![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 2 years ago
#8875 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Opening and closing of "Visualize" in XMAS UI
Fatal Python error: Segmentation fault
Thread 0x000000031bb06000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031ab03000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000310eaf000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000002047f32c0 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.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" : 300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 49170,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-04-20 11:13:40.0347 +0800",
"incident" : "747CA9D7-5485-427D-BF90-81E9820C9434",
"pid" : 15844,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-04-19 14:19:50.4204 +0800",
"procStartAbsTime" : 6480459312661,
"procExitAbsTime" : 7244066229264,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"15477C43-E67C-53BA-A76B-21D43DBB4CAE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CE9BADAD-40EC-8646-A78D-263FEB67B985",
"throttleTimeout" : 2147483647,
"wakeTime" : 5645,
"sleepWakeUUID" : "22050C11-1564-4CBB-BC9E-A108107FEFFE",
"sip" : "enabled",
"vmRegionInfo" : "0x273dd984de08 is not in any region. Bytes after previous region: 42665559514633 Bytes before following region: 62406520414712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000273dd984de08","rawCodes":[1,43146595851784],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000273dd984de08"},
"vmregioninfo" : "0x273dd984de08 is not in any region. Bytes after previous region: 42665559514633 Bytes before following region: 62406520414712\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"size" : 4964352,
"uuid" : "f36760e5-d1e7-3a93-ae8c-1c3e55e3fc35",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5003345920,
"size" : 2801664,
"uuid" : "babd94e3-ec19-3110-ab5b-11c39432d8c5",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4946911232,
"size" : 5259264,
"uuid" : "35b47b1c-6952-3d39-a5e7-711f3ca228f2",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5084471296,
"size" : 655360,
"uuid" : "4bf756eb-ff87-3f7f-8c98-b1eda6463b81",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703273390080,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4816896,
"uuid" : "be859dcd-e5ee-3aab-97e4-13231468695f",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703439982592,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112958,
"uuid" : "7bf47984-29cb-319e-a6da-0884d158f96a",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703324549120,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16814067,
"uuid" : "540cedfd-5a35-3f35-8953-dcb7c4834eb5",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.40.118"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4513710080,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4369608704,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 4096,
"uuid" : "5df621ee-554e-36a8-b448-93b2334e5480",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 8664707072,
"size" : 622592,
"uuid" : "bba77709-6cad-3592-ab03-09d0f7b8610e",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 140703127437312,
"size" : 196608,
"uuid" : "f066db2c-ed38-3f37-8d21-81d15fa908fe",
"path" : "\/usr\/libexec\/rosetta\/runtime",
"name" : "runtime"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4608962560,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5234360320,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5222494208,
"size" : 147456,
"uuid" : "9a744198-7fb3-3c4f-b935-3646fa131615",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numexpr\/interpreter.cpython-39-darwin.so",
"name" : "interpreter.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 6109786112,
"size" : 63373312,
"uuid" : "ccf8b470-9ccf-3558-9748-04374e88d1ea",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5032435712,
"size" : 6979584,
"uuid" : "49d915f7-1c6d-3bbd-b96f-064260e7d998",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 960K 67 \nColorSync 248K 29 \nCoreAnimation 808K 92 \nCoreGraphics 24K 4 \nCoreServices 624K 2 \nCoreUI image data 1556K 22 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.8G 163 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 584.0M 8 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1740K 432 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1140K 114 \nRosetta Thread Context 1140K 114 \nSTACK GUARD 44K 11 \nStack 225.8M 58 \nStack Guard 56.2M 47 \nVM_ALLOCATE 164.4M 432 \nVM_ALLOCATE (reserved) 384.1M 16 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 52.3M 919 \n__DATA_CONST 40.2M 395 \n__DATA_DIRTY 1845K 231 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 219.7M 288 \n__OBJC_RO 65.4M 1 \n__OBJC_RW 1987K 2 \n__TEXT 1.0G 901 \ndyld private memory 768K 4 \nmapped file 4.7G 2134 \nshared memory 1004K 32 \nunshared pmap 14.4M 9 \n=========== ======= ======= \nTOTAL 9.4G 6566 \nTOTAL, minus reserved VM space 8.5G 6566 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs
Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
level 0.11, step 1, values float32
Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375,
step 1, values float32
Log from Wed Apr 19 14:11:57 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_MS_Wint/XMAS
> files/NS1-apoAI_models-forwint_forAlvin.cxs"
Log from Mon Apr 3 16:43:31 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Log from Mon Apr 3 15:19:20 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint.cxs
Log from Sat Apr 1 16:55:32 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Thu Mar 30 23:52:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab-
> ApoAI_Ab562_compare.cxs"
Opened sNS1wt-Ab562.mrc as #2, grid size 352,352,352, pixel 0.85, shown at
level 0.17, step 1, values float32
Opened sNS1wt-Fab562.mrc as #8, grid size 416,416,416, pixel 0.85, shown at
level 0.0754, step 1, values float32
Log from Sat Nov 19 10:30:44 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-
> ApoAI_hdl.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.17, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
416,416,416, pixel 0.85, shown at level 0.0687, step 1, values float32
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0754, step 1, values float32
Log from Thu Mar 24 12:02:48 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
> Fab-ApoAI_hdl.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Log from Sat Mar 12 14:58:51 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-
> Fab-ApoAI_hdl_Compare-NS1ts.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32
Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
416,416,416, pixel 0.858, shown at level 0.135, step 1, values float32
Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.79, shown at level 0.318, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Log from Fri Mar 11 18:14:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
> Fab-ApoAI_hdl.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.127, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.191, step 1, values float32
Log from Thu Mar 3 21:24:07 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
352,352,352, pixel 0.85, shown at level 0.0969, step 1, values float32
Log from Thu Mar 3 19:50:19 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab5-DL.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.05, step 1, values float32
Log from Thu Mar 3 12:01:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\dahailuo\\\OneDrive - Nanyang Technological
> University\\\Temporal\\\202112_FlaviNS1\\\Data_EM_Alvin\\\20220302_D2NS1ts-
> Ab56-apoa1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:18:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220302_D2NS1ts-
> Ab56-apoa1.cxs" format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:08:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 22:03:06 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56-AA1.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 21:54:19 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.421, step 2, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at level 0.471, step 1, values float32
Log from Tue Feb 22 21:05:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J91_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J91_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0468, step 2, values float32
> surface dust #1 size 8.58
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #2, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.58
> close #2
> close #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J20_004_volume_map_sharp.mrc"
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/D2NS1.pdb"
Summary of feedback from opening D:/OneDrive - Nanyang Technological
University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
sNS1-Fab56-2/D2NS1.pdb
---
warning | Ignored bad PDB record found on line 5732
END
Chain information for D2NS1.pdb #3
---
Chain | Description
B C | No description available
> hide #!2 models
> volume #1 level 0.07524
> volume #1 level 0.07
> volume #1 level 0.072
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.89628,-0.44038,-0.052381,101.61,0.096778,0.078954,0.99217,-38.919,-0.43279,-0.89433,0.11338,384.44
> view matrix models
> #3,0.99109,-0.12056,-0.056551,31.91,0.0080432,0.4781,-0.87827,242.8,0.13292,0.86999,0.47482,-76.088
> view matrix models
> #3,0.79841,-0.57175,0.18879,97.95,-0.1953,0.050686,0.97943,19.471,-0.56956,-0.81886,-0.071196,428.68
> view matrix models
> #3,0.82022,-0.53629,0.19907,86.322,-0.4792,-0.8342,-0.2729,441.29,0.31242,0.12845,-0.94122,269.29
> view matrix models
> #3,0.33094,0.34033,0.88014,-96.351,-0.87516,0.45954,0.15137,217.82,-0.35295,-0.82036,0.44993,298
> view matrix models
> #3,0.12486,-0.10929,0.98614,-3.3941,-0.98525,0.10355,0.13622,299.73,-0.117,-0.9886,-0.094748,381.83
> view matrix models
> #3,-0.013734,0.34293,0.93926,-46.701,0.87722,0.45496,-0.15328,-35.332,-0.47989,0.82183,-0.30707,179.08
> view matrix models
> #3,-0.024741,-0.048477,0.99852,10.486,0.22627,0.97263,0.052827,-44.605,-0.97375,0.22725,-0.013095,313.53
> view matrix models
> #3,0.22803,-0.14862,0.96224,-10.67,-0.86757,-0.4796,0.13152,377.92,0.44195,-0.86481,-0.23831,288.28
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.594,-0.90644,0.38234,-0.1794,295.23,-0.4125,-0.89262,0.18187,368.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.895,-0.90644,0.38234,-0.1794,305.2,-0.4125,-0.89262,0.18187,368.62
> view matrix models
> #3,-0.090598,0.23885,0.96682,-18.453,-0.90644,0.38234,-0.1794,307.34,-0.4125,-0.89262,0.18187,380.09
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 72
shifted from previous position = 2.04
rotated from previous position = 4.6 degrees
atoms outside contour = 3319, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06802577 0.24460859 0.96723274 -24.08767794
-0.87342564 0.45395004 -0.17623011 287.61942533
-0.48218273 -0.85679405 0.18276711 387.90605974
Axis -0.34848182 0.74217118 -0.57248788
Axis point 265.32854097 -0.00000000 317.95880744
Rotation angle (degrees) 102.45391693
Shift along axis -0.21455122
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.017 degrees
atoms outside contour = 3323, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800908 0.24437415 0.96729317 -24.07786550
-0.87335170 0.45412951 -0.17613415 287.55836847
-0.48231900 -0.85676584 0.18253965 387.96533381
Axis -0.34851775 0.74227452 -0.57233199
Axis point 265.31869899 0.00000000 317.91033718
Rotation angle (degrees) 102.45483514
Shift along axis -0.20615891
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 44
shifted from previous position = 0.00415
rotated from previous position = 0.0128 degrees
atoms outside contour = 3322, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06778785 0.24439903 0.96730241 -24.12733834
-0.87337367 0.45415748 -0.17595301 287.52563608
-0.48231036 -0.85674392 0.18266531 387.93712068
Axis -0.34858450 0.74224338 -0.57233173
Axis point 265.33740374 0.00000000 317.91776063
Rotation angle (degrees) 102.44383763
Shift along axis -0.20430725
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.013 degrees
atoms outside contour = 3321, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06797653 0.24451862 0.96725895 -24.09141306
-0.87335854 0.45410159 -0.17617224 287.57257739
-0.48231121 -0.85673942 0.18268417 387.93432608
Axis -0.34847884 0.74224049 -0.57239982
Axis point 265.31882258 -0.00000000 317.92823841
Rotation angle (degrees) 102.45045928
Shift along axis -0.21017795
> transparency #1.1 50
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/F562a.pdb"
Chain information for F562a.pdb #4
---
Chain | Description
B | No description available
C | No description available
> ui tool show "Color Actions"
> color sel bychain
> color sel bychain
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> color sel bychain
> color sel bychain
> color sel bychain
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/7bsc_DEN2 NS1c.pdb"
7bsc_DEN2 NS1c.pdb title:
Complex structure of 1G5.3 fab bound to DENV2 NS1C [more info...]
Chain information for 7bsc_DEN2 NS1c.pdb #5
---
Chain | Description
A | non-structural protein 1
H | 1G5.3 fab heavy chain
L | 1G5.3 fab light chain
> mmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with 7bsc_DEN2 NS1c.pdb, chain A (#5),
sequence alignment score = 896.9
RMSD between 162 pruned atom pairs is 0.535 angstroms; (across all 177 pairs:
2.714)
> mmaker #4 to #5
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 7bsc_DEN2 NS1c.pdb, chain H (#5) with F562a.pdb, chain B (#4),
sequence alignment score = 1028.9
RMSD between 105 pruned atom pairs is 0.627 angstroms; (across all 215 pairs:
11.308)
> ~select #4
Nothing selected
> hide #!5 models
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #4,0.59089,-0.15644,-0.79144,253.32,0.26071,0.96541,0.0038114,-36.876,0.76347,-0.20859,0.61123,8.3612
> view matrix models
> #4,0.59089,-0.15644,-0.79144,249.54,0.26071,0.96541,0.0038114,-38.171,0.76347,-0.20859,0.61123,-6.5674
> view matrix models
> #4,0.59089,-0.15644,-0.79144,250.18,0.26071,0.96541,0.0038114,-52.258,0.76347,-0.20859,0.61123,-8.7931
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.08302, steps = 284
shifted from previous position = 3.86
rotated from previous position = 9.32 degrees
atoms outside contour = 2026, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.70756240 -0.18104725 -0.68306467 216.74116501
0.24257753 0.97011437 -0.00585274 -48.06381473
0.66371047 -0.16155497 0.73033445 -11.10097449
Axis -0.10961944 -0.94817357 0.29824565
Axis point 132.17662306 0.00000000 263.68811665
Rotation angle (degrees) 45.25073566
Shift along axis 18.50297639
> transparency #1.1 0
> view matrix models
> #4,0.70756,-0.18105,-0.68306,218.9,0.24258,0.97011,-0.0058527,-47.556,0.66371,-0.16155,0.73033,-11.137
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.60929,0.056492,-0.79093,206.86,0.79214,-0.088481,0.60389,-30.096,-0.035867,-0.99447,-0.09866,369.53
> view matrix models
> #4,0.13536,-0.077461,-0.98776,343.37,0.97999,0.15727,0.12197,-53.095,0.1459,-0.98451,0.097201,310.49
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 96
shifted from previous position = 8.35
rotated from previous position = 5.73 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18515527 -0.12030538 -0.97531746 334.84540290
0.98054878 0.08839233 0.17524520 -44.47549541
0.06512764 -0.98879392 0.13433160 327.48525231
Axis -0.60933659 -0.54463915 0.57626133
Axis point 0.00000000 23.05515362 346.04002443
Rotation angle (degrees) 107.22113422
Shift along axis 8.90662490
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 28
shifted from previous position = 0.017
rotated from previous position = 0.0169 degrees
atoms outside contour = 1608, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18543237 -0.12023134 -0.97527394 334.76776945
0.98049261 0.08847529 0.17551742 -44.49851310
0.06518495 -0.98879550 0.13429212 327.47372226
Axis -0.60944823 -0.54461805 0.57616320
Axis point 0.00000000 23.10963968 345.96113737
Rotation angle (degrees) 107.21151966
Shift along axis 8.88937821
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 44
shifted from previous position = 0.0205
rotated from previous position = 0.0218 degrees
atoms outside contour = 1604, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18554107 -0.12011878 -0.97526714 334.73699226
