![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#10188 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304150037 (2023-04-15 00:37:23 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84fb24b40 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 497 in swap_buffers
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 191 in draw
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.6-rc2023.04.15.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-rc2023.04.15.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-rc2023.04.15.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-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.15.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" : 130000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 2265,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2023-11-18 21:54:10.8138 +0100",
"codeSigningMonitor" : 0,
"incident" : "95359877-8FE4-4627-AA9A-3C689C7C4153",
"pid" : 33432,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-11-18 14:35:49.0946 +0100",
"procStartAbsTime" : 112971244334222,
"procExitAbsTime" : 139242777199613,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3C18038A-1839-5728-A3A7-57BDBB3C7A0C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9B98626C-34AA-4037-BF37-43F9688AEC0C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 17198,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "22AF1C2B-8420-4833-A4D3-4FB594BEC4C4",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":33432},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/T7SS2.cxs"
Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.2, shown at level 0.109, step 1, values float32
Log from Fri Nov 17 13:21:00 2023UCSF ChimeraX version: 1.6rc202304150037
(2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/gabrielumajioka/Downloads/T7SS-docking-9.cxs
Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.2, shown at level 0.109, step 1, values float32
Log from Tue Nov 14 13:40:55 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-8.cxs format session
Opened cryosparc_P14_J498_004_volume_map_sharp(1).mrc as #6, grid size
400,400,400, pixel 1.2, shown at level 0.0856, step 1, values float32
Log from Mon Nov 13 18:48:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-5.cxs format session
Opened cryosparc_P14_J452_004_volume_map_sharp(1).mrc as #11, grid size
400,400,400, pixel 1.2, shown at level 0.139, step 1, values float32
Log from Mon Nov 13 10:11:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-4.cxs format session
Opened cryosparc_P14_J436_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.2, shown at level 0.203, step 2, values float32
Opened map 10 as #6, grid size 64,63,78, pixel 3.33, shown at level 0.0631,
step 1, values float32
Opened mask-assym.mrc as #8, grid size 400,400,400, pixel 1.2, shown at level
0.0631, step 1, values float32
Log from Sun Nov 12 21:44:36 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-3.cxs format session
Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32
Log from Wed Nov 1 11:49:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-2.cxs format session
Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32
Log from Tue Oct 31 18:38:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking-2.cxs format session
Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 1.2, shown at level 0.295, step 2, values float32
Log from Tue Oct 31 18:30:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking.cxs format session
Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
480,480,480, pixel 1.2, shown at level 0.255, step 1, values float32
Log from Tue Oct 31 16:44:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/remi/Desktop/T7SS-docking.cxs
Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
480,480,480, pixel 1.2, shown at level 0.255, step 1, values float32
Log from Tue Oct 31 16:39:50 2023UCSF 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/remi/Downloads/cryosparc_P14_J56_002_volume_map_sharp.mrc
Opened cryosparc_P14_J56_002_volume_map_sharp.mrc as #1, grid size
480,480,480, pixel 1.2, shown at level 0.041, step 2, values float32
> volume #1 level 0.1564
> volume #1 level 0.2549
> open /Users/remi/Desktop/assym-T7SS.pdb format pdb
Summary of feedback from opening /Users/remi/Desktop/assym-T7SS.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 246
LEU A 251 1 6
Start residue of secondary structure not found: HELIX 2 2 PRO A 252 ILE A 266
1 15
Start residue of secondary structure not found: HELIX 3 3 PHE A 272 HIS A 334
1 63
Start residue of secondary structure not found: HELIX 4 4 LEU B 246 LEU B 251
1 6
Start residue of secondary structure not found: HELIX 5 5 PRO B 252 ILE B 266
1 15
63 messages similar to the above omitted
Chain information for assym-T7SS.pdb
---
Chain | Description
2.3/A | No description available
2.2/B | No description available
2.3/D | No description available
2.1/E | No description available
> ui tool show "Model Panel"
> close #2
> open /Users/remi/Desktop/assymT7SS.pdb format pdb
Chain information for assymT7SS.pdb #2
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
> select add #2
15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.91551,-0.29814,-0.2701,38.646,-0.25751,0.95013,-0.17592,3.0638,0.30908,-0.091506,-0.94662,-36.622
> view matrix models
> #2,-0.6347,-0.62055,-0.46051,15.794,-0.77144,0.47404,0.42446,6.3839,-0.045101,0.62466,-0.77959,3.3795
> view matrix models
> #2,-0.6347,-0.62055,-0.46051,-41.56,-0.77144,0.47404,0.42446,216.14,-0.045101,0.62466,-0.77959,318.45
> view matrix models
> #2,0.69412,-0.60038,-0.39717,-77.217,-0.47864,0.027184,-0.87759,174.16,0.53768,0.79925,-0.26849,315.34
> view matrix models
> #2,0.15505,-0.9879,0.0036659,-72.231,-0.78554,-0.12554,-0.60595,180.19,0.59908,0.091072,-0.79549,279.35
> view matrix models
> #2,-0.037366,-0.96806,0.24794,-63.003,-0.88151,-0.084931,-0.46446,186.24,0.47068,-0.23591,-0.85018,269.49
> view matrix models
> #2,-0.037366,-0.96806,0.24794,209.07,-0.88151,-0.084931,-0.46446,339.9,0.47068,-0.23591,-0.85018,252.24
> view matrix models
> #2,0.32978,0.84002,0.43082,271.72,0.87854,-0.10604,-0.46575,289.73,-0.34556,0.53209,-0.77297,306.09
> view matrix models
> #2,0.33158,0.83971,0.43004,333.47,0.87799,-0.10785,-0.46637,288.63,-0.34524,0.53222,-0.77302,251.42
> view matrix models
> #2,0.24058,0.84481,0.47794,336.82,0.9342,-0.067887,-0.35024,290.07,-0.26344,0.53075,-0.80555,248.67
> view matrix models
> #2,0.24058,0.84481,0.47794,335.59,0.9342,-0.067887,-0.35024,295.89,-0.26344,0.53075,-0.80555,246.49
> view matrix models
> #2,0.21808,0.84057,0.49587,336.28,0.89113,0.035659,-0.45235,299.86,-0.39791,0.54054,-0.74127,251.44
> view matrix models
> #2,0.21999,0.84041,0.49529,327.22,0.89076,0.033926,-0.45321,299.01,-0.39769,0.54089,-0.74114,253.45
> view matrix models
> #2,0.10676,0.96445,0.24175,332.07,0.82308,0.050679,-0.56566,300.15,-0.5578,0.25937,-0.7884,246.34
> fitmap #2 inMap #1
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) using 15580 atoms
average map value = 0.1148, steps = 228
shifted from previous position = 14
rotated from previous position = 13.9 degrees
atoms outside contour = 12209, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.24950001 0.90537255 0.34358452 336.12410985
0.88549670 -0.06968627 -0.45939030 284.75162857
-0.39197623 0.41886084 -0.81909111 246.20223303
Axis 0.76652168 0.64198410 -0.01734728
Axis point 0.00000000 -50.49604260 127.87593764
Rotation angle (degrees) 145.04864097
Shift along axis 436.18149689
> view matrix models
> #2,0.83486,-0.37823,-0.39993,260.25,-0.46711,-0.87118,-0.15119,295.2,-0.29123,0.31303,-0.90399,238.18
> select #1
2 models selected
> select /B:62
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /B:91
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
138 atoms, 141 bonds, 16 residues, 1 model selected
> select up
2587 atoms, 2647 bonds, 337 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #2
12993 atoms, 13269 bonds, 19 pseudobonds, 1607 residues, 2 models selected
> view matrix models
> #2,0.81525,0.579,-0.011729,289.02,0.3716,-0.53854,-0.75623,294.76,-0.44417,0.61216,-0.6542,248.98
Drag select of 55 residues
> select add #2
12993 atoms, 13269 bonds, 19 pseudobonds, 1607 residues, 2 models selected
> view matrix models
> #2,0.81525,0.579,-0.011729,319.44,0.3716,-0.53854,-0.75623,271.37,-0.44417,0.61216,-0.6542,277.35
> view matrix models
> #2,0.73427,0.45171,-0.50675,329,-0.10859,-0.65871,-0.74452,282.37,-0.67011,0.60171,-0.43462,279.21
> select clear
> select /B:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
54 atoms, 54 bonds, 6 residues, 1 model selected
> select up
244 atoms, 247 bonds, 32 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #2
12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected
> view matrix models
> #2,0.53471,0.82963,0.16065,334.45,0.67364,-0.3037,-0.67377,268.52,-0.51019,0.46849,-0.72126,275.54
> view matrix models
> #2,0.535,0.82996,0.15794,342.1,0.67294,-0.30559,-0.67362,292.11,-0.51082,0.46667,-0.722,252.39
> view matrix models
> #2,0.27161,0.91841,0.28768,351.22,0.92273,-0.16356,-0.34904,281.59,-0.2735,0.36025,-0.89186,244.4
> view matrix models
> #2,0.8986,0.16311,-0.40732,317.47,0.058952,-0.9648,-0.2563,276.8,-0.43479,0.2063,-0.87658,243.39
> view matrix models
> #2,-0.12163,0.95617,0.26635,366.29,0.9373,0.19894,-0.28617,293.76,-0.32661,0.21485,-0.92042,241.17
> view matrix models
> #2,-0.11789,0.95691,0.26537,332.13,0.9375,0.19535,-0.28797,289.17,-0.3274,0.21484,-0.92014,246.09
> view matrix models
> #2,0.55179,0.81486,0.17756,306.4,0.81092,-0.4745,-0.34243,268.51,-0.19478,0.33294,-0.92261,246.35
> view matrix models
> #2,0.39927,0.8132,0.42342,305.53,0.88401,-0.21899,-0.413,277.75,-0.24313,0.53921,-0.80631,253.24
> view matrix models
> #2,0.39357,0.91717,0.062389,318.42,0.78658,-0.30086,-0.53924,280.81,-0.4758,0.2613,-0.83984,250.92
> view matrix models
> #2,0.39357,0.91717,0.062389,314.83,0.78658,-0.30086,-0.53924,279.02,-0.4758,0.2613,-0.83984,262.26
> view matrix models
> #2,0.18232,0.98126,0.062348,324.37,0.83317,-0.12051,-0.53972,284.53,-0.52209,0.15035,-0.83953,259.46
> fitmap #2 inMap #1
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) using 12749 atoms
average map value = 0.1294, steps = 648
shifted from previous position = 22.9
rotated from previous position = 16.4 degrees
atoms outside contour = 9692, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.05284042 0.99262308 0.10912075 341.39459842
0.95272311 -0.01736940 -0.30334306 291.60594776
-0.29920996 0.11999063 -0.94661273 268.09004886
Axis 0.71809527 0.69264591 -0.06768179
Axis point 0.00000000 -50.02823723 149.55303999
Rotation angle (degrees) 162.85676305
Shift along axis 428.98870025
> select up
12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected
> volume flip #1
Opened cryosparc_P14_J56_002_volume_map_sharp.mrc z flip as #3, grid size
480,480,480, pixel 1.2, shown at step 1, values float32
> view matrix models
> #2,-0.78462,0.61223,0.097677,354.67,-0.59918,-0.70838,-0.37306,317.9,-0.1592,-0.35123,0.92265,200.31
> close #1
> view matrix models
> #2,-0.62743,0.70516,0.33026,347.51,-0.73861,-0.67326,0.034292,314.17,0.24653,-0.22242,0.94327,191.35
> view matrix models
> #2,0.46112,0.87653,-0.1381,329.19,-0.55503,0.40635,0.72582,333.71,0.69232,-0.25804,0.67388,181.57
> view matrix models
> #2,0.45616,0.87988,-0.13314,328.04,-0.55968,0.39998,0.72579,344.42,0.69187,-0.25656,0.67491,300.14
> view matrix models
> #2,0.88496,0.32953,-0.32901,296.96,-0.14732,0.86838,0.47352,355.03,0.44174,-0.37058,0.81703,300.61
> view matrix models
> #2,0.75126,0.45329,-0.47972,309.85,-0.35619,0.89037,0.28351,367.39,0.55563,-0.042118,0.83036,309.33
> view matrix models
> #2,0.75126,0.45329,-0.47972,314.13,-0.35619,0.89037,0.28351,360.19,0.55563,-0.042118,0.83036,319.87
> view matrix models
> #2,0.83453,0.50026,-0.23087,307.24,-0.36052,0.81268,0.45779,353.13,0.41664,-0.2988,0.85856,313.79
> view matrix models
> #2,0.81985,-0.049041,-0.57048,294.39,0.46363,0.64153,0.61114,315.36,0.33601,-0.76553,0.54869,305.64
> view matrix models
> #2,-0.97033,0.21068,0.1186,347.62,-0.23574,-0.93337,-0.27063,298.17,0.053679,-0.29056,0.95535,323.87
> view matrix models
> #2,-0.97033,0.21068,0.1186,350.14,-0.23574,-0.93337,-0.27063,287.61,0.053679,-0.29056,0.95535,326.05
> view matrix models
> #2,-0.96136,0.24111,0.13286,312.37,-0.26855,-0.92749,-0.26009,268.17,0.060514,-0.28572,0.9564,320.81
> view matrix models
> #2,-0.73875,0.66728,0.094853,322.53,-0.6735,-0.72551,-0.14153,286.7,-0.025626,-0.16844,0.98538,327.57
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 12749 atoms
average map value = 0.1323, steps = 496
shifted from previous position = 37.6
rotated from previous position = 25 degrees
atoms outside contour = 9355, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.71542707 0.50286009 0.48507307 335.20734608
-0.60763885 -0.79050019 -0.07671068 286.71361276
0.34487561 -0.34963013 0.87110253 324.27644999
Axis -0.23688745 0.12168799 -0.96388608
Axis point 182.04187295 122.61966787 0.00000000
Rotation angle (degrees) 144.82659237
Shift along axis -357.08236454
> volume #3 color #aeaeae
> volume #3 color #aeaeae89
> open /Users/remi/Desktop/assymT7SS.pdb format pdb
Chain information for assymT7SS.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
> select add #3
12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 4 models selected
> select subtract #2
2 models selected
> select add #1
15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 4 models selected
> select add #2
28329 atoms, 28938 bonds, 39 pseudobonds, 3519 residues, 6 models selected
> select subtract #2
15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 4 models selected
> select subtract #3
15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected
> view matrix models
> #1,0.7628,-0.060227,-0.64382,-3.7713,0.13958,0.98752,0.072994,-3.4849,0.63139,-0.14554,0.76169,-26.366
> view matrix models
> #1,0.7628,-0.060227,-0.64382,13.29,0.13958,0.98752,0.072994,317.65,0.63139,-0.14554,0.76169,326.48
> view matrix models
> #1,-0.4098,-0.80531,-0.42841,19.735,0.85765,-0.18023,-0.48162,244.95,0.31065,-0.56479,0.76453,319.12
> view matrix models
