,212.28,0,1,0,201.47,0,0,1,106.94
> volume erase #2 center 212.28,201.47,106.94 radius 32.12
> view matrix models #3,1,0,0,220.92,0,1,0,166.89,0,0,1,106.53
> view matrix models #3,1,0,0,227.3,0,1,0,168.78,0,0,1,111.01
> volume erase #2 center 227.3,168.78,111.01 radius 32.12
> view matrix models #3,1,0,0,241.37,0,1,0,186.51,0,0,1,178.42
> view matrix models #3,1,0,0,265.96,0,1,0,195.56,0,0,1,150.36
> view matrix models #3,1,0,0,267.41,0,1,0,191.95,0,0,1,151.06
> view matrix models #3,1,0,0,267.98,0,1,0,191.29,0,0,1,150.88
> volume erase #2 center 267.98,191.29,150.88 radius 32.12
> view matrix models #3,1,0,0,249.24,0,1,0,183.14,0,0,1,169.43
> view matrix models #3,1,0,0,247.96,0,1,0,180.13,0,0,1,176.94
> view matrix models #3,1,0,0,247.62,0,1,0,180.93,0,0,1,175.55
> volume erase #2 center 247.62,180.93,175.55 radius 14.85
> view matrix models #3,1,0,0,230.85,0,1,0,183.35,0,0,1,140.43
> view matrix models #3,1,0,0,227.29,0,1,0,181.05,0,0,1,132.78
> volume erase #2 center 227.29,181.05,132.78 radius 14.85
> hide #3 models
> select subtract #3
Nothing selected
> show #!1 models
> volume #1 level 0.03006
> hide #!2 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> volume erase #1 center 139.02,180.94,179.91 radius 22.182
Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
0.74, shown at step 1, values float32
> volume erase #4 center 135.12,201.97,197.24 radius 22.164
> volume erase #4 center 153.11,212.48,222.77 radius 22.164
> volume erase #4 center 189.01,222.98,218.1 radius 22.164
> volume erase #4 center 207.63,218.66,207.51 radius 22.164
> volume erase #4 center 205.67,233.05,195.36 radius 22.164
> volume erase #4 center 240.61,226.55,200.09 radius 22.164
> volume erase #4 center 234.06,210.34,215.07 radius 22.164
> volume erase #4 center 165.06,178.19,208.63 radius 22.164
> volume erase #4 center 147.44,141.75,161.18 radius 22.164
> volume erase #4 center 168.46,130.94,174.07 radius 22.164
> volume erase #4 center 170.77,147.86,164.7 radius 22.164
> volume erase #4 center 150.68,174.81,163.92 radius 22.164
> volume erase #4 center 158.83,159.78,197.76 radius 22.164
> hide #3 models
> select subtract #3
Nothing selected
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #3 models
> select add #3
1 model selected
> volume erase #4 center 163.24,190.1,158.8 radius 22.164
> volume erase #4 center 165.54,184.04,168.19 radius 22.164
> volume erase #4 center 171.2,201.05,166.92 radius 22.164
> undo
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> ui tool show "Side View"
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> volume erase #4 center 223.42,218.19,178.35 radius 17.475
> volume erase #4 center 211.53,221.7,173.87 radius 17.475
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> select subtract #3
Nothing selected
> lighting soft
> ui tool show "Color Zone"
> color zone #4 near #7 distance 4.44
> color zone #4 near #7 distance 4.6
> color zone #4 near #7 distance 72.5
> lighting simple
> lighting soft
> surface dust #2 size 7.4
> surface dust #4 size 7.4
> color zone #4 near #7 distance 74.79
> color zone #4 near #7 distance 58.36
> lighting simple
> lighting soft
> volume #4 level 0.04729
> lighting simple
> volume #4 level 0.06407
> lighting soft
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_localref.cxs" includeMaps true
——— End of log from Thu Oct 31 16:48:37 2024 ———
opened ChimeraX session
> lighting simple
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> open
> /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
> coot-56.pdb
Summary of feedback from opening
/Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
coot-56.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
ALA A 6 1 4
Start residue of secondary structure not found: HELIX 2 2 LEU A 7 ARG A 9 1 3
Start residue of secondary structure not found: HELIX 3 3 SER A 15 ASN A 24 1
10
Start residue of secondary structure not found: HELIX 4 4 PRO A 96 ALA A 98 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN A 100 ALA A 103
1 4
24 messages similar to the above omitted
P64_J12_model-coot-56.pdb title:
Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
(Q9NXR7) [more info...]
Chain information for P64_J12_model-coot-56.pdb #3
---
Chain | Description
A | brisc and BRCA1-A complex member 2
B C D L S T | No description available
F | No description available
G | No description available
I | No description available
J | No description available
M | No description available
N | 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
Z | No description available
Non-standard residues in P64_J12_model-coot-56.pdb #3
---
ZN — (ZN)
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> hide #!4 models
> select subtract #3
Nothing selected
> colour #3/G,X,M,U #0096FF
> colour #3/Q,F,J,W #00F900
> colour #3/H,Y,D,I,V #9437FF
> colour #3/L,O,R,S,T,C,B,A #FF9300
> colour #3/E,K,N,P #EF4E5D
> select #3/D
602 atoms, 608 bonds, 76 residues, 1 model selected
> color sel orange
> select #3/A
1839 atoms, 1884 bonds, 231 residues, 1 model selected
> color sel #ff7e79ff
> color sel byelement
> color sel #ff2600ff
> color sel #ff7e79ff
> select #3/Z
4866 atoms, 4939 bonds, 3 pseudobonds, 340 residues, 2 models selected
> color (#!3 & sel) #9437ffff
> select #3/V
1998 atoms, 2019 bonds, 5 pseudobonds, 153 residues, 2 models selected
> color (#!3 & sel) lime
> ui mousemode right select
> select clear
> select #3/J
4726 atoms, 4795 bonds, 6 pseudobonds, 322 residues, 2 models selected
> color (#!3 & sel) #ff40ffff
> color (#!3 & sel) #9437ffff
> select clear
> dssp
> show #8 models
> hide #8 models
> select #3/S,T
2394 atoms, 2406 bonds, 152 residues, 1 model selected
> hide sel cartoons
> show #8 models
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/SQ
Nothing selected
> select #3/Q
2420 atoms, 2446 bonds, 3 pseudobonds, 183 residues, 2 models selected
> color (#!3 & sel) #0096ffff
> select #3/M
2382 atoms, 2408 bonds, 4 pseudobonds, 192 residues, 2 models selected
> color (#!3 & sel) #00f900ff
> select clear
> cartoon style width 1
> cartoon style width 5
> cartoon style width 2
> cartoon style thickness 2
> cartoon style thickness 1
> cartoon style thickness 0.9
> cartoon style width 2
> cartoon style width 3
> lighting soft
> cartoon style width 2
> cartoon style thickness 0.8
> cartoon style thickness 0.7
> lighting full
> lighting soft
> lighting simple
> select #3/N
3760 atoms, 3805 bonds, 237 residues, 1 model selected
> color sel #ff7e79ff
> select clear
> select #3/X,U
5022 atoms, 5072 bonds, 10 pseudobonds, 378 residues, 2 models selected
> color (#!3 & sel) #0433ffff
> color (#!3 & sel) #7a81ffff
> color (#!3 & sel) #0433ffff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #00fdffff
> color (#!3 & sel) #005493ff
[Repeated 1 time(s)]
> color (#!3 & sel) #005493a3
> color (#!3 & sel) #00549385
> color (#!3 & sel) #00549380
> color (#!3 & sel) #0096ffff
> select clear
> select #3/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #3/O:76
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> style #8#!3 stick
Changed 56848 atom styles
> show #8#!3 surfaces
> surface transparency 50
> surface transparency 80
> hide #!3,8 surfaces
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #A,Y,W
Expected an objects specifier or a keyword
> select #3A,Y,W
Expected an objects specifier or a keyword
> select #3/A,Y,W
9248 atoms, 9394 bonds, 8 pseudobonds, 805 residues, 2 models selected
> color (#!3 & sel) light gray
[Repeated 1 time(s)]
> color (#!3 & sel) #c0c0c0ff
> select #3/X,U,V