0.98049338 0.08814571 0.17567888 -44.47566373
0.06486328 -0.98883862 0.13413032 327.56427605
Axis -0.60959315 -0.54447990 0.57614045
Axis point 0.00000000 23.17721063 345.92539580
Rotation angle (degrees) 107.22299700
Shift along axis 8.88575635
> transparency #1.1 50
> view matrix models
> #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104
> view matrix models
> #4,0.75847,0.64831,0.066474,-35.582,0.26049,-0.20809,-0.94278,276.59,-0.59738,0.73239,-0.32671,193.1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09049, steps = 88
shifted from previous position = 2.42
rotated from previous position = 6.19 degrees
atoms outside contour = 1911, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72637414 0.68694818 -0.02197301 -24.03798979
0.18664733 -0.22792648 -0.95562142 294.38643021
-0.66147062 0.69003748 -0.29377694 209.53189487
Axis 0.89678670 0.34848835 -0.27263435
Axis point 0.00000000 72.78629578 205.81231454
Rotation angle (degrees) 113.43226483
Shift along axis 23.90769923
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0905, steps = 44
shifted from previous position = 0.0137
rotated from previous position = 0.0204 degrees
atoms outside contour = 1906, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72623985 0.68709241 -0.02190190 -24.03578291
0.18654834 -0.22764140 -0.95570869 294.36480593
-0.66164597 0.68998798 -0.29349821 209.53312556
Axis 0.89671635 0.34858730 -0.27273923
Axis point 0.00000000 72.74870511 205.83733915
Rotation angle (degrees) 113.41885466
Shift along axis 23.91065009
> view matrix models
> #4,0.4777,0.81916,-0.31746,33.473,0.28288,-0.48553,-0.82719,308.03,-0.83173,0.30535,-0.46366,331.51
> view matrix models
> #4,0.53443,0.7221,-0.43927,54.882,0.15416,-0.59427,-0.78935,347.48,-0.83104,0.35413,-0.42891,318.4
> view matrix models
> #4,0.55861,0.65321,-0.51116,71.372,0.070767,-0.65156,-0.75529,369.52,-0.82641,0.38574,-0.41019,309.57
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 104
shifted from previous position = 3.1
rotated from previous position = 2.07 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58731938 0.63730986 -0.49889086 69.51709433
0.06189895 -0.64996950 -0.75743526 371.85473470
-0.80698480 0.41397558 -0.42118849 304.38816914
Axis 0.87354940 0.22975311 -0.42909784
Axis point 0.00000000 108.25389938 250.40641939
Rotation angle (degrees) 137.89516888
Shift along axis 15.54909083
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 100
shifted from previous position = 0.0102
rotated from previous position = 0.0178 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58732049 0.63712467 -0.49912604 69.58840441
0.06165901 -0.65012663 -0.75731997 371.91413492
-0.80700236 0.41401391 -0.42111716 304.37603978
Axis 0.87355306 0.22960687 -0.42916866
Axis point 0.00000000 108.28874120 250.42594564
Rotation angle (degrees) 137.89878759
Shift along axis 15.55454641
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 84
shifted from previous position = 0.011
rotated from previous position = 0.0172 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58733885 0.63729229 -0.49889038 69.51578518
0.06188954 -0.64997620 -0.75743028 371.85701767
-0.80697135 0.41399213 -0.42119800 304.38350057
Axis 0.87355567 0.22974281 -0.42909059
Axis point 0.00000000 108.25696578 250.40359329
Rotation angle (degrees) 137.89502914
Shift along axis 15.54928904
> view matrix models
> #4,0.65819,-0.32045,-0.68124,252,0.74547,0.15105,0.6492,-68.256,-0.10513,-0.93515,0.3383,328.44
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.102, steps = 172
shifted from previous position = 4.22
rotated from previous position = 10.1 degrees
atoms outside contour = 1745, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62980729 -0.32213914 -0.70680207 259.21419516
0.77615676 0.29659722 0.55642680 -86.34491343
0.03038868 -0.89903085 0.43682956 282.25072430
Axis -0.74003611 -0.37482903 0.55843509
Axis point 0.00000000 121.16366768 309.58820660
Rotation angle (degrees) 79.53603811
Shift along axis -1.84457671
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0802
rotated from previous position = 0.389 degrees
atoms outside contour = 1748, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62493642 -0.32416938 -0.71018919 260.92042942
0.78000765 0.29690303 0.55085085 -86.37873091
0.03228835 -0.89819976 0.43840012 281.55642716
Axis -0.73657217 -0.37741145 0.56126823
Axis point 0.00000000 119.97837519 311.01534570
Rotation angle (degrees) 79.62326298
Shift along axis -1.55772605
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 44
shifted from previous position = 0.00561
rotated from previous position = 0.0322 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62451536 -0.32441238 -0.71044858 261.07250560
0.78034368 0.29682398 0.55041736 -86.36985039
0.03231597 -0.89813815 0.43852428 281.52393140
Axis -0.73629476 -0.37754414 0.56154292
Axis point 0.00000000 119.89834457 311.14057931
Rotation angle (degrees) 79.63421202
Shift along axis -1.53011648
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 80
shifted from previous position = 0.189
rotated from previous position = 1.07 degrees
atoms outside contour = 1750, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61106207 -0.33151468 -0.71881930 265.86650256
0.79073980 0.29753498 0.53497991 -86.41685086
0.03652019 -0.89530496 0.44395419 279.51480621
Axis -0.72651910 -0.38367781 0.57005380
Axis point 0.00000000 116.77430340 315.34054751
Rotation angle (degrees) 79.84710044
Shift along axis -0.66238880
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.014
rotated from previous position = 0.0403 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61056528 -0.33194773 -0.71904155 266.05161554
0.79112724 0.29741686 0.53447255 -86.39981112
0.03643813 -0.89518374 0.44420530 279.47442312
Axis -0.72617579 -0.38373633 0.57045170
Axis point 0.00000000 116.70216550 315.50779421
Rotation angle (degrees) 79.85768786
Shift along axis -0.61883651
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 56
shifted from previous position = 0.00922
rotated from previous position = 0.0302 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61096453 -0.33178461 -0.71877766 265.91505542
0.79082389 0.29745317 0.53490111 -86.40973158
0.03633074 -0.89523215 0.44411653 279.51627475
Axis -0.72644097 -0.38355984 0.57023274
Axis point -0.00000000 116.79213793 315.39803173
Rotation angle (degrees) 79.84759520
Shift along axis -0.63895706
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.0112
rotated from previous position = 0.0392 degrees
atoms outside contour = 1755, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61092141 -0.33119723 -0.71908514 265.86201413
0.79084444 0.29729954 0.53495614 -86.39268360
0.03660768 -0.89550063 0.44355214 279.58799940
Axis -0.72655505 -0.38383015 0.56990540
Axis point 0.00000000 116.72048670 315.29183470
Rotation angle (degrees) 79.86974659
Shift along axis -0.66456157
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0779 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61046660 -0.33218219 -0.71901706 266.11491018
0.79119095 0.29782655 0.53415002 -86.45092816
0.03670725 -0.89496053 0.44463270 279.33262127
Axis -0.72594735 -0.38388637 0.57064148
Axis point 0.00000000 116.64464322 315.61501173
Rotation angle (degrees) 79.83619740
Shift along axis -0.59930216
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 36
shifted from previous position = 0.00553
rotated from previous position = 0.0185 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61052405 -0.33197184 -0.71906543 266.07628678
0.79114928 0.29764543 0.53431266 -86.42628442
0.03664978 -0.89509882 0.44435898 279.40085187
Axis -0.72607396 -0.38386786 0.57049283
Axis point 0.00000000 116.66062451 315.54721201
Rotation angle (degrees) 79.84776315
Shift along axis -0.61860883
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0181
rotated from previous position = 0.0284 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61082613 -0.33169276 -0.71893766 265.95113585
0.79091989 0.29755592 0.53470198 -86.43037190
0.03656738 -0.89523203 0.44409733 279.47798684
Axis -0.72633614 -0.38375939 0.57023200
Axis point -0.00000000 116.71858763 315.43181746
Rotation angle (degrees) 79.84919126
Shift along axis -0.63416214
> view matrix models
> #4,0.4439,-0.28201,-0.85054,303.77,0.88884,0.018251,0.45784,-44.907,-0.11359,-0.95924,0.25876,341.18
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 424
shifted from previous position = 2.2
rotated from previous position = 6.39 degrees
atoms outside contour = 1635, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47014986 -0.27680804 -0.83805515 296.29282889
0.88242695 0.12936746 0.45231266 -60.98673857
-0.01678672 -0.95217718 0.30508496 317.15529629
Axis -0.70304515 -0.41110215 0.58027799
Axis point 0.00000000 97.60706796 321.98215187
Rotation angle (degrees) 92.73398070
Shift along axis 0.80277942
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 44
shifted from previous position = 0.0281
rotated from previous position = 0.296 degrees
atoms outside contour = 1634, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47131282 -0.27849458 -0.83684228 296.21168106
0.88186020 0.13410185 0.45203904 -61.71403302
-0.01366832 -0.95102969 0.30879721 315.93242787
Axis -0.70218063 -0.41196614 0.58071186
Axis point 0.00000000 97.40904882 322.29816415
Rotation angle (degrees) 92.45840264
Shift along axis 0.89569574
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.16 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47202347 -0.27915399 -0.83622180 296.12646474
0.88150690 0.13674791 0.45193539 -62.12511633
-0.01180798 -0.95045940 0.31062439 315.27843547
Axis -0.70176755 -0.41254208 0.58080232
Axis point 0.00000000 97.28028496 322.43137386
Rotation angle (degrees) 92.30976635
Shift along axis 0.93172962
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.193 degrees
atoms outside contour = 1638, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47308077 -0.28050864 -0.83517034 296.03384583
0.88096007 0.13964438 0.45211592 -62.58112928
-0.01019558 -0.94963907 0.31317998 314.52160203
Axis -0.70135897 -0.41277074 0.58113330
Axis point 0.00000000 97.26838533 322.61659552
Rotation angle (degrees) 92.12314752
Shift along axis 0.98464198
> transparency #1.1 0
> view matrix models
> #4,0.84021,-0.0035817,-0.54224,142.19,-0.39021,0.69038,-0.60919,201.03,0.37654,0.72344,0.57867,-93.731
> view matrix models
> #4,0.79315,-0.11192,-0.59866,177.39,0.50761,-0.42168,0.75135,74.2,-0.33653,-0.89981,-0.27764,436.47
> view matrix models
> #4,0.7358,0.3335,-0.58938,106.02,-0.64815,0.094684,-0.7556,375.07,-0.19619,0.93798,0.28583,9.2542
> view matrix models
> #4,0.79115,-0.59673,-0.13416,211.08,0.60994,0.75351,0.24535,-98.992,-0.045318,-0.27593,0.96011,122.12
> view matrix models
> #4,0.66555,-0.4336,-0.60749,260.88,0.69641,0.65352,0.29652,-103.07,0.26843,-0.62041,0.73691,152.31
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 416
shifted from previous position = 2.7
rotated from previous position = 17.5 degrees
atoms outside contour = 1774, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67732915 -0.28469604 -0.67836083 239.91883502
0.71088577 0.49065254 0.50388643 -103.74543128
0.18938499 -0.82353401 0.53471962 227.48787848
Axis -0.70890735 -0.46341865 0.53168931
Axis point 0.00000000 101.86597662 309.82596584
Rotation angle (degrees) 69.43005060
Shift along axis -1.04978373
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 44
shifted from previous position = 0.00594
rotated from previous position = 0.0194 degrees
atoms outside contour = 1776, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67756361 -0.28454385 -0.67819052 239.83133941
0.71064745 0.49081816 0.50406126 -103.75597407
0.18944069 -0.82348792 0.53477088 227.46549023
Axis -0.70904026 -0.46339937 0.53152886
Axis point 0.00000000 101.90886125 309.76335536
Rotation angle (degrees) 69.41623953
Shift along axis -1.06514982
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09997, steps = 40
shifted from previous position = 0.0133
rotated from previous position = 0.00996 degrees
atoms outside contour = 1778, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67763562 -0.28462709 -0.67808363 239.81516361
0.71058849 0.49090368 0.50406111 -103.75178064
0.18940430 -0.82340817 0.53490655 227.43306000
Axis -0.70903930 -0.46335011 0.53157309
Axis point 0.00000000 101.93201901 309.76345143
Rotation angle (degrees) 69.40726713
Shift along axis -1.06768104
> view matrix models
> #4,0.67386,0.21665,-0.70638,152.68,-0.73712,0.13162,-0.66282,370.99,-0.050625,0.96733,0.2484,-19.457
> view matrix models
> #4,0.26977,0.74198,-0.61375,121.96,-0.64983,-0.33008,-0.68467,441.19,-0.7106,0.58353,0.39312,157.04
> view matrix models
> #4,0.83537,0.35405,-0.42048,63.612,-0.53507,0.34852,-0.76957,306.25,-0.12592,0.86786,0.48059,-14.673
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 108
shifted from previous position = 1.02
rotated from previous position = 11.1 degrees
atoms outside contour = 1639, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88907475 0.29063713 -0.35366111 56.95234558
-0.45699328 0.51877555 -0.72251581 256.52548266
-0.02651919 0.80399130 0.59404945 -35.16228912
Axis 0.88188843 -0.18899530 -0.43191847
Axis point 0.00000000 161.74872048 251.74241852
Rotation angle (degrees) 59.93713751
Shift along axis 16.93074519
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 44
shifted from previous position = 0.0122
rotated from previous position = 0.077 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88924092 0.29042756 -0.35341541 56.93133633
-0.45670512 0.51991995 -0.72187513 256.18534624
-0.02590471 0.80332752 0.59497383 -35.27785394
Axis 0.88179482 -0.18935008 -0.43195422
Axis point -0.00000000 161.74523741 251.76190662
Rotation angle (degrees) 59.86313127
Shift along axis 16.93146051
> view matrix models
> #4,0.83879,0.21495,-0.50022,97.467,-0.52296,0.062549,-0.85006,366.96,-0.15144,0.97462,0.16488,7.9202
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1097, steps = 264
shifted from previous position = 0.803
rotated from previous position = 13.4 degrees
atoms outside contour = 1566, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.90125965 0.23249395 -0.36561951 66.81826163
-0.42074684 0.26813163 -0.86664730 312.38684742
-0.10345610 0.93490749 0.33947732 -14.03685609
Axis 0.93143071 -0.13554240 -0.33773523
Axis point 0.00000000 165.03559591 224.93775063
Rotation angle (degrees) 75.25993272
Shift along axis 24.63566001
> view matrix models
> #4,0.85035,0.35218,-0.39099,57.593,-0.48265,0.22596,-0.84616,329.25,-0.20965,0.90825,0.36212,8.0544
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85035,0.35218,-0.39099,60.231,-0.48265,0.22596,-0.84616,326.26,-0.20965,0.90825,0.36212,12.759
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 168
shifted from previous position = 2.33
rotated from previous position = 5.98 degrees
atoms outside contour = 1596, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88028089 0.25385290 -0.40082949 74.19694561
-0.45618497 0.22068248 -0.86208731 322.45385437
-0.13038732 0.94173137 0.31006645 -3.17418883
Axis 0.92158142 -0.13817047 -0.36276246
Axis point 0.00000000 162.85511452 230.82234394
Rotation angle (degrees) 78.14035717
Shift along axis 24.97640109
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.011
rotated from previous position = 0.0221 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88011312 0.25412437 -0.40102585 74.19170998
-0.45646647 0.22069435 -0.86193525 322.48434036
-0.13053461 0.94165537 0.31023525 -3.15440043
Axis 0.92146618 -0.13819573 -0.36304548
Axis point 0.00000000 162.86097718 230.89097488
Rotation angle (degrees) 78.13997962
Shift along axis 24.94438268
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.00421
rotated from previous position = 0.0136 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88018838 0.25419012 -0.40081894 74.13944294
-0.45629950 0.22079847 -0.86199700 322.44263683
-0.13061091 0.94161321 0.31033107 -3.14778151
Axis 0.92150340 -0.13805512 -0.36300449
Axis point 0.00000000 162.82540766 230.87431985
Rotation angle (degrees) 78.13192347
Shift along axis 24.94755119
> view matrix models
> #4,0.88019,0.25419,-0.40082,73.448,-0.4563,0.2208,-0.862,321.07,-0.13061,0.94161,0.31033,-5.8994
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 160
shifted from previous position = 2.99
rotated from previous position = 8.44 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327534 0.17162879 -0.45599755 97.28727310