> #1,-0.4098,-0.80531,-0.42841,231.03,0.85765,-0.18023,-0.48162,275.13,0.31065,-0.56479,0.76453,311.21
> view matrix models
> #1,-0.56725,-0.75762,-0.32285,238.63,0.75799,-0.32703,-0.56437,271.15,0.322,-0.56486,0.75977,310.83
> view matrix models
> #1,-0.56725,-0.75762,-0.32285,228.51,0.75799,-0.32703,-0.56437,269.81,0.322,-0.56486,0.75977,321.81
> view matrix models
> #1,-0.7432,0.25566,0.6183,284.83,-0.44295,-0.8806,-0.16832,286.8,0.50144,-0.39897,0.76771,323.36
> view matrix models
> #1,-0.89095,0.033236,0.45289,278.2,-0.19382,-0.92974,-0.31307,276.08,0.41066,-0.3667,0.8348,328.01
> view matrix models
> #1,-0.89095,0.033236,0.45289,276.78,-0.19382,-0.92974,-0.31307,225.9,0.41066,-0.3667,0.8348,328.47
> view matrix models
> #1,-0.45718,0.67481,0.57933,291.28,-0.78705,-0.61032,0.089801,260.05,0.41417,-0.41491,0.81013,326.18
> view matrix models
> #1,-0.45718,0.67481,0.57933,315.13,-0.78705,-0.61032,0.089801,257.34,0.41417,-0.41491,0.81013,333.35
> view matrix models
> #1,0.086003,0.96645,0.24203,307.08,-0.87012,-0.045465,0.49073,286.76,0.48527,-0.2528,0.83702,338.03
> view matrix models
> #1,0.086003,0.96645,0.24203,314.78,-0.87012,-0.045465,0.49073,295.01,0.48527,-0.2528,0.83702,333.49
> fitmap #1 inMap #3
Fit molecule assymT7SS.pdb (#1) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 15580 atoms
average map value = 0.1379, steps = 368
shifted from previous position = 41.3
rotated from previous position = 23.3 degrees
atoms outside contour = 11338, contour level = 0.25488
Position of assymT7SS.pdb (#1) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.29623652 0.85245381 0.43077421 335.00418906
-0.93660606 0.17091236 0.30587259 284.36395152
0.18711762 -0.49407637 0.84904390 322.59951367
Axis -0.40506875 0.12337996 -0.90592312
Axis point 310.83111180 50.30752618 0.00000000
Rotation angle (degrees) 80.90357899
Shift along axis -392.86527276
> select #1/B:301
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
77 atoms, 76 bonds, 11 residues, 1 model selected
> select up
2587 atoms, 2647 bonds, 337 residues, 1 model selected
> open /Users/remi/Desktop/assymT7SS.pdb format pdb
Chain information for assymT7SS.pdb #4
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
> select clear
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #!2 to #4
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 assymT7SS.pdb, chain A (#4) with assymT7SS.pdb, chain A (#2),
sequence alignment score = 7110.1
RMSD between 1378 pruned atom pairs is 0.000 angstroms; (across all 1378
pairs: 0.000)
> matchmaker #!2 to #4
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 assymT7SS.pdb, chain A (#4) with assymT7SS.pdb, chain A (#2),
sequence alignment score = 7110.1
RMSD between 1378 pruned atom pairs is 0.000 angstroms; (across all 1378
pairs: 0.000)
> close #4
> select clear
> select add #2
12749 atoms, 13022 bonds, 19 pseudobonds, 1575 residues, 2 models selected
> view matrix models
> #2,0.99989,0.0078678,0.012325,4.0241,-0.0078934,0.99997,0.0020257,73.605,-0.012309,-0.0021227,0.99992,241.51
> view matrix models
> #2,-0.85905,-0.50148,0.10268,43.808,0.37886,-0.75777,-0.53128,4.8094,0.34423,-0.4175,0.84095,217.22
> view matrix models
> #2,-0.81776,-0.50158,0.28228,38.135,0.31441,-0.8001,-0.51086,4.8107,0.48209,-0.32901,0.812,216.78
> close #2
> open /Users/remi/Desktop/assymT7SS.pdb format pdb
Chain information for assymT7SS.pdb #2
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
> select add #2
15580 atoms, 15916 bonds, 20 pseudobonds, 1944 residues, 2 models selected
> view matrix models
> #2,0.99999,-0.00041742,0.0039933,-10.051,0.00041645,1,0.0002435,358.05,-0.0039934,-0.00024183,0.99999,346.1
> view matrix models
> #2,0.99999,-0.00041742,0.0039933,232.44,0.00041645,1,0.0002435,447.54,-0.0039934,-0.00024183,0.99999,349.8
> view matrix models
> #2,-0.71695,0.55472,0.42222,307.49,-0.68122,-0.68612,-0.25531,397.56,0.14807,-0.47067,0.8698,325.53
> view matrix models
> #2,-0.72959,0.54589,0.41194,312.55,-0.6687,-0.69567,-0.26245,288.55,0.14331,-0.46695,0.8726,330.35
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 15580 atoms
average map value = 0.1436, steps = 368
shifted from previous position = 31.8
rotated from previous position = 16.4 degrees
atoms outside contour = 11144, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.64998586 0.45300920 0.61016478 336.13537293
-0.63743189 -0.76214809 -0.11318519 287.19803248
0.41376199 -0.46250726 0.78414798 323.37304671
Axis -0.30068624 0.16905779 -0.93861986
Axis point 175.52913680 133.64480487 0.00000000
Rotation angle (degrees) 144.48791123
Shift along axis -356.04258138
> select clear
Drag select of 3 cryosparc_P14_J56_002_volume_map_sharp.mrc z flip , 1338
residues
> select up
11186 atoms, 11428 bonds, 1379 residues, 4 models selected
> select up
18784 atoms, 19190 bonds, 2316 residues, 4 models selected
> hide #!3 models
> select clear
Drag select of 1251 residues
> select up
10530 atoms, 10753 bonds, 1299 residues, 2 models selected
> select up
18784 atoms, 19190 bonds, 2316 residues, 2 models selected
> select down
10530 atoms, 10753 bonds, 1299 residues, 2 models selected
> select #1/A:618
6 atoms, 5 bonds, 1 residue, 1 model selected
> select :1-618
17070 atoms, 17438 bonds, 40 pseudobonds, 2134 residues, 4 models selected
> select :618-
Expected an objects specifier or a keyword
> select :618-end
14102 atoms, 14404 bonds, 1756 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> show #!3 models
> select add #1
8529 atoms, 8713 bonds, 20 pseudobonds, 1066 residues, 2 models selected
> fitmap #1 inMap #3
Fit molecule assymT7SS.pdb (#1) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms
average map value = 0.2526, steps = 64
shifted from previous position = 0.358
rotated from previous position = 0.102 degrees
atoms outside contour = 4297, contour level = 0.25488
Position of assymT7SS.pdb (#1) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.29578493 0.85335289 0.42930190 335.03321557
-0.93662425 0.17075429 0.30590519 284.32893315
0.18773994 -0.49257671 0.84977756 323.05057485
Axis -0.40432995 0.12232054 -0.90639670
Axis point 310.57331623 50.13128968 0.00000000
Rotation angle (degrees) 80.89998128
Shift along axis -393.49667050
> select add #2
17058 atoms, 17426 bonds, 40 pseudobonds, 2132 residues, 4 models selected
> select subtract #1
8529 atoms, 8713 bonds, 20 pseudobonds, 1066 residues, 2 models selected
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms
average map value = 0.2573, steps = 52
shifted from previous position = 0.521
rotated from previous position = 0.329 degrees
atoms outside contour = 4132, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.65268600 0.45212702 0.60793268 336.22452046
-0.63386216 -0.76539768 -0.11128861 287.11378647
0.41499368 -0.45798204 0.78615057 324.13408296
Axis -0.29985640 0.16687364 -0.93927596
Axis point 175.13402757 133.53178381 0.00000000
Rotation angle (degrees) 144.68304548
Shift along axis -357.35870250
> view matrix models
> #2,-0.64983,0.45512,0.60876,336.36,-0.635,-0.76524,-0.10574,287.55,0.41772,-0.45527,0.78628,324.21
> save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
> open "/Users/remi/Documents/IECB/grant
> applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
> format pdb
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #4
---
Chain | Description
B C | No description available
> view matrix models
> #2,-0.64893,0.45363,0.61083,336.46,-0.63441,-0.7658,-0.10526,287.57,0.42002,-0.45582,0.78473,324.05
> view matrix models
> #2,-0.62011,0.48096,0.6198,337.78,-0.66369,-0.74286,-0.087571,289.89,0.41831,-0.46566,0.77986,323.38
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms
average map value = 0.2573, steps = 60
shifted from previous position = 0.548
rotated from previous position = 2.59 degrees
atoms outside contour = 4134, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.65263927 0.45219031 0.60793578 336.22431474
-0.63397319 -0.76529615 -0.11135436 287.10755499
0.41489756 -0.45808922 0.78613885 324.13155085
Axis -0.29984225 0.16693164 -0.93927017
Axis point 175.15057476 133.52838162 0.00000000
Rotation angle (degrees) 144.67627919
Shift along axis -357.33401936
> view matrix models
> #2,-0.28274,0.74119,0.60885,342.46,-0.88749,-0.44296,0.12711,317.68,0.36391,-0.50441,0.78303,322.84
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms
average map value = 0.2573, steps = 148
shifted from previous position = 6.29
rotated from previous position = 27.4 degrees
atoms outside contour = 4133, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.65259853 0.45219005 0.60797971 336.22292178
-0.63393823 -0.76534293 -0.11123184 287.10957267
0.41501504 -0.45801132 0.78612223 324.13182531
Axis -0.29988913 0.16687264 -0.93926569
Axis point 175.13742617 133.52514170 0.00000000
Rotation angle (degrees) 144.67740203
Shift along axis -357.36476921
> view matrix models
> #2,-0.64962,0.45343,0.61024,336.41,-0.63685,-0.76295,-0.11105,287.22,0.41523,-0.46077,0.7844,323.91
> view matrix models
> #2,-0.69536,0.47409,0.5401,332.06,-0.60282,-0.79393,-0.07922,288.41,0.39125,-0.38067,0.83786,330.75
> fitmap #2 inMap #3
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) using 8529 atoms
average map value = 0.2573, steps = 104
shifted from previous position = 2.41
rotated from previous position = 5.58 degrees
atoms outside contour = 4132, contour level = 0.25488
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J56_002_volume_map_sharp.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.65265924 0.45216740 0.60793138 336.22551079
-0.63390146 -0.76536710 -0.11127505 287.11305306
0.41497572 -0.45799328 0.78615349 324.13379193
Axis -0.29985579 0.16687576 -0.93927578
Axis point 175.13995760 133.52801339 0.00000000
Rotation angle (degrees) 144.68005904
Shift along axis -357.35797534
> ui tool show Matchmaker
> matchmaker #4 to #1
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 assymT7SS.pdb, chain B (#1) with
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain C (#4), sequence alignment
score = 1854.4
RMSD between 156 pruned atom pairs is 0.663 angstroms; (across all 369 pairs:
6.931)
> select :1-200
10698 atoms, 10932 bonds, 2 pseudobonds, 1342 residues, 5 models selected
> hide #!3 models
> hide #4 models
> select :1-224
11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 5 models selected
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 7 models selected
> show #4 models
> select subtract #3
11916 atoms, 12184 bonds, 8 pseudobonds, 1486 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #4 to #1 & sel
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 assymT7SS.pdb, chain B (#1) with
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#4), sequence alignment
score = 1065.9
RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
1.541)
> open "/Users/remi/Documents/IECB/grant
> applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
> format pdb
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #5
---
Chain | Description
B C | No description available
> ui tool show Matchmaker
> matchmaker #5 to #1 & sel
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 assymT7SS.pdb, chain B (#1) with
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#5), sequence alignment
score = 1065.9
RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
1.541)
> save /Users/remi/Desktop/T7SS-docking.cxs
——— End of log from Tue Oct 31 16:39:50 2023 ———
opened ChimeraX session
> open "/Users/remi/Documents/IECB/grant
> applications/ANR-T7SS-2023/YukCdimer_3fc44.result/YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb"
> format pdb
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb #6
---
Chain | Description
B C | No description available
> ui tool show Matchmaker
> matchmaker #5 to #1
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 assymT7SS.pdb, chain B (#1) with
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain C (#5), sequence alignment
score = 1854.4
RMSD between 156 pruned atom pairs is 0.663 angstroms; (across all 369 pairs:
6.931)
> matchmaker #5 to #2 & sel
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 assymT7SS.pdb, chain B (#2) with
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb, chain B (#5), sequence alignment
score = 1065.9
RMSD between 197 pruned atom pairs is 0.624 angstroms; (across all 216 pairs:
1.541)
> ui tool show "Model Panel"
> close #6
> save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
> hide #4 models
> hide #5 models
> select #2/B:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/B:373
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
144 atoms, 142 bonds, 28 residues, 2 models selected
> select up
5174 atoms, 5294 bonds, 674 residues, 2 models selected
> select up
5224 atoms, 5342 bonds, 680 residues, 2 models selected
> select down
5174 atoms, 5294 bonds, 674 residues, 2 models selected
> select up
5224 atoms, 5342 bonds, 680 residues, 2 models selected
> select up
5662 atoms, 5788 bonds, 738 residues, 2 models selected
> select up
5666 atoms, 5788 bonds, 742 residues, 2 models selected
> select up
17058 atoms, 17426 bonds, 2132 residues, 2 models selected
> select down
5666 atoms, 5788 bonds, 742 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #4-5
14740 atoms, 15012 bonds, 1804 residues, 2 models selected
> select #4,5
14740 atoms, 15012 bonds, 1804 residues, 2 models selected
> show #4 models
> show #5 models
> select #3
2 models selected
> select #3
2 models selected
> select #3
2 models selected
> select #3
2 models selected
> select subtract #3
Nothing selected
> select clear
> select #5/B:358
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4,5 : 358-end
3056 atoms, 3052 bonds, 376 residues, 2 models selected
> save /Users/remi/Desktop/T7SS-docking.cxs includeMaps true
> delete atoms sel
> delete bonds sel
> save /Users/remi/Desktop/T7SS-docking.cxs
——— End of log from Tue Oct 31 16:44:53 2023 ———
opened ChimeraX session
> open /Users/remi/Downloads/cryosparc_P14_J66_004_volume_map_sharp.mrc format
> mrc
Opened cryosparc_P14_J66_004_volume_map_sharp.mrc as #6, grid size
480,480,480, pixel 1.2, shown at level 0.068, step 2, values float32
> volume #6 level 0.1911
> close #3
> volume #6 level 0.2454
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 1 maps.