7020 atoms, 7091 bonds, 15 pseudobonds, 531 residues, 2 models selected
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #c0c0c0ff
> select #3/Z,N
8626 atoms, 8744 bonds, 3 pseudobonds, 577 residues, 2 models selected
> color (#!3 & sel) #a9a9a9ff
> color (#!3 & sel) #c0c0c0ff
> select clear
> select #3/I,M,Q
9765 atoms, 9908 bonds, 7 pseudobonds, 758 residues, 2 models selected
> color (#!3 & sel) dim gray
> select #3/G,F
7112 atoms, 7179 bonds, 4 pseudobonds, 479 residues, 2 models selected
> select #3/G,F,J
11838 atoms, 11974 bonds, 10 pseudobonds, 801 residues, 2 models selected
> color (#!3 & sel) dim gray
> select clear
> ui tool show "Side View"
> spin 360
Unknown command: spin 360
> roll 360
Expected an axis vector or a keyword
> roll x 360
[Repeated 2 time(s)]
> roll x 1 360
> roll y 1 360
> roll x 1 90
> roll x 2 90
> roll x -1 90
> roll y 1 360
> roll x -1 90
> roll y 1 360
> wait 20
> roll x -1 90
> roll y 1 360
> wait 150
> roll x -1 90
> roll y 1 360
> wait 250
> roll x -1 90
> roll y 1 360
> wait 500
> roll x -1 90
> roll y 1 360
> wait 450
> roll x -1 90
> roll y 1 360
> wait 420
> roll x -1 90
> roll y 1 360
> wait 400
> roll x -1 90
> color #3,8 #0096ffff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> Color #3/G,Q #0096FF
Unknown command: Color #3/G,Q #0096FF
> Sel #3/G,Q color sel #0096FF
Unknown command: Sel #3/G,Q color sel #0096FF
> Sel #3/G,Q
Unknown command: Sel #3/G,Q
> select #3/G,Q
6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #3/G,Q color sel #0096FF
Expected a keyword
> select #3/G,Q
6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected
> color sel #0096FF
> select clear
> color #3/G,Q #0096FF
> color #3,8 #797979ff
> color #3,8 #919191ff
> undo
[Repeated 1 time(s)]
> color #3,8 dim gray
> undo
[Repeated 4 time(s)]
> select clear
> color #3/G,Q #0096FF
> wait 150
> color #3/G,Q dimgray
> color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> color fade #3/G,Q #0096FF
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> wait 50
> color #3/G,Q dimgray
> Crossfade color #3/G,Q #0096FF
Unknown command: Crossfade color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> Crossfade; color #3/G,Q #0096FF; wait 50
Unknown command: Crossfade; color #3/G,Q #0096FF; wait 50
> crossfade
> color #3/G,Q #0096FF
> wait 50
> crossfade
> color #3/G,Q #0096FF
> wait 50
> undo
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> select #3/Z:275
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!3 & sel) #9437ffff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> select clear
> select #3/Z:274
21 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!3 & sel) light gray
> select clear
> undo
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #c0c0c0ff
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> select clear
> roll x -1 90
> roll x 1 90
> open
> /Users/zbxg977/Desktop/BRISC_project/BRISC_pentaUb_structure_Dan/cryosparc_P1_DeepEmhancer_J202_highres.mrc
Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
512,512,512, pixel 0.74, shown at level 0.00204, step 2, values float32
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> volume #5 step 1
> volume #5 level 0.1134
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95422,-0.27698,-0.11292,74.797,0.20162,0.87447,-0.44119,60.309,0.22095,0.39822,0.89028,-89.115
> undo
> select subtract #3
22 models selected
> select add #5
4 models selected
> view matrix models
> #5,0.89102,-0.11592,0.43892,-23.542,0.30523,0.86866,-0.39021,37.491,-0.33604,0.48165,0.80938,-20.252
> view matrix models
> #5,0.42416,-0.27299,0.86346,9.9416,0.79723,0.56483,-0.21305,5.4897,-0.42955,0.77875,0.45721,-15.846
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.42416,-0.27299,0.86346,6.061,0.79723,0.56483,-0.21305,-17.432,-0.42955,0.77875,0.45721,24.788
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.81844,-0.43282,0.37791,50.121,0.50998,0.24418,-0.8248,164.2,0.26471,0.86778,0.42057,-78.781
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.81844,-0.43282,0.37791,40.926,0.50998,0.24418,-0.8248,160.85,0.26471,0.86778,0.42057,-105.12
> view matrix models
> #5,0.81844,-0.43282,0.37791,56.133,0.50998,0.24418,-0.8248,169.15,0.26471,0.86778,0.42057,-100.7
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.79885,-0.084636,0.59554,174.83,-0.6013,0.13968,-0.78672,330.58,-0.016603,-0.98657,-0.16248,364.87
> view matrix models
> #5,-0.70691,-0.21333,0.67436,176.16,-0.70654,0.25721,-0.65928,305.02,-0.032808,-0.94251,-0.33255,381.88
> view matrix models
> #5,-0.86037,-0.37738,0.34257,272.5,-0.34072,-0.074004,-0.93725,356.83,0.37905,-0.9231,-0.06491,287.32
> view matrix models
> #5,0.27598,-0.92698,0.25405,237.73,-0.926,-0.32726,-0.18819,379.89,0.25759,-0.18332,-0.94871,284.51
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.27598,-0.92698,0.25405,261.38,-0.926,-0.32726,-0.18819,442.24,0.25759,-0.18332,-0.94871,329.72
> view matrix models
> #5,0.27598,-0.92698,0.25405,270.85,-0.926,-0.32726,-0.18819,441.82,0.25759,-0.18332,-0.94871,354.73
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.76194,0.56796,0.31124,118.96,-0.39996,-0.034665,-0.91588,416.29,-0.5094,-0.82232,0.25357,412.69
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.76194,0.56796,0.31124,167.06,-0.39996,-0.034665,-0.91588,433.46,-0.5094,-0.82232,0.25357,417.86
> ui tool show "Fit in Map"
> fitmap #3 inMap #5
Fit molecule P64_J12_model-coot-56.pdb (#3) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 53424 atoms
average map value = 0.07452, steps = 284
shifted from previous position = 23.8
rotated from previous position = 6.83 degrees
atoms outside contour = 43940, contour level = 0.1134
Position of P64_J12_model-coot-56.pdb (#3) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
-0.76336194 -0.42876028 -0.48315957 509.75254988
0.58594633 -0.14473464 -0.79731974 262.25309824
0.27192911 -0.89174912 0.36171543 201.03833376
Axis -0.07445072 -0.59533266 0.80002257
Axis point 210.03507452 319.31513667 0.00000000
Rotation angle (degrees) 140.64127053
Shift along axis -33.24407263
> select subtract #5
Nothing selected
> open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
Chain information for penta_Ub_merged.pdb #6
---
Chain | Description
A B C L | No description available
O | No description available
> select add #6
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> view matrix models #6,1,0,0,14.12,0,1,0,22.571,0,0,1,27.031
> view matrix models #6,1,0,0,15.745,0,1,0,4.9213,0,0,1,39.269
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.03084, steps = 240
shifted from previous position = 5.63
rotated from previous position = 11.6 degrees
atoms outside contour = 3177, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
-0.81522555 -0.25341032 -0.52075956 465.22557231
0.51830802 0.08193703 -0.85125972 235.13444893
0.25838749 -0.96388253 0.06454744 304.69339704
Axis -0.10216074 -0.70676837 0.70002975
Axis point 150.78544864 0.00000000 367.68057814
Rotation angle (degrees) 146.55035104
Shift along axis -0.41893617
> hide sel atoms
> show sel cartoons
> hide #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9837,-0.11362,0.13936,21.477,0.056651,0.93143,0.35949,-55.449,-0.17065,-0.34573,0.92269,154.42
> view matrix models
> #6,0.37349,-0.79347,0.48053,230.48,-0.0081346,0.5152,0.85703,-41.298,-0.9276,-0.324,0.18597,433.9
> view matrix models
> #6,0.30923,-0.43531,0.8455,121.42,-0.36441,0.76697,0.52816,42.616,-0.8784,-0.47144,0.078541,467.05
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.30923,-0.43531,0.8455,102.31,-0.36441,0.76697,0.52816,47.152,-0.8784,-0.47144,0.078541,461.46