-0.48720393 0.31672140 -0.81383039 304.58441441
0.00474745 0.93286180 0.36020320 -32.68286674
Axis 0.90839597 -0.23961801 -0.34263678
Axis point 0.00000000 182.33141527 229.00675692
Rotation angle (degrees) 74.03202850
Shift along axis 26.58980844
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 80
shifted from previous position = 0.0187
rotated from previous position = 0.0503 degrees
atoms outside contour = 1606, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307788 0.17102576 -0.45660182 97.51562460
-0.48755025 0.31670719 -0.81362849 304.62173537
0.00545764 0.93297736 0.35989370 -32.78455753
Axis 0.90828067 -0.24028299 -0.34247673
Axis point 0.00000000 182.48861826 229.00019788
Rotation angle (degrees) 74.04755731
Shift along axis 26.60408358
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 64
shifted from previous position = 0.00983
rotated from previous position = 0.00562 degrees
atoms outside contour = 1605, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87308357 0.17093159 -0.45662622 97.52642834
-0.48753906 0.31671935 -0.81363046 304.61327140
0.00554721 0.93299049 0.35985828 -32.79571036
Axis 0.90828615 -0.24034163 -0.34242104
Axis point 0.00000000 182.49871036 228.98437979
Rotation angle (degrees) 74.04808080
Shift along axis 26.60059602
> ui mousemode right "rotate selected models"
> transparency #1.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.87308,0.17093,-0.45663,98.781,-0.48754,0.31672,-0.81363,307.95,0.0055472,0.93299,0.35986,-31.624
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 152
shifted from previous position = 1.66
rotated from previous position = 10.1 degrees
atoms outside contour = 1670, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85430945 0.22816829 -0.46700601 94.00588935
-0.50530889 0.15416741 -0.84905556 345.08239658
-0.12173045 0.96133847 0.24700214 -1.12292161
Axis 0.91267386 -0.17406375 -0.36976782
Axis point 0.00000000 176.18270876 236.27702715
Rotation angle (degrees) 82.66101368
Shift along axis 26.14560144
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 60
shifted from previous position = 0.00837
rotated from previous position = 0.0183 degrees
atoms outside contour = 1667, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85416080 0.22824487 -0.46724044 94.04888675
-0.50553655 0.15397090 -0.84895570 345.14108146
-0.12182835 0.96135179 0.24690203 -1.09962552
Axis 0.91260386 -0.17412755 -0.36991051
Axis point 0.00000000 176.20594034 236.31033169
Rotation angle (degrees) 82.67387511
Shift along axis 26.13756946
> view matrix models
> #4,0.85416,0.22824,-0.46724,92.304,-0.50554,0.15397,-0.84896,343.85,-0.12183,0.96135,0.2469,-1.3966
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 132
shifted from previous position = 2.46
rotated from previous position = 10.1 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327321 0.17148581 -0.45605541 97.32164807
-0.48720576 0.31684479 -0.81378127 304.55640572
0.00494684 0.93284619 0.36024093 -32.71905415
Axis 0.90838381 -0.23975747 -0.34257148
Axis point 0.00000000 182.35784967 228.99751317
Rotation angle (degrees) 74.02729082
Shift along axis 26.59434986
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0199
rotated from previous position = 0.0492 degrees
atoms outside contour = 1607, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87291436 0.17135958 -0.45678926 97.50396396
-0.48784609 0.31650499 -0.81352984 304.69020219
0.00516995 0.93298473 0.35987885 -32.73221582
Axis 0.90818184 -0.24021727 -0.34278478
Axis point 0.00000000 182.47945606 229.06508608
Rotation angle (degrees) 74.05889597
Shift along axis 26.57958591
> volume #1 step 1
> volume #1 level 0.08
> volume #2 step 1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 96
shifted from previous position = 0.0269
rotated from previous position = 0.0588 degrees
atoms outside contour = 1705, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87339018 0.17133657 -0.45588748 97.30726750
-0.48699588 0.31678456 -0.81393032 304.55388891
0.00496208 0.93289407 0.36011672 -32.71648369
Axis 0.90847710 -0.23967565 -0.34238127
Axis point 0.00000000 182.34480224 228.95151912
Rotation angle (degrees) 74.02930115
Shift along axis 26.60878416
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 60
shifted from previous position = 0.0234
rotated from previous position = 0.0504 degrees
atoms outside contour = 1711, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307658 0.17097372 -0.45662380 97.51998587
-0.48755237 0.31664803 -0.81365025 304.63116274
0.00547621 0.93300698 0.35981662 -32.78056504
Axis 0.90828882 -0.24029916 -0.34244377
Axis point 0.00000000 182.49216804 228.98849803
Rotation angle (degrees) 74.05165523
Shift along axis 26.59919907
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 84
shifted from previous position = 0.0236
rotated from previous position = 0.0512 degrees
atoms outside contour = 1709, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87330072 0.17150987 -0.45599367 97.31366850
-0.48715626 0.31696366 -0.81376461 304.52650710
0.00496476 0.93280138 0.36035670 -32.73218629
Axis 0.90838730 -0.23974404 -0.34257162
Axis point 0.00000000 182.35082823 229.00016180
Rotation angle (degrees) 74.01947881
Shift along axis 26.60320358
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0146 degrees
atoms outside contour = 3383, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06781116 0.24433459 0.96731706 -24.10970616
-0.87336663 0.45417416 -0.17594486 287.52120019
-0.48231982 -0.85675345 0.18259559 387.95373087
Axis -0.34859656 0.74226213 -0.57230007
Axis point 265.34079550 0.00000000 317.90521257
Rotation angle (degrees) 102.44607735
Shift along axis -0.20528738
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 40
shifted from previous position = 0.00617
rotated from previous position = 0.0174 degrees
atoms outside contour = 3388, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800223 0.24456045 0.96724657 -24.09574276
-0.87334229 0.45411451 -0.17621946 287.57652794
-0.48233700 -0.85672063 0.18270418 387.93151574
Axis -0.34844475 0.74224675 -0.57241245
Axis point 265.30857487 0.00000000 317.93174566
Rotation angle (degrees) 102.45024724
Shift along axis -0.20805003
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.8783,0.21948,-0.42476,83.959,-0.47606,0.31931,-0.81939,302.68,-0.044211,0.92188,0.38494,-24.427
> view matrix models
> #4,0.88185,0.18737,-0.43271,90.075,-0.47057,0.40846,-0.78213,281.03,0.030198,0.89334,0.44837,-40.684
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 108
shifted from previous position = 0.192
rotated from previous position = 5.8 degrees
atoms outside contour = 1706, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87316782 0.17153805 -0.45623751 97.35347505
-0.48739404 0.31688450 -0.81365305 304.56284709
0.00500214 0.93282310 0.36029997 -32.73417130
Axis 0.90830421 -0.23988070 -0.34269623
Axis point 0.00000000 182.38522859 229.02890887
Rotation angle (degrees) 74.02748836
Shift along axis 26.58569939
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0157
rotated from previous position = 0.0308 degrees
atoms outside contour = 1714, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87319228 0.17106442 -0.45636852 97.46138911
-0.48734683 0.31669009 -0.81375701 304.60534678
0.00532251 0.93297608 0.35989904 -32.76360108
Axis 0.90836070 -0.24009506 -0.34239627
Axis point 0.00000000 182.44525999 228.97324319
Rotation angle (degrees) 74.04449916
Shift along axis 26.61399150
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 76
shifted from previous position = 0.0215
rotated from previous position = 0.0496 degrees
atoms outside contour = 1707, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87344661 0.17154945 -0.45569927 97.23463453
-0.48689717 0.31676739 -0.81399606 304.54231699
0.00471009 0.93286078 0.36020634 -32.68225206
Axis 0.90851141 -0.23945131 -0.34244721
Axis point 0.00000000 182.29150588 228.95203805
Rotation angle (degrees) 74.02546087
Shift along axis 26.60766517
> close #5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb"
Chain information for F562b.pdb #5
---
Chain | Description
B | No description available
C | No description available
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,0.88246,-0.46571,0.066244,91.139,0.4452,0.87234,0.20206,-101.84,-0.15189,-0.14881,0.97713,59.494
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.88246,-0.46571,0.066244,31.321,0.4452,0.87234,0.20206,-110.9,-0.15189,-0.14881,0.97713,2.868
> view matrix models
> #5,0.88246,-0.46571,0.066244,29.937,0.4452,0.87234,0.20206,-111.7,-0.15189,-0.14881,0.97713,-4.3706
> view matrix models
> #5,0.91945,-0.24365,-0.30863,71.496,-0.34812,-0.86933,-0.35081,481.22,-0.18283,0.42999,-0.88413,336.53
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1014, steps = 252
shifted from previous position = 4.97
rotated from previous position = 12.4 degrees
atoms outside contour = 1810, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96186420 -0.19777272 -0.18895294 31.32789418
-0.26901427 -0.80896731 -0.52268846 497.86596548
-0.04948323 0.55358635 -0.83132038 280.55853441
Axis 0.98957826 -0.12823509 -0.06550286
Axis point 0.00000000 209.55045747 214.71270936
Rotation angle (degrees) 147.05697484
Shift along axis -51.21986933
> view matrix models
> #5,0.96186,-0.19777,-0.18895,31.586,-0.26901,-0.80897,-0.52269,497.84,-0.049483,0.55359,-0.83132,280.45
> view matrix models
> #5,0.96186,-0.19777,-0.18895,30.409,-0.26901,-0.80897,-0.52269,498.49,-0.049483,0.55359,-0.83132,281.14
> view matrix models
> #5,0.88111,-0.30725,-0.35949,105.37,-0.46365,-0.71093,-0.52878,515.6,-0.093104,0.63259,-0.76887,259.2
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 3.4
rotated from previous position = 5.08 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88807867 -0.23238898 -0.39662534 101.69393944
-0.43540490 -0.70196949 -0.56361460 519.59851714
-0.14744106 0.67322671 -0.72458742 250.51818794
Axis 0.96785351 -0.19499177 -0.15886409
Axis point 0.00000000 224.56879044 228.99496698
Rotation angle (degrees) 140.28561169
Shift along axis -42.69094177
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 0.0823 degrees
atoms outside contour = 1771, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88749875 -0.23316934 -0.39746451 102.13143422
-0.43663025 -0.70123937 -0.56357554 519.69347155
-0.14730923 0.67371761 -0.72415784 250.30786189
Axis 0.96767878 -0.19564479 -0.15912543
Axis point 0.00000000 224.69705024 229.03906748
Rotation angle (degrees) 140.25962425
Shift along axis -42.67524524
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0089
rotated from previous position = 0.0313 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88726809 -0.23348649 -0.39779316 102.30830437
-0.43710961 -0.70099140 -0.56351243 519.72597500
-0.14727705 0.67386581 -0.72402648 250.24321586
Axis 0.96761002 -0.19589960 -0.15923003
Axis point 0.00000000 224.74651301 229.05595353
Rotation angle (degrees) 140.25296234
Shift along axis -42.66580653
> view matrix models
> #5,0.90434,-0.19289,-0.38074,87.744,-0.3816,-0.76498,-0.51883,511.31,-0.19118,0.61449,-0.76541,278.75
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 100
shifted from previous position = 0.228
rotated from previous position = 5.49 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88741151 -0.23323538 -0.39762052 102.19303295
-0.43675670 -0.70132020 -0.56337694 519.68635289
-0.14745987 0.67361061 -0.72422672 250.37123988
Axis 0.96765550 -0.19569262 -0.15920817
Axis point 0.00000000 224.70331960 229.05340664
Rotation angle (degrees) 140.27024302
Shift along axis -42.67227987
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 0.0119
rotated from previous position = 0.0244 degrees
atoms outside contour = 1769, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88757691 -0.23309386 -0.39733424 102.06718757
-0.43649500 -0.70124393 -0.56367462 519.68560309
-0.14723913 0.67373898 -0.72415222 250.29116827
Axis 0.96770087 -0.19558315 -0.15906683
Axis point 0.00000000 224.68268474 229.02792313
Rotation angle (degrees) 140.25607412
Shift along axis -42.68426633
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 64
shifted from previous position = 0.0443
rotated from previous position = 0.146 degrees
atoms outside contour = 1761, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88644690 -0.23468134 -0.39891925 102.92117215
-0.43878232 -0.70033958 -0.56302270 519.80857088
-0.14724801 0.67412844 -0.72378787 250.13865633
Axis 0.96736944 -0.19679007 -0.15959331
Axis point 0.00000000 224.90663730 229.11626097
Rotation angle (degrees) 140.24985998
Shift along axis -42.65082531
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.0509 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88682818 -0.23410569 -0.39840974 102.63155782
-0.43798841 -0.70069517 -0.56319841 519.75407402
-0.14731582 0.67395906 -0.72393179 250.21245718
Axis 0.96748195 -0.19636048 -0.15944037
Axis point 0.00000000 224.82302925 229.08819200
Rotation angle (degrees) 140.25515764
Shift along axis -42.65894548
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0277
rotated from previous position = 0.119 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88773516 -0.23286893 -0.39711253 101.94821925
-0.43614356 -0.70150514 -0.56362163 519.65415902
-0.14732651 0.67354481 -0.72431506 250.37946507
Axis 0.96774956 -0.19539029 -0.15900765
Axis point 0.00000000 224.64447067 229.01845950
Rotation angle (degrees) 140.26798555
Shift along axis -42.68728231
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0384 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88743039 -0.23323831 -0.39757668 102.17484111
-0.43673470 -0.70130263 -0.56341586 519.68061974
-0.14741140 0.67362788 -0.72422052 250.35767544
Axis 0.96766061 -0.19568838 -0.15918228
Axis point 0.00000000 224.69868010 229.04697101
Rotation angle (degrees) 140.26833165
Shift along axis -42.67739283
> ~select #5
Nothing selected
> show #!2 models
> select #2
2 models selected
> view matrix models
> #2,0.19536,0.75362,0.62761,-85.152,-0.79186,-0.25635,0.5543,213.6,0.57862,-0.60527,0.54668,70.661
> view matrix models
> #2,0.11282,0.94881,0.29501,-45.954,-0.85716,-0.057225,0.51186,202.13,0.50254,-0.31062,0.80683,-2.2981
> view matrix models
> #2,0.11282,0.94881,0.29501,-10.942,-0.85716,-0.057225,0.51186,230.24,0.50254,-0.31062,0.80683,26.411
> view matrix models
> #2,-0.3673,0.80202,0.47101,56.376,-0.91933,-0.38991,-0.052965,380.04,0.14117,-0.45246,0.88054,91.186
> view matrix models
> #2,-0.37949,0.87152,0.31056,74.515,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,198.78
> view matrix models
> #2,-0.37949,0.87152,0.31056,77.692,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,195.9
> view matrix models
> #2,-0.4416,0.17153,0.88066,94.799,-0.84825,0.23999,-0.47209,346.93,-0.29232,-0.9555,0.039518,365.71
> view matrix models
> #2,-0.16701,0.27438,0.94701,26.293,-0.9691,-0.22254,-0.10643,372.5,0.18155,-0.93552,0.30307,245.76
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 816, shift = 17.1, angle = 92.5 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884246 0.36253629 0.90084502 32.04958536
-0.12095024 0.90936326 -0.39803210 133.21868643
-0.96349643 -0.20402438 -0.17334571 390.21884814
Axis 0.10022302 0.96310562 -0.24976572
Axis point 169.19260085 0.00000000 200.88498104
Rotation angle (degrees) 104.56110947
Shift along axis 34.05247827
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 0.000646, angle = 0.0027 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884389 0.36253338 0.90084582 32.04982504
-0.12099611 0.90935469 -0.39803771 133.22769414
-0.96349031 -0.20406771 -0.17332869 390.22127920
Axis 0.10020344 0.96310196 -0.24978768
Axis point 169.19590472 0.00000000 200.88843406
Rotation angle (degrees) 104.56090162
Shift along axis 34.05088824
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 2.75e-05, angle = 5.91e-05 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884450 0.36253261 0.90084597 32.05002579
-0.12099600 0.90935500 -0.39803705 133.22750949
-0.96349017 -0.20406771 -0.17332945 390.22138385
Axis 0.10020311 0.96310210 -0.24978726
Axis point 169.19595961 -0.00000000 200.88835343
Rotation angle (degrees) 104.56093288
Shift along axis 34.05087684
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24143,0.39089,0.88821,30.445,-0.11992,0.89625,-0.42703,139.68,-0.96298,-0.20961,-0.16951,390.31