> ui tool show "Model Panel"
> select add #1
5696 atoms, 5819 bonds, 19 pseudobonds, 695 residues, 2 models selected
> fitmap #1 inMap #6
Fit molecule assymT7SS.pdb (#1) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5696 atoms
average map value = 0.2873, steps = 76
shifted from previous position = 1.28
rotated from previous position = 4.86 degrees
atoms outside contour = 2399, contour level = 0.24544
Position of assymT7SS.pdb (#1) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.25842480 0.87271194 0.41423481 336.29794647
-0.95762926 0.17499857 0.22873935 283.53418241
0.12713307 -0.45579530 0.88095847 324.94865022
Axis -0.34657588 0.14535793 -0.92669101
Axis point 321.23956161 37.12486653 0.00000000
Rotation angle (degrees) 80.95611541
Shift along axis -376.46580795
> select add #2
11392 atoms, 11638 bonds, 38 pseudobonds, 1390 residues, 4 models selected
> select subtract #1
5696 atoms, 5819 bonds, 19 pseudobonds, 695 residues, 2 models selected
> fitmap #2 inMap #6
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5696 atoms
average map value = 0.2892, steps = 92
shifted from previous position = 3.3
rotated from previous position = 7.37 degrees
atoms outside contour = 2170, contour level = 0.24544
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.71622533 0.48361825 0.50312489 335.56769935
-0.60727525 -0.78713420 -0.10787273 286.03161351
0.34385759 -0.38279648 0.85745485 326.44258633
Axis -0.24196331 0.14017284 -0.96010694
Axis point 181.13626464 126.30627263 0.00000000
Rotation angle (degrees) 145.38143563
Shift along axis -354.52099736
> volume #6 style mesh
> select add #4
11538 atoms, 11797 bonds, 19 pseudobonds, 1409 residues, 3 models selected
> select subtract #2
5842 atoms, 5978 bonds, 714 residues, 1 model selected
> fitmap #4 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5842 atoms
average map value = 0.2593, steps = 108
shifted from previous position = 11.3
rotated from previous position = 7.04 degrees
atoms outside contour = 2573, contour level = 0.24544
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.86311987 0.08070962 -0.49850782 276.76821254
-0.45008955 -0.57059383 0.68690762 253.56059819
-0.22900543 0.81725678 0.52881743 271.59811939
Axis 0.21389700 -0.44224109 -0.87101716
Axis point 182.97824011 27.48927179 0.00000000
Rotation angle (degrees) 162.25983857
Shift along axis -289.50164740
> select subtract #4
Nothing selected
> select add #5
5842 atoms, 5978 bonds, 714 residues, 1 model selected
> fitmap #5 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 5842 atoms
average map value = 0.3, steps = 96
shifted from previous position = 11.6
rotated from previous position = 5.64 degrees
atoms outside contour = 1928, contour level = 0.24544
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.89300837 -0.28408098 0.34904735 278.41998222
0.43520701 -0.34763597 0.83050833 320.32779713
-0.11459021 0.89355874 0.43407587 275.96838979
Axis 0.07347802 0.54031641 0.83824767
Axis point 114.91035289 104.46109670 0.00000000
Rotation angle (degrees) 154.59318082
Shift along axis 424.86597441
> volume #6 level 0.2949
> save /Users/remi/Desktop/T7SS-docking-2.cxs
——— End of log from Tue Oct 31 18:30:09 2023 ———
opened ChimeraX session
> open /Users/remi/Desktop/YukB-TM.pdb
Summary of feedback from opening /Users/remi/Desktop/YukB-TM.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 246
LEU A 251 1 6
Start residue of secondary structure not found: HELIX 2 2 PRO A 252 ILE A 266
1 15
Start residue of secondary structure not found: HELIX 3 3 PHE A 272 HIS A 334
1 63
Start residue of secondary structure not found: HELIX 10 10 LEU D 246 LEU D
251 1 6
Start residue of secondary structure not found: HELIX 11 11 PRO D 252 ILE D
266 1 15
11 messages similar to the above omitted
Chain information for YukB-TM.pdb #3
---
Chain | Description
B C | No description available
> ui tool show "Model Panel"
> select add #3
7776 atoms, 7950 bonds, 946 residues, 2 models selected
> select subtract #5
1934 atoms, 1972 bonds, 232 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models #3,1,0,0,50.691,0,1,0,310.77,0,0,1,302.6
> view matrix models #3,1,0,0,135.33,0,1,0,286.44,0,0,1,296.82
> view matrix models #3,1,0,0,263.66,0,1,0,250.66,0,0,1,271.76
> view matrix models #3,1,0,0,325.25,0,1,0,231.16,0,0,1,293.65
> view matrix models
> #3,0.70359,-0.62334,-0.34118,327.13,0.69609,0.70113,0.15451,262.52,0.14291,-0.3462,0.92721,305.8
> view matrix models
> #3,0.70218,-0.62463,-0.34173,324.93,0.69752,0.69979,0.15413,280.81,0.14287,-0.34659,0.92707,317.69
> view matrix models
> #3,0.88594,-0.37771,-0.26916,323.6,0.44174,0.86402,0.24154,272.65,0.14133,-0.33289,0.93232,317.39
> view matrix models
> #3,0.88594,-0.37771,-0.26916,333.31,0.44174,0.86402,0.24154,268.45,0.14133,-0.33289,0.93232,316.72
> fitmap #3 inMap #6
Fit molecule YukB-TM.pdb (#3) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms
average map value = 0.263, steps = 272
shifted from previous position = 22.3
rotated from previous position = 18.8 degrees
atoms outside contour = 1247, contour level = 0.29485
Position of YukB-TM.pdb (#3) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.73075945 -0.54752577 -0.40768389 333.46652490
0.67599522 0.66351928 0.32058171 285.76200058
0.09497938 -0.50986047 0.85499779 341.59285647
Axis -0.53171151 -0.32184281 0.78339011
Axis point -96.07052368 654.65487038 -0.00000000
Rotation angle (degrees) 51.34435840
Shift along axis -1.67796933
> view matrix models
> #3,0.71991,-0.52048,-0.45916,330.66,0.68265,0.65046,0.333,286.74,0.12535,-0.55317,0.82358,342.63
> view matrix models
> #3,0.71991,-0.52048,-0.45916,336.05,0.68265,0.65046,0.333,282.9,0.12535,-0.55317,0.82358,317.22
> fitmap #3 inMap #6
Fit molecule YukB-TM.pdb (#3) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms
average map value = 0.263, steps = 244
shifted from previous position = 26.4
rotated from previous position = 3.54 degrees
atoms outside contour = 1247, contour level = 0.29485
Position of YukB-TM.pdb (#3) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.73074010 -0.54750143 -0.40775126 333.47153017
0.67600176 0.66354672 0.32051111 285.77815164
0.09508172 -0.50985089 0.85499213 341.59476560
Axis -0.53166083 -0.32195188 0.78337970
Axis point -96.09353373 654.68448428 0.00000000
Rotation angle (degrees) 51.34426931
Shift along axis -1.70216043
> view matrix models
> #3,0.73074,-0.5475,-0.40775,337.27,0.676,0.66355,0.32051,282.88,0.095082,-0.50985,0.85499,319.9
> ui tool show Matchmaker
> matchmaker #3 to #1
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 assymT7SS.pdb, chain A (#1) with YukB-TM.pdb, chain B (#3),
sequence alignment score = 1703.3
Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
TM.pdb, chain B
> matchmaker #3 to #2
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 assymT7SS.pdb, chain A (#2) with YukB-TM.pdb, chain B (#3),
sequence alignment score = 1703.3
Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
TM.pdb, chain B
> ui tool show Matchmaker
> matchmaker #3 to #2
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 assymT7SS.pdb, chain A (#2) with YukB-TM.pdb, chain B (#3),
sequence alignment score = 1703.3
Fewer than 3 residues aligned; cannot match assymT7SS.pdb, chain A with YukB-
TM.pdb, chain B
> select #3/B:290
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:291
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
548 atoms, 555 bonds, 63 residues, 1 model selected
> select up
967 atoms, 986 bonds, 116 residues, 1 model selected
> fitmap #3 inMap #6
Fit molecule YukB-TM.pdb (#3) to map
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) using 1934 atoms
average map value = 0.263, steps = 252
shifted from previous position = 22.2
rotated from previous position = 0.00743 degrees
atoms outside contour = 1248, contour level = 0.29485
Position of YukB-TM.pdb (#3) relative to
cryosparc_P14_J66_004_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.73071533 -0.54746344 -0.40784664 333.47096692
0.67601075 0.66357297 0.32043780 285.76894231
0.09520802 -0.50985753 0.85497411 341.59833133
Axis -0.53161364 -0.32209109 0.78335449
Axis point -96.08229491 654.70202551 0.00000000
Rotation angle (degrees) 51.34487596
Shift along axis -1.72875718
> view matrix models
> #3,0.73072,-0.54746,-0.40785,336.34,0.67601,0.66357,0.32044,284.44,0.095208,-0.50986,0.85497,328.93
> select #1/E:294
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/E:297
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
548 atoms, 557 bonds, 63 residues, 1 model selected
> select up
566 atoms, 577 bonds, 65 residues, 1 model selected
> select up
967 atoms, 987 bonds, 116 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/E:276
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
548 atoms, 557 bonds, 63 residues, 1 model selected
> select up
566 atoms, 577 bonds, 65 residues, 1 model selected
> select up
967 atoms, 987 bonds, 116 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/remi/Desktop/T7SS-docking-2.cxs
——— End of log from Tue Oct 31 18:38:05 2023 ———
opened ChimeraX session
> save /Users/remi/Desktop/T7SS-docking-3.cxs includeMaps true
——— End of log from Wed Nov 1 11:49:41 2023 ———
opened ChimeraX session
> open /Users/remi/Downloads/cryosparc_P14_J436_004_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P14_J436_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.2, shown at level 0.0937, step 2, values float32
> volume #7 level 0.1419
> ui tool show "Model Panel"
> select add #1
4729 atoms, 4832 bonds, 1 pseudobond, 579 residues, 2 models selected
> select add #2
9458 atoms, 9664 bonds, 2 pseudobonds, 1158 residues, 4 models selected
> select add #3
11392 atoms, 11636 bonds, 2 pseudobonds, 1390 residues, 5 models selected
> select add #4
17234 atoms, 17614 bonds, 2 pseudobonds, 2104 residues, 6 models selected
> select add #5
23076 atoms, 23592 bonds, 2 pseudobonds, 2818 residues, 7 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.021944,0.89209,0.45133,330.91,0.97559,0.11777,-0.18534,312.97,-0.21849,0.43625,-0.8729,242.41,#2,-0.86176,0.24802,0.44255,330.89,0.34943,0.92261,0.16338,310.24,-0.36778,0.29544,-0.88173,241.16,#4,-0.95193,-0.092145,-0.29213,266,0.21153,0.49202,-0.8445,330.03,0.22155,-0.86569,-0.44887,295.17,#5,-0.73376,-0.38067,0.56275,286.25,-0.65379,0.17032,-0.73726,266.25,0.18481,-0.90889,-0.37385,296.5,#3,0.88976,-0.33341,-0.3117,331.15,-0.45191,-0.73929,-0.49923,311.75,-0.063989,0.58506,-0.80846,238.53
> view matrix models
> #1,-0.021944,0.89209,0.45133,282.15,0.97559,0.11777,-0.18534,299.8,-0.21849,0.43625,-0.8729,204.25,#2,-0.86176,0.24802,0.44255,282.14,0.34943,0.92261,0.16338,297.07,-0.36778,0.29544,-0.88173,203,#4,-0.95193,-0.092145,-0.29213,217.24,0.21153,0.49202,-0.8445,316.85,0.22155,-0.86569,-0.44887,257.01,#5,-0.73376,-0.38067,0.56275,237.5,-0.65379,0.17032,-0.73726,253.07,0.18481,-0.90889,-0.37385,258.33,#3,0.88976,-0.33341,-0.3117,282.4,-0.45191,-0.73929,-0.49923,298.57,-0.063989,0.58506,-0.80846,200.36
> view matrix models
> #1,-0.021944,0.89209,0.45133,292.48,0.97559,0.11777,-0.18534,260.11,-0.21849,0.43625,-0.8729,210.7,#2,-0.86176,0.24802,0.44255,292.46,0.34943,0.92261,0.16338,257.38,-0.36778,0.29544,-0.88173,209.45,#4,-0.95193,-0.092145,-0.29213,227.57,0.21153,0.49202,-0.8445,277.17,0.22155,-0.86569,-0.44887,263.46,#5,-0.73376,-0.38067,0.56275,247.82,-0.65379,0.17032,-0.73726,213.39,0.18481,-0.90889,-0.37385,264.78,#3,0.88976,-0.33341,-0.3117,292.73,-0.45191,-0.73929,-0.49923,258.89,-0.063989,0.58506,-0.80846,206.81
> ui tool show "Fit in Map"
> fitmap sel inMap #7
Fit molecules assymT7SS.pdb (#1), assymT7SS.pdb (#2),
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4),
YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5), YukB-TM.pdb (#3) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 23076 atoms
average map value = 0.1434, steps = 144
shifted from previous position = 13.4
rotated from previous position = 15.5 degrees
atoms outside contour = 12526, contour level = 0.1419
Position of assymT7SS.pdb (#1) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.22608012 0.88164601 0.41423192 285.54542347
0.96667767 -0.15063411 -0.20698704 245.61380651
-0.12009184 0.44722441 -0.88632289 205.31128703
Axis 0.77060776 0.62938984 0.10016037
Axis point 0.00000000 -17.75681651 83.64802640
Rotation angle (degrees) 154.88239910
Shift along axis 395.19440967
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.73839608 0.46086884 0.49231203 284.88461594
0.58673515 0.79892911 0.13211418 243.10775111
-0.33243510 0.38640936 -0.86033407 203.79957019
Axis 0.29155924 0.94560439 0.14431057
Axis point 123.70226930 0.00000000 60.88753693
Rotation angle (degrees) 154.14499461
Shift along axis 342.35493104
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.87540369 0.05540811 -0.48020653 225.51072062
0.41957424 0.58042355 -0.69790111 273.13753574
0.24005380 -0.81242750 -0.53135274 259.41085155
Axis -0.14049323 -0.88356666 0.44673438
Axis point 51.30311012 0.00000000 223.28090352
Rotation angle (degrees) 155.94666474
Shift along axis -157.13020362
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.87740715 -0.30254740 0.37231942 229.29818644
-0.46513505 0.34639976 -0.81465121 206.50279255
0.11749925 -0.88795961 -0.44465903 254.39561897
Axis -0.23569252 0.81926776 -0.52273260
Axis point 156.05432032 0.00000000 182.32981571
Rotation angle (degrees) 171.05321655
Shift along axis -17.84367262
Position of YukB-TM.pdb (#3) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.75151986 -0.52139048 -0.40419038 285.58145951
-0.65091569 -0.68574055 -0.32568185 244.74527457
-0.10736231 0.50785024 -0.85472888 201.32402682
Axis 0.93211564 -0.33193453 -0.14484442
Axis point 0.00000000 144.87717120 160.38244388
Rotation angle (degrees) 153.44104706
Shift along axis 155.79487573
> close #6
> fitmap #1 inMap #7
Fit molecule assymT7SS.pdb (#1) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 4729 atoms
average map value = 0.1628, steps = 56
shifted from previous position = 1.27
rotated from previous position = 2.38 degrees
atoms outside contour = 2275, contour level = 0.1419
Position of assymT7SS.pdb (#1) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.25886376 0.86389663 0.43205574 284.56519739
0.95872519 -0.17532969 -0.22384259 244.17062848
-0.11762466 0.47216745 -0.87362597 205.58322627
Axis 0.78032593 0.61626966 0.10631626
Axis point 0.00000000 -14.96165689 83.57550674
Rotation angle (degrees) 153.51433265
Shift along axis 394.38539217
> fitmap #2 inMap #7
Fit molecule assymT7SS.pdb (#2) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 4729 atoms
average map value = 0.1628, steps = 92
shifted from previous position = 2.86
rotated from previous position = 2.4 degrees
atoms outside contour = 2210, contour level = 0.1419
Position of assymT7SS.pdb (#2) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.72054757 0.46296298 0.51621360 285.82202748
0.60797648 0.77979515 0.14927868 242.74548594
-0.33343036 0.42140812 -0.84335011 203.27007081
Axis 0.30107194 0.94000841 0.16043650
Axis point 122.79273314 0.00000000 57.87300408
Rotation angle (degrees) 153.13214980
Shift along axis 346.84773162
> fitmap #3 inMap #7
Fit molecule YukB-TM.pdb (#3) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 1934 atoms
average map value = 0.1651, steps = 160
shifted from previous position = 2.54
rotated from previous position = 6.53 degrees
atoms outside contour = 1081, contour level = 0.1419
Position of YukB-TM.pdb (#3) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.73100700 -0.58685167 -0.34818655 288.18371158
-0.67538579 -0.69506413 -0.24645465 246.19000576
-0.09737966 0.41532032 -0.90444802 201.46250567
Axis 0.92786411 -0.35165234 -0.12413227
Axis point 0.00000000 155.76763872 149.91090232
Rotation angle (degrees) 159.10772688
Shift along axis 155.81403511
> fitmap #4 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 5842 atoms
average map value = 0.1355, steps = 132
shifted from previous position = 8.14
rotated from previous position = 4.73 degrees
atoms outside contour = 3351, contour level = 0.1419
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.85472470 0.12343654 -0.50419153 222.89478895
0.48265532 0.54643305 -0.68443755 272.18875179
0.19102232 -0.82835641 -0.52662713 267.10096997
Axis -0.18088010 -0.87375867 0.45147335
Axis point 43.11660241 0.00000000 226.95085493