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.92947,-0.26671,-0.25485,104.32,-0.27908,-0.96018,-0.012978,433.1,-0.24124,0.083187,-0.96689,379.48
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.92947,-0.26671,-0.25485,106.56,-0.27908,-0.96018,-0.012978,437.85,-0.24124,0.083187,-0.96689,383.68
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.92611,0.0034423,-0.37724,76.233,-0.10302,-0.95964,-0.26168,437.28,-0.36292,0.28121,-0.88838,361.8
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.58955,0.42781,-0.68513,120.44,-0.084315,-0.81099,-0.57896,454.97,-0.80332,0.39909,-0.44205,368.48
> view matrix models
> #6,0.43235,-0.37451,-0.82026,325.47,-0.65274,-0.75758,0.0018353,481.19,-0.6221,0.53463,-0.57199,323.19
> view matrix models
> #6,0.66075,-0.25513,-0.70591,234.59,-0.3588,-0.93341,0.0015123,448.38,-0.65929,0.25228,-0.7083,405.14
> view matrix models
> #6,0.53137,-0.26167,-0.80572,280.2,-0.12418,-0.96488,0.23147,366.1,-0.83799,-0.022937,-0.5452,470.63
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.04473, steps = 216
shifted from previous position = 8.49
rotated from previous position = 8.17 degrees
atoms outside contour = 3016, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.07651590 0.64458117 0.76069733 -87.66333612
0.99486624 0.00132160 -0.10119000 11.31246327
-0.06623051 0.76453474 -0.64117092 155.61742874
Axis 0.69402741 0.66292501 0.28081378
Axis point 0.00000000 7.59449819 100.00864003
Rotation angle (degrees) 141.41343192
Shift along axis -9.64192415
> view matrix models
> #6,0.27731,-0.24257,-0.92965,347.92,-0.0086426,-0.96819,0.25005,334.1,-0.96074,-0.061309,-0.27059,467.65
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.27731,-0.24257,-0.92965,352.22,-0.0086426,-0.96819,0.25005,333.08,-0.96074,-0.061309,-0.27059,463.08
> view matrix models
> #6,0.27731,-0.24257,-0.92965,355.74,-0.0086426,-0.96819,0.25005,333.93,-0.96074,-0.061309,-0.27059,466.06
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.29679,-0.35595,-0.88612,365.66,0.10608,-0.9099,0.40103,274.01,-0.94903,-0.21303,-0.23229,485.65
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.29679,-0.35595,-0.88612,367.16,0.10608,-0.9099,0.40103,280.02,-0.94903,-0.21303,-0.23229,486.54
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.04044, steps = 88
shifted from previous position = 2.76
rotated from previous position = 5.25 degrees
atoms outside contour = 3054, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.15609642 0.72235882 0.67367027 -116.00954017
0.96951994 0.01835015 -0.24432426 42.58067044
-0.18885174 0.69127491 -0.69747689 205.63722394
Axis 0.72174910 0.66537520 0.19066746
Axis point 0.00000000 21.56062234 131.74159871
Rotation angle (degrees) 139.59795370
Shift along axis -16.18933184
> view matrix models
> #6,0.37294,-0.32482,-0.86914,348.3,0.076925,-0.92267,0.37783,289.83,-0.92466,-0.20777,-0.31911,493.61
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.06226, steps = 212
shifted from previous position = 3.45
rotated from previous position = 19.4 degrees
atoms outside contour = 2811, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.00314523 0.52331352 0.85213441 -73.49266478
0.95223623 0.25863119 -0.16234552 -8.10699426
-0.30534615 0.81194388 -0.49750464 178.68162582
Axis 0.61955240 0.73604400 0.27275273
Axis point 25.90526356 0.00000000 114.54079787
Rotation angle (degrees) 128.16032758
Shift along axis -2.76376043
> select subtract #6
Nothing selected
> hide #!5 models
> show #!3 models
> color #6 #ff9300ff
> ui tool show "Side View"
> select #6
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> hide #6
> view matrix models
> #6,0.4434,0.00086618,-0.89632,274.04,0.24539,-0.96191,0.12046,299.3,-0.86208,-0.27336,-0.42673,507.15
> hide cartoons #6
Expected ',' or a keyword
> view matrix models
> #6,0.4434,0.00086618,-0.89632,274.06,0.24539,-0.96191,0.12046,299.25,-0.86208,-0.27336,-0.42673,507.17
> ui mousemode right select
> select clear
> crossfade #6
Expected an integer >= 1 or a keyword
> hide #6 models
> crossfade
> hide #3/O,L,D,C,B
> wait 50
> crossfade
> hide cartoons #3/O,L,D,C,B; wait 50
Expected ',' or a keyword
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> undo
> show #6 models
> hide #6 models
> show #6 models
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> undo
> hide #6 models
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon show #3/O,L,A,C,B; wait 50
Expected an atoms specifier or a keyword
> show #6 models
> crossfade
> cartoon hide #3/O,L,A,C,B
> wait 50
> undo
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon show #6/O,L,A,C,B; wait 50
Expected an atoms specifier or a keyword
> undo
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> 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
> hide #!8 models
> show #!8 models
> undo
[Repeated 9 time(s)]
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #6 models
> show #!2 models
> hide #!2 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #8/O to #3/R pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain R (#3) with penta_Ub_merged.pdb,
chain O (#8), sequence alignment score = 374
RMSD between 76 pruned atom pairs is 0.217 angstroms; (across all 76 pairs:
0.217)
> select clear
> show #6 models
> hide #!8 models
> show #!8 models
> hide #6 models
> show #6 models
> crossfade
> color #3/Q #0096FF, color #3/Z #C0C0C0; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> wait 50
> crossfade
> color #3/Q #0096FF
> color #3/Z #C0C0C0
> wait 50
> select clear
> undo
[Repeated 3 time(s)]
> crossfade
> color #3/Q #0096FF, #3/Z #C0C0C0; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> crossfade
> color #3/Q #0096FF & #3/Z #C0C0C0; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF & color #3/Z #C0C0C0; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF #3/Z #9437FF; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF, #3/Z #9437FF; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> crossfade
> color #3/Q #0096FF & #3/Z #9437FF; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF
> undo
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> undo
[Repeated 1 time(s)]
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> 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
> 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
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> 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 50
> 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 50
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> wait 50
> 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 50
> 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 50
> 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 dimgray
> color #3/I #C0C0C0
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I dimgrey
> wait 50
> undo
[Repeated 2 time(s)]
> redo
> 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 80
> 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 80
> 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 dimgray
> 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 dimgray
> color #3/I dimgrey
> wait 50
> crossfade
> color #3/V C0C0C0; color #3/I dimgrey; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> 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
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/Abraxas2 alphafold.pdb"
Abraxas2 alphafold.pdb title:
Alphafold monomer V2.0 prediction for brisc complex subunit abraxas 2 (Q15018)
[more info...]