> view matrix models
> #2,-0.24371,0.41583,0.87618,29.184,-0.11889,0.8838,-0.45252,145.47,-0.96253,-0.21445,-0.16596,390.36
> view matrix models
> #2,-0.23248,0.44368,0.86551,25.173,-0.098419,0.87459,-0.47477,147.23,-0.96761,-0.19556,-0.15966,387.41
> view matrix models
> #2,-0.015904,0.29362,0.95579,-1.8481,0.11672,0.94992,-0.28987,72.596,-0.99304,0.10695,-0.049378,329.9
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3636, correlation about mean = 0.2345, overlap = 5800
steps = 160, shift = 4.43, angle = 14.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23589350 0.38613188 0.89177153 30.30521757
0.14116968 0.92155092 -0.36168365 84.35973344
-0.96147045 0.04057228 -0.27189798 372.10342069
Axis 0.21036827 0.96919218 -0.12810818
Axis point 149.90554609 -0.00000000 183.31483684
Rotation angle (degrees) 107.04485499
Shift along axis 40.46655914
> transparency sel 50
> view matrix models
> #2,-0.32117,0.35848,0.87655,50.083,0.35637,0.9033,-0.23885,33.297,-0.87741,0.23567,-0.41786,354.8
> view matrix models
> #2,-0.25849,0.33315,0.90675,38.999,0.20781,0.93585,-0.2846,59.301,-0.9434,0.11486,-0.31114,365.02
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> show #3 models
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C E | No description available
D | No description available
F | No description available
> close #6
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1.pdb" models #3
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb" models #4
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb" models #5
> relModel #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C | No description available
> close #6
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
A B | No description available
C E | No description available
D F | No description available
> hide atoms
> show cartoons
> hide #3 models
> hide #5 models
> hide #4 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.0103
rotated from previous position = 0.00699 degrees
atoms outside contour = 6863, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007640 -0.00005950 0.01644925
0.00007639 0.99999999 -0.00007418 0.00540007
0.00005950 0.00007417 1.00000000 -0.02042262
Axis 0.60809281 -0.48779755 0.62631995
Axis point -36.04322257 258.47150214 0.00000000
Rotation angle (degrees) 0.00698874
Shift along axis -0.00542257
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 12404 atoms
average map value = 0.1322, steps = 204
shifted from previous position = 3.17
rotated from previous position = 16.9 degrees
atoms outside contour = 7037, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.15126719 0.47107682 -0.86902521 263.21094843
0.40313494 0.83210747 0.38089281 -155.24920226
0.90255217 -0.29271785 -0.31577809 100.07490639
Axis -0.35517923 -0.93411153 -0.03582417
Axis point 121.90346818 0.00000000 160.98219047
Rotation angle (degrees) 108.50992410
Shift along axis 47.94790735
> show #3 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> hide #3 models
> ui mousemode right "map eraser"
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J59_004_volume_map_sharp
> (3).mrc"
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.366, step 2, values float32
> close #7
> hide #!2 models
> surface dust #8 size 8.5
> select #8
2 models selected
> close #7
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,35.396,0,1,0,60.903,0,0,1,32.921
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.3457,-0.50036,0.79381,208.17,-0.017535,0.84927,0.52767,14.154,-0.93818,0.1685,-0.30237,329.15
> view matrix models
> #8,-0.51948,-0.14515,0.84206,178.05,0.63577,0.59277,0.49439,-45.989,-0.57091,0.79219,-0.21565,171.93
> view matrix models
> #8,-0.55842,-0.30769,0.77039,216.83,0.59819,0.49406,0.63093,-44.478,-0.57475,0.81316,-0.09184,152.9
> view matrix models
> #8,-0.55842,-0.30769,0.77039,191.12,0.59819,0.49406,0.63093,-46.563,-0.57475,0.81316,-0.09184,158.22
> show #6 models
> ~select #8
Nothing selected
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 168
shifted from previous position = 1.67
rotated from previous position = 11.8 degrees
atoms outside contour = 6854, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00007634 0.00003096 356.91445101
-0.00007636 -0.99999975 -0.00069729 357.06728170
0.00003091 -0.00069729 0.99999976 0.11956672
Axis -0.00001547 0.00034864 -0.99999994
Axis point 178.46403997 178.52684922 0.00000000
Rotation angle (degrees) 179.99562555
Shift along axis -0.00059852
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.00373
rotated from previous position = 0.0435 degrees
atoms outside contour = 6861, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00004453 0.00006393 356.91507698
-0.00004452 -1.00000000 0.00006135 356.92005524
0.00006393 0.00006135 1.00000000 -0.02104448
Axis -0.00003196 -0.00003068 -1.00000000
Axis point 178.46151168 178.45605515 0.00000000
Rotation angle (degrees) 179.99744898
Shift along axis -0.00131278
> select #8
2 models selected
> view matrix models
> #8,-0.55842,-0.30769,0.77039,144.53,0.59819,0.49406,0.63093,-60.652,-0.57475,0.81316,-0.09184,256.77
> view matrix models
> #8,-0.55842,-0.30769,0.77039,188.5,0.59819,0.49406,0.63093,-43.585,-0.57475,0.81316,-0.09184,207.1
> view matrix models
> #8,0.20416,-0.32979,0.92171,53.292,0.8306,0.55667,0.015197,-5.7187,-0.5181,0.76247,0.38758,141.12
> view matrix models
> #8,-0.17775,-0.55408,0.81327,158.88,0.42359,0.70287,0.57144,-38.275,-0.88824,0.44606,0.10977,280.75
> view matrix models
> #8,-0.44365,-0.53212,0.72113,209.28,0.54415,0.47941,0.68853,-40.877,-0.71209,0.69787,0.076868,222.08
> view matrix models
> #8,-0.44365,-0.53212,0.72113,201.21,0.54415,0.47941,0.68853,-58.258,-0.71209,0.69787,0.076868,191.6
> view matrix models
> #8,-0.44365,-0.53212,0.72113,198.44,0.54415,0.47941,0.68853,-54.781,-0.71209,0.69787,0.076868,186.46
> view matrix models
> #8,-0.078986,-0.30105,0.95033,78.334,0.99624,-0.057911,0.064456,35.555,0.03563,0.95185,0.30449,4.0251
> view matrix models
> #8,-0.078986,-0.30105,0.95033,83.821,0.99624,-0.057911,0.064456,34.166,0.03563,0.95185,0.30449,22.679
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.12,0.9291,0.27408,0.24829,-27.377,-0.34419,0.88644,0.30946,90.098
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.41,0.9291,0.27408,0.24829,-25.4,-0.34419,0.88644,0.30946,74.434
> view matrix models
> #8,0.021026,-0.64563,0.76336,142.78,0.95068,0.24925,0.18463,-16.653,-0.30947,0.72183,0.61903,50.881
> view matrix models
> #8,0.18242,-0.5728,0.79914,102.63,0.95907,0.28269,-0.016302,4.2907,-0.21658,0.76941,0.60092,32.168
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.51,0.95907,0.28269,-0.016302,-14.792,-0.21658,0.76941,0.60092,29.021
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.75,0.95907,0.28269,-0.016302,-13.773,-0.21658,0.76941,0.60092,25.236
> view matrix models
> #8,0.19689,-0.59123,0.7821,106.42,0.95308,0.30251,-0.011255,-16.342,-0.22993,0.74762,0.62305,27.429
> view matrix models
> #8,0.16349,-0.53138,0.83121,96.478,0.91695,0.39269,0.070685,-34.591,-0.36397,0.75062,0.55145,57.366
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2099, correlation about mean = -0.0466, overlap = 1148
steps = 220, shift = 8.88, angle = 20.7 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.16970377 -0.22411591 0.95967322 38.04053966
0.82808228 0.56039048 -0.01556391 -26.95927500
-0.53430362 0.79732965 0.28068680 115.40605181
Axis 0.40645268 0.74699927 0.52610674
Axis point 84.17805896 0.00000000 56.92499809
Rotation angle (degrees) 89.69114416
Shift along axis 56.03902271
> hide #!8 models
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.17985,-0.20944,0.96114,34.185,0.82577,0.56311,-0.031812,-24.805,-0.53457,0.7994,0.27422,116.02
> view matrix models
> #8,-0.19365,-0.33381,0.92253,114.87,-0.70512,-0.60645,-0.36745,423.6,0.68213,-0.72166,-0.11794,196.81
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 196, shift = 4.16, angle = 13 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07683115 -0.17561277 0.98145662 66.44166832
-0.66408769 -0.72522667 -0.18175198 411.16957530
0.74369650 -0.66573749 -0.06090228 170.05104945
Axis -0.66519466 0.32677996 -0.67136497
Axis point 7.75299271 239.88960504 0.00000000
Rotation angle (degrees) 158.66671698
Shift along axis -24.00098327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00106, angle = 0.00247 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07685176 -0.17562808 0.98145227 66.44848746
-0.66411122 -0.72519937 -0.18177500 411.17240045
0.74367337 -0.66576320 -0.06090373 170.05786271
Axis -0.66518608 0.32679973 -0.67136385
Axis point 7.75566835 239.89404572 0.00000000
Rotation angle (degrees) 158.66630362
Shift along axis -24.00027887
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00214, angle = 0.00428 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680221 -0.17565442 0.98145143 66.44396733
-0.66407552 -0.72523465 -0.18176462 411.17025225
0.74371036 -0.66571781 -0.06094818 170.05404481
Axis -0.66520863 0.32678246 -0.67134991
Axis point 7.74491366 239.89221167 -0.00000000
Rotation angle (degrees) 158.66868085
Shift along axis -24.00164195
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select down
2 models selected
> volume flip #8
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip as #9, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> hide #!9 models
> show #!9 models
> select #9
2 models selected
> view matrix models
> #9,0.04932,0.5784,-0.81426,225.85,0.77832,-0.53317,-0.33159,193.54,-0.62593,-0.6174,-0.47647,432.54
> view matrix models
> #9,0.49864,0.44515,-0.74377,167.72,0.18866,-0.89322,-0.40812,346.38,-0.84603,0.063187,-0.52938,372.95
> view matrix models
> #9,0.41566,0.19473,-0.88843,240.37,-0.83603,-0.30285,-0.45753,418.6,-0.35815,0.93293,0.036921,80.781
> view matrix models
> #9,0.18699,-0.28999,-0.93858,354,0.30934,-0.88945,0.33644,207.89,-0.93239,-0.35325,-0.076615,374.31
> view matrix models
> #9,0.12166,-0.27135,-0.95476,363.51,0.35041,-0.88823,0.29709,207.97,-0.92866,-0.37071,-0.01298,366.08
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.12166,-0.27135,-0.95476,343.55,0.35041,-0.88823,0.29709,204.63,-0.92866,-0.37071,-0.01298,384.14
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03988, overlap = 1580
steps = 48, shift = 0.0161, angle = 0.00778 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07667600 -0.17562499 0.98146657 66.40220937
-0.66405605 -0.72527845 -0.18166098 411.15872420
0.74374077 -0.66567786 -0.06101339 170.05477366
Axis -0.66525588 0.32674168 -0.67132294
Axis point 7.71835621 239.88762888 0.00000000
Rotation angle (degrees) 158.66732589
Shift along axis -23.99344049
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 84, shift = 0.0157, angle = 0.009 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07682622 -0.17562423 0.98145496 66.44206918
-0.66408132 -0.72523107 -0.18175771 411.17012882
0.74370270 -0.66572968 -0.06091201 170.05004664
Axis -0.66519758 0.32677973 -0.67136219
Axis point 7.75121505 239.88987802 0.00000000
Rotation angle (degrees) 158.66744100
Shift along axis -24.00021217
> view matrix models
> #9,0.12166,-0.27135,-0.95476,338.02,0.35041,-0.88823,0.29709,203.08,-0.92866,-0.37071,-0.01298,379.52
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.30016,-0.86169,-0.40914,310.95,-0.62921,-0.50123,0.59402,242.86,-0.71693,0.079138,-0.69264,391.26
> view matrix models
> #9,0.079463,-0.47579,-0.87596,361.79,-0.033015,-0.87952,0.47472,229.87,-0.99629,-0.0088031,-0.085597,347.7
> view matrix models
> #9,0.41919,-0.72698,-0.54387,295.14,-0.54116,-0.68106,0.49326,272.69,-0.729,0.087548,-0.6789,389.59
> view matrix models
> #9,-0.24911,-0.67335,-0.6961,410.62,-0.72999,-0.34178,0.59185,234.54,-0.63644,0.65558,-0.4064,247.91
> view matrix models
> #9,0.38176,-0.48586,-0.78626,304.1,-0.52937,-0.81227,0.24491,330.41,-0.75764,0.32273,-0.56729,341.04
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.000846, angle = 0.00177 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680654 -0.17560484 0.98145997 66.43537485
-0.66409320 -0.72522729 -0.18172939 411.16781129
0.74369413 -0.66573891 -0.06091578 170.05270073
Axis -0.66520310 0.32677576 -0.67135865
Axis point 7.74972828 239.88942606 0.00000000
Rotation angle (degrees) 158.66589087
Shift along axis -23.99969612
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.00125, angle = 0.00125 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07681767 -0.17562278 0.98145589 66.43984164
-0.66408848 -0.72522635 -0.18175040 411.16938528
0.74369719 -0.66573520 -0.06091887 170.05309874
Axis -0.66520021 0.32678120 -0.67135886
Axis point 7.74944501 239.89073787 0.00000000
Rotation angle (degrees) 158.66693629
Shift along axis -24.00002709
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 435032 points
correlation = 0.2522, correlation about mean = -0.0372, overlap = 1.179e+04
steps = 324, shift = 5.58, angle = 29.2 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip (#9)
relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.07209466 -0.25700523 -0.96371709 344.01508219
-0.25749943 -0.93827144 0.23095609 315.15876008
-0.96358516 0.23150590 -0.13382306 321.33072132
Axis 0.73215596 -0.17567940 -0.65809148
Axis point 0.00000000 198.81231893 315.31278484
Rotation angle (degrees) 179.97848683
Shift along axis -14.95921604
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!2 models
> ~select #9
Nothing selected
> show #7 models
> hide #6 models
> hide #!1 models
> select #7
1 model selected
> view matrix models
> #7,0.28314,0.80804,0.51663,178.11,-0.89657,0.0317,0.44178,178.55,0.34059,-0.58828,0.73343,173.27
> view matrix models
> #7,-0.85167,0.44193,-0.28171,178.2,0.13709,-0.33096,-0.93363,178.47,-0.50584,-0.83376,0.22128,173.34
> view matrix models
> #7,-0.052894,0.17656,-0.98287,178.14,0.95344,0.30156,0.0028629,178.4,0.2969,-0.93695,-0.18429,173.28
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.052894,0.17656,-0.98287,123.75,0.95344,0.30156,0.0028629,168.98,0.2969,-0.93695,-0.18429,135.65
> view matrix models
> #7,-0.052894,0.17656,-0.98287,171.65,0.95344,0.30156,0.0028629,239.46,0.2969,-0.93695,-0.18429,240.81
> view matrix models
> #7,-0.052894,0.17656,-0.98287,168.29,0.95344,0.30156,0.0028629,214.9,0.2969,-0.93695,-0.18429,234.8
> transparency #2.1 0
> volume erase #2 center 168.29,214.9,234.8 radius 57.895
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.31,0.95344,0.30156,0.0028629,232.11,0.2969,-0.93695,-0.18429,231.78
> volume erase #10 center 158.31,232.11,231.78 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,179.95,0.95344,0.30156,0.0028629,219.57,0.2969,-0.93695,-0.18429,237.28
> view matrix models
> #7,-0.052894,0.17656,-0.98287,196.31,0.95344,0.30156,0.0028629,220.25,0.2969,-0.93695,-0.18429,246.32
> volume erase #10 center 196.31,220.25,246.32 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,185.48,0.95344,0.30156,0.0028629,234.46,0.2969,-0.93695,-0.18429,244.14
> view matrix models
> #7,-0.052894,0.17656,-0.98287,151.71,0.95344,0.30156,0.0028629,160.15,0.2969,-0.93695,-0.18429,262.05
> view matrix models
> #7,-0.052894,0.17656,-0.98287,147.93,0.95344,0.30156,0.0028629,158.34,0.2969,-0.93695,-0.18429,267.59
> view matrix models
> #7,-0.052894,0.17656,-0.98287,139.18,0.95344,0.30156,0.0028629,153.5,0.2969,-0.93695,-0.18429,267
> volume erase #10 center 139.18,153.5,267 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,140,0.95344,0.30156,0.0028629,152.53,0.2969,-0.93695,-0.18429,263.01
> view matrix models
> #7,-0.052894,0.17656,-0.98287,156.67,0.95344,0.30156,0.0028629,178.21,0.2969,-0.93695,-0.18429,266.42
> volume erase #10 center 156.67,178.21,266.42 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.47,0.95344,0.30156,0.0028629,179.86,0.2969,-0.93695,-0.18429,260.63
> view matrix models
> #7,-0.052894,0.17656,-0.98287,146.27,0.95344,0.30156,0.0028629,179.75,0.2969,-0.93695,-0.18429,264.96
> view matrix models
> #7,-0.052894,0.17656,-0.98287,136.73,0.95344,0.30156,0.0028629,165.7,0.2969,-0.93695,-0.18429,256.45
> volume erase #10 center 136.73,165.7,256.45 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,170.65,0.95344,0.30156,0.0028629,257.57,0.2969,-0.93695,-0.18429,281.54
> view matrix models
> #7,-0.052894,0.17656,-0.98287,198.12,0.95344,0.30156,0.0028629,237.97,0.2969,-0.93695,-0.18429,234.34
> volume erase #10 center 198.12,237.97,234.34 radius 57.895
> close #7
> show #!1 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1732, overlap = 5606