Rotation angle (degrees) 156.55744346
Shift along axis -157.55554269
> fitmap #5 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) to map
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) using 5842 atoms
average map value = 0.1797, steps = 92
shifted from previous position = 8.57
rotated from previous position = 4.78 degrees
atoms outside contour = 2643, contour level = 0.1419
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) relative to
cryosparc_P14_J436_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.83545712 -0.35744614 0.41742504 228.62561401
-0.52796328 0.31123083 -0.79018361 205.35695099
0.15253254 -0.88054962 -0.44873845 262.85138211
Axis -0.27572899 0.80825240 -0.52028990
Axis point 161.85636230 0.00000000 186.33101316
Rotation angle (degrees) 170.56855211
Shift along axis -33.81738013
> show #!7 models
> volume #7 level 0.2029
> molmap sel 10
Opened map 10 as #6, grid size 64,63,78, pixel 3.33, shown at level 0.0631,
step 1, values float32
> vop resample #8 ongrid #7
[Repeated 1 time(s)]
> vop resample #6 ongrid #7
Opened map 10 resampled as #8, grid size 400,400,400, pixel 1.2, shown at step
1, values float32
> save /Users/remi/Desktop/mask-assym.mrc models #8
> save /Users/remi/Desktop/T7SS-docking-4.cxs includeMaps true
——— End of log from Sun Nov 12 21:44:36 2023 ———
opened ChimeraX session
> select #1.1:1-204
Nothing selected
> select #1.1:1-204
Nothing selected
> split all
Split assymT7SS.pdb (#1) into 2 models
Split assymT7SS.pdb (#2) into 2 models
Split YukB-TM.pdb (#3) into 2 models
Split YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#4) into 2 models
Split YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb (#5) into 2 models
Chain information for assymT7SS.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for assymT7SS.pdb D #1.2
---
Chain | Description
D | No description available
Chain information for assymT7SS.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for assymT7SS.pdb D #2.2
---
Chain | Description
D | No description available
Chain information for YukB-TM.pdb B #3.1
---
Chain | Description
B | No description available
Chain information for YukB-TM.pdb C #3.2
---
Chain | Description
C | No description available
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B #4.1
---
Chain | Description
B | No description available
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C #4.2
---
Chain | Description
C | No description available
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B #5.1
---
Chain | Description
B | No description available
Chain information for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C #5.2
---
Chain | Description
C | No description available
> select #1.1:1-204
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.1:1-204
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/remi/Desktop/FHA-1.pdb /Users/remi/Desktop/FHA-2.pdb
Summary of feedback from opening /Users/remi/Desktop/FHA-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR B 8
LEU B 13 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG B 30 LYS B 32 1
3
Start residue of secondary structure not found: HELIX 3 3 GLY B 38 ASP B 46 1
9
Start residue of secondary structure not found: HELIX 4 4 PHE B 75 ALA B 80 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS B 83 GLN B 99 1
17
49 messages similar to the above omitted
Summary of feedback from opening /Users/remi/Desktop/FHA-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR B 8
LEU B 13 1 6
Start residue of secondary structure not found: HELIX 2 2 ARG B 30 LYS B 32 1
3
Start residue of secondary structure not found: HELIX 3 3 GLY B 38 ASP B 46 1
9
Start residue of secondary structure not found: HELIX 4 4 PHE B 75 ALA B 80 1
6
Start residue of secondary structure not found: HELIX 5 5 LYS B 83 GLN B 99 1
17
49 messages similar to the above omitted
Chain information for FHA-1.pdb #9
---
Chain | Description
A | No description available
Chain information for FHA-2.pdb #10
---
Chain | Description
A | No description available
> open /Users/remi/Downloads/cryosparc_P14_J452_004_volume_map_sharp(1).mrc
Opened cryosparc_P14_J452_004_volume_map_sharp(1).mrc as #11, grid size
400,400,400, pixel 1.2, shown at level 0.048, step 2, values float32
> close #8
> close #6
> close #7
> volume #11 step 1
> volume #11 level 0.129
> volume #11 style mesh
> ui tool show "Model Panel"
> select add #1.1
2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected
> fitmap #1.1 inMap #11
Fit molecule assymT7SS.pdb A (#1.1) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2485 atoms
average map value = 0.1513, steps = 48
shifted from previous position = 0.959
rotated from previous position = 1.5 degrees
atoms outside contour = 1030, contour level = 0.12903
Position of assymT7SS.pdb A (#1.1) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.25350703 0.86285371 0.43728441 285.23871409
0.95707270 -0.15806001 -0.24295856 244.09660484
-0.14052052 0.48010468 -0.86588306 206.41132849
Axis 0.77719258 0.62106006 0.10127234
Axis point 0.00000000 -18.34928408 84.50766871
Rotation angle (degrees) 152.27836324
Shift along axis 394.18782414
> select add #1.2
3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 3 models selected
> select subtract #1.1
637 atoms, 651 bonds, 79 residues, 1 model selected
> fitmap #1.2 inMap #11
Fit molecule assymT7SS.pdb D (#1.2) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 637 atoms
average map value = 0.1125, steps = 36
shifted from previous position = 1.83
rotated from previous position = 6.52 degrees
atoms outside contour = 365, contour level = 0.12903
Position of assymT7SS.pdb D (#1.2) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.26867845 0.81301352 0.51654709 282.94622350
0.96248237 -0.20547831 -0.17721835 243.33517348
-0.03794169 0.54478222 -0.83771878 208.34532416
Axis 0.78262089 0.60104455 0.16201849
Axis point 0.00000000 -9.35906561 75.20423453
Rotation angle (degrees) 152.53084968
Shift along axis 401.45070029
> select subtract #1.2
Nothing selected
> select add #2
3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 12 atomic models, 1 maps.
> select subtract #2.1
637 atoms, 651 bonds, 79 residues, 2 models selected
> select add #2
3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected
> select subtract #2
Nothing selected
> select add #2.1
2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected
> fitmap #2.1 inMap #11
Fit molecule assymT7SS.pdb A (#2.1) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2485 atoms
average map value = 0.152, steps = 64
shifted from previous position = 1.49
rotated from previous position = 2.67 degrees
atoms outside contour = 994, contour level = 0.12903
Position of assymT7SS.pdb A (#2.1) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.73561811 0.42365331 0.52856775 285.85940769
0.57468039 0.80339908 0.15586009 243.88343620
-0.35862020 0.41841103 -0.83446017 203.59571871
Axis 0.28006415 0.94636699 0.16110119
Axis point 126.33437429 0.00000000 56.10661311
Rotation angle (degrees) 152.04787883
Shift along axis 343.66171823
> select add #2.2
3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 3 models selected
> select subtract #2.1
637 atoms, 651 bonds, 79 residues, 1 model selected
> fitmap #2.2 inMap #11
Fit molecule assymT7SS.pdb D (#2.2) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 637 atoms
average map value = 0.1281, steps = 88
shifted from previous position = 5.42
rotated from previous position = 7.03 degrees
atoms outside contour = 317, contour level = 0.12903
Position of assymT7SS.pdb D (#2.2) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.69061390 0.52765072 0.49460809 291.43330149
0.62103505 0.78314223 0.03168140 242.78379891
-0.37063177 0.32904858 -0.86853851 192.39532545
Axis 0.32334213 0.94081837 0.10154143
Axis point 124.40229542 0.00000000 59.69478635
Rotation angle (degrees) 152.62362755
Shift along axis 342.18422030
> select subtract #2.2
Nothing selected
> select add #3
1934 atoms, 1972 bonds, 232 residues, 3 models selected
> select subtract #3.1
967 atoms, 986 bonds, 116 residues, 2 models selected
> select add #3
1934 atoms, 1972 bonds, 232 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3.1
967 atoms, 986 bonds, 116 residues, 1 model selected
> fitmap #3.1 inMap #11
Fit molecule YukB-TM.pdb B (#3.1) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 967 atoms
average map value = 0.136, steps = 144
shifted from previous position = 1.41
rotated from previous position = 4.71 degrees
atoms outside contour = 559, contour level = 0.12903
Position of YukB-TM.pdb B (#3.1) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.77877801 -0.54726206 -0.30660894 287.65397249
-0.62476349 -0.72057338 -0.30074008 247.09818678
-0.05635060 0.42576783 -0.90307606 201.17610227
Axis 0.94070516 -0.32404232 -0.10035127
Axis point 0.00000000 149.78962958 148.20503069
Rotation angle (degrees) 157.28480446
Shift along axis 170.33902927
> select add #3.2
1934 atoms, 1972 bonds, 232 residues, 2 models selected
> select subtract #3.1
967 atoms, 986 bonds, 116 residues, 1 model selected
> fitmap #3.2 inMap #11
Fit molecule YukB-TM.pdb C (#3.2) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 967 atoms
average map value = 0.1383, steps = 84
shifted from previous position = 3.98
rotated from previous position = 2.99 degrees
atoms outside contour = 580, contour level = 0.12903
Position of YukB-TM.pdb C (#3.2) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.75076359 -0.55641703 -0.35602545 289.25125500
-0.64677155 -0.72876716 -0.22491107 247.73865976
-0.13431531 0.39912217 -0.90700656 204.15357376
Axis 0.93364517 -0.33171086 -0.13518359
Axis point 0.00000000 154.44686631 150.74110092
Rotation angle (degrees) 160.47659701
Shift along axis 160.28221955
> select add #3
1934 atoms, 1972 bonds, 232 residues, 3 models selected
> select add #4
7776 atoms, 7950 bonds, 946 residues, 6 models selected
> select subtract #3
5842 atoms, 5978 bonds, 714 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #4.1
2921 atoms, 2989 bonds, 357 residues, 1 model selected
> fitmap #4.1 inMap #11
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms
average map value = 0.1155, steps = 144
shifted from previous position = 5.46
rotated from previous position = 5.91 degrees
atoms outside contour = 1738, contour level = 0.12903
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.80316762 0.10520960 -0.58638956 225.43800474
0.53415526 0.56304447 -0.63060216 271.58470368
0.26381800 -0.81970230 -0.50841735 261.36686153
Axis -0.19477209 -0.87570904 0.44181163
Axis point 33.00237324 0.00000000 227.74236623
Rotation angle (degrees) 150.95872730
Shift along axis -166.26329161
> select subtract #4.1
Nothing selected
> select add #4.2
2921 atoms, 2989 bonds, 357 residues, 1 model selected
> fitmap #4.2 inMap #11
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms
average map value = 0.1178, steps = 88
shifted from previous position = 1.95
rotated from previous position = 1.1 degrees
atoms outside contour = 1771, contour level = 0.12903
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.84669010 0.11785659 -0.51886964 224.89936836
0.49036519 0.55135994 -0.67494014 272.18843289
0.20653779 -0.82590074 -0.52462377 267.61952032
Axis -0.18202990 -0.87470400 0.44917483
Axis point 42.06353806 0.00000000 228.01876294
Rotation angle (degrees) 155.50216856
Shift along axis -158.81476674
> select add #5.1
5842 atoms, 5978 bonds, 714 residues, 2 models selected
> select subtract #5.1
2921 atoms, 2989 bonds, 357 residues, 1 model selected
> select add #4
5842 atoms, 5978 bonds, 714 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #5.1
2921 atoms, 2989 bonds, 357 residues, 1 model selected
> fitmap #5.1 inMap #11
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms
average map value = 0.1479, steps = 64
shifted from previous position = 5.02
rotated from previous position = 4.72 degrees
atoms outside contour = 1226, contour level = 0.12903
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.80980501 -0.40893524 0.42069919 230.56169398
-0.54216618 0.24756601 -0.80297379 207.71276690
0.22421346 -0.87834107 -0.42219105 257.76689331
Axis -0.30259116 0.78886809 -0.53490722
Axis point 164.40264514 0.00000000 190.69516105
Rotation angle (degrees) 172.84601007
Shift along axis -43.78932744
> select subtract #5.1
Nothing selected
> select add #5.2
2921 atoms, 2989 bonds, 357 residues, 1 model selected
> fitmap #5.2 inMap #11
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 2921 atoms
average map value = 0.1624, steps = 48
shifted from previous position = 1.56
rotated from previous position = 1.09 degrees
atoms outside contour = 1220, contour level = 0.12903
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
-0.82759155 -0.37391184 0.41866712 230.22405264
-0.53729975 0.31177697 -0.78364795 205.60859814
0.16248447 -0.87349016 -0.45892672 263.39251680
Axis -0.28354406 0.80851823 -0.51565594
Axis point 163.26367726 -0.00000000 186.40032914
Rotation angle (degrees) 170.88437974
Shift along axis -34.86027669
> select subtract #5.2
Nothing selected
> select add #9
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> fitmap #9 inMap #11
Fit molecule FHA-1.pdb (#9) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms
average map value = 0.1561, steps = 80
shifted from previous position = 8.74
rotated from previous position = 16.7 degrees
atoms outside contour = 621, contour level = 0.12903
Position of FHA-1.pdb (#9) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.98388207 -0.16008706 0.07967561 19.56803312
0.17401712 0.95972685 -0.22055025 12.71286023
-0.04115958 0.23086036 0.97211593 -22.93584404
Axis 0.78580706 0.21034760 0.58160222
Axis point 0.00000000 115.09932169 32.13073443
Rotation angle (degrees) 16.69203612
Shift along axis 4.71128035
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.98388,-0.16009,0.079676,21.798,0.17402,0.95973,-0.22055,12.954,-0.04116,0.23086,0.97212,-40.142
> view matrix models
> #9,0.98388,-0.16009,0.079676,20.258,0.17402,0.95973,-0.22055,10.904,-0.04116,0.23086,0.97212,-43.857
> fitmap #9 inMap #11
Fit molecule FHA-1.pdb (#9) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms
average map value = 0.1413, steps = 76
shifted from previous position = 5.55
rotated from previous position = 18.6 degrees
atoms outside contour = 705, contour level = 0.12903
Position of FHA-1.pdb (#9) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.98782986 0.03476648 -0.15160296 23.21561903
-0.04988970 0.99402134 -0.09712155 32.66734210
0.14732001 0.10350299 0.98365845 -58.01587898
Axis 0.54248250 -0.80827843 -0.22890766
Axis point 408.19402927 0.00000000 122.26235600
Rotation angle (degrees) 10.65608161
Shift along axis -0.52996150
> select subtract #9
Nothing selected
> select add #10
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> view matrix models #10,1,0,0,-2.9386,0,1,0,0.56538,0,0,1,-9.0423
> fitmap #10 inMap #11
Fit molecule FHA-2.pdb (#10) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms
average map value = 0.1273, steps = 88
shifted from previous position = 9.93
rotated from previous position = 2.8 degrees
atoms outside contour = 832, contour level = 0.12903
Position of FHA-2.pdb (#10) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.99908131 0.00404660 -0.04266327 6.28219628
-0.00503920 0.99971851 -0.02318409 6.78410757
0.04255744 0.02337778 0.99882048 -15.16654365
Axis 0.47738501 -0.87374246 -0.09315403
Axis point 364.02992804 0.00000000 156.37209775
Rotation angle (degrees) 2.79528860
Shift along axis -1.51571179
> view matrix models
> #10,0.99908,0.0040466,-0.042663,4.4253,-0.0050392,0.99972,-0.023184,6.0808,0.042557,0.023378,0.99882,-31.912
> view matrix models
> #10,0.99711,0.061525,-0.044568,-11.472,-0.062639,0.99775,-0.024045,19.473,0.042989,0.026768,0.99872,-32.971
> view matrix models
> #10,0.99711,0.061525,-0.044568,-11.003,-0.062639,0.99775,-0.024045,28,0.042989,0.026768,0.99872,-26.228
> fitmap #10 inMap #11
Fit molecule FHA-2.pdb (#10) to map
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) using 1607 atoms
average map value = 0.1273, steps = 104
shifted from previous position = 12.8
rotated from previous position = 3.3 degrees
atoms outside contour = 832, contour level = 0.12903
Position of FHA-2.pdb (#10) relative to
cryosparc_P14_J452_004_volume_map_sharp(1).mrc (#11) coordinates:
Matrix rotation and translation
0.99905298 0.00400340 -0.04332569 6.43148939
-0.00503549 0.99970551 -0.02373881 6.88424484
0.04321790 0.02393450 0.99877893 -15.46733824
Axis 0.48048984 -0.87225574 -0.09110127
Axis point 365.50552770 0.00000000 157.15173383
Rotation angle (degrees) 2.84355753
Shift along axis -1.50546264
> volume #11 level 0.1391
> select #4.1:207-end
1248 atoms, 1279 bonds, 151 residues, 1 model selected
> select #4.1:207-end #4.2:207-end
2496 atoms, 2558 bonds, 302 residues, 2 models selected
> save /Users/remi/Desktop/YukC-TM-ext-1.pdb selectedOnly true relModel #11
> save /Users/remi/Desktop/T7SS-docking-5.cxs includeMaps true
——— End of log from Mon Nov 13 10:11:02 2023 ———
opened ChimeraX session
> select #4:260-end
1614 atoms, 1648 bonds, 196 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #5:260-end
1614 atoms, 1648 bonds, 196 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> open /Users/remi/Downloads/cryosparc_P14_J498_004_volume_map_sharp(1).mrc
> format mrc
Opened cryosparc_P14_J498_004_volume_map_sharp(1).mrc as #6, grid size
400,400,400, pixel 1.2, shown at level 0.0503, step 2, values float32
> close #11
> volume #6 level 0.1294
> save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
> volume #6 step 1
> ui tool show "Fit in Map"
> fitmap #1.1 inMap #6
Fit molecule assymT7SS.pdb A (#1.1) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2485 atoms
average map value = 0.1511, steps = 68
shifted from previous position = 1.94
rotated from previous position = 0.361 degrees
atoms outside contour = 1052, contour level = 0.12937
Position of assymT7SS.pdb A (#1.1) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.25087391 0.86162213 0.44121375 286.17040814
0.95733893 -0.15331482 -0.24494231 244.85172869
-0.14340311 0.48384074 -0.86332710 204.99147866
Axis 0.77597617 0.62247435 0.10191504
Axis point 0.00000000 -18.82158856 83.50169937
Rotation angle (degrees) 151.99224087
Shift along axis 395.36705066
> fitmap #1.2 inMap #6
Fit molecule assymT7SS.pdb D (#1.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms
average map value = 0.1241, steps = 56
shifted from previous position = 1.46
rotated from previous position = 5.37 degrees
atoms outside contour = 337, contour level = 0.12937
Position of assymT7SS.pdb D (#1.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.26824266 0.84658248 0.45972163 285.20079573
0.95590315 -0.17467933 -0.23608534 245.30020872
-0.11956185 0.50277752 -0.85610731 205.31097875
Axis 0.78168443 0.61285646 0.11565647
Axis point 0.00000000 -14.76446624 81.87577514
Rotation angle (degrees) 151.79618610
Shift along axis 397.01638013
> fitmap #2.1 inMap #6
Fit molecule assymT7SS.pdb A (#2.1) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2485 atoms
average map value = 0.1637, steps = 44
shifted from previous position = 1.11
rotated from previous position = 0.471 degrees
atoms outside contour = 893, contour level = 0.12937
Position of assymT7SS.pdb A (#2.1) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.73408712 0.42677833 0.52818213 286.66780869
0.57977068 0.79885515 0.16030099 244.17231087
-0.35352803 0.42389941 -0.83386284 203.04714623
Axis 0.28255787 0.94512763 0.16399640
Axis point 126.01194453 0.00000000 55.56992545
Rotation angle (degrees) 152.19587569
Shift along axis 345.07324385
> fitmap #2.2 inMap #6
Fit molecule assymT7SS.pdb D (#2.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms
average map value = 0.149, steps = 48
shifted from previous position = 0.55
rotated from previous position = 8.45 degrees
atoms outside contour = 263, contour level = 0.12937
Position of assymT7SS.pdb D (#2.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.76330845 0.47102695 0.44214684 287.71549892
0.58555271 0.79356395 0.16548195 245.59716883
-0.27292533 0.38521405 -0.88154518 194.98739648
Axis 0.29034867 0.94487904 0.15133156
Axis point 120.96818265 0.00000000 58.32802205
Rotation angle (degrees) 157.76579239
Shift along axis 345.10517912
> fitmap #2.2 inMap #6
Fit molecule assymT7SS.pdb D (#2.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 637 atoms
average map value = 0.149, steps = 40
shifted from previous position = 0.0251
rotated from previous position = 0.0339 degrees
atoms outside contour = 262, contour level = 0.12937
Position of assymT7SS.pdb D (#2.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.76304574 0.47124642 0.44236639 287.71163299
0.58594786 0.79322692 0.16569902 245.56719155
-0.27281186 0.38563957 -0.88139425 194.99894104
Axis 0.29055218 0.94478529 0.15152619
Axis point 120.93960100 0.00000000 58.31088988
Rotation angle (degrees) 157.75999327
Shift along axis 345.15095927
> fitmap #3.1 inMap #6
Fit molecule YukB-TM.pdb B (#3.1) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 967 atoms
average map value = 0.1398, steps = 88
shifted from previous position = 1.55
rotated from previous position = 3.46 degrees
atoms outside contour = 562, contour level = 0.12937
Position of YukB-TM.pdb B (#3.1) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.80521184 -0.49941155 -0.31972174 286.59601859
-0.58554684 -0.75478078 -0.29570402 249.00766180
-0.09364182 0.42531644 -0.90018728 199.88102583
Axis 0.94805324 -0.29726729 -0.11325731
Axis point 0.00000000 146.54485870 148.42457055
Rotation angle (degrees) 157.64998225
Shift along axis 175.04846175
> fitmap #3.2 inMap #6
Fit molecule YukB-TM.pdb C (#3.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 967 atoms
average map value = 0.1387, steps = 88
shifted from previous position = 1.29
rotated from previous position = 2.37 degrees
atoms outside contour = 581, contour level = 0.12937
Position of YukB-TM.pdb C (#3.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.72766479 -0.56710553 -0.38586950 288.97649126
-0.67047201 -0.70681297 -0.22557196 246.66083796
-0.14481446 0.42285547 -0.89455129 203.80509765
Axis 0.92703436 -0.34462808 -0.14777950
Axis point 0.00000000 154.99719606 154.08518826
Rotation angle (degrees) 159.52906697
Shift along axis 152.76666819
> volume #6 style mesh
> fitmap #4.1 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms
average map value = 0.1456, steps = 64
shifted from previous position = 2.75
rotated from previous position = 4.56 degrees
atoms outside contour = 874, contour level = 0.12937
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.84794123 0.09462712 -0.52157586 224.36704846
0.47586168 0.56941353 -0.67031626 272.56070395
0.23356226 -0.81658676 -0.52785863 264.55748256
Axis -0.17038537 -0.87963389 0.44408676
Axis point 42.73319139 0.00000000 226.33802162
Rotation angle (degrees) 154.58102154
Shift along axis -160.49601874
> fitmap #4.2 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms
average map value = 0.1547, steps = 60
shifted from previous position = 1.25
rotated from previous position = 3.29 degrees
atoms outside contour = 907, contour level = 0.12937
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.83851639 0.12070264 -0.53133901 225.47693135
0.48967805 0.59460979 -0.63769476 270.16380167
0.23896793 -0.79490255 -0.55769549 268.49270536
Axis -0.18101818 -0.88697613 0.42485971
Axis point 41.49154009 0.00000000 224.10852552
Rotation angle (degrees) 154.26356131
Shift along axis -166.37253474
> fitmap #5.1 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms
average map value = 0.1722, steps = 56
shifted from previous position = 3.66
rotated from previous position = 3.19 degrees
atoms outside contour = 642, contour level = 0.12937
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.83369611 -0.35893916 0.41965876 229.01428818
-0.52152230 0.26190737 -0.81204619 206.80433804
0.18156346 -0.89586115 -0.40554593 261.83363371
Axis -0.27915439 0.79300103 -0.54149995
Axis point 162.29438708 -0.00000000 191.17874464
Rotation angle (degrees) 171.36594830
Shift along axis -41.71719172
> fitmap #5.2 inMap #6
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 2114 atoms
average map value = 0.1832, steps = 52
shifted from previous position = 1.14
rotated from previous position = 2.82 degrees
atoms outside contour = 695, contour level = 0.12937
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
-0.81980064 -0.41042535 0.39934690 232.39386740
-0.53239936 0.28943480 -0.79547370 206.70864938
0.21089768 -0.86474189 -0.45578903 264.08678920
Axis -0.29485474 0.80217417 -0.51920833
Axis point 163.12837611 0.00000000 190.83410136
Rotation angle (degrees) 173.25437673
Shift along axis -39.82215423
> fitmap #9 inMap #6
Fit molecule FHA-1.pdb (#9) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 1607 atoms
average map value = 0.148, steps = 56
shifted from previous position = 1.46
rotated from previous position = 0.636 degrees
atoms outside contour = 667, contour level = 0.12937
Position of FHA-1.pdb (#9) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.98862566 0.04288194 -0.14415421 20.39092579
-0.05726132 0.99362324 -0.09712876 34.98987893
0.13906991 0.10427844 0.98477691 -57.85486031
Axis 0.55687210 -0.78308823 -0.27688677
Axis point 427.86337835 0.00000000 107.79164253
Rotation angle (degrees) 10.41857101
Shift along axis -0.02577914
> fitmap #10 inMap #6
Fit molecule FHA-2.pdb (#10) to map
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) using 1607 atoms
average map value = 0.1383, steps = 64
shifted from previous position = 5.08
rotated from previous position = 5.48 degrees
atoms outside contour = 768, contour level = 0.12937
Position of FHA-2.pdb (#10) relative to
cryosparc_P14_J498_004_volume_map_sharp(1).mrc (#6) coordinates:
Matrix rotation and translation
0.99686754 0.05861708 -0.05309566 -5.44038327
-0.05559903 0.99684540 0.05663911 5.11562851
0.05624819 -0.05350962 0.99698188 0.26212914
Axis -0.57160077 -0.56742396 -0.59270786
Axis point 87.03489235 96.95987405 0.00000000
Rotation angle (degrees) 5.52908900
Shift along axis 0.05163109
> save /Users/remi/Desktop/T7SS-docking-8.cxs
> save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
Drag select of 69 residues
Drag select of 29 residues
> select up
823 atoms, 843 bonds, 100 residues, 3 models selected
> select up
5195 atoms, 5314 bonds, 634 residues, 3 models selected
Drag select of 45 residues
> select up
5987 atoms, 6126 bonds, 730 residues, 5 models selected
> select up
9423 atoms, 9642 bonds, 1152 residues, 5 models selected
> color sel cornflower blue
> select clear
> select #3.1/B:291
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #3.2/C:296
20 atoms, 19 bonds, 2 residues, 2 models selected
> select add #1.1/A:610
28 atoms, 26 bonds, 3 residues, 3 models selected
> select add #2.1/A:366
39 atoms, 36 bonds, 4 residues, 4 models selected
> select up
1216 atoms, 1229 bonds, 142 residues, 4 models selected
> select up
6616 atoms, 6756 bonds, 792 residues, 4 models selected
> select up
6790 atoms, 6936 bonds, 810 residues, 4 models selected
> select up
6904 atoms, 7050 bonds, 824 residues, 4 models selected
> select up
7541 atoms, 7701 bonds, 903 residues, 5 models selected
> select up
8178 atoms, 8352 bonds, 982 residues, 6 models selected
> select down
7541 atoms, 7701 bonds, 903 residues, 5 models selected
> select down
6904 atoms, 7050 bonds, 824 residues, 4 models selected
> color sel orange
> select #1.2/D:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #10/A:66
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #9/A:68
16 atoms, 14 bonds, 2 residues, 2 models selected
> select up
82 atoms, 80 bonds, 12 residues, 2 models selected
> select up
3214 atoms, 3282 bonds, 408 residues, 2 models selected
> select up
3214 atoms, 3282 bonds, 408 residues, 9 models selected
> color (#9-10 & sel) orange
> select #1.2/D:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2.2/D:4
16 atoms, 14 bonds, 2 residues, 2 models selected
> select up
157 atoms, 158 bonds, 19 residues, 2 models selected
> select up
1274 atoms, 1302 bonds, 158 residues, 2 models selected
> color sel hot pink
> select clear
> volume #6 level 0.1231
> ui tool show "Color Zone"
> color zone #6 near #1.1 distance 7.2
Drag select of 2426 residues, 2 pseudobonds
> color zone #6 near #1.1 distance 7.2
> color zone #6 near #1.1 distance 8
> color zone #6 near sel distance 8
> select clear
> volume #6 style surface
> volume #6 level 0.08563
> graphics silhouettes true
> lighting full
> save /Users/remi/Desktop/T7SS-docking-8.cxs includeMaps true
——— End of log from Mon Nov 13 18:48:45 2023 ———
opened ChimeraX session
> open
> /Users/remi/Downloads/cryosparc_P14_J549_class_00_00060_volume_sharp.mrc
> format mrc
Opened cryosparc_P14_J549_class_00_00060_volume_sharp.mrc as #7, grid size
128,128,128, pixel 3.75, shown at level 0.147, step 1, values float32
> close #7
> open /Users/remi/Downloads/cryosparc_P14_J542_004_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P14_J542_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 1.2, shown at level 0.0238, step 2, values float32
> volume #7 step 1
> volume #7 level 0.0855
> volume #7 level 0.09809
> volume #7 style mesh
> volume #7 color #6d888a
> volume #7 color #6d888a59
> volume #7 color #6d888a89
> volume #7 color #a6ced189
> volume #7 level 0.1094
> close #6
> ui tool show "Fit in Map"
> fitmap #1.1 inMap #7
Fit molecule assymT7SS.pdb A (#1.1) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2485 atoms
average map value = 0.1383, steps = 72
shifted from previous position = 1.62
rotated from previous position = 0.602 degrees
atoms outside contour = 906, contour level = 0.10941
Position of assymT7SS.pdb A (#1.1) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.25719778 0.85816587 0.44429791 286.83108815
0.95682925 -0.16174110 -0.24149036 245.14804543
-0.13537756 0.48722803 -0.86271766 203.82556556
Axis 0.77823773 0.61906674 0.10536795
Axis point -0.00000000 -17.38715279 82.44922026
Rotation angle (degrees) 152.08345759
Shift along axis 396.46245948
> fitmap #1.2 inMap #7
Fit molecule assymT7SS.pdb D (#1.2) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 637 atoms
average map value = 0.1138, steps = 64
shifted from previous position = 1.44
rotated from previous position = 0.892 degrees
atoms outside contour = 282, contour level = 0.10941
Position of assymT7SS.pdb D (#1.2) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.27592201 0.84526327 0.45759922 285.40546542
0.95521356 -0.18817657 -0.22837823 245.02452788
-0.10693028 0.50011956 -0.85932900 203.62868501
Axis 0.78487899 0.60822057 0.11845977
Axis point 0.00000000 -12.61891842 80.81963616
Rotation angle (degrees) 152.34911668
Shift along axis 397.15951648
> fitmap #2.1 inMap #7
Fit molecule assymT7SS.pdb A (#2.1) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2485 atoms
average map value = 0.1511, steps = 44
shifted from previous position = 1.21
rotated from previous position = 1.25 degrees
atoms outside contour = 719, contour level = 0.10941
Position of assymT7SS.pdb A (#2.1) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.72055560 0.43526099 0.53976616 287.39045253
0.59508387 0.78774263 0.15917519 244.55931385
-0.35591406 0.43590071 -0.82662915 202.69526744
Axis 0.29098977 0.94184945 0.16806120
Axis point 125.28117101 0.00000000 54.53511835
Rotation angle (degrees) 151.60873321
Shift along axis 348.03094705
> fitmap #2.2 inMap #7
Fit molecule assymT7SS.pdb D (#2.2) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 637 atoms
average map value = 0.1348, steps = 52
shifted from previous position = 0.589
rotated from previous position = 4.04 degrees
atoms outside contour = 218, contour level = 0.10941
Position of assymT7SS.pdb D (#2.2) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.73119001 0.46720983 0.49706755 287.65845963
0.61371762 0.76866524 0.18028985 244.23452197
-0.29784536 0.43688525 -0.84877525 199.25379349
Axis 0.30257035 0.93733977 0.17275802
Axis point 120.87527248 0.00000000 55.56051962
Rotation angle (degrees) 154.91097045
Shift along axis 350.39034219
> fitmap #3.1 inMap #7
Fit molecule YukB-TM.pdb B (#3.1) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 967 atoms
average map value = 0.1269, steps = 224
shifted from previous position = 1.16
rotated from previous position = 6.57 degrees
atoms outside contour = 460, contour level = 0.10941
Position of YukB-TM.pdb B (#3.1) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.74345767 -0.58853654 -0.31764040 290.12902281
-0.66744069 -0.68301464 -0.29667142 245.94403283
-0.04235107 0.43256877 -0.90060571 200.44406551