Chain information for Abraxas2 alphafold.pdb #2
---
Chain | Description | UniProt
A | brisc complex subunit abraxas 2 | ABRX2_HUMAN 1-415
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/Brcc36 alphafold.pdb"
Brcc36 alphafold.pdb title:
Alphafold monomer V2.0 prediction for lys-63-specific deubiquitinase BRCC36
(P46736) [more info...]
Chain information for Brcc36 alphafold.pdb #4
---
Chain | Description | UniProt
A | lys-63-specific deubiquitinase BRCC36 | BRCC3_HUMAN 1-316
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/Brcc45 alphafold.pdb"
Brcc45 alphafold.pdb title:
Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
(Q9NXR7) [more info...]
Chain information for Brcc45 alphafold.pdb #5
---
Chain | Description | UniProt
A | brisc and BRCA1-A complex member 2 | BABA2_HUMAN 1-383
Drag select of 4 residues
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,49.333,0,1,0,-85.824,0,0,1,90.52
> view matrix models #2,1,0,0,161.85,0,1,0,44.609,0,0,1,140.07
> view matrix models #2,1,0,0,249.46,0,1,0,94.779,0,0,1,323.36
> ui mousemode right translate
> ui tool show Matchmaker
> matchmaker #2/A to #3/M pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain M (#3) with Abraxas2
alphafold.pdb, chain A (#2), sequence alignment score = 819.5
RMSD between 169 pruned atom pairs is 1.047 angstroms; (across all 192 pairs:
2.148)
> select #2/A:32-52
172 atoms, 173 bonds, 21 residues, 1 model selected
> select up
311 atoms, 317 bonds, 38 residues, 1 model selected
> select up
3301 atoms, 3372 bonds, 415 residues, 1 model selected
> hide sel cartoons
> select #2/A:32-52
172 atoms, 173 bonds, 21 residues, 1 model selected
> show sel cartoons
> color sel lime
> select #2/A:32-54
187 atoms, 188 bonds, 23 residues, 1 model selected
> show sel cartoons
> color sel dim gray
> select #2/A:37-50
110 atoms, 111 bonds, 14 residues, 1 model selected
> color sel lime
> ui mousemode right select
> select clear
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/Brcc36 alphafold.pdb"
Brcc36 alphafold.pdb title:
Alphafold monomer V2.0 prediction for lys-63-specific deubiquitinase BRCC36
(P46736) [more info...]
Chain information for Brcc36 alphafold.pdb #6
---
Chain | Description | UniProt
A | lys-63-specific deubiquitinase BRCC36 | BRCC3_HUMAN 1-316
> select clear
> ui mousemode right translate
> ui mousemode right "move picked models"
> view matrix models #4,1,0,0,-56.122,0,1,0,-84.255,0,0,1,51.498
> view matrix models #6,1,0,0,68.2,0,1,0,52.979,0,0,1,4.8463
> ui mousemode right select
Drag select of 356 residues
Drag select of 363 residues
Drag select of 316 residues
> select clear
Drag select of 316 residues
> delete
Missing or invalid "atoms" argument: empty atom specifier
> select clear
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "move picked models"
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui tool show Matchmaker
> matchmaker #4/A to #3/G pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain G (#3) with Brcc36 alphafold.pdb,
chain A (#4), sequence alignment score = 1180.5
RMSD between 235 pruned atom pairs is 0.786 angstroms; (across all 250 pairs:
1.302)
> select #4/A:184-208
207 atoms, 212 bonds, 25 residues, 1 model selected
> color sel cyan
> color sel light sea green
> color sel cyan
> select up
251 atoms, 256 bonds, 31 residues, 1 model selected
> select up
2529 atoms, 2575 bonds, 316 residues, 1 model selected
> hide sel cartoons
> select #4/A:184-208
207 atoms, 212 bonds, 25 residues, 1 model selected
> show sel cartoons
> select #4/A:180-208
237 atoms, 242 bonds, 29 residues, 1 model selected
> show sel cartoons
> select #4/A:176-208
268 atoms, 273 bonds, 33 residues, 1 model selected
> show sel cartoons
> select #4/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:182
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:181
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:176-183
61 atoms, 60 bonds, 8 residues, 1 model selected
> color sel dim gray
> ui mousemode right select
> select clear
> select #3/G:88
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 7 atom styles
> color (#!3 & sel) cyan
> select #3/G:145
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 17 atom styles
> color (#!3 & sel) cyan
> ui tool show Matchmaker
> matchmaker #5/A to #3/Y pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain Y (#3) with Brcc45 alphafold.pdb,
chain A (#5), sequence alignment score = 1634.1
RMSD between 209 pruned atom pairs is 1.153 angstroms; (across all 351 pairs:
2.724)
> select #5/A:378
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
79 atoms, 81 bonds, 10 residues, 1 model selected
> select up
3078 atoms, 3169 bonds, 383 residues, 1 model selected
> ui mousemode right "move picked models"
> view matrix models
> #5,0.82998,0.35439,0.43074,135.5,0.40064,-0.91606,-0.018284,95.563,0.3881,0.18775,-0.90229,157.7
> view matrix models
> #5,0.82998,0.35439,0.43074,143.32,0.40064,-0.91606,-0.018284,35.228,0.3881,0.18775,-0.90229,66.629
> show sel cartoons
> hide sel cartoons
> select #6/A:98
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
133 atoms, 133 bonds, 18 residues, 1 model selected
> select up
2529 atoms, 2575 bonds, 316 residues, 1 model selected
> hide sel cartoons
> select #3/Y:263
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 20 atom styles
> style sel ball
Changed 20 atom styles
> color (#!3 & sel) purple
> color (#!3 & sel) #b13dffff
> select #3/Y:320
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> show sel atoms
> color (#!3 & sel) #b13dffff
> select #3/Y:140
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!3 & sel) #b13dffff
> style sel ball
Changed 20 atom styles
> ui mousemode right select
> select clear
> save "/Users/sxfp8838/OneDrive - University of Leeds/BRISC/BRISC all
> mutations coloured.cxs"
> select #3/Y:165
Nothing selected
> select #3/Y:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:160
Nothing selected
> view
> select #3/Y:160
Nothing selected
> select #3/Y:150
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/M:21
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/M:72
Nothing selected
> select #3/M:99
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/M:105
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/M:107
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/M:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/M:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/M:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/M:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/M:208
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/M:219
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/M:223
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/M:240
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/M:267
Nothing selected
> select #3/M:406
Nothing selected
> select #3/F:21
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/F:72
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/F:99
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/F:105
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #3/F:107
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/F:117
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/F:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/F:122
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #3/F:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/F:161
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #3/G:59
Nothing selected
> select #3/G:60
Nothing selected
> select #3/G:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/G:187
Nothing selected
> select #3/G:190
Nothing selected
> select #3/G:191
Nothing selected
> select #3/G:195
Nothing selected
> select #3/G:200
Nothing selected
> select #3/Y:5
Nothing selected
> select #3/Y:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right translate
> select #3/Y:50
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:60
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/Y:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:109
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #3/Y:133
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/Y:139
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/Y:203
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/Y:157
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:162
Nothing selected
> select #3/Y:172
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:186
Nothing selected
> select #4/A:184
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
251 atoms, 256 bonds, 31 residues, 1 model selected
> select up
2529 atoms, 2575 bonds, 316 residues, 1 model selected
> select up
68285 atoms, 69226 bonds, 5893 residues, 8 models selected
> select down
2529 atoms, 2575 bonds, 316 residues, 28 models selected
> show sel cartoons
> undo
> ui mousemode right select
> select clear
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/Brcc45 alphafold.pdb"
Brcc45 alphafold.pdb title:
Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
(Q9NXR7) [more info...]