steps = 100, shift = 2.13, angle = 5.64 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26232817 0.42310640 0.86727444 32.84932501
0.23389320 0.89982892 -0.36824168 75.35914970
-0.93620401 0.10624943 -0.33501218 371.04180450
Axis 0.25313923 0.96214902 -0.10094453
Axis point 142.07695422 0.00000000 181.57625532
Rotation angle (degrees) 110.41122784
Shift along axis 43.36754334
> select #10
2 models selected
> view matrix models
> #10,-0.26233,0.42311,0.86727,32.251,0.23389,0.89983,-0.36824,72.484,-0.9362,0.10625,-0.33501,370.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.13878,0.40417,0.9041,8.8226,0.22067,0.9026,-0.36963,74.459,-0.96543,0.14821,-0.21445,349.11
> view matrix models
> #10,0.081829,0.24713,0.96552,-14.455,0.27881,0.92441,-0.26024,43.68,-0.95685,0.29049,0.0067426,290.35
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1733, overlap = 5606
steps = 228, shift = 2.88, angle = 23.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26246485 0.42303734 0.86726677 32.87464761
0.23392580 0.89986112 -0.36814227 75.32527217
-0.93615756 0.10625167 -0.33514125 371.06459232
Axis 0.25309913 0.96216476 -0.10089498
Axis point 142.08264269 0.00000000 181.57434136
Rotation angle (degrees) 110.41836671
Shift along axis 43.35731307
> show #6 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> hide #!10 models
> show #!8 models
> hide #!1 models
> ~select #10
Nothing selected
> hide #6 models
> select #7
1 model selected
> view matrix models
> #7,0.92464,0.25458,-0.28325,178.06,0.04684,0.66208,0.74796,178.47,0.37795,-0.70486,0.60026,173.27
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.92464,0.25458,-0.28325,204.47,0.04684,0.66208,0.74796,168.78,0.37795,-0.70486,0.60026,117.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,205.35,0.04684,0.66208,0.74796,172.6,0.37795,-0.70486,0.60026,132.71
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.38,0.04684,0.66208,0.74796,170.72,0.37795,-0.70486,0.60026,135.25
> view matrix models
> #7,0.92464,0.25458,-0.28325,208.14,0.04684,0.66208,0.74796,169.1,0.37795,-0.70486,0.60026,122.9
> volume #8 level 0.8304
> view matrix models
> #7,0.92464,0.25458,-0.28325,209.46,0.04684,0.66208,0.74796,167.64,0.37795,-0.70486,0.60026,121.48
> volume erase #8 center 209.46,167.64,121.48 radius 64.178
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.68,0.04684,0.66208,0.74796,128.68,0.37795,-0.70486,0.60026,117.72
> volume erase #11 center 202.68,128.68,117.72 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,183.78,0.04684,0.66208,0.74796,136.58,0.37795,-0.70486,0.60026,112.38
> volume erase #11 center 183.78,136.58,112.38 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,262.78,0.04684,0.66208,0.74796,132.37,0.37795,-0.70486,0.60026,184.94
> view matrix models
> #7,0.92464,0.25458,-0.28325,269.47,0.04684,0.66208,0.74796,136.95,0.37795,-0.70486,0.60026,179.85
> view matrix models
> #7,0.92464,0.25458,-0.28325,267.59,0.04684,0.66208,0.74796,127.26,0.37795,-0.70486,0.60026,154.16
> view matrix models
> #7,0.92464,0.25458,-0.28325,261.44,0.04684,0.66208,0.74796,136.21,0.37795,-0.70486,0.60026,158.39
> volume erase #11 center 261.44,136.21,158.39 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,234.76,0.04684,0.66208,0.74796,204.63,0.37795,-0.70486,0.60026,115.7
> view matrix models
> #7,0.92464,0.25458,-0.28325,232.48,0.04684,0.66208,0.74796,207.24,0.37795,-0.70486,0.60026,119.09
> volume erase #11 center 232.48,207.24,119.09 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,211.86,0.04684,0.66208,0.74796,185.05,0.37795,-0.70486,0.60026,105.87
> view matrix models
> #7,0.92464,0.25458,-0.28325,195.04,0.04684,0.66208,0.74796,187.39,0.37795,-0.70486,0.60026,114.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,201.04,0.04684,0.66208,0.74796,190.35,0.37795,-0.70486,0.60026,113.3
> volume erase #11 center 201.04,190.35,113.3 radius 64.178
> show #!1 models
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3648, correlation about mean = -0.1049, overlap = 2621
steps = 72, shift = 2.57, angle = 2.92 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05111081 -0.21510165 0.97525327 67.52834138
-0.64952035 -0.73462917 -0.19606954 411.11615250
0.75862440 -0.64346813 -0.10216541 168.35220279
Axis -0.67771084 0.32814528 -0.65804915
Axis point 0.00000000 241.21252430 -1.00026216
Rotation angle (degrees) 160.72632370
Shift along axis -21.64288928
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 40, shift = 0.0141, angle = 0.00956 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05107225 -0.21496635 0.97528512 67.48907810
-0.64946346 -0.73471119 -0.19595064 411.10839498
0.75867570 -0.64341970 -0.10208944 168.33302170
Axis -0.67772214 0.32806961 -0.65807524
Axis point 0.00000000 241.19521972 -0.99729201
Rotation angle (degrees) 160.72350203
Shift along axis -21.64246440
Correlation = 0.3649, Correlation about mean = -0.1049, Overlap = 2621
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 28, shift = 0.011, angle = 0.00422 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05110002 -0.21502631 0.97527045 67.51163904
-0.64943800 -0.73471600 -0.19601698 411.10850225
0.75869563 -0.64339417 -0.10210226 168.32377829
Axis -0.67771626 0.32808172 -0.65807526
Axis point 0.00000000 241.19615320 -1.00289431
Rotation angle (degrees) 160.72744238
Shift along axis -21.64626553
> close #7
> volume #8 level 0.4211
> hide #!8 models
> volume #11 level 0.6377
> volume #11 level 0.4713
> show #!10 models
> hide #!10 models
> show #!10 models
> select #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.14971,0.63965,-0.75394,191.13,-0.95888,-0.2799,-0.047058,377.99,-0.24113,0.71589,0.65525,40.47
> view matrix models
> #11,-0.069022,0.30969,-0.94833,249.55,0.96027,0.27828,0.020987,-16.584,0.2704,-0.9092,-0.3166,311.78
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.069022,0.30969,-0.94833,292.24,0.96027,0.27828,0.020987,-16.748,0.2704,-0.9092,-0.3166,306.11
> view matrix models
> #11,-0.069022,0.30969,-0.94833,288.83,0.96027,0.27828,0.020987,-15.141,0.2704,-0.9092,-0.3166,305.54
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.12042,0.37081,-0.92087,284.98,0.89214,0.44729,0.063446,-33.276,0.43542,-0.8139,-0.38467,274.73
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3705, correlation about mean = -0.01342, overlap = 9885
steps = 84, shift = 3.3, angle = 7.24 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08967779 0.29999028 -0.94971770 295.49237204
0.84493489 0.52775912 0.08692132 -41.96570345
0.52729773 -0.79465472 -0.30080053 248.18221209
Axis -0.48858097 -0.81858128 0.30201543
Axis point 60.64458577 -0.00000000 223.51625228
Rotation angle (degrees) 115.55387500
Shift along axis -35.06475327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3706, correlation about mean = -0.01331, overlap = 9885
steps = 40, shift = 0.0143, angle = 0.0103 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08981970 0.29998685 -0.94970537 295.52003565
0.84486634 0.52788229 0.08683967 -41.94876855
0.52738342 -0.79457419 -0.30086302 248.17026594
Axis -0.48850161 -0.81863956 0.30198584
Axis point 60.66605513 0.00000000 223.51111811
Rotation angle (degrees) 115.55645450
Shift along axis -35.07718649
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> close #9
> show #!2 models
> hide #!11 models
> ~select #11
Nothing selected
> show #6 models
> hide #!2 models
> show #!2 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 434908 points
correlation = 0.8681, correlation about mean = 0.7943, overlap = 2.493e+04
steps = 100, shift = 2.6, angle = 5.47 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.99999417 -0.00078818 -0.00332112 0.86833791
0.00079720 0.99999599 0.00271726 -0.70720618
0.00331897 -0.00271989 0.99999079 0.00769659
Axis -0.62300052 -0.76083593 0.18165636
Axis point -1.67706066 0.00000000 261.17922578
Rotation angle (degrees) 0.25002110
Shift along axis -0.00150896
> hide #!1 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 124
shifted from previous position = 2.69
rotated from previous position = 12.5 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25275147 -0.43670415 -0.86336907 353.51447381
-0.44938591 -0.84323715 0.29496333 308.88812835
-0.85683660 0.31343349 -0.40937812 323.84932290
Axis 0.79143097 -0.27991074 -0.54340316
Axis point 0.00000000 215.73050893 284.44415750
Rotation angle (degrees) 179.33140963
Shift along axis 17.34045325
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 36
shifted from previous position = 0.00249
rotated from previous position = 0.00661 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25279114 -0.43660663 -0.86340677 353.49888697
-0.44933375 -0.84329450 0.29487884 308.90364784
-0.85685225 0.31341505 -0.40935948 323.85331097
Axis 0.79144345 -0.27985911 -0.54341158
Axis point 0.00000000 215.71863017 284.44492018
Rotation angle (degrees) 179.32902903
Shift along axis 17.33923677
> transparency #2.1#10.1 50
> hide #!2 models
> show #!8 models
> select #8
2 models selected
> view matrix models
> #8,0.33902,0.03981,-0.93994,229.8,-0.92382,-0.17477,-0.34061,394.45,-0.17784,0.9838,-0.022475,72.918
> view matrix models
> #8,-0.19081,0.15972,-0.96855,298.63,-0.9771,-0.1256,0.17178,326.79,-0.094217,0.97914,0.18003,33.4
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.19081,0.15972,-0.96855,333.9,-0.9771,-0.1256,0.17178,339.76,-0.094217,0.97914,0.18003,31.589
> view matrix models
> #8,-0.19081,0.15972,-0.96855,336.31,-0.9771,-0.1256,0.17178,330.87,-0.094217,0.97914,0.18003,34.463
> view matrix models
> #8,-0.19081,0.15972,-0.96855,332.19,-0.9771,-0.1256,0.17178,338.81,-0.094217,0.97914,0.18003,28.17
> view matrix models
> #8,-0.19081,0.15972,-0.96855,344.81,-0.9771,-0.1256,0.17178,333.8,-0.094217,0.97914,0.18003,27.752
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,233.97,0.79273,0.40527,0.45534,-53.893,0.46395,-0.88565,-0.019473,233.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,225.01,0.79273,0.40527,0.45534,-60.792,0.46395,-0.88565,-0.019473,244.4
> view matrix models
> #8,0.39538,0.22669,-0.8901,226.27,0.79273,0.40527,0.45534,-67.659,0.46395,-0.88565,-0.019473,244.84
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 47154 points
correlation = 0.3601, correlation about mean = -0.01926, overlap = 2801
steps = 244, shift = 6.57, angle = 20.9 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.50275518 0.77664634 0.37954926 71.44698114
0.77480667 0.59955666 -0.20051529 -35.12156246
-0.38329076 0.19326720 -0.90318100 318.59922133
Axis 0.45869577 0.88859079 -0.00214294
Axis point 85.22138435 0.00000000 150.24137730
Rotation angle (degrees) 154.58056842
Shift along axis 0.88099311
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:05:12 2022 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!1 models
> show #!2 models
> close #11
> close #8
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.1/B 7.2/B 7.3/B
7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B | apolipoprotein A-I
> close #7.2-10
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!2 models
> hide #!1 models
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 352
shifted from previous position = 4.55
rotated from previous position = 50.7 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51892205 0.80965860 -0.27417668 164.22917225
-0.84272074 -0.43077092 0.32289035 300.54198392
0.14332362 0.39860929 0.90585262 -107.70830576
Axis 0.04438420 -0.24472630 -0.96857580
Axis point 169.29706156 116.85077370 0.00000000
Rotation angle (degrees) 121.46114137
Shift along axis 38.06231174
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 40
shifted from previous position = 0.00569
rotated from previous position = 0.00161 degrees
atoms outside contour = 2609, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894067 0.80965192 -0.27416117 164.23500046
-0.84270669 -0.43078495 0.32290828 300.54258112
0.14333881 0.39860769 0.90585092 -107.71085737
Axis 0.04437330 -0.24472913 -0.96857558
Axis point 169.29862447 116.85084764 0.00000000
Rotation angle (degrees) 121.46229524
Shift along axis 38.06223078
> show #4 models
> hide #!7 models
> hide #6 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 184
shifted from previous position = 2.68
rotated from previous position = 43.1 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696585 -0.97040692 -0.04644960 286.31819473
0.13996862 0.08141367 -0.98680321 234.14224375
0.96138231 0.22733718 0.15511878 -33.92541253
Axis 0.62926604 -0.52234025 0.57548668
Axis point 0.00000000 269.88096267 6.34604794
Rotation angle (degrees) 105.26304401
Shift along axis 38.34477607
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0184 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699244 -0.97040417 -0.04637137 286.30251238
0.14028426 0.08141314 -0.98675843 234.09383454
0.96132975 0.22734912 0.15542673 -33.96007421
Axis 0.62921931 -0.52224780 0.57562166
Axis point 0.00000000 269.87054516 6.30278577
Rotation angle (degrees) 105.25312557
Shift along axis 38.34392482
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0177
rotated from previous position = 0.024 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699037 -0.97040260 -0.04641486 286.30808679
0.13987427 0.08136006 -0.98682101 234.17141287
0.96139000 0.22737483 0.15501591 -33.91830894
Axis 0.62930653 -0.52233598 0.57544628
Axis point 0.00000000 269.87165306 6.36745226
Rotation angle (degrees) 105.26696289
Shift along axis 38.34122922
> show #3 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0174
rotated from previous position = 0.02 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696878 -0.97040926 -0.04638578 286.31082660
0.14021616 0.08140780 -0.98676855 234.10798884
0.96134552 0.22732931 0.15535816 -33.95179699
Axis 0.62922296 -0.52227064 0.57559694
Axis point 0.00000000 269.87770153 6.30937551
Rotation angle (degrees) 105.25602295
Shift along axis 38.34306534
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0232 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23695180 -0.97040946 -0.04646826 286.32373425
0.13981736 0.08139458 -0.98682623 234.17404048
0.96140779 0.22733318 0.15496668 -33.91113966
Axis 0.62929239 -0.52237681 0.57542468
Axis point 0.00000000 269.88626156 6.36736238
Rotation angle (degrees) 105.26854490
Shift along axis 38.34095150
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.00386
rotated from previous position = 0.0076 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23701158 -0.97039892 -0.04638334 286.30019564
0.13991374 0.08134082 -0.98681700 234.16833276
0.96137903 0.22739739 0.15505086 -33.92599735
Axis 0.62931286 -0.52231123 0.57546182
Axis point 0.00000000 269.86512738 6.36383820
Rotation angle (degrees) 105.26586629
Shift along axis 38.34052770
> show #!2 models
> show #6 models
> hide #!2 models
> hide #!10 models
> hide #6 models
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!2 models
> show #!1 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.4911, correlation about mean = 0.2779, overlap = 6002
steps = 1308, shift = 0.661, angle = 22 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27793747 -0.14035072 -0.95029069 409.92559615
0.39452131 0.88530641 -0.24614115 -49.02432671
0.87584454 -0.44332178 -0.19068848 109.24693947
Axis -0.10307165 -0.95457032 0.27959209
Axis point 169.03926821 0.00000000 207.85299225
Rotation angle (degrees) 106.95735055
Shift along axis 35.09003774
> show #!10 models
> hide #!2 models
> hide #!1 models
> show #!2 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00219
rotated from previous position = 0.0172 degrees
atoms outside contour = 2607, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51889139 0.80974271 -0.27398626 164.17754795
-0.84268736 -0.43067692 0.32310277 300.48501792
0.14363056 0.39854000 0.90583449 -107.74724207
Axis 0.04421738 -0.24478525 -0.96856853
Axis point 169.27126594 116.83993981 0.00000000
Rotation angle (degrees) 121.45756347
Shift along axis 38.06578928
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00282
rotated from previous position = 0.00397 degrees
atoms outside contour = 2606, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894411 0.80971407 -0.27397106 164.19040191
-0.84265984 -0.43073928 0.32309143 300.49449446
0.14360158 0.39853079 0.90584314 -107.74009884
Axis 0.04422032 -0.24476870 -0.96857258
Axis point 169.27313448 116.84271119 0.00000000
Rotation angle (degrees) 121.46113819
Shift along axis 38.06301215