Axis 0.93080066 -0.35137873 -0.10071309
Axis point 0.00000000 153.96309711 149.16549351
Rotation angle (degrees) 156.93797581
Shift along axis 163.44544357
> fitmap #3.2 inMap #7
Fit molecule YukB-TM.pdb C (#3.2) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 967 atoms
average map value = 0.1274, steps = 52
shifted from previous position = 1.03
rotated from previous position = 1.53 degrees
atoms outside contour = 530, contour level = 0.10941
Position of YukB-TM.pdb C (#3.2) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.71543110 -0.58096387 -0.38812282 289.66689571
-0.68095115 -0.70414919 -0.20119506 246.54504150
-0.15640931 0.40823388 -0.89937824 203.33539719
Axis 0.92391582 -0.35128588 -0.15158425
Axis point 0.00000000 157.58167242 152.90959860
Rotation angle (degrees) 160.74290144
Shift along axis 150.19759317
> fitmap #4.1 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms
average map value = 0.1397, steps = 52
shifted from previous position = 0.87
rotated from previous position = 1.26 degrees
atoms outside contour = 652, contour level = 0.10941
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#4.1) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.83888706 0.08310779 -0.53792341 225.62403252
0.48290993 0.56960656 -0.66509124 272.36305740
0.25113044 -0.81770499 -0.51796915 264.56023633
Axis -0.17001865 -0.87904182 0.44539774
Axis point 41.20238270 0.00000000 228.03245237
Rotation angle (degrees) 153.33233577
Shift along axis -159.94427921
> fitmap #4.2 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms
average map value = 0.1479, steps = 44
shifted from previous position = 1.04
rotated from previous position = 1.15 degrees
atoms outside contour = 714, contour level = 0.10941
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#4.2) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.83220637 0.13424052 -0.53797030 225.82199093
0.50520957 0.58336960 -0.63595849 270.99818461
0.22846412 -0.80103645 -0.55330349 267.65812071
Axis -0.19032520 -0.88365393 0.42770556
Axis point 39.90467106 0.00000000 224.43542980
Rotation angle (degrees) 154.29908935
Shift along axis -167.96936281
> fitmap #5.1 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms
average map value = 0.1618, steps = 48
shifted from previous position = 1.13
rotated from previous position = 0.978 degrees
atoms outside contour = 456, contour level = 0.10941
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (#5.1) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.83187868 -0.37254088 0.41132851 230.35775653
-0.52076326 0.26787755 -0.81058450 207.07344041
0.19179019 -0.88851275 -0.41684723 262.25101633
Axis -0.28223062 0.79509602 -0.53681300
Axis point 162.40604083 0.00000000 191.48767206
Rotation angle (degrees) 172.06452805
Shift along axis -41.15050093
> fitmap #5.2 inMap #7
Fit molecule YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 2114 atoms
average map value = 0.1642, steps = 56
shifted from previous position = 0.336
rotated from previous position = 1.39 degrees
atoms outside contour = 543, contour level = 0.10941
Position of YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (#5.2) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
-0.81931778 -0.39500688 0.41555738 232.11682695
-0.54133025 0.29416935 -0.78767122 206.50573719
0.18889131 -0.87030682 -0.45484735 263.68427876
Axis -0.29286343 0.80331243 -0.51857512
Axis point 164.44834446 0.00000000 188.75579165
Rotation angle (degrees) 171.88953035
Shift along axis -38.83001248
> fitmap #9 inMap #7
Fit molecule FHA-1.pdb (#9) to map cryosparc_P14_J542_004_volume_map_sharp.mrc
(#7) using 1607 atoms
average map value = 0.1374, steps = 64
shifted from previous position = 0.856
rotated from previous position = 1.74 degrees
atoms outside contour = 549, contour level = 0.10941
Position of FHA-1.pdb (#9) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99188388 0.03534957 -0.12213427 17.62461393
-0.04525595 0.99582199 -0.07931249 29.05417982
0.11882033 0.08419609 0.98933955 -50.48702997
Axis 0.54115984 -0.79748079 -0.26677786
Axis point 435.68399653 0.00000000 116.07783059
Rotation angle (degrees) 8.68907603
Shift along axis -0.16359535
> fitmap #10 inMap #7
Fit molecule FHA-2.pdb (#10) to map
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) using 1607 atoms
average map value = 0.1363, steps = 52
shifted from previous position = 1.4
rotated from previous position = 1.85 degrees
atoms outside contour = 564, contour level = 0.10941
Position of FHA-2.pdb (#10) relative to
cryosparc_P14_J542_004_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99755585 0.03435302 -0.06084564 3.82910164
-0.03223415 0.99885077 0.03546973 3.77839117
0.06199421 -0.03342173 0.99751677 -8.04223974
Axis -0.44221636 -0.78851281 -0.42742513
Axis point 140.17713571 0.00000000 48.32369250
Rotation angle (degrees) 4.46748737
Shift along axis -1.23514588
> save /Users/remi/Desktop/T7SS-docking-9.cxs includeMaps true
——— End of log from Tue Nov 14 13:40:55 2023 ———
opened ChimeraX session
> show surfaces
[Repeated 1 time(s)]
> mlp
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
-4.13, maximum 25.08
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
-4.867, maximum 25.11
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
-4.127, maximum 25.05
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
-4.866, maximum 25.1
Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
-1.53, maximum 22.46
Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
maximum 25.59
Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
maximum 25.27
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -27.88, mean -3.48, maximum 23.57
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -29.17, mean -3.443, maximum 22.54
Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
-1.439, maximum 22.4
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -28.29, mean -3.483, maximum 23.72
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -28.96, mean -3.44, maximum 22.7
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 11 time(s)]Coulombic values for assymT7SS.pdb A_A SES surface
#1.1.2: minimum, -16.49, mean -2.18, maximum 12.35
Coulombic values for assymT7SS.pdb D_D SES surface #1.2.1: minimum, -10.22,
mean -0.66, maximum 8.70
Coulombic values for assymT7SS.pdb A_A SES surface #2.1.2: minimum, -16.49,
mean -2.18, maximum 12.35
Coulombic values for assymT7SS.pdb D_D SES surface #2.2.1: minimum, -10.22,
mean -0.66, maximum 8.70
Coulombic values for YukB-TM.pdb B_B SES surface #3.1.1: minimum, -13.72, mean
1.13, maximum 12.66
Coulombic values for YukB-TM.pdb C_C SES surface #3.2.1: minimum, -14.06, mean
1.14, maximum 13.61
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface #4.1.1: minimum, -18.31, mean -1.89, maximum 32.59
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface #4.2.1: minimum, -19.05, mean -1.87, maximum 22.55
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface #5.1.1: minimum, -18.31, mean -1.89, maximum 32.59
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface #5.2.1: minimum, -19.05, mean -1.87, maximum 22.55
Coulombic values for FHA-1.pdb_A SES surface #9.1: minimum, -15.53, mean
-3.48, maximum 8.33
Coulombic values for FHA-2.pdb_A SES surface #10.1: minimum, -22.75, mean
-3.50, maximum 8.14
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
-4.13, maximum 25.08
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
-4.867, maximum 25.11
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
-4.127, maximum 25.05
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
-4.866, maximum 25.1
Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
-1.53, maximum 22.46
Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
maximum 25.59
Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
maximum 25.27
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -27.88, mean -3.48, maximum 23.57
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -29.17, mean -3.443, maximum 22.54
Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
-1.439, maximum 22.4
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -28.29, mean -3.483, maximum 23.72
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -28.96, mean -3.44, maximum 22.7
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic
Coulombic values for assymT7SS.pdb A_A SES surface #1.1.2: minimum, -16.49,
mean -2.18, maximum 12.35
Coulombic values for assymT7SS.pdb D_D SES surface #1.2.1: minimum, -10.22,
mean -0.66, maximum 8.70
Coulombic values for assymT7SS.pdb A_A SES surface #2.1.2: minimum, -16.49,
mean -2.18, maximum 12.35
Coulombic values for assymT7SS.pdb D_D SES surface #2.2.1: minimum, -10.22,
mean -0.66, maximum 8.70
Coulombic values for YukB-TM.pdb B_B SES surface #3.1.1: minimum, -13.72, mean
1.13, maximum 12.66
Coulombic values for YukB-TM.pdb C_C SES surface #3.2.1: minimum, -14.06, mean
1.14, maximum 13.61
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface #4.1.1: minimum, -18.31, mean -1.89, maximum 32.59
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface #4.2.1: minimum, -19.05, mean -1.87, maximum 22.55
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface #5.1.1: minimum, -18.31, mean -1.89, maximum 32.59
Coulombic values for YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface #5.2.1: minimum, -19.05, mean -1.87, maximum 22.55
Coulombic values for FHA-1.pdb_A SES surface #9.1: minimum, -15.53, mean
-3.48, maximum 8.33
Coulombic values for FHA-2.pdb_A SES surface #10.1: minimum, -22.75, mean
-3.50, maximum 8.14
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
-4.13, maximum 25.08
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
-4.867, maximum 25.11
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
-4.127, maximum 25.05
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
-4.866, maximum 25.1
Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
-1.53, maximum 22.46
Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
maximum 25.59
Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
maximum 25.27
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -27.88, mean -3.48, maximum 23.57
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -29.17, mean -3.443, maximum 22.54
Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
-1.439, maximum 22.4
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -28.29, mean -3.483, maximum 23.72
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -28.96, mean -3.44, maximum 22.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> mlp
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -26.05, mean
-4.13, maximum 25.08
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.01, mean
-4.867, maximum 25.11
Map values for surface "assymT7SS.pdb D_D SES surface": minimum -25.92, mean
-4.127, maximum 25.05
Map values for surface "assymT7SS.pdb A_A SES surface": minimum -27.05, mean
-4.866, maximum 25.1
Map values for surface "YukB-TM.pdb B_B SES surface": minimum -24.75, mean
-1.53, maximum 22.46
Map values for surface "FHA-1.pdb_A SES surface": minimum -27.39, mean -5.877,
maximum 25.59
Map values for surface "FHA-2.pdb_A SES surface": minimum -26.33, mean -5.795,
maximum 25.27
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -27.88, mean -3.48, maximum 23.57
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -29.17, mean -3.443, maximum 22.54
Map values for surface "YukB-TM.pdb C_C SES surface": minimum -25.43, mean
-1.439, maximum 22.4
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B_B SES
surface": minimum -28.29, mean -3.483, maximum 23.72
Map values for surface "YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C_C SES
surface": minimum -28.96, mean -3.44, maximum 22.7
To also show corresponding color key, enter the above mlp command and add key
true
> hide surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #4.1/B #4.2/C #5.1/B #5.2/C
Alignment identifier is 1
> select #4.1/B:219-220 #4.2/C:219-220 #5.1/B:219-220 #5.2/C:219-220
92 atoms, 92 bonds, 8 residues, 4 models selected
> select #4.1/B:219-241 #4.2/C:219-241 #5.1/B:219-241 #5.2/C:219-241
732 atoms, 748 bonds, 92 residues, 4 models selected
1 [ID: 1] region 4 chains [219-241] RMSD: 49.851
> color (#!4.1-2#!5.1-2 & sel) white
> ui tool show "Show Sequence Viewer"
> sequence chain #3.1/B #3.2/C
Alignment identifier is 1
> select #3.1/B:247 #3.2/C:247
28 atoms, 30 bonds, 2 residues, 2 models selected
> select #3.1/B:247-335 #3.2/C:247-335
1500 atoms, 1526 bonds, 178 residues, 2 models selected
1 [ID: 1] region chains B,C [27-115] RMSD: 22.120
> select clear
> select #3.1/B:246-247 #3.2/C:246-247
44 atoms, 46 bonds, 4 residues, 2 models selected
> select #3.1/B:246-266 #3.2/C:246-266
320 atoms, 326 bonds, 42 residues, 2 models selected
1 [ID: 1] region chains B,C [26-46] RMSD: 11.217
> color (#!3.1-2 & sel) white
> select #3.1/B:271 #3.2/C:271
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #3.1/B:271-291 #3.2/C:271-291
334 atoms, 338 bonds, 42 residues, 2 models selected
1 [ID: 1] region chains B,C [51-71] RMSD: 12.019
> color (#!3.1-2 & sel) magenta
> color (#!3.1-2 & sel) white
> select clear
> save "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/T7SS2.cxs"
——— End of log from Fri Nov 17 13:21:00 2023 ———
opened ChimeraX session
> hide #!7 models
> open "/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure
> related/YukC.fa"
Summary of feedback from opening /Users/gabrielumajioka/Desktop/project T7SS
/T7SS structure related/YukC.fa
---
notes | Alignment identifier is YukC.fa
Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (4.1) chain B to
WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
with 0 mismatches
Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (4.2) chain C to
WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
with 0 mismatches
Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb B (5.1) chain B to
WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
with 0 mismatches
Associated YukCdimer_3fc44_unrelaxed_rank_1_model_5.pdb C (5.2) chain C to
WP_003243575.1/1-451 MULTISPECIES: type VII secretion protein EssB [Bacillus]
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment YukC.fa
Opened 393 sequences from YukC.fa
> ui tool show "Render By Attribute"
> select #4.1/B:2 #4.2/C:2 #5.1/B:2 #5.2/C:2
24 atoms, 20 bonds, 4 residues, 4 models selected
> select #4.1/B:2 #4.2/C:2 #5.1/B:2 #5.2/C:2
24 atoms, 20 bonds, 4 residues, 4 models selected
YukC.fa [ID: YukC.fa] region WP_003243575.1/1-451 MULTISPECIES: type VII
secretion protein EssB [Bacillus] [2] RMSD: 89.085
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> ui tool show "Render By Attribute"
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,blue:1.048,white:3.463,red
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,blue:0.0486897,white:1.56235,red
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,blue:0.18585,white:1.56235,red
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,blue:0.430779,white:3.4532,red
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,blue:-0.196239,white:1.43499,red
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.43499,#9e205e
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1-2#!5.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
6342 atoms, 777 residues, 3 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!5.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!4.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
Window position QRect(818,959 576x67) outside any known screen, using primary
screen
Window position QRect(818,1022 576x72) outside any known screen, using primary
screen
> select add #5.2
2132 atoms, 2179 bonds, 262 residues, 8 models selected
> color byattribute r:seq_conservation #!4.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> hide #!5.2 models
> select subtract #5.2
18 atoms, 15 bonds, 3 residues, 7 models selected
> hide #!5.1 models
> select add #5.1
2126 atoms, 2174 bonds, 261 residues, 6 models selected
> select subtract #5.1
12 atoms, 10 bonds, 2 residues, 5 models selected
> hide #!5 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2.2 models
> show #!2.1 models
> show #!3 models
> show #!3.1 models
> show #!5 models
> show #!5.1 models