Chain information for Brcc45 alphafold.pdb #7
---
Chain | Description | UniProt
A | brisc and BRCA1-A complex member 2 | BABA2_HUMAN 1-383
> ui mousemode right "move picked models"
> view matrix models #7,1,0,0,123.09,0,1,0,171.58,0,0,1,39.68
> ui tool show Matchmaker
> matchmaker #7/A to #3/Y pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain Y (#3) with Brcc45 alphafold.pdb,
chain A (#7), sequence alignment score = 1634.1
RMSD between 209 pruned atom pairs is 1.153 angstroms; (across all 351 pairs:
2.724)
> select #3/Y:172
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:186
Nothing selected
> select #3/Y:186
Nothing selected
> select #3/Y:206
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/Y:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #7/A:167
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
89 atoms, 91 bonds, 11 residues, 1 model selected
> select up
3078 atoms, 3169 bonds, 383 residues, 1 model selected
> hide sel cartoons
> select #3/Y:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/Y:220
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/Y:227
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:266
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #3,1,-0.00034178,0.0018431,-11.971,0.00034053,1,0.00068229,19.772,-0.0018434,-0.00068166,1,-12.284
> select #3/Y:287
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/Y:2300
Nothing selected
> select #3/Y:300
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/Y:366
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/Y:348
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/Y:330
7 atoms, 6 bonds, 1 residue, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/BRISC coloured .cxs"
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 Tue Feb 25 14:10:22 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/sxfp8838/Library/CloudStorage/OneDrive-
> UniversityofLeeds/BRISC/BRISC.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 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
> volume #1 level 0.1462
> hide #!1 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,177.62,0,1,0,221.79,0,0,1,116.11
> volume erase #2 center 177.62,221.79,116.11 radius 32.12
> view matrix models #3,1,0,0,188.72,0,1,0,194.5,0,0,1,112.11
> view matrix models #3,1,0,0,212.28,0,1,0,201.47,0,0,1,106.94
> volume erase #2 center 212.28,201.47,106.94 radius 32.12
> view matrix models #3,1,0,0,220.92,0,1,0,166.89,0,0,1,106.53
> view matrix models #3,1,0,0,227.3,0,1,0,168.78,0,0,1,111.01
> volume erase #2 center 227.3,168.78,111.01 radius 32.12
> view matrix models #3,1,0,0,241.37,0,1,0,186.51,0,0,1,178.42
> view matrix models #3,1,0,0,265.96,0,1,0,195.56,0,0,1,150.36
> view matrix models #3,1,0,0,267.41,0,1,0,191.95,0,0,1,151.06
> view matrix models #3,1,0,0,267.98,0,1,0,191.29,0,0,1,150.88
> volume erase #2 center 267.98,191.29,150.88 radius 32.12
> view matrix models #3,1,0,0,249.24,0,1,0,183.14,0,0,1,169.43
> view matrix models #3,1,0,0,247.96,0,1,0,180.13,0,0,1,176.94
> view matrix models #3,1,0,0,247.62,0,1,0,180.93,0,0,1,175.55
> volume erase #2 center 247.62,180.93,175.55 radius 14.85
> view matrix models #3,1,0,0,230.85,0,1,0,183.35,0,0,1,140.43
> view matrix models #3,1,0,0,227.29,0,1,0,181.05,0,0,1,132.78
> volume erase #2 center 227.29,181.05,132.78 radius 14.85
> hide #3 models
> select subtract #3
Nothing selected
> show #!1 models
> volume #1 level 0.03006
> hide #!2 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> volume erase #1 center 139.02,180.94,179.91 radius 22.182
Opened P64_W2_J50_tightTarget.mrc copy as #4, grid size 512,512,512, pixel
0.74, shown at step 1, values float32
> volume erase #4 center 135.12,201.97,197.24 radius 22.164
> volume erase #4 center 153.11,212.48,222.77 radius 22.164
> volume erase #4 center 189.01,222.98,218.1 radius 22.164
> volume erase #4 center 207.63,218.66,207.51 radius 22.164
> volume erase #4 center 205.67,233.05,195.36 radius 22.164
> volume erase #4 center 240.61,226.55,200.09 radius 22.164
> volume erase #4 center 234.06,210.34,215.07 radius 22.164
> volume erase #4 center 165.06,178.19,208.63 radius 22.164
> volume erase #4 center 147.44,141.75,161.18 radius 22.164
> volume erase #4 center 168.46,130.94,174.07 radius 22.164
> volume erase #4 center 170.77,147.86,164.7 radius 22.164
> volume erase #4 center 150.68,174.81,163.92 radius 22.164
> volume erase #4 center 158.83,159.78,197.76 radius 22.164
> hide #3 models
> select subtract #3
Nothing selected
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #3 models
> select add #3
1 model selected
> volume erase #4 center 163.24,190.1,158.8 radius 22.164
> volume erase #4 center 165.54,184.04,168.19 radius 22.164
> volume erase #4 center 171.2,201.05,166.92 radius 22.164
> undo
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> ui tool show "Side View"
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> ui tool show "Map Eraser"
> select add #3
1 model selected
> volume erase #4 center 223.42,218.19,178.35 radius 17.475
> volume erase #4 center 211.53,221.7,173.87 radius 17.475
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #3 models
> select subtract #3
Nothing selected
> lighting soft
> ui tool show "Color Zone"
> color zone #4 near #7 distance 4.44
> color zone #4 near #7 distance 4.6
> color zone #4 near #7 distance 72.5
> lighting simple
> lighting soft
> surface dust #2 size 7.4
> surface dust #4 size 7.4
> color zone #4 near #7 distance 74.79
> color zone #4 near #7 distance 58.36
> lighting simple
> lighting soft
> volume #4 level 0.04729
> lighting simple
> volume #4 level 0.06407
> lighting soft
> save "/Users/zbxg977/Desktop/BRISC_project/Main figures/Figure
> 2/Map_localref.cxs" includeMaps true
——— End of log from Thu Oct 31 16:48:37 2024 ———
opened ChimeraX session
> lighting simple
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> open
> /Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
> coot-56.pdb
Summary of feedback from opening
/Users/zbxg977/Desktop/BRISC_project/Phenix/RealSpaceRefine_51/P64_J12_model-
coot-56.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 3
ALA A 6 1 4
Start residue of secondary structure not found: HELIX 2 2 LEU A 7 ARG A 9 1 3
Start residue of secondary structure not found: HELIX 3 3 SER A 15 ASN A 24 1
10
Start residue of secondary structure not found: HELIX 4 4 PRO A 96 ALA A 98 1
3
Start residue of secondary structure not found: HELIX 5 5 GLN A 100 ALA A 103
1 4
24 messages similar to the above omitted
P64_J12_model-coot-56.pdb title:
Alphafold monomer V2.0 prediction for brisc and BRCA1-A complex member 2
(Q9NXR7) [more info...]