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14665,-0.10019,0.9841,42.803,-0.93066,-0.32317,-0.17158,431.35,0.33522,-0.94102,-0.045847,294.18
> view matrix models
> #3,-0.24212,-0.16715,0.95574,75.904,-0.91312,-0.29375,-0.2827,443.12,0.328,-0.94116,-0.081503,301.82
> view matrix models
> #3,-0.22781,0.0025001,0.9737,41.665,-0.95433,-0.19906,-0.22277,423.77,0.19327,-0.97998,0.047735,309.02
> view matrix models
> #3,-0.31679,-0.24249,0.91698,108.61,-0.87534,-0.29756,-0.38109,454.64,0.36527,-0.92339,-0.118,298.78
> view matrix models
> #3,-0.20831,0.16138,0.96466,13.134,-0.97765,-0.063166,-0.20055,401.06,0.028569,-0.98487,0.17093,316.86
> view matrix models
> #3,-0.18189,0.029376,0.98288,27.434,-0.97841,0.094327,-0.18388,371.75,-0.098114,-0.99511,0.011585,369.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.18189,0.029376,0.98288,26.801,-0.97841,0.094327,-0.18388,370.7,-0.098114,-0.99511,0.011585,365.44
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 220
shifted from previous position = 5.16
rotated from previous position = 26.4 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51865164 0.80982057 -0.27420999 164.16314366
-0.84285174 -0.43044060 0.32298891 300.49787860
0.14353196 0.39863709 0.90580740 -107.73453379
Axis 0.04433389 -0.24481919 -0.96855463
Axis point 169.29026360 116.83700867 0.00000000
Rotation angle (degrees) 121.44248630
Shift along axis 38.05712471
> hide #!2 models
> view matrix models
> #3,-0.095949,-0.048917,0.99418,23.903,-0.93262,-0.34465,-0.10697,422.69,0.34788,-0.93745,-0.012552,284.37
> view matrix models
> #3,-0.095949,-0.048917,0.99418,24.499,-0.93262,-0.34465,-0.10697,420.51,0.34788,-0.93745,-0.012552,282.55
> ui mousemode right "map eraser"
> volume erase #10 center 197.01,182.51,231.59 radius 31.633
> volume erase #10 center 213.27,171.82,231.83 radius 31.633
> volume erase #10 center 199.27,226.74,192.59 radius 31.633
> volume erase #10 center 201.83,210.63,213.73 radius 31.633
> close #8
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 84
shifted from previous position = 4.01
rotated from previous position = 2.96 degrees
atoms outside contour = 2586, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47450864 0.83236882 -0.28636287 154.63058051
-0.86693279 -0.38553270 0.31589884 297.74905925
0.15254210 0.39815408 0.90454642 -108.87748698
Axis 0.04681588 -0.24980441 -0.96716391
Axis point 169.11832797 115.96117517 0.00000000
Rotation angle (degrees) 118.53838807
Shift along axis 38.16251411
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 48
shifted from previous position = 0.00277
rotated from previous position = 0.00477 degrees
atoms outside contour = 2584, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47448892 0.83239630 -0.28631566 154.61369255
-0.86692974 -0.38549828 0.31594921 297.73456104
0.15262076 0.39812996 0.90454377 -108.88430164
Axis 0.04677274 -0.24981834 -0.96716240
Axis point 169.11102884 115.95863363 0.00000000
Rotation angle (degrees) 118.53670909
Shift along axis 38.16095498
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 60
shifted from previous position = 0.0162
rotated from previous position = 0.0207 degrees
atoms outside contour = 2591, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47456944 0.83227118 -0.28654585 154.70120447
-0.86694397 -0.38562941 0.31575007 297.80757285
0.15228918 0.39826452 0.90454042 -108.84769154
Axis 0.04696579 -0.24977725 -0.96716366
Axis point 169.15292707 115.96995015 0.00000000
Rotation angle (degrees) 118.54372018
Shift along axis 38.15363917
> show #!2 models
> show #!7 models
> show #7.1 models
> select #7.1
5464 atoms, 5510 bonds, 334 residues, 1 model selected
> close #8
> close #8
> ui mousemode right "translate selected models"
> view matrix models #7.1,1,0,0,169.78,0,1,0,228.66,0,0,1,242.62
> view matrix models #7.1,1,0,0,141.19,0,1,0,179.49,0,0,1,253.16
> view matrix models #7.1,1,0,0,139.34,0,1,0,181.33,0,0,1,279.32
> view matrix models #7.1,1,0,0,140.66,0,1,0,199.74,0,0,1,261.78
> view matrix models #7.1,1,0,0,152.52,0,1,0,194.28,0,0,1,257.24
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.96441,0.048869,0.25985,165.75,0.098602,0.8454,-0.52495,167.67,-0.24533,0.53189,0.8105,246.45
> view matrix models
> #7.1,0.52404,0.070357,0.84878,205.22,0.25659,0.93724,-0.23611,177.31,-0.81212,0.34152,0.4731,245.12
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.96,0.25659,0.93724,-0.23611,166.4,-0.81212,0.34152,0.4731,253.15
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.06,0.25659,0.93724,-0.23611,172.5,-0.81212,0.34152,0.4731,255.75
> view matrix models
> #7.1,0.52404,0.070357,0.84878,220.15,0.25659,0.93724,-0.23611,172.23,-0.81212,0.34152,0.4731,250.53
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.93,0.25659,0.93724,-0.23611,169.22,-0.81212,0.34152,0.4731,253.47
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.24,0.25659,0.93724,-0.23611,170.23,-0.81212,0.34152,0.4731,253.64
> view matrix models
> #7.1,0.52404,0.070357,0.84878,216.82,0.25659,0.93724,-0.23611,165.96,-0.81212,0.34152,0.4731,248.26
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.73952,-0.17388,0.65029,205.07,0.14405,0.98456,0.099452,184.79,-0.65754,0.020126,0.75315,262.95
> view matrix models
> #7.1,0.73125,-0.084624,0.67684,205.42,0.062378,0.99641,0.057187,184.4,-0.67925,0.00040129,0.73391,262.74
> view matrix models
> #7.1,0.69799,-0.10334,0.70861,208.03,0.074484,0.99464,0.071682,184.87,-0.71222,0.0027467,0.70195,261.87
> view matrix models
> #7.1,0.63726,0.053079,0.76882,210.42,0.18684,0.95722,-0.22096,168.07,-0.74766,0.28445,0.60008,253.89
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.63726,0.053079,0.76882,208.69,0.18684,0.95722,-0.22096,171.97,-0.74766,0.28445,0.60008,254.92
> view matrix models
> #7.1,0.63726,0.053079,0.76882,209.09,0.18684,0.95722,-0.22096,174.45,-0.74766,0.28445,0.60008,259.11
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.62362,0.070465,0.77855,209.66,0.22628,0.93702,-0.26606,171.53,-0.74826,0.34209,0.5684,256.78
> view matrix models
> #7.1,0.61203,0.086506,0.78609,210.1,0.26096,0.91623,-0.30401,169.1,-0.74654,0.3912,0.53819,254.58
> ui mousemode right "rotate selected models"
> ~select #7.1
Nothing selected
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:54:19 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.1/B 8.2/B 8.3/B
8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B | apolipoprotein A-I
> mmaker #8 to #7
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 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.1), sequence
alignment score = 889.9
RMSD between 167 pruned atom pairs is 0.000 angstroms; (across all 167 pairs:
0.000)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.2), sequence
alignment score = 889.9
RMSD between 99 pruned atom pairs is 0.967 angstroms; (across all 167 pairs:
2.405)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.3), sequence
alignment score = 882.7
RMSD between 146 pruned atom pairs is 0.614 angstroms; (across all 167 pairs:
6.590)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.4), sequence
alignment score = 879.1
RMSD between 90 pruned atom pairs is 0.877 angstroms; (across all 167 pairs:
6.733)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.5), sequence
alignment score = 886.3
RMSD between 83 pruned atom pairs is 0.781 angstroms; (across all 167 pairs:
7.288)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.6), sequence
alignment score = 889.9
RMSD between 150 pruned atom pairs is 0.625 angstroms; (across all 167 pairs:
4.094)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.7), sequence
alignment score = 886.3
RMSD between 150 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
2.428)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.8), sequence
alignment score = 882.7
RMSD between 114 pruned atom pairs is 1.220 angstroms; (across all 167 pairs:
8.487)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.9), sequence
alignment score = 886.3
RMSD between 137 pruned atom pairs is 0.954 angstroms; (across all 167 pairs:
7.152)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.10), sequence
alignment score = 886.3
RMSD between 149 pruned atom pairs is 0.855 angstroms; (across all 167 pairs:
1.629)
> close #7
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 22:03:06 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb #7
---
Chain | Description
B C | No description available
> select #7
4272 atoms, 4342 bonds, 530 residues, 1 model selected
> view matrix models #7,1,0,0,155.3,0,1,0,-32.66,0,0,1,15.862
> view matrix models #7,1,0,0,227.55,0,1,0,182.45,0,0,1,257.42
> view matrix models #7,1,0,0,226.69,0,1,0,184.64,0,0,1,255.63
> view matrix models #7,1,0,0,204.58,0,1,0,234.23,0,0,1,235.65
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.55,-0.4966,0.03861,-0.86712,237.02,-0.54821,0.76058,0.34783,236.07
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,202.23,-0.4966,0.03861,-0.86712,223.37,-0.54821,0.76058,0.34783,214.9
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.71,-0.4966,0.03861,-0.86712,212.44,-0.54821,0.76058,0.34783,207.19
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.77,-0.4966,0.03861,-0.86712,212.73,-0.54821,0.76058,0.34783,213.42
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.7,-0.4966,0.03861,-0.86712,204.73,-0.54821,0.76058,0.34783,218.41
> view matrix models
> #7,0.67294,0.6481,-0.35654,169.65,-0.4966,0.03861,-0.86712,208.53,-0.54821,0.76058,0.34783,221.42
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.74751,0.56918,-0.34243,169.65,-0.52825,0.19685,-0.82595,208.32,-0.40271,0.7983,0.44782,221.09
> view matrix models
> #7,0.17157,-0.18647,-0.96736,171.99,0.92678,0.36358,0.094287,205.38,0.33413,-0.91271,0.23519,222.64
> view matrix models
> #7,-0.43014,-0.90269,-0.011358,172.47,-0.7035,0.32728,0.63086,206.67,-0.56575,0.27935,-0.77582,223.35
> view matrix models
> #7,-0.56096,-0.12743,-0.81798,172.58,-0.79405,0.36224,0.48812,206.9,0.2341,0.92333,-0.30439,221.07
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,172.56,-0.84174,0.37778,0.38568,207.05,0.27385,0.91443,-0.29802,221.03
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,175.91,-0.84174,0.37778,0.38568,203.89,0.27385,0.91443,-0.29802,211.39
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.08,-0.84174,0.37778,0.38568,206.07,0.27385,0.91443,-0.29802,215.64
> hide #!8 models
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.65,-0.84174,0.37778,0.38568,206.88,0.27385,0.91443,-0.29802,212.06
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:08:07 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb
#9
---
Chain | Description
B C | No description available
> mmaker #9 to #10
No 'to' model specified
> mmaker #9 to #7
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 ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb, chain B (#7) with
ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb, chain B (#9),
sequence alignment score = 1084.5
RMSD between 74 pruned atom pairs is 0.985 angstroms; (across all 207 pairs:
10.547)
> hide #7 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.52533,-0.58815,-0.61491,177.85,0.0047201,0.72466,-0.68909,201.87,0.85089,0.35909,0.38346,210.74
> view matrix models
> #9,0.45946,-0.88174,0.10689,181.58,0.8882,0.45638,-0.053134,204.22,-0.0019327,0.11935,0.99285,214.69
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.45946,-0.88174,0.10689,177.6,0.8882,0.45638,-0.053134,197.13,-0.0019327,0.11935,0.99285,218.41
> view matrix models
> #9,0.45946,-0.88174,0.10689,175.75,0.8882,0.45638,-0.053134,203.48,-0.0019327,0.11935,0.99285,218.85
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.69,0.8882,0.45638,-0.053134,196.29,-0.0019327,0.11935,0.99285,214.81
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.27,0.8882,0.45638,-0.053134,199.29,-0.0019327,0.11935,0.99285,212.88
> view matrix models
> #9,0.45946,-0.88174,0.10689,173.56,0.8882,0.45638,-0.053134,203.27,-0.0019327,0.11935,0.99285,212.35
> view matrix models
> #9,0.45946,-0.88174,0.10689,176.72,0.8882,0.45638,-0.053134,202,-0.0019327,0.11935,0.99285,212.91
> view matrix models
> #9,0.45946,-0.88174,0.10689,172.24,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.78
> view matrix models
> #9,0.45946,-0.88174,0.10689,171.54,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.45
> ui tool show "Fit in Map"
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 3334 atoms
average map value = 0.1014, steps = 288
shifted from previous position = 26.2
rotated from previous position = 35.6 degrees
atoms outside contour = 2236, contour level = 0.14151
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.15030095 -0.25689088 -0.95468145 159.80559539
0.91205850 0.40867945 0.03362089 142.63963221
0.38152180 -0.87577859 0.29572442 147.85545078
Axis -0.45590440 -0.66987165 0.58602316
Axis point -104.50370211 0.00000000 221.35941513
Rotation angle (degrees) 94.16607036
Shift along axis -81.75960077
> view matrix models
> #9,0.67727,-0.51922,0.52127,172.73,0.71543,0.63007,-0.30194,194.77,-0.17166,0.57742,0.7982,218.78
> view matrix models
> #9,0.67727,-0.51922,0.52127,173.99,0.71543,0.63007,-0.30194,197.51,-0.17166,0.57742,0.7982,212.36
> view matrix models
> #9,0.67727,-0.51922,0.52127,174.96,0.71543,0.63007,-0.30194,195,-0.17166,0.57742,0.7982,208.97
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.66193,-0.59819,0.45168,174.95,0.73725,0.62836,-0.24824,195.18,-0.13532,0.49732,0.85695,209.41
> view matrix models
> #9,0.64956,-0.67275,0.35424,174.82,0.71372,0.70012,0.020895,196.02,-0.26207,0.23925,0.93492,210.62
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:18:18 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #9 models
> hide #!10 models
> show #6 models
> hide #4 models
> hide #3 models
> ui tool show "Fit in Map"
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.07482, steps = 364
shifted from previous position = 2.61
rotated from previous position = 17.1 degrees
atoms outside contour = 8195, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99640848 0.07252019 0.04371456 331.26650068
-0.01695668 -0.67668277 0.73607941 166.80204366
0.08296151 0.73269451 0.67548215 -88.38561339
Axis -0.03462299 -0.40144391 -0.91522895
Axis point 169.54681270 98.35816249 0.00000000
Rotation angle (degrees) 177.19813771
Shift along axis 2.46197109
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.64956,-0.67275,0.35424,175.54,0.71372,0.70012,0.020895,189.47,-0.26207,0.23925,0.93492,190.81
> ~select #9
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,-0.99797,0.039575,0.049905,338.25,-0.014392,-0.90338,0.42859,266.52,0.062045,0.42701,0.90212,-62.663
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.99623,0.082033,0.028348,334.24,-0.086585,-0.91673,-0.39002,429.14,-0.006007,-0.391,0.92037,92.117
> view matrix models
> #6,-0.99623,0.082033,0.028348,335.42,-0.086585,-0.91673,-0.39002,430.38,-0.006007,-0.391,0.92037,88.929
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09493, steps = 84
shifted from previous position = 3.13
rotated from previous position = 3.82 degrees
atoms outside contour = 7003, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820989 0.05968746 0.00379835 345.43779112
-0.05973880 -0.99809742 -0.01525811 372.27574829
0.00288041 -0.01545771 0.99987637 1.80150722
Axis -0.00167123 0.00768605 -0.99996907
Axis point 178.28007958 180.98306790 0.00000000
Rotation angle (degrees) 176.57654715
Shift along axis 0.48257203
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09495, steps = 48
shifted from previous position = 0.019
rotated from previous position = 0.00432 degrees
atoms outside contour = 7012, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820895 0.05970074 0.00383565 345.40975009
-0.05975246 -0.99809759 -0.01519388 372.26991158
0.00292127 -0.01539585 0.99987721 1.78218185
Axis -0.00169079 0.00765450 -0.99996927
Axis point 178.26722509 180.97930211 0.00000000
Rotation angle (degrees) 176.57577490
Shift along axis 0.48339683
> set bgColor white
> lighting full
> ~select #6
Nothing selected
> hide #6 models
> show #6 models
> color #6 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> select #1
2 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> ~select #1
Nothing selected
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #4 models
> hide #6 models
> volume #2 color #a7a49f80
> volume #2 color #b8b5af80
> color #3-4 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 12 atomic
models, 1 maps.