> show #!5.2 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!9 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> hide #!2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> hide #!3 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3.2 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.2 models
> show #!4.2 models
> show #!5.1 models
> hide #!5.1 models
> show sel surfaces
> select add #4.2
2120 atoms, 2169 bonds, 260 residues, 4 models selected
> select add #4.1
4228 atoms, 4328 bonds, 518 residues, 4 models selected
> show sel surfaces
> select subtract #4.2
2114 atoms, 2164 bonds, 259 residues, 3 models selected
> select add #4.2
4228 atoms, 4328 bonds, 518 residues, 3 models selected
> select subtract #4.2
2114 atoms, 2164 bonds, 259 residues, 3 models selected
> select subtract #4.1
1 model selected
> ui tool show "Side View"
> select add #10
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select add #1.2
2244 atoms, 2292 bonds, 283 residues, 3 models selected
> select add #3
4178 atoms, 4264 bonds, 515 residues, 7 models selected
> select subtract #3
2244 atoms, 2292 bonds, 283 residues, 6 models selected
> select add #3
4178 atoms, 4264 bonds, 515 residues, 7 models selected
> select subtract #3
2244 atoms, 2292 bonds, 283 residues, 6 models selected
> select add #3
4178 atoms, 4264 bonds, 515 residues, 7 models selected
> show #!3.1 models
> hide #!3.1 models
> show #!3.2 models
> show #!3.1 models
> hide #!4 models
> show #!4 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.1 models
> select add #1.1
6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected
> select subtract #1.1
4178 atoms, 4264 bonds, 515 residues, 10 models selected
> select add #1.1
6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected
> select subtract #1.1
4178 atoms, 4264 bonds, 515 residues, 10 models selected
> select add #1.1
6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 11 models selected
> select add #1
6663 atoms, 6803 bonds, 1 pseudobond, 811 residues, 13 models selected
> select subtract #1.2
6026 atoms, 6152 bonds, 1 pseudobond, 732 residues, 12 models selected
> select subtract #1.1
3541 atoms, 3613 bonds, 436 residues, 9 models selected
> show #!2.1 models
> show #!2.2 models
> show #!3.1 models
> show #!5.1 models
> show #!5.2 models
> show #!7 models
> show #!9 models
> select subtract #10
1934 atoms, 1972 bonds, 232 residues, 7 models selected
> select subtract #3.2
967 atoms, 986 bonds, 116 residues, 5 models selected
> select subtract #3.1
3 models selected
> select add #3
1934 atoms, 1972 bonds, 232 residues, 4 models selected
> select add #1
5056 atoms, 5162 bonds, 1 pseudobond, 607 residues, 9 models selected
> select subtract #1
1934 atoms, 1972 bonds, 232 residues, 7 models selected
> select add #1.1
4419 atoms, 4511 bonds, 1 pseudobond, 528 residues, 7 models selected
> select add #1
5056 atoms, 5162 bonds, 1 pseudobond, 607 residues, 10 models selected
> select subtract #1
1934 atoms, 1972 bonds, 232 residues, 7 models selected
> select subtract #3
2 models selected
> hide surfaces
> hide #!7 models
> turm 90
Unknown command: turm 90
> turm x 90
Unknown command: turm x 90
> turm x 90
Unknown command: turm x 90
> turm 90 90
Unknown command: turm 90 90
> turm x 90
Unknown command: turm x 90
> turn x 90
> turn y 90
> turn y -90
> turn z -90
> turn y -90
> select #4.2/C
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Model Panel"
> select add #4
4228 atoms, 4328 bonds, 518 residues, 4 models selected
> select subtract #4
2 models selected
> select add #4.1
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select subtract #4.1
1 model selected
> select add #4.2
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select subtract #4.2
1 model selected
> select add #5.1
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select subtract #5.1
1 model selected
> select add #5.2
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select subtract #5.2
1 model selected
> select add #5.2
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> color byattribute r:seq_conservation #!4.2 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!5.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> select subtract #5.2
1 model selected
> select add #5.2.1
2114 atoms, 259 residues, 1 model selected
> color byattribute r:seq_conservation #!5.1 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> color byattribute r:seq_conservation #!5.2 target abcs palette
> -1.367,#0fc7cf:-0.196239,#b2b2b2:1.18026,#9e205e
2114 atoms, 259 residues, 1 surfaces, atom seq_conservation range -1.37 to
3.46
> hide #5.2.1 models
> select subtract #5.2.1
1 model selected
> show #5.2.1 models
> show surfaces
> hide surfaces
> select add #5.2.1
2114 atoms, 259 residues, 1 model selected
> select add #5.1
4228 atoms, 2164 bonds, 518 residues, 3 models selected
> select add #4.2
6342 atoms, 4328 bonds, 777 residues, 5 models selected
> select add #4.1
8456 atoms, 6492 bonds, 1036 residues, 7 models selected
> show sel surfaces
> select subtract #5.2.1
6342 atoms, 6492 bonds, 777 residues, 7 models selected
> select subtract #5.1
4228 atoms, 4328 bonds, 518 residues, 5 models selected
> select add #5
8456 atoms, 8656 bonds, 1036 residues, 7 models selected
> select subtract #4.2
6342 atoms, 6492 bonds, 777 residues, 8 models selected
> select subtract #5
2114 atoms, 2164 bonds, 259 residues, 4 models selected
> select subtract #4.1
1 model selected
> select add #4
4228 atoms, 4328 bonds, 518 residues, 3 models selected
> turn y -90
> select subtract #4
2 models selected
> hide surfaces
> select add #4
4228 atoms, 4328 bonds, 518 residues, 3 models selected
> select add #5
8456 atoms, 8656 bonds, 1036 residues, 8 models selected
> hide sel surfaces
> select subtract #4
4228 atoms, 4328 bonds, 518 residues, 7 models selected
> select subtract #5
2 models selected
> select #4.2/C:28
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4.2/C:62
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4.2/C:64
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4.2/C:62
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4.2/C:64
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #4.2/C:28
26 atoms, 24 bonds, 3 residues, 1 model selected
> show (#!4.2 & sel) target ab
> select #4.2/C:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (#!4.2 & sel) target ab
> hide #!10 models
> hide #!9 models
> hide #5.2.1 models
> show #5.2.1 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!3 models
> hide #!3.1 models
> hide #!3.2 models
> hide #!4 models
> hide #!4.1 models
> show #!5.1-2 surfaces
> hide #!5.1-2 surfaces
> select #5.1/B:39
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4.1/B #4.2/C #5.1/B #5.2/C
Alignment identifier is 1
> select #4.1/B:50-98 #4.2/C:50-98 #5.1/B:50-98 #5.2/C:50-98
1656 atoms, 1700 bonds, 196 residues, 4 models selected
> select #4.1/B:50-103 #4.2/C:50-103 #5.1/B:50-103 #5.2/C:50-103
1820 atoms, 1868 bonds, 216 residues, 4 models selected
1 [ID: 1] region 4 chains [50-103] RMSD: 67.077
> select #4.1/B:101-102 #4.2/C:101-102 #5.1/B:101-102 #5.2/C:101-102
64 atoms, 60 bonds, 8 residues, 4 models selected
> select #4.1/B:101 #4.2/C:101 #5.1/B:101 #5.2/C:101
32 atoms, 28 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [101] RMSD: 64.978
> select clear
> select #5.1/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5.1/B:31
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5.1/B:131
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #5.1/B:33
26 atoms, 23 bonds, 3 residues, 2 models selected
> select add #5.1/B:32
35 atoms, 31 bonds, 4 residues, 2 models selected
> select add #5.1/B:60
43 atoms, 38 bonds, 5 residues, 2 models selected
> select add #5.1/B:40
52 atoms, 46 bonds, 6 residues, 2 models selected
> show (#!5.1 & sel) target ab
> show sel surfaces
> hide sel surfaces
> select
> #4.1/B:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
> #4.2/C:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
> #5.1/B:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
> #5.2/C:8-13,30-32,38-46,75-80,83-99,111-113,140-155,161-166,175-181,186-206,212-258
4664 atoms, 4720 bonds, 564 residues, 4 models selected
> select clear
> show #!5.1-2 surfaces
> hide #!5.1-2 surfaces
> transparency #5 50
> show #!5.1-2 surfaces
> hide #!5.1-2 cartoons
> hide #!5.1-2 atoms
Unsupported scale factor (0.000000) detected on Display0
> interfaces #!5.1-2 & ~solvent
1 buried areas: #5.1/B #5.2/C 1645
> transparency #5 0
> show #!5.1-2 cartoons
> hide #!5.1-2 surfaces
> show #!5.1-2 surfaces
> turn y -180
> turn z -90
> turn x 90
> turn x -90
> turn y 180
> hide #!5.1-2 surfaces
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!7 models
> hide #!7 models
> show #!3.2 models
> hide #!3.2 models
> show #!3.1 models
> hide #!3 models
> show #!3 models
> show #!2.2 models
> hide #!2.2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!1.1 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> show #!2.2 models
> hide #!1 models
> hide #!2.1 models
> show #!2.1 models
> show #!7 models
> hide #!7 models
> show #!10 models
> show #!4.1 models
> show #!3.2 models
> show #!1.2 models
> show #!1.1 models
> show surfaces
> hide surfaces
> hide #!1.1 models
> show #!1.1 models
> select add #5.1
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select add #5.2
4228 atoms, 4328 bonds, 518 residues, 3 models selected
> select add #4.2
6342 atoms, 6492 bonds, 777 residues, 5 models selected
> select add #4.1
8456 atoms, 8656 bonds, 1036 residues, 7 models selected
> show sel surfaces
> select add #4
8456 atoms, 8656 bonds, 1036 residues, 9 models selected
> select subtract #4
4228 atoms, 4328 bonds, 518 residues, 6 models selected
> select add #5
4228 atoms, 4328 bonds, 518 residues, 5 models selected
> select subtract #5
2 models selected
> select add #1.2
637 atoms, 651 bonds, 79 residues, 1 model selected
> select add #1.1
3122 atoms, 3190 bonds, 1 pseudobond, 375 residues, 4 models selected
> select add #2
6244 atoms, 6380 bonds, 2 pseudobonds, 750 residues, 9 models selected
> select add #3
8178 atoms, 8352 bonds, 2 pseudobonds, 982 residues, 14 models selected
> select add #4
12406 atoms, 12680 bonds, 2 pseudobonds, 1500 residues, 19 models selected
> select subtract #4
8178 atoms, 8352 bonds, 2 pseudobonds, 982 residues, 18 models selected
> select add #9
9785 atoms, 9993 bonds, 2 pseudobonds, 1186 residues, 17 models selected
> select add #10
11392 atoms, 11634 bonds, 2 pseudobonds, 1390 residues, 19 models selected
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> hide sel surfaces
> select add #4
15620 atoms, 15962 bonds, 2 pseudobonds, 1908 residues, 23 models selected
> select subtract #4.1
13506 atoms, 13798 bonds, 2 pseudobonds, 1649 residues, 24 models selected
> select add #5
17734 atoms, 18126 bonds, 2 pseudobonds, 2167 residues, 26 models selected
> select add #4.1
19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 29 models selected
> hide sel surfaces
> select add #1
19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 31 models selected
> select subtract #1
16726 atoms, 17100 bonds, 1 pseudobond, 2051 residues, 27 models selected
> select subtract #2
13604 atoms, 13910 bonds, 1676 residues, 21 models selected
> select subtract #3
11670 atoms, 11938 bonds, 1444 residues, 16 models selected
> select subtract #4
7442 atoms, 7610 bonds, 926 residues, 11 models selected
> select subtract #5
3214 atoms, 3282 bonds, 408 residues, 6 models selected
> select subtract #9
1607 atoms, 1641 bonds, 204 residues, 3 models selected
> select subtract #10
1 model selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #5.2.1 models
> hide #!5.2 models
> hide #!5.1 models
> hide #!5 models
> show #!5 models
> show #!5.2 models
> show #!5.1 models
> show #5.2.1 models
> hide #!4 models
> show #!4 models
> hide #!3.2 models
> hide #!3.1 models
> hide #!3 models
> hide #!2.2 models
> hide #!2.1 models
> hide #!2 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!4.1-2#!5.1-2 surfaces
> transparency #4-5#!1 0
> hide #!4.1-2#!5.1-2 surfaces
> show #!9 models
> hide #!9 models
> show #!9 models
> select #9/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/A:140
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5.1/B:40
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 56 residues
Drag select of 33 residues
Drag select of 149 residues
> show (#!9#!5.1-2 & sel) target ab
> select clear
> select #4.1/B:96 #4.2/C:96 #5.1/B:96 #5.2/C:96
20 atoms, 16 bonds, 4 residues, 4 models selected
> select #4.1/B:96 #4.2/C:96 #5.1/B:96 #5.2/C:96
20 atoms, 16 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [96] RMSD: 62.642
> select
19848 atoms, 20290 bonds, 2 pseudobonds, 2426 residues, 21 models selected
> hide (#!9#!4.1-2#!5.1-2 & sel) target a
> select clear
> select #5.1/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (#!5.1 & sel) target ab
> select #9/A:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:138
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (#!9 & sel) target ab
> select #9/A:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:134
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #9/A:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:110
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/A:148
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show (#!9 & sel) target ab
> select #9/A:149
6 atoms, 5 bonds, 1 residue, 1 model selected
> show (#!9 & sel) target ab
> select #9/A:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:135
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #9/A:136
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #9/A:137
22 atoms, 19 bonds, 3 residues, 2 models selected
> select add #9/A:108
30 atoms, 26 bonds, 4 residues, 2 models selected
> select add #9/A:109
37 atoms, 32 bonds, 5 residues, 2 models selected
> select add #9/A:146
48 atoms, 42 bonds, 6 residues, 2 models selected
> select add #9/A:187
57 atoms, 50 bonds, 7 residues, 2 models selected
> select subtract #9/A:187
48 atoms, 42 bonds, 6 residues, 2 models selected
> select add #9/A:147
55 atoms, 49 bonds, 7 residues, 2 models selected
> show (#!9 & sel) target ab
> select clear
> select #9/A:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.1/B:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5.1/B:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #5.1/B:40
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:140
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #5.1/B:40
9 atoms, 8 bonds, 1 residue, 1 model selected
> show (#!5.1 & sel) target ab
> select #5.1/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A:140
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5.1/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.1/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:140
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5.1/B:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5.1/B:98
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #5.1/B:100
27 atoms, 25 bonds, 3 residues, 2 models selected
> select #5.1/B:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select add #9/A:142
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5.2/C:17
11 atoms, 9 bonds, 2 residues, 3 models selected
> select clear
> select add #9/A:142
6 atoms, 5 bonds, 1 residue, 1 model selected
> select subtract #9/A:142
1 model selected
> select add #9/A:142
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select add #9/A:140
8 atoms, 8 bonds, 2 residues, 2 models selected
Drag select of 49 atoms, 46 residues, 39 bonds
> show (#!9#!5.1 & sel) target ab
> select clear
> ui tool show Distances
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true dashes 3
210 contacts
> ui tool show Distances
Drag select of 16 residues
> ui tool show Contacts
> contacts intraMol false ignoreHiddenModels true dashes 3
210 contacts
> contacts intraMol false ignoreHiddenModels true dashes 3
210 contacts
> contacts intraMol false ignoreHiddenModels true dashes 3
210 contacts
> show (#!9#!5.2 & sel) target ab
Drag select of 142 atoms, 92 residues, 119 bonds, 118 pseudobonds
> ui tool show Distances
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
210 contacts
> show (#!9#!5.1-2 & sel) target ab
> select clear
> ui tool show "Side View"
> select #9/A:146
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.1/B:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A #2.1/A