Chain information for P64_J12_model-coot-56.pdb #3
---
Chain | Description
A | brisc and BRCA1-A complex member 2
B C D L S T | No description available
F | No description available
G | No description available
I | No description available
J | No description available
M | No description available
N | 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
Z | No description available
Non-standard residues in P64_J12_model-coot-56.pdb #3
---
ZN — (ZN)
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> hide #!4 models
> select subtract #3
Nothing selected
> colour #3/G,X,M,U #0096FF
> colour #3/Q,F,J,W #00F900
> colour #3/H,Y,D,I,V #9437FF
> colour #3/L,O,R,S,T,C,B,A #FF9300
> colour #3/E,K,N,P #EF4E5D
> select #3/D
602 atoms, 608 bonds, 76 residues, 1 model selected
> color sel orange
> select #3/A
1839 atoms, 1884 bonds, 231 residues, 1 model selected
> color sel #ff7e79ff
> color sel byelement
> color sel #ff2600ff
> color sel #ff7e79ff
> select #3/Z
4866 atoms, 4939 bonds, 3 pseudobonds, 340 residues, 2 models selected
> color (#!3 & sel) #9437ffff
> select #3/V
1998 atoms, 2019 bonds, 5 pseudobonds, 153 residues, 2 models selected
> color (#!3 & sel) lime
> ui mousemode right select
> select clear
> select #3/J
4726 atoms, 4795 bonds, 6 pseudobonds, 322 residues, 2 models selected
> color (#!3 & sel) #ff40ffff
> color (#!3 & sel) #9437ffff
> select clear
> dssp
> show #8 models
> hide #8 models
> select #3/S,T
2394 atoms, 2406 bonds, 152 residues, 1 model selected
> hide sel cartoons
> show #8 models
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/SQ
Nothing selected
> select #3/Q
2420 atoms, 2446 bonds, 3 pseudobonds, 183 residues, 2 models selected
> color (#!3 & sel) #0096ffff
> select #3/M
2382 atoms, 2408 bonds, 4 pseudobonds, 192 residues, 2 models selected
> color (#!3 & sel) #00f900ff
> select clear
> cartoon style width 1
> cartoon style width 5
> cartoon style width 2
> cartoon style thickness 2
> cartoon style thickness 1
> cartoon style thickness 0.9
> cartoon style width 2
> cartoon style width 3
> lighting soft
> cartoon style width 2
> cartoon style thickness 0.8
> cartoon style thickness 0.7
> lighting full
> lighting soft
> lighting simple
> select #3/N
3760 atoms, 3805 bonds, 237 residues, 1 model selected
> color sel #ff7e79ff
> select clear
> select #3/X,U
5022 atoms, 5072 bonds, 10 pseudobonds, 378 residues, 2 models selected
> color (#!3 & sel) #0433ffff
> color (#!3 & sel) #7a81ffff
> color (#!3 & sel) #0433ffff
> color (#!3 & sel) #0096ffff
> color (#!3 & sel) #00fdffff
> color (#!3 & sel) #005493ff
[Repeated 1 time(s)]
> color (#!3 & sel) #005493a3
> color (#!3 & sel) #00549385
> color (#!3 & sel) #00549380
> color (#!3 & sel) #0096ffff
> select clear
> select #3/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> select #3/O:76
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3/B:63
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> style #8#!3 stick
Changed 56848 atom styles
> show #8#!3 surfaces
> surface transparency 50
> surface transparency 80
> hide #!3,8 surfaces
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select #A,Y,W
Expected an objects specifier or a keyword
> select #3A,Y,W
Expected an objects specifier or a keyword
> select #3/A,Y,W
9248 atoms, 9394 bonds, 8 pseudobonds, 805 residues, 2 models selected
> color (#!3 & sel) light gray
[Repeated 1 time(s)]
> color (#!3 & sel) #c0c0c0ff
> select #3/X,U,V
7020 atoms, 7091 bonds, 15 pseudobonds, 531 residues, 2 models selected
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #c0c0c0ff
> select #3/Z,N
8626 atoms, 8744 bonds, 3 pseudobonds, 577 residues, 2 models selected
> color (#!3 & sel) #a9a9a9ff
> color (#!3 & sel) #c0c0c0ff
> select clear
> select #3/I,M,Q
9765 atoms, 9908 bonds, 7 pseudobonds, 758 residues, 2 models selected
> color (#!3 & sel) dim gray
> select #3/G,F
7112 atoms, 7179 bonds, 4 pseudobonds, 479 residues, 2 models selected
> select #3/G,F,J
11838 atoms, 11974 bonds, 10 pseudobonds, 801 residues, 2 models selected
> color (#!3 & sel) dim gray
> select clear
> ui tool show "Side View"
> spin 360
Unknown command: spin 360
> roll 360
Expected an axis vector or a keyword
> roll x 360
[Repeated 2 time(s)]
> roll x 1 360
> roll y 1 360
> roll x 1 90
> roll x 2 90
> roll x -1 90
> roll y 1 360
> roll x -1 90
> roll y 1 360
> wait 20
> roll x -1 90
> roll y 1 360
> wait 150
> roll x -1 90
> roll y 1 360
> wait 250
> roll x -1 90
> roll y 1 360
> wait 500
> roll x -1 90
> roll y 1 360
> wait 450
> roll x -1 90
> roll y 1 360
> wait 420
> roll x -1 90
> roll y 1 360
> wait 400
> roll x -1 90
> color #3,8 #0096ffff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> Color #3/G,Q #0096FF
Unknown command: Color #3/G,Q #0096FF
> Sel #3/G,Q color sel #0096FF
Unknown command: Sel #3/G,Q color sel #0096FF
> Sel #3/G,Q
Unknown command: Sel #3/G,Q
> select #3/G,Q
6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #3/G,Q color sel #0096FF
Expected a keyword
> select #3/G,Q
6163 atoms, 6223 bonds, 5 pseudobonds, 433 residues, 2 models selected
> color sel #0096FF
> select clear
> color #3/G,Q #0096FF
> color #3,8 #797979ff
> color #3,8 #919191ff
> undo
[Repeated 1 time(s)]
> color #3,8 dim gray
> undo
[Repeated 4 time(s)]
> select clear
> color #3/G,Q #0096FF
> wait 150
> color #3/G,Q dimgray
> color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> color fade #3/G,Q #0096FF
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> wait 50
> color #3/G,Q dimgray
> Crossfade color #3/G,Q #0096FF
Unknown command: Crossfade color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> color #3/G,Q #0096FF
> wait 50
> color #3/G,Q dimgray
> Crossfade; color #3/G,Q #0096FF; wait 50
Unknown command: Crossfade; color #3/G,Q #0096FF; wait 50
> crossfade
> color #3/G,Q #0096FF
> wait 50
> crossfade
> color #3/G,Q #0096FF
> wait 50
> undo
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q #0096FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/G,Q dimgray
> wait 50
> select #3/Z:275
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!3 & sel) #9437ffff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> select clear
> select #3/Z:274
21 atoms, 21 bonds, 1 residue, 1 model selected
> color (#!3 & sel) light gray
> select clear
> undo
> color (#!3 & sel) #d6d6d6ff
> color (#!3 & sel) #c0c0c0ff
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #9437FF
> wait 50
[Repeated 1 time(s)]
> crossfade
> color #3/Y,Z #C0C0C0
> wait 50