> hide #4 models
> show #4 models
> hide #4 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select #2
2 models selected
> ~select #2
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> show #4 models
> ui tool show "Segment Map"
> show #9 models
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.64956,-0.67275,0.35424,173.28,0.71372,0.70012,0.020895,203.74,-0.26207,0.23925,0.93492,217.24
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.42545,-0.83111,0.35811,174.01,0.88507,0.46469,0.026952,204.31,-0.18881,0.30548,0.93329,216.96
> view matrix models
> #9,0.36854,-0.89204,0.26163,173.89,0.89839,0.4141,0.14638,204.91,-0.23892,0.18109,0.954,217.47
> view matrix models
> #9,0.39748,-0.85333,0.3374,174.03,0.89601,0.44024,0.057848,204.49,-0.1979,0.27932,0.93958,217.07
> view matrix models
> #9,0.4249,-0.82293,0.37715,174.06,0.89397,0.44699,-0.03185,204.13,-0.14237,0.3507,0.9256,216.74
> view matrix models
> #9,0.30959,-0.88763,0.34097,174.24,0.94929,0.30918,-0.057041,204.4,-0.05479,0.34134,0.93834,216.73
> ~select #9
Nothing selected
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.30959,-0.88763,0.34097,171.78,0.94929,0.30918,-0.057041,200.45,-0.05479,0.34134,0.93834,215.77
> ~select #9
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\dahailuo\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\movie2.mp4"
Movie saved to \C:Users\\...\Data_EM_Alvin\movie2.mp4
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> mmaker #6 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 F562a.pdb, chain B (#4) with D2NS1-F562.pdb, chain C (#6), sequence
alignment score = 1200
RMSD between 228 pruned atom pairs is 0.000 angstroms; (across all 228 pairs:
0.000)
> hide #!2 models
> hide #9 models
> hide #3 models
> hide #4 models
> show #!2 models
> hide #6 models
> show #!1 models
> show #!10 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 48, shift = 0.0601, angle = 0.109 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27792284 -0.14164293 -0.95010322 410.09306464
0.39540197 0.88452622 -0.24752902 -48.83916554
0.87545196 -0.44446666 -0.18982414 109.38604242
Axis -0.10294301 -0.95425209 0.28072349
Axis point 169.05771360 0.00000000 208.04394464
Rotation angle (degrees) 106.95439226
Shift along axis 35.09589160
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2809, overlap = 5991
steps = 48, shift = 0.0078, angle = 0.0885 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27794843 -0.14312388 -0.94987377 410.31424613
0.39534589 0.88416435 -0.24890760 -48.51539453
0.87546917 -0.44471217 -0.18916865 109.30275225
Axis -0.10234637 -0.95410041 0.28145627
Axis point 169.16249688 0.00000000 208.15543264
Rotation angle (degrees) 106.94636481
Shift along axis 35.05832906
> hide #!2 models
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.74046,0.62541,0.24616,-107.44,-0.65719,0.75044,0.070241,152.95,-0.1408,-0.21378,0.96668,70.267
> view matrix models
> #1,0.72193,-0.13867,0.67793,-42.597,0.2204,0.97477,-0.035306,-25.414,-0.65593,0.1749,0.73428,133.11
> view matrix models
> #1,0.74615,0.64297,-0.17276,-38.999,0.62682,-0.76589,-0.14322,231.4,-0.22441,-0.0014231,-0.97449,383.68
> view matrix models
> #1,0.80841,0.29993,0.50648,-106.59,0.51816,-0.77083,-0.37058,291.07,0.27926,0.56202,-0.77856,159.28
> view matrix models
> #1,0.96135,-0.23483,0.14371,24.411,0.25186,0.96097,-0.11451,-14.839,-0.11121,0.14628,0.98297,-2.0945
> view matrix models
> #1,0.99141,-0.075528,-0.10677,34.022,0.051461,0.97582,-0.21244,35.244,0.12024,0.20512,0.97132,-51.881
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 716, shift = 1.66, angle = 12.6 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27785362 -0.14026525 -0.95032783 409.88132947
0.39567157 0.88475643 -0.24627224 -49.16134094
0.87535212 -0.44444535 -0.19033380 109.50506725
Axis -0.10359229 -0.95434929 0.28015367
Axis point 168.94433960 0.00000000 207.96495201
Rotation angle (degrees) 106.96068830
Shift along axis 35.13479072
> show #!2 models
> hide #!2 models
> show #!2 models
> ~select #1
Nothing selected
> select #1
2 models selected
> view matrix models
> #1,0.9987,0.030982,-0.040533,2.2432,0.0036821,0.74864,0.66296,-67.414,0.050884,-0.66225,0.74755,154.04
> view matrix models
> #1,0.87306,0.20075,-0.44437,64.348,0.48063,-0.20061,0.85367,-16.172,0.082229,-0.95888,-0.27163,378
> view matrix models
> #1,0.83244,0.37492,-0.40802,34.215,0.55119,-0.48475,0.67912,52.19,0.056831,-0.79023,-0.61017,411.1
> view matrix models
> #1,0.68639,0.56283,-0.46053,35.845,0.69489,-0.69435,0.1871,149.22,-0.21447,-0.44844,-0.8677,443.15
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> view matrix models
> #1,0.82844,0.50873,-0.23428,-19.057,0.47101,-0.40647,0.7829,34.547,0.30305,-0.75893,-0.57635,355.71
> view matrix models
> #1,0.84453,-0.094928,-0.52703,136.53,-0.025459,-0.99017,0.13755,339.15,-0.5349,-0.10275,-0.83864,433.6
> view matrix models
> #1,0.97799,-0.18464,-0.097184,54.238,-0.1969,-0.66248,-0.72274,460.34,0.069068,0.72597,-0.68425,151.17
> view matrix models
> #1,0.97796,-0.19168,-0.082782,53.003,-0.16644,-0.47632,-0.86337,446.06,0.12606,0.85812,-0.49773,85.086
> view matrix models
> #1,0.99726,0.035713,-0.06472,5.846,-0.039623,-0.48086,-0.8759,426.41,-0.062402,0.87607,-0.47813,112.12
> view matrix models
> #1,-0.96752,0.24305,-0.069446,320.31,-0.20699,-0.60408,0.76957,193.12,0.14509,0.75896,0.63477,-96.862
> view matrix models
> #1,-0.85416,0.24266,-0.45992,367.81,-0.51768,-0.48048,0.70792,237.19,-0.049202,0.84277,0.53603,-60.033
> view matrix models
> #1,-0.98697,0.14048,-0.078425,343.64,-0.16057,-0.82904,0.53564,265.52,0.010232,0.54125,0.8408,-69.644
> view matrix models
> #1,-0.99016,0.10292,-0.094853,353.76,-0.13794,-0.83244,0.53668,261.91,-0.023726,0.54448,0.83844,-63.751
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99016,0.10292,-0.094853,357.93,-0.13794,-0.83244,0.53668,248.71,-0.023726,0.54448,0.83844,-68.308
> view matrix models
> #1,-0.99016,0.10292,-0.094853,358.29,-0.13794,-0.83244,0.53668,250.68,-0.023726,0.54448,0.83844,-68.894
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.9422,-0.030752,0.33364,299.34,0.13856,-0.9424,0.30443,261.21,0.30506,0.33307,0.89219,-99.156
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.5,0.28029,-0.94609,-0.16233,317.46,0.56574,0.026196,0.82416,-79.125
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.77548,-0.32284,0.54259,268.3,0.28029,-0.94609,-0.16233,334.8,0.56574,0.026196,0.82416,-67.645
> view matrix models
> #1,-0.77548,-0.32284,0.54259,265.58,0.28029,-0.94609,-0.16233,338.57,0.56574,0.026196,0.82416,-65.98
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.03,0.28029,-0.94609,-0.16233,352.61,0.56574,0.026196,0.82416,-59.271
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91194,-0.17978,0.36883,313.96,0.10929,-0.97286,-0.20397,395.12,0.39549,-0.1457,0.90684,-12.537
> view matrix models
> #1,-0.91113,-0.10679,0.39805,295.73,0.021642,-0.97691,-0.21254,412.97,0.41156,-0.18504,0.8924,-5.8812
> view matrix models
> #1,-0.99135,-0.088862,0.096564,359.09,0.037913,-0.89841,-0.43753,435.05,0.12563,-0.43008,0.894,88.599
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99135,-0.088862,0.096564,361.35,0.037913,-0.89841,-0.43753,415.99,0.12563,-0.43008,0.894,90.946
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.47,-0.013738,-0.97125,-0.23766,403.58,0.13986,-0.23721,0.96134,42.319
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.46,-0.013738,-0.97125,-0.23766,399.55,0.13986,-0.23721,0.96134,42.616
> view matrix models
> #1,-0.99008,-0.020034,0.1391,338.93,-0.013738,-0.97125,-0.23766,400.44,0.13986,-0.23721,0.96134,32.494
> view matrix models
> #1,-0.99008,-0.020034,0.1391,335.49,-0.013738,-0.97125,-0.23766,400.28,0.13986,-0.23721,0.96134,33.65
> view matrix models
> #1,-0.99008,-0.020034,0.1391,333.14,-0.013738,-0.97125,-0.23766,400.18,0.13986,-0.23721,0.96134,33.756
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99347,-0.11227,0.020092,370.83,0.11149,-0.99309,-0.036498,346.87,0.024051,-0.03402,0.99913,11.612
> view matrix models
> #1,-0.99314,-0.11513,0.02023,371.26,0.11367,-0.99155,-0.06254,350.72,0.027259,-0.059812,0.99784,15.866
> view matrix models
> #1,-0.99502,-0.048682,0.086949,348.18,0.043004,-0.99689,-0.06602,364.89,0.089893,-0.061952,0.99402,5.7314
> view matrix models
> #1,-0.9999,-0.011841,0.0079016,356.17,0.012535,-0.99545,0.094484,342.25,0.0067469,0.094574,0.9955,-7.6193
> view matrix models
> #1,-0.99955,0.029264,0.006465,349.02,-0.028596,-0.99584,0.086513,351.05,0.0089699,0.086289,0.99623,-6.6648
> show #!2 models
> hide #!2 models
> view matrix models
> #1,-0.99431,-0.012476,0.10579,338.32,0.013343,-0.99988,0.0074894,357.98,0.10568,0.0088583,0.99436,-9.7821
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 948, shift = 10.3, angle = 23.5 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.27780939 0.13998726 -0.95038174 260.70800172
-0.39575740 -0.88479067 -0.24601119 407.82841194
-0.87532735 0.44446484 -0.19040216 263.31428797
Axis 0.78717074 -0.08556506 -0.61077070
Axis point 0.00000000 178.59809032 292.75645151
Rotation angle (degrees) 153.98663078
Shift along axis 9.50119898
> hide #!10 models
> show #6 models
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,0.80584,-0.033933,0.59116,-60.641,-0.18803,0.93202,0.30982,-22.728,-0.56149,-0.36082,0.74468,228.14
> view matrix models
> #6,0.84169,0.23741,0.48497,-96.336,-0.031206,0.91804,-0.39525,78.603,-0.53906,0.31754,0.78012,96.759
> view matrix models
> #6,0.95752,0.28708,0.027255,-43.538,-0.26323,0.90873,-0.32391,108.93,-0.11776,0.30298,0.94569,-5.8011
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.95752,0.28708,0.027255,-47.959,-0.26323,0.90873,-0.32391,118,-0.11776,0.30298,0.94569,-22.337
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99918,0.040001,0.0063686,-7.5857,-0.036305,0.95416,-0.29708,64.472,-0.01796,0.2966,0.95483,-40.695
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 96
shifted from previous position = 4.3
rotated from previous position = 4.93 degrees
atoms outside contour = 6857, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 -0.00003889 0.00000390 356.92132489
0.00003889 -0.99999983 -0.00059770 357.02795185
0.00000392 -0.00059770 0.99999983 0.10572384
Axis -0.00000446 -0.00030232 0.99999995
Axis point 178.45719114 178.51746241 0.00000000
Rotation angle (degrees) 179.99777155
Shift along axis -0.00380630
> ~select #6
Nothing selected
> interfaces #6 & ~solvent
7 buried areas: A B 2354, E F 2040, C D 2040, B C 1572, A F 1542, B D 1312, A
E 1190
> open "C:/Users/dahailuo/Downloads/cryosparc_P35_J100_005_volume_map_sharp
> (1).mrc"
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.0415, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1102+1920+23 (frame:
1936x1141+1912-8) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1920x1017+1920+23 (frame:
1936x1056+1912-8) margins: 8, 31, 8, 8 minimum size: 493x1102 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=509,1141 maxtrack=0,0)
> volume #11 step 1
> surface dust #1 size 8.58
> surface dust #11 size 8.58
> volume #11 level 0.045
> volume #11 level 0.05
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) using 12404 atoms
average map value = 0.08442, steps = 152
shifted from previous position = 1.4
rotated from previous position = 4.71 degrees
atoms outside contour = 5898, contour level = 0.05
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) coordinates:
Matrix rotation and translation
0.99897026 0.04182548 -0.01757995 -4.15590074
-0.04516063 0.95385198 -0.29686178 69.02604187
0.00435228 0.29735001 0.95475862 -45.20466997
Axis 0.98879513 -0.03649622 -0.14474879
Axis point 0.00000000 183.11150795 204.04343868
Rotation angle (degrees) 17.48599398
Shift along axis -0.08520266
> transparency #11.1 50
> show #3 models
> mmaker #3 to #6
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 D2NS1-F562.pdb, chain A (#6) with D2NS1.pdb, chain B (#3), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 60
shifted from previous position = 1.1
rotated from previous position = 2.61 degrees
atoms outside contour = 3025, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14875593 -0.08639183 -0.98509297 342.36735832
0.98470147 -0.07847453 0.15557896 -15.12271804
-0.09074546 -0.99316577 0.07339661 361.18209695
Axis -0.63557683 -0.49482408 0.59261389
Axis point 0.00000000 37.80172615 346.76474569
Rotation angle (degrees) 115.35090835
Shift along axis 3.92385104
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07339, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.00688 degrees
atoms outside contour = 3021, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14885535 -0.08637602 -0.98507934 342.35458834
0.98468094 -0.07852972 0.15568097 -15.13336069
-0.09080510 -0.99316278 0.07336326 361.19655370
Axis -0.63562980 -0.49478213 0.59259210
Axis point 0.00000000 37.81870419 346.75288311
Rotation angle (degrees) 115.35056364
Shift along axis 3.91916090
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.0195 degrees
atoms outside contour = 3027, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14869429 -0.08663603 -0.98508083 342.41395707
0.98471526 -0.07839157 0.15553350 -15.12882419
-0.09069683 -0.99315105 0.07365544 361.12491138
Axis -0.63549687 -0.49480794 0.59271311
Axis point 0.00000000 37.79183158 346.80910583
Rotation angle (degrees) 115.34202749
Shift along axis 3.92633355
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,0.052602,-0.042076,-0.99773,354.08,0.96197,-0.26603,0.061936,37.093,-0.26803,-0.96305,0.026482,395.65
> view matrix models
> #3,0.0070452,-0.012575,-0.9999,357.51,0.93425,-0.35645,0.011066,66.236,-0.35656,-0.93423,0.0092369,409.45
> view matrix models
> #3,-0.0058622,0.0073093,-0.99996,356.45,0.91272,-0.40851,-0.0083368,82.232,-0.40855,-0.91272,-0.0042765,417.39
> view matrix models
> #3,-0.020074,-0.027951,-0.99941,364.78,0.92365,-0.38315,-0.0078364,75.954,-0.3827,-0.92326,0.033508,407.88
> view matrix models
> #3,0.0017745,-0.041136,-0.99915,363.11,0.92163,-0.38766,0.017597,72.537,-0.38806,-0.92088,0.037224,407.76
> view matrix models
> #3,-0.017771,-0.12129,-0.99246,378.83,0.9086,-0.41622,0.034596,76.603,-0.41728,-0.90114,0.1176,395.26
> view matrix models
> #3,0.012861,-0.10916,-0.99394,371.67,0.88601,-0.45952,0.061933,82.986,-0.46349,-0.88144,0.09081,404.85
> view matrix models
> #3,0.012034,-0.092833,-0.99561,369.37,0.88338,-0.46553,0.054084,85.858,-0.46851,-0.88015,0.076405,408.08
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.56,0.88274,-0.46516,0.066341,83.724,-0.46934,-0.8796,0.077605,407.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.16,0.88274,-0.46516,0.066341,83.998,-0.46934,-0.8796,0.077605,407.23
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.06,0.88274,-0.46516,0.066341,83.639,-0.46934,-0.8796,0.077605,407.78
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.91,0.88274,-0.46516,0.066341,85.463,-0.46934,-0.8796,0.077605,407.43
> ~select #3
Nothing selected
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> show #4 models
> hide #4 models
> show #4 models
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 64
shifted from previous position = 1.84
rotated from previous position = 3.05 degrees
atoms outside contour = 1419, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82616267 0.51307542 -0.23282799 17.45941536
-0.12390784 -0.23766697 -0.96341127 357.00880636
-0.54963816 0.82478363 -0.13277751 149.37621508
Axis 0.92916660 0.16461820 -0.33098381
Axis point 0.00000000 112.71394709 221.40097809
Rotation angle (degrees) 105.79170262
Shift along axis 25.55174348
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 48
shifted from previous position = 0.011
rotated from previous position = 0.0276 degrees
atoms outside contour = 1418, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82596970 0.51342982 -0.23273140 17.41926576
-0.12364669 -0.23778983 -0.96341451 356.97717269
-0.54998689 0.82452765 -0.13292329 149.51361297
Axis 0.92909832 0.16486078 -0.33105473
Axis point 0.00000000 112.65571575 221.42366392
Rotation angle (degrees) 105.80544612
Shift along axis 25.53855668
> hide #6 models
> show #5 models
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1083, steps = 76
shifted from previous position = 0.951
rotated from previous position = 3.36 degrees
atoms outside contour = 1258, contour level = 0.05
Position of F562b.pdb (#5) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.91100184 -0.19027699 -0.36588295 82.97740999
-0.38499639 -0.71041595 -0.58914087 517.50161240
-0.14782913 0.67757202 -0.72044619 248.76959820
Axis 0.97438742 -0.16773248 -0.14978305
Axis point 0.00000000 219.97208546 227.46670853
Rotation angle (degrees) 139.45804049
Shift along axis -43.21115606
> color #3-5 bychain
> hide #!11 models
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab56
> .cxs"
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-
> Fab5-DL.cxs" includeMaps true
——— End of log from Thu Mar 3 12:01:46 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #5
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #7 models
> hide #!8 models
> hide #9 models
> close #8
> show #9 models
> hide #9 models
> show #7 models
> show #9 models
> hide #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:9-11
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B:1-207
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-86
208 atoms, 215 bonds, 23 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an
ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-
tuples-or ndarrays with different lengths or shapes) is deprecated. If you
meant to do this, you must specify 'dtype=object' when creating the ndarray
return array(a, dtype, copy=False, order=order)
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel blue
> color sel cornflower blue
> select #9/B:151-152
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #9/B:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel cornflower blue
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> close #10
> close #11
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #3 models
> show #4 models
> show #5 models
> hide #5 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> hide #4 models
> show #4 models
> hide #4 models
> select #9/C:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/C:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel medium blue
> select #9/C:151
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/C:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel medium blue
> close #7
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> close #6
> show #4 models
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J142_005_volume_map_sharp.mrc"
Opened cryosparc_P47_J142_005_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0449, step 2, values float32
> volume #6 step 1
> volume #6 level 0.1656
> volume #6 level 0.06061
> close #6
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J128_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0566, step 2, values float32
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!6 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> show #!6 models
> volume #6 step 1
> volume #6 level 0.116
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J132_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J132_002_volume_map_sharp.mrc as #7, grid size
360,360,360, pixel 0.85, shown at level 0.0558, step 2, values float32
> volume #7 step 1
> volume #7 level 0.189
> volume #6 level 0.148
> volume #6 level 0.1384
> volume #7 level 0.08193
> volume #7 level 0.04862
> volume #6 level 0.06462
> close #7
> volume #6 level 0.1336
> volume #6 level 0.1256
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #6
2 models selected
> view matrix models
> #6,-0.83996,0.011508,0.54253,184.02,0.50426,0.3859,0.77253,-105.68,-0.20047,0.92247,-0.32995,103.36
> view matrix models
> #6,0.1848,-0.18014,0.96613,-8.4193,0.46665,-0.84908,-0.24758,260.82,0.86492,0.4966,-0.072852,-31.125
> view matrix models
> #6,0.25195,-0.19005,0.94889,-14.067,0.4832,-0.82485,-0.29351,262.08,0.83847,0.53245,-0.11599,-25.726
> view matrix models
> #6,-0.035938,-0.13733,0.98987,13.939,0.38333,-0.91664,-0.11325,261.83,0.92291,0.37538,0.085583,-46.756
> view matrix models
> #6,0.1558,-0.53982,0.82724,75.077,-0.30263,-0.82328,-0.48024,409.8,0.94029,-0.17552,-0.29163,98.871
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.1558,-0.53982,0.82724,121.85,-0.30263,-0.82328,-0.48024,428.76,0.94029,-0.17552,-0.29163,116.7
> view matrix models
> #6,0.1558,-0.53982,0.82724,122.7,-0.30263,-0.82328,-0.48024,438.5,0.94029,-0.17552,-0.29163,113.43
> view matrix models
> #6,0.1558,-0.53982,0.82724,123.68,-0.30263,-0.82328,-0.48024,449.46,0.94029,-0.17552,-0.29163,118.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.15847,-0.55227,0.81847,126.67,-0.30396,-0.81597,-0.49173,450.39,0.93941,-0.17086,-0.29717,118.9
> view matrix models
> #6,0.31733,-0.49565,0.80848,95.704,-0.41983,-0.83787,-0.34888,447.71,0.85032,-0.22872,-0.47397,170.26
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.921,-0.41983,-0.83787,-0.34888,440.31,0.85032,-0.22872,-0.47397,180.5
> view matrix models
> #6,0.31733,-0.49565,0.80848,96.096,-0.41983,-0.83787,-0.34888,439.7,0.85032,-0.22872,-0.47397,180.02
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.946,-0.41983,-0.83787,-0.34888,439.56,0.85032,-0.22872,-0.47397,179.06
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.851,-0.41983,-0.83787,-0.34888,439.42,0.85032,-0.22872,-0.47397,178.96
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.32806,-0.48111,0.81296,90.235,-0.37939,-0.85524,-0.35303,436.79,0.86512,-0.19262,-0.4631,169.31
> view matrix models
> #6,0.36269,-0.41122,0.83627,70.284,-0.30986,-0.89953,-0.30795,425.95,0.87889,-0.14743,-0.45367,158.62
> view matrix models
> #6,0.36637,-0.44198,0.8188,77.421,-0.35476,-0.87986,-0.31621,430.93,0.86019,-0.17462,-0.47915,169.85
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.762,-0.30034,-0.9051,-0.30097,424.26,0.88299,-0.1445,-0.44659,156.39
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.7,-0.30034,-0.9051,-0.30097,421.64,0.88299,-0.1445,-0.44659,155.81
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.281,-0.30034,-0.9051,-0.30097,420.24,0.88299,-0.1445,-0.44659,157.09
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.528,-0.30034,-0.9051,-0.30097,421,0.88299,-0.1445,-0.44659,156.78
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36427,-0.41429,0.83407,72.656,-0.28999,-0.90154,-0.32115,422.2,0.88499,-0.12489,-0.44854,153.73
> view matrix models
> #6,0.35177,-0.40975,0.84164,72.569,-0.29057,-0.90249,-0.31793,421.91,0.88984,-0.13272,-0.43653,152.26
> view matrix models
> #6,0.3599,-0.44231,0.82148,79.767,-0.28748,-0.89021,-0.35338,425.33,0.8876,-0.10898,-0.44754,150.68
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.749,-0.29539,-0.89136,-0.34382,425.13,0.87766,-0.11101,-0.46626,155.55
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37744,-0.43949,0.8151,76.75,-0.29539,-0.89136,-0.34382,424.99,0.87766,-0.11101,-0.46626,155.59
> view matrix models
> #6,0.37744,-0.43949,0.8151,75.665,-0.29539,-0.89136,-0.34382,426.6,0.87766,-0.11101,-0.46626,156.42
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.299,-0.29539,-0.89136,-0.34382,425.99,0.87766,-0.11101,-0.46626,155.38
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.803,-0.29539,-0.89136,-0.34382,426.26,0.87766,-0.11101,-0.46626,155.31
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.3964,-0.4154,0.81873,70.6,-0.31009,-0.89996,-0.30647,423.68,0.86412,-0.13239,-0.48555,163.85
> view matrix models
> #6,0.36188,-0.4339,0.82509,77.612,-0.3531,-0.88293,-0.30945,427.92,0.86276,-0.17936,-0.47273,169.32
> view matrix models
> #6,0.34333,-0.43629,0.83173,79.67,-0.33947,-0.88333,-0.32323,428.21,0.87572,-0.17137,-0.45138,162.63
> view matrix models
> #6,0.36882,-0.43654,0.82061,77.724,-0.34143,-0.88476,-0.31721,427.74,0.86452,-0.16319,-0.47537,166.95
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.88,-0.33111,-0.89091,-0.31088,426.13,0.86644,-0.15658,-0.47409,165.42
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37369,-0.42634,0.82377,75.079,-0.33111,-0.89091,-0.31088,425.43,0.86644,-0.15658,-0.47409,165.61
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.521,-0.33111,-0.89091,-0.31088,425.67,0.86644,-0.15658,-0.47409,165.89
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.154,-0.33111,-0.89091,-0.31088,425.74,0.86644,-0.15658,-0.47409,166.14
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.447,-0.33111,-0.89091,-0.31088,425.75,0.86644,-0.15658,-0.47409,166.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.5154,-0.37111,0.77242,53.045,-0.24207,-0.9277,-0.2842,413.84,0.82205,-0.040509,-0.56797,170.41
> view matrix models
> #6,0.49373,-0.37696,0.78367,55.354,-0.26058,-0.92389,-0.28024,415.36,0.82966,-0.065846,-0.55437,171.02
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ~select #6
Nothing selected
> vop resample #6 onGrid #2
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> close #6
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> volume #7 level 0.09689
Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 175454 points
correlation = 0.8828, correlation about mean = 0.547, overlap = 7225
steps = 168, shift = 7.84, angle = 17 degrees
Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95949380 0.09544158 -0.26507085 39.26017660
-0.07373087 0.99314477 0.09070403 -7.34539260
0.27191066 -0.06748605 0.95995324 -23.66014125
Axis -0.27050228 -0.91822900 -0.28928192
Axis point 103.77985456 0.00000000 135.28320696
Rotation angle (degrees) 17.00173416
Shift along axis 2.96923623
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_ac.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError:
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
->
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> -> : Error while saving session data for 'tools' ->
->
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Thu Mar 3 19:50:19 2022 ———
opened ChimeraX session
> show #9 models
> hide #!7 models
> show #3 models
> show #!7 models
> volume #7 level 0.1304
> hide #9 models
> hide #!2 models
> select #7
2 models selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.047588,-0.1037,-0.99347,365.91,0.86244,-0.4975,0.093243,89.677,-0.50392,-0.86124,0.065763,412.54
> view matrix models
> #3,0.06743,-0.16738,-0.98358,371.36,0.85706,-0.49497,0.14299,81.335,-0.51078,-0.85264,0.11008,404.4
> view matrix models
> #3,0.096228,-0.19565,-0.97594,369.69,0.85361,-0.48807,0.18201,73.83,-0.51194,-0.85059,0.12005,402.49
> view matrix models
> #3,0.12326,-0.1737,-0.97705,361.44,0.80994,-0.55129,0.20019,88.903,-0.57341,-0.81603,0.072729,415.92
> view matrix models
> #3,0.16662,-0.22348,-0.96036,359.21,0.80001,-0.5387,0.26416,77.136,-0.57639,-0.81231,0.089027,412.91
> view matrix models
> #3,0.16293,-0.22083,-0.96161,359.64,0.8006,-0.54002,0.25966,78.055,-0.57663,-0.81217,0.088811,412.97
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.16293,-0.22083,-0.96161,359.93,0.8006,-0.54002,0.25966,80.609,-0.57663,-0.81217,0.088811,411.39
> view matrix models
> #3,0.16293,-0.22083,-0.96161,360.07,0.8006,-0.54002,0.25966,81.287,-0.57663,-0.81217,0.088811,412.29
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.17153,-0.1861,-0.96744,353.75,0.81713,-0.52169,0.24523,77.868,-0.55034,-0.83259,0.062584,415.78
> view matrix models
> #3,0.18128,-0.16143,-0.97009,348.36,0.82389,-0.51369,0.23944,76.368,-0.53698,-0.84265,0.03988,419.16
> view matrix models
> #3,0.15753,-0.14621,-0.97663,351.15,0.82063,-0.53075,0.21182,84.727,-0.54931,-0.83482,0.03638,420.64
> view matrix models
> #3,0.14559,-0.14302,-0.97895,353.12,0.82526,-0.52818,0.1999,85.606,-0.54566,-0.837,0.04113,419.52
> view matrix models
> #3,0.10891,-0.20392,-0.97291,368.74,0.80086,-0.56179,0.20739,94.212,-0.58886,-0.80175,0.10213,410.32
> view matrix models
> #3,7.5917e-05,-0.38124,-0.92448,409.06,0.76186,-0.5988,0.247,100.24,-0.64774,-0.70434,0.29041,370.76
> view matrix models
> #3,0.020851,-0.42125,-0.9067,408.97,0.8145,-0.51877,0.25975,75.255,-0.57979,-0.74392,0.33229,358
> view matrix models
> #3,0.0058992,-0.41587,-0.90941,411.17,0.80554,-0.53687,0.25074,81.477,-0.59251,-0.73405,0.33183,358.66
> view matrix models
> #3,0.010117,-0.39918,-0.91682,408.95,0.78121,-0.56916,0.25643,90.171,-0.62418,-0.71883,0.30608,366.25
> show #!2 models
> show #4 models
> hide #!2 models
> hide #4 models
> hide #!7 models
> show #!2 models
> volume #2 level 0.1739
> volume #2 level 0.2952
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> select #3/B:2,7,40,94,101,112-114,116,120,122,233
96 atoms, 87 bonds, 12 residues, 1 model selected
> color sel red
> color sel red
> volume #2 level 0.275
> volume #2 level 0.2628
> show #!7 models
> show #9 models
> hide #!7 models
> hide #!2 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.38721,-0.79412,0.46845,171.91,0.90831,0.41577,-0.04598,200.21,-0.15825,0.4433,0.88229,215.35
> view matrix models
> #9,-0.087483,-0.4123,0.90684,172.91,0.99343,0.031343,0.11009,201.89,-0.073812,0.91051,0.40685,212.01
> view matrix models
> #9,-0.28915,-0.67075,0.68299,173.05,0.95728,-0.20238,0.20652,203.01,-0.00030104,0.71353,0.70062,213.67
> view matrix models
> #9,-0.26136,-0.69506,0.66977,173.04,0.95462,-0.083484,0.28588,202.96,-0.14278,0.71409,0.68534,213.75
> view matrix models
> #9,-0.24903,-0.6779,0.69169,173.06,0.94836,-0.025801,0.31615,202.9,-0.19647,0.7347,0.64932,213.61
> view matrix models
> #9,-0.29521,-0.62627,0.72155,173.07,0.95342,-0.14413,0.26498,203.06,-0.061948,0.76617,0.63965,213.33
> view matrix models
> #9,-0.20952,-0.51342,0.83217,173.06,0.97542,-0.05031,0.21455,202.56,-0.068285,0.85666,0.51134,212.57
> view matrix models
> #9,0.10294,-0.34459,0.93309,172.61,0.93996,0.34057,0.022073,200.66,-0.32539,0.8748,0.35896,212.2
> view matrix models
> #9,-0.16022,-0.18462,0.96966,172.53,0.98145,0.074958,0.17644,202.03,-0.10526,0.97995,0.16919,210.92
> show #!2 models
> view matrix models
> #9,-0.15367,-0.25507,0.95464,172.68,0.9497,-0.30492,0.0714,202.82,0.27288,0.91759,0.28909,211.18
> view matrix models
> #9,-0.5038,0.50581,0.70024,169.74,0.53017,-0.45894,0.71295,206.18,0.68199,0.73043,-0.036959,210.08
> view matrix models
> #9,-0.57338,0.5803,0.57834,169.11,0.40927,-0.40864,0.81579,206.54,0.70974,0.70446,-0.0031917,210.27
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.57338,0.5803,0.57834,169.15,0.40927,-0.40864,0.81579,203.59,0.70974,0.70446,-0.0031917,212
> view matrix models
> #3,0.010117,-0.39918,-0.91682,409.31,0.78121,-0.56916,0.25643,90.718,-0.62418,-0.71883,0.30608,366.04
> view matrix models
> #3,0.010117,-0.39918,-0.91682,409.6,0.78121,-0.56916,0.25643,90.515,-0.62418,-0.71883,0.30608,366.16
> view matrix models
> #2,-0.25925,0.42088,0.86928,32.265,0.23342,0.90067,-0.36647,74.017,-0.93718,0.1079,-0.33174,370.87
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.61844,0.56215,0.54911,169.14,0.3784,-0.39939,0.83505,203.67,0.68873,0.72421,0.034284,212.11
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.61844,0.56215,0.54911,177.9,0.3784,-0.39939,0.83505,199.13,0.68873,0.72421,0.034284,214.65
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.4,0.3784,-0.39939,0.83505,196.45,0.68873,0.72421,0.034284,215.17
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.59,0.3784,-0.39939,0.83505,195.92,0.68873,0.72421,0.034284,215.89
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 5602 atoms
average map value = 0.1891, steps = 236
shifted from previous position = 3.82
rotated from previous position = 35.5 degrees
atoms outside contour = 3840, contour level = 0.26284
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97831960 0.09903901 0.18188469 -62.54218727
0.12885075 -0.97864261 -0.16017526 308.84298175
0.16213651 0.18013858 -0.97018650 260.99607581
Axis 0.99452465 0.05771160 0.08712110
Axis point 0.00000000 144.84592078 146.67317576
Rotation angle (degrees) 170.14858369
Shift along axis -21.63765850
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.56,0.3784,-0.39939,0.83505,195.48,0.68873,0.72421,0.034284,215.15
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.6283,0.53153,0.56808,178.73,0.62001,-0.098962,0.77833,194.1,0.46993,0.84124,-0.26738,213.86
> view matrix models
> #9,-0.75088,0.39219,0.53138,179.14,0.55722,-0.055683,0.82849,194.22,0.35452,0.9182,-0.17673,214.09
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.41,0.62601,-0.03822,0.77888,193.91,0.31059,0.92838,-0.20408,214
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.53,0.31059,0.92838,-0.20408,211.04
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.99,0.31059,0.92838,-0.20408,210.24
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.97,0.76527,0.12677,0.63111,197.77,-0.078317,0.99147,-0.10419,210.83
> select #3/C:2,7,40,94,101,112-114,116,120,122,233
96 atoms, 87 bonds, 12 residues, 1 model selected
> color sel red
> show #4 models
Average map value = 0.2376 for 3401 atoms, 1878 outside contour
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 3401 atoms
average map value = 0.2415, steps = 72
shifted from previous position = 1.54
rotated from previous position = 3.06 degrees
atoms outside contour = 1864, contour level = 0.26284
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.23699392 -0.97040420 -0.04636322 286.30117001
0.14025454 0.08139807 -0.98676390 234.10565599
0.96133372 0.22735440 0.15539445 -33.95669350
Axis 0.62922896 -0.52224902 0.57561001
Axis point 0.00000000 269.86990420 6.31008896
Rotation angle (degrees) 105.25448782
Shift along axis 38.34172327
Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 81674 points
correlation = 0.9169, correlation about mean = 0.5151, overlap = 5213
steps = 48, shift = 1.14, angle = 0.0547 degrees