Alignment identifier is 2
> ui tool show "Show Sequence Viewer"
> sequence chain #4.1/B #4.2/C #5.1/B #5.2/C
Alignment identifier is 3
> select #4.1/B:108 #4.2/C:108 #5.1/B:108 #5.2/C:108
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #4.1/B:108-158 #4.2/C:108-158 #5.1/B:108-158 #5.2/C:108-158
1620 atoms, 1664 bonds, 204 residues, 4 models selected
3 [ID: 3] region 4 chains [108-158] RMSD: 67.396
> select #4.1/B:19-27 #4.2/C:19-27 #5.1/B:19-27 #5.2/C:19-27
280 atoms, 284 bonds, 36 residues, 4 models selected
> select #4.1/B:27-47 #4.2/C:27-47 #5.1/B:27-47 #5.2/C:27-47
684 atoms, 684 bonds, 84 residues, 4 models selected
3 [ID: 3] region 4 chains [27-47] RMSD: 74.213
> select #1.1/A:399 #2.1/A:399
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1.1/A:399-535 #2.1/A:399-535
2348 atoms, 2414 bonds, 274 residues, 2 models selected
2 [ID: 2] region 2 chains [282-418] RMSD: 48.897
> select #1.1/A:536 #2.1/A:536
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1.1/A:536-617 #2.1/A:536-617
1352 atoms, 1372 bonds, 164 residues, 2 models selected
2 [ID: 2] region 2 chains [419-500] RMSD: 48.564
> select #4.1/B:97-99 #4.2/C:97-99 #5.1/B:97-99 #5.2/C:97-99
100 atoms, 96 bonds, 12 residues, 4 models selected
> select #4.1/B:97-110 #4.2/C:97-110 #5.1/B:97-110 #5.2/C:97-110
448 atoms, 448 bonds, 56 residues, 4 models selected
3 [ID: 3] region 4 chains [97-110] RMSD: 66.188
> select #4.1/B:146-147 #4.2/C:146-147 #5.1/B:146-147 #5.2/C:146-147
68 atoms, 64 bonds, 8 residues, 4 models selected
> select #4.1/B:146-199 #4.2/C:146-199 #5.1/B:146-199 #5.2/C:146-199
1680 atoms, 1704 bonds, 216 residues, 4 models selected
3 [ID: 3] region 4 chains [146-199] RMSD: 68.483
> select clear
> select #4.1/B:131-132 #4.2/C:131-132 #5.1/B:131-132 #5.2/C:131-132
60 atoms, 56 bonds, 8 residues, 4 models selected
> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131
36 atoms, 32 bonds, 4 residues, 4 models selected
3 [ID: 3] region 4 chains [131] RMSD: 72.867
> select #4.1/B:1-2 #4.2/C:1-2 #5.1/B:1-2 #5.2/C:1-2
56 atoms, 52 bonds, 8 residues, 4 models selected
> select #4.1/B:1-258 #4.2/C:1-258 #5.1/B:1-258 #5.2/C:1-258
8424 atoms, 8624 bonds, 1032 residues, 4 models selected
3 [ID: 3] region 4 chains [1-258] RMSD: 65.941
> select #4.1/B:1 #4.2/C:1 #5.1/B:1 #5.2/C:1
32 atoms, 28 bonds, 4 residues, 4 models selected
> select #4.1/B #4.2/C #5.1/B #5.2/C
8456 atoms, 8656 bonds, 1036 residues, 4 models selected
3 [ID: 3] region 4 chains [1-357] RMSD: 65.871
> select clear
> select #4.1/B:132 #4.2/C:132 #5.1/B:132 #5.2/C:132
24 atoms, 20 bonds, 4 residues, 4 models selected
> select #4.1/B:131-132 #4.2/C:131-132 #5.1/B:131-132 #5.2/C:131-132
60 atoms, 56 bonds, 8 residues, 4 models selected
1 [ID: 1] region 4 chains [131-132] RMSD: 72.960
> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131
36 atoms, 32 bonds, 4 residues, 4 models selected
> select #4.1/B:131 #4.2/C:131 #5.1/B:131 #5.2/C:131
36 atoms, 32 bonds, 4 residues, 4 models selected
1 [ID: 1] region 4 chains [131] RMSD: 72.867
Drag select of 1 residues
> select #5.1/B:130@CA
1 atom, 1 residue, 1 model selected
> select add #5.1/B:103@CA
2 atoms, 2 residues, 1 model selected
> select add #5.1/B:104
13 atoms, 10 bonds, 3 residues, 2 models selected
> select add #5.1/B:102
21 atoms, 17 bonds, 4 residues, 2 models selected
> select add #5.1/B:105
29 atoms, 24 bonds, 5 residues, 2 models selected
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
210 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
210 contacts
> select clear
> select add #5.1/B:130
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5.1/B:131
18 atoms, 16 bonds, 2 residues, 2 models selected
> select add #5.1/B:104
29 atoms, 26 bonds, 3 residues, 2 models selected
> select add #5.1/B:102@CA
30 atoms, 27 bonds, 4 residues, 2 models selected
> interfaces select #1.1/A & ::polymer_type>0 contacting #10/A &
> ::polymer_type>0 areaCutoff 0
1 contacting residues
> interfaces select #1.1/A & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> select #1.1/A
2485 atoms, 2539 bonds, 1 pseudobond, 296 residues, 2 models selected
> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> interfaces select #4.1/B & ::polymer_type>0 contacting #9/A &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
Drag select of 2 residues
> select add #5.1/B:131
22 atoms, 8 bonds, 3 residues, 2 models selected
> select subtract #5.1/B:41
17 atoms, 8 bonds, 2 residues, 2 models selected
> select subtract #5.1/B:42
9 atoms, 8 bonds, 1 residue, 2 models selected
> label (#!5.1 & sel) attribute name
> label (#!5.1 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> select add #9/A:145
16 atoms, 14 bonds, 2 residues, 3 models selected
> select subtract #9/A:145
9 atoms, 8 bonds, 1 residue, 2 models selected
> select add #9/A:146
20 atoms, 18 bonds, 2 residues, 3 models selected
> select add #5.1/B:130
29 atoms, 26 bonds, 3 residues, 4 models selected
> select add #5.1/B:104
40 atoms, 36 bonds, 4 residues, 4 models selected
> select add #5.1/B:103
46 atoms, 41 bonds, 5 residues, 4 models selected
> select add #5.1/B:102
54 atoms, 48 bonds, 6 residues, 4 models selected
> select add #9/A:101
65 atoms, 59 bonds, 7 residues, 4 models selected
> select add #9/A:109
72 atoms, 65 bonds, 8 residues, 4 models selected
> select add #9/A:107
81 atoms, 73 bonds, 9 residues, 4 models selected
> select add #9/A:148@CA
82 atoms, 73 bonds, 10 residues, 4 models selected
> select subtract #9/A:148
81 atoms, 73 bonds, 9 residues, 4 models selected
> label (#!9#!5.1 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> select clear
> ui tool show "Side View"
> select #9/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/A:140
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #9/A:141
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/A:201
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.1/B:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:139
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
210 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true
> makePseudobonds false dashes 3
210 contacts
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055
210 contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055
210 contacts
> contacts saveFile "/Users/gabrielumajioka/Desktop/project T7SS /T7SS
> structure related/contact" intraModel false intraMol false
> ignoreHiddenModels true dashes 3 radius 0.055
210 contacts
> cartoon hide (#!9 & sel)
> select
19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 24 models selected
> cartoon hide (#!9#!4.1-2#!5.1-2 & sel)
> select clear
Drag select of 37 atoms, 35 bonds
> hide (#!9 & sel) target a
Drag select of 1 atoms
Drag select of 26 atoms, 25 bonds
> hide (#!9 & sel) target a
Drag select of 1 atoms
> hide (#!9 & sel) target a
> select clear
Drag select of 57 atoms, 56 bonds
> hide (#!9 & sel) target a
Drag select of 296 atoms, 298 bonds
> hide (#!5.2 & sel) target a
Drag select of 23 atoms, 21 bonds
> hide (#!5.2 & sel) target a
Drag select of 17 atoms, 15 bonds
Drag select of 29 atoms, 25 bonds
Drag select of 4 atoms, 6 bonds
Drag select of 24 atoms, 26 bonds
Drag select of 1 atoms
Drag select of 3 atoms, 2 bonds
Drag select of 9 atoms, 7 bonds
Drag select of 3 atoms, 2 bonds
Drag select of 10 atoms, 8 bonds
Drag select of 7 atoms, 7 bonds
Drag select of 8 atoms, 9 bonds
> hide (#!9#!5.1-2 & sel) target a
Drag select of 5 atoms
> hide (#!9#!5.1-2 & sel) target a
Drag select of 44 atoms, 43 bonds
> hide (#!9#!5.1-2 & sel) target a
Drag select of 18 atoms, 17 bonds
Drag select of 10 atoms, 11 bonds
Drag select of 17 atoms, 17 bonds
> hide (#!9#!5.1-2 & sel) target a
Drag select of 1 atoms, 2 bonds, 11 pseudobonds
> select #5.1/B:43@N
1 atom, 1 residue, 1 model selected
> select clear
> show #!9#!4.1-2#!5.1-2 cartoons
> hide #!9#!4.1-2#!5.1-2 cartoons
Drag select of 4 atoms, 6 bonds
> select clear
> select #5.1/B:47@CD1
1 atom, 1 residue, 1 model selected
> select add #5.1/B:47@CG2
1 atom, 1 bond, 1 residue, 1 model selected
> hide (#!5.1 & sel) target ab
Drag select of 6 atoms, 2 bonds
> hide (#!5.1 & sel) target a
Drag select of 8 atoms, 7 bonds
> hide (#!5.1 & sel) target a
Drag select of 7 atoms, 6 bonds
> hide (#!5.1 & sel) target a
Drag select of 4 atoms, 3 bonds
> hide (#!9 & sel) target a
> hide sel cartoons
> show sel cartoons
> select
19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 24 models selected
> show sel & #!9#!4.1-2#!5.1-2 cartoons
> hide sel & #!9#!4.1-2#!5.1-2 cartoons
> select clear
> select #9/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> show sel cartoons
> select #4.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #5.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> show sel cartoons
> select #5.2/C
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> show sel cartoons
> select #4.2/C
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #9/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select #5.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> show sel atoms
> select #10/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select #2.2/D
637 atoms, 651 bonds, 79 residues, 1 model selected
> select #10/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select #9/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> show sel atoms
> select #4.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #5.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #4.2/C
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #5.2/C
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> show sel atoms
> ui tool show Contacts
> contacts intraModel false intraMol false ignoreHiddenModels true dashes 3
> radius 0.055
210 contacts
> interfaces select #9/A & ::polymer_type>0 contacting #4.1/B &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> interfaces select #10/A & ::polymer_type>0 contacting #4.1/B &
> ::polymer_type>0 areaCutoff 0
10 contacting residues
> hide #!9#!4.1-2#!5.1-2 cartoons
Drag select of 526 atoms, 535 bonds
> hide (#!5.2 & sel) target a
Drag select of 335 atoms, 307 bonds, 4 pseudobonds
> hide (#!9#!5.2 & sel) target a
Drag select of 1241 atoms, 1266 bonds
> hide (#!9#!5.2 & sel) target a
Drag select of 2503 atoms, 2553 bonds
> hide (#!9#!5.1-2 & sel) target a
> select clear
Drag select of 365 atoms, 355 bonds
> hide (#!5.1 & sel) target a
Drag select of 441 atoms, 431 bonds, 17 pseudobonds
Drag select of 479 atoms, 460 bonds, 23 pseudobonds
Drag select of 459 atoms, 443 bonds, 19 pseudobonds
Drag select of 270 atoms, 264 bonds, 2 pseudobonds
> select clear
Drag select of 305 atoms, 295 bonds
> select subtract #5.2/C:46@CB
304 atoms, 293 bonds, 50 residues, 4 models selected
> select subtract #5.2/C:46@CG
303 atoms, 292 bonds, 50 residues, 5 models selected
> select subtract #5.2/C:46@OD1
302 atoms, 292 bonds, 50 residues, 5 models selected
> select clear
Drag select of 175 atoms, 170 bonds
> hide (#!5.2 & sel) target a
Drag select of 50 atoms, 37 bonds
> hide (#!5.2 & sel) target a
Drag select of 32 atoms, 26 bonds
> hide (#!5.1-2 & sel) target a
Drag select of 65 atoms, 59 bonds
> hide (#!5.1-2 & sel) target a
Drag select of 11 atoms, 11 bonds
Drag select of 27 atoms, 23 bonds
> select clear
Drag select of 21 atoms, 18 bonds
Drag select of 7 atoms, 6 bonds
> hide (#!5.1 & sel) target a
Drag select of 87 atoms, 85 bonds
Drag select of 33 atoms, 29 bonds
Drag select of 31 atoms, 33 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 37 atoms, 31 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 26 atoms, 26 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 16 atoms, 14 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 27 atoms, 25 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 25 atoms, 24 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 10 atoms, 6 bonds
> hide (#!9#!5.1 & sel) target a
Drag select of 2 atoms
> hide (#!9#!5.1 & sel) target a
> select helix
8282 atoms, 8370 bonds, 986 residues, 12 models selected
> select clear
> show #!9#!4.1-2#!5.1-2 cartoons
> select #5.1/B:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.2/C:104
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (#!5.2 & sel) target ab
> label (#!5.2 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> select clear
> select #9/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #9/A:185
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #9/A:204
24 atoms, 22 bonds, 3 residues, 2 models selected
> label (#!9 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> select clear
> select #5.2/C:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> label (#!5.2 & sel) text "/{0.chain_id} {0.name}
> {0.number}{0.insertion_code}"
> select #5.2/C:43
7 atoms, 6 bonds, 1 residue, 1 model selected
> show (#!5.2 & sel) target ab
> select #9/A:200
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:199
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> color sel byhetero
> select clear
> hide #!9#!4.1-2#!5.1-2 cartoons
Drag select of 1 atoms
> hide (#!5.2 & sel) target a
Drag select of 1 atoms
> hide sel target a
Drag select of 1 atoms
> hide sel target a
Drag select of 1 atoms
> select clear
Drag select of 1 atoms
> hide (#!9 & sel) target a
Drag select of 2 atoms
> hide (#!9 & sel) target a
> select clear
Drag select of 5 atoms, 4 bonds
> hide sel target a
Drag select of 1 atoms
> hide sel target a
Drag select of 1 atoms
> hide (#!9 & sel) target a
Drag select of 7 atoms, 6 bonds
Drag select of 4 atoms, 2 bonds
> hide (#!5.1 & sel) target ab
Drag select of 2 atoms
> hide (#!5.1 & sel) target a
Drag select of 9 atoms, 10 bonds
> hide (#!9#!5.1 & sel) target a
> show sel cartoons
> select #10/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select #10/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> select #9/A
1607 atoms, 1641 bonds, 204 residues, 1 model selected
> show sel cartoons
> select clear
> select
19848 atoms, 20290 bonds, 212 pseudobonds, 2426 residues, 25 models selected
> show sel & #!9#!4.1-2#!5.1-2 cartoons
> select clear
> select add #5.1
2114 atoms, 2164 bonds, 259 residues, 2 models selected
> show #!1.1 models
> show #!1.2 models
> show #!2 models
> show #!2.1 models
> show #!2.2 models
> show #!3 models
> show #!3.1 models
> show #!3.2 models
> select clear
> show #!7 models
> show #!10 models
> hide #!7 models
Drag select of 94 residues
Drag select of 11 residues
> select clear
> ui tool show "Side View"
> help help:user/tools/sideview.html
Drag select of 2 residues
Drag select of 172 residues, 1 pseudobonds
> ui tool show "Side View"
> select clear
> ui tool show "Side View"
> ui autostart true "Side View"
> ui tool show "Side View"
Drag select of 47 residues
> show (#!1.1#!2.1#!3.1#!4.2#!5.2 & sel) target ab
> select clear
> ui tool show "Side View"
> hide #6 models
> show #6 models
> hide #6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> ui tool show "Side View"
> hide #!7 models
> ui tool show "Side View"
> select #4.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select #5.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select clear
> select #5.1/B
2114 atoms, 2164 bonds, 259 residues, 1 model selected
> select clear
> ui tool show "Side View"
Drag select of 121 atoms, 64 residues, 104 bonds
> style sel sphere
Changed 524 atom styles
> hide (#!2.1#!3.1#!4.1#!5.2 & sel) target a
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.1.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
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: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2,3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 3 days, 10 hours, 53 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
MT5531:
Resolution: 1360 x 768
UI Looks like: 1360 x 768 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7,55
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
ChimeraX-AddH: 2.2.4
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: 1.6rc202304150037
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: 2.7.1
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: 1.10.2
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: 6.4.1
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: 3.2.0
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: 6.2
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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