> select clear
> roll x -1 90
> roll x 1 90
> open
> /Users/zbxg977/Desktop/BRISC_project/BRISC_pentaUb_structure_Dan/cryosparc_P1_DeepEmhancer_J202_highres.mrc
Opened cryosparc_P1_DeepEmhancer_J202_highres.mrc as #5, grid size
512,512,512, pixel 0.74, shown at level 0.00204, step 2, values float32
> select add #3
53424 atoms, 54081 bonds, 43 pseudobonds, 4083 residues, 2 models selected
> volume #5 step 1
> volume #5 level 0.1134
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95422,-0.27698,-0.11292,74.797,0.20162,0.87447,-0.44119,60.309,0.22095,0.39822,0.89028,-89.115
> undo
> select subtract #3
22 models selected
> select add #5
4 models selected
> view matrix models
> #5,0.89102,-0.11592,0.43892,-23.542,0.30523,0.86866,-0.39021,37.491,-0.33604,0.48165,0.80938,-20.252
> view matrix models
> #5,0.42416,-0.27299,0.86346,9.9416,0.79723,0.56483,-0.21305,5.4897,-0.42955,0.77875,0.45721,-15.846
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.42416,-0.27299,0.86346,6.061,0.79723,0.56483,-0.21305,-17.432,-0.42955,0.77875,0.45721,24.788
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.81844,-0.43282,0.37791,50.121,0.50998,0.24418,-0.8248,164.2,0.26471,0.86778,0.42057,-78.781
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.81844,-0.43282,0.37791,40.926,0.50998,0.24418,-0.8248,160.85,0.26471,0.86778,0.42057,-105.12
> view matrix models
> #5,0.81844,-0.43282,0.37791,56.133,0.50998,0.24418,-0.8248,169.15,0.26471,0.86778,0.42057,-100.7
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.79885,-0.084636,0.59554,174.83,-0.6013,0.13968,-0.78672,330.58,-0.016603,-0.98657,-0.16248,364.87
> view matrix models
> #5,-0.70691,-0.21333,0.67436,176.16,-0.70654,0.25721,-0.65928,305.02,-0.032808,-0.94251,-0.33255,381.88
> view matrix models
> #5,-0.86037,-0.37738,0.34257,272.5,-0.34072,-0.074004,-0.93725,356.83,0.37905,-0.9231,-0.06491,287.32
> view matrix models
> #5,0.27598,-0.92698,0.25405,237.73,-0.926,-0.32726,-0.18819,379.89,0.25759,-0.18332,-0.94871,284.51
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.27598,-0.92698,0.25405,261.38,-0.926,-0.32726,-0.18819,442.24,0.25759,-0.18332,-0.94871,329.72
> view matrix models
> #5,0.27598,-0.92698,0.25405,270.85,-0.926,-0.32726,-0.18819,441.82,0.25759,-0.18332,-0.94871,354.73
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.76194,0.56796,0.31124,118.96,-0.39996,-0.034665,-0.91588,416.29,-0.5094,-0.82232,0.25357,412.69
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.76194,0.56796,0.31124,167.06,-0.39996,-0.034665,-0.91588,433.46,-0.5094,-0.82232,0.25357,417.86
> ui tool show "Fit in Map"
> fitmap #3 inMap #5
Fit molecule P64_J12_model-coot-56.pdb (#3) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 53424 atoms
average map value = 0.07452, steps = 284
shifted from previous position = 23.8
rotated from previous position = 6.83 degrees
atoms outside contour = 43940, contour level = 0.1134
Position of P64_J12_model-coot-56.pdb (#3) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
-0.76336194 -0.42876028 -0.48315957 509.75254988
0.58594633 -0.14473464 -0.79731974 262.25309824
0.27192911 -0.89174912 0.36171543 201.03833376
Axis -0.07445072 -0.59533266 0.80002257
Axis point 210.03507452 319.31513667 0.00000000
Rotation angle (degrees) 140.64127053
Shift along axis -33.24407263
> select subtract #5
Nothing selected
> open /Users/zbxg977/Desktop/penta_Ub_merged.pdb
Chain information for penta_Ub_merged.pdb #6
---
Chain | Description
A B C L | No description available
O | No description available
> select add #6
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> view matrix models #6,1,0,0,14.12,0,1,0,22.571,0,0,1,27.031
> view matrix models #6,1,0,0,15.745,0,1,0,4.9213,0,0,1,39.269
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.03084, steps = 240
shifted from previous position = 5.63
rotated from previous position = 11.6 degrees
atoms outside contour = 3177, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
-0.81522555 -0.25341032 -0.52075956 465.22557231
0.51830802 0.08193703 -0.85125972 235.13444893
0.25838749 -0.96388253 0.06454744 304.69339704
Axis -0.10216074 -0.70676837 0.70002975
Axis point 150.78544864 0.00000000 367.68057814
Rotation angle (degrees) 146.55035104
Shift along axis -0.41893617
> hide sel atoms
> show sel cartoons
> hide #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9837,-0.11362,0.13936,21.477,0.056651,0.93143,0.35949,-55.449,-0.17065,-0.34573,0.92269,154.42
> view matrix models
> #6,0.37349,-0.79347,0.48053,230.48,-0.0081346,0.5152,0.85703,-41.298,-0.9276,-0.324,0.18597,433.9
> view matrix models
> #6,0.30923,-0.43531,0.8455,121.42,-0.36441,0.76697,0.52816,42.616,-0.8784,-0.47144,0.078541,467.05
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.30923,-0.43531,0.8455,102.31,-0.36441,0.76697,0.52816,47.152,-0.8784,-0.47144,0.078541,461.46
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.92947,-0.26671,-0.25485,104.32,-0.27908,-0.96018,-0.012978,433.1,-0.24124,0.083187,-0.96689,379.48
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.92947,-0.26671,-0.25485,106.56,-0.27908,-0.96018,-0.012978,437.85,-0.24124,0.083187,-0.96689,383.68
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.92611,0.0034423,-0.37724,76.233,-0.10302,-0.95964,-0.26168,437.28,-0.36292,0.28121,-0.88838,361.8
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.58955,0.42781,-0.68513,120.44,-0.084315,-0.81099,-0.57896,454.97,-0.80332,0.39909,-0.44205,368.48
> view matrix models
> #6,0.43235,-0.37451,-0.82026,325.47,-0.65274,-0.75758,0.0018353,481.19,-0.6221,0.53463,-0.57199,323.19
> view matrix models
> #6,0.66075,-0.25513,-0.70591,234.59,-0.3588,-0.93341,0.0015123,448.38,-0.65929,0.25228,-0.7083,405.14
> view matrix models
> #6,0.53137,-0.26167,-0.80572,280.2,-0.12418,-0.96488,0.23147,366.1,-0.83799,-0.022937,-0.5452,470.63
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.04473, steps = 216
shifted from previous position = 8.49
rotated from previous position = 8.17 degrees
atoms outside contour = 3016, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.07651590 0.64458117 0.76069733 -87.66333612
0.99486624 0.00132160 -0.10119000 11.31246327
-0.06623051 0.76453474 -0.64117092 155.61742874
Axis 0.69402741 0.66292501 0.28081378
Axis point 0.00000000 7.59449819 100.00864003
Rotation angle (degrees) 141.41343192
Shift along axis -9.64192415
> view matrix models
> #6,0.27731,-0.24257,-0.92965,347.92,-0.0086426,-0.96819,0.25005,334.1,-0.96074,-0.061309,-0.27059,467.65
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.27731,-0.24257,-0.92965,352.22,-0.0086426,-0.96819,0.25005,333.08,-0.96074,-0.061309,-0.27059,463.08
> view matrix models
> #6,0.27731,-0.24257,-0.92965,355.74,-0.0086426,-0.96819,0.25005,333.93,-0.96074,-0.061309,-0.27059,466.06
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.29679,-0.35595,-0.88612,365.66,0.10608,-0.9099,0.40103,274.01,-0.94903,-0.21303,-0.23229,485.65
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.29679,-0.35595,-0.88612,367.16,0.10608,-0.9099,0.40103,280.02,-0.94903,-0.21303,-0.23229,486.54
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.04044, steps = 88
shifted from previous position = 2.76
rotated from previous position = 5.25 degrees
atoms outside contour = 3054, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.15609642 0.72235882 0.67367027 -116.00954017
0.96951994 0.01835015 -0.24432426 42.58067044
-0.18885174 0.69127491 -0.69747689 205.63722394
Axis 0.72174910 0.66537520 0.19066746
Axis point 0.00000000 21.56062234 131.74159871
Rotation angle (degrees) 139.59795370
Shift along axis -16.18933184
> view matrix models
> #6,0.37294,-0.32482,-0.86914,348.3,0.076925,-0.92267,0.37783,289.83,-0.92466,-0.20777,-0.31911,493.61
> fitmap #6 inMap #5
Fit molecule penta_Ub_merged.pdb (#6) to map
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) using 3424 atoms
average map value = 0.06226, steps = 212
shifted from previous position = 3.45
rotated from previous position = 19.4 degrees
atoms outside contour = 2811, contour level = 0.1134
Position of penta_Ub_merged.pdb (#6) relative to
cryosparc_P1_DeepEmhancer_J202_highres.mrc (#5) coordinates:
Matrix rotation and translation
0.00314523 0.52331352 0.85213441 -73.49266478
0.95223623 0.25863119 -0.16234552 -8.10699426
-0.30534615 0.81194388 -0.49750464 178.68162582
Axis 0.61955240 0.73604400 0.27275273
Axis point 25.90526356 0.00000000 114.54079787
Rotation angle (degrees) 128.16032758
Shift along axis -2.76376043
> select subtract #6
Nothing selected
> hide #!5 models
> show #!3 models
> color #6 #ff9300ff
> ui tool show "Side View"
> select #6
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> hide #6
> view matrix models
> #6,0.4434,0.00086618,-0.89632,274.04,0.24539,-0.96191,0.12046,299.3,-0.86208,-0.27336,-0.42673,507.15
> hide cartoons #6
Expected ',' or a keyword
> view matrix models
> #6,0.4434,0.00086618,-0.89632,274.06,0.24539,-0.96191,0.12046,299.25,-0.86208,-0.27336,-0.42673,507.17
> ui mousemode right select
> select clear
> crossfade #6
Expected an integer >= 1 or a keyword
> hide #6 models
> crossfade
> hide #3/O,L,D,C,B
> wait 50
> crossfade
> hide cartoons #3/O,L,D,C,B; wait 50
Expected ',' or a keyword
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> undo
> show #6 models
> hide #6 models
> show #6 models
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> undo
> hide #6 models
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon show #3/O,L,A,C,B; wait 50
Expected an atoms specifier or a keyword
> show #6 models
> crossfade
> cartoon hide #3/O,L,A,C,B
> wait 50
> undo
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> crossfade
> cartoon hide #3/O,L,D,C,B
> wait 50
> crossfade
> cartoon show #6/O,L,A,C,B; wait 50
Expected an atoms specifier or a keyword
> undo
> crossfade
> cartoon #6/O,L,A,C,B
> wait 50
> 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
> hide #!8 models
> show #!8 models
> undo
[Repeated 9 time(s)]
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #6 models
> show #!2 models
> hide #!2 models
> hide #6 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
3424 atoms, 3454 bonds, 380 residues, 1 model selected
> show sel cartoons
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #8/O to #3/R pairing ss
Parameters
---
Chain pairing | ss
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-56.pdb, chain R (#3) with penta_Ub_merged.pdb,
chain O (#8), sequence alignment score = 374
RMSD between 76 pruned atom pairs is 0.217 angstroms; (across all 76 pairs:
0.217)
> select clear
> show #6 models
> hide #!8 models
> show #!8 models
> hide #6 models
> show #6 models
> crossfade
> color #3/Q #0096FF, color #3/Z #C0C0C0; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> wait 50
> crossfade
> color #3/Q #0096FF
> color #3/Z #C0C0C0
> wait 50
> select clear
> undo
[Repeated 3 time(s)]
> crossfade
> color #3/Q #0096FF, #3/Z #C0C0C0; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> crossfade
> color #3/Q #0096FF & #3/Z #C0C0C0; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF & color #3/Z #C0C0C0; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF #3/Z #9437FF; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF, #3/Z #9437FF; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> crossfade
> color #3/Q #0096FF & #3/Z #9437FF; wait 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> crossfade
> color #3/Q #0096FF
> undo
> crossfade
> color #3/Q #0096FF
> color #3/Z #9437FF
> wait 50
> undo
[Repeated 1 time(s)]
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> 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
> 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
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> 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 50
> 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 50
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> roll y 1 360
> wait 390
> roll x -1 90
> wait 50
> 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 50
> 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 50
> 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 dimgray
> color #3/I #C0C0C0
> 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 dimgray
> color #3/I #C0C0C0
> wait 50
> crossfade
> cartoon hide #6/O,L,A,C,B
> wait 50
> crossfade
> cartoon #3/O,L,D,C,B
> wait 50
> crossfade
> color #3/V #0096FF
> color #3/I dimgrey
> wait 50
> undo
[Repeated 2 time(s)]
> redo
> 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 80
> 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 80
> 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 dimgray
> 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 dimgray
> color #3/I dimgrey
> wait 50
> crossfade
> color #3/V C0C0C0; color #3/I dimgrey; wait 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> 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
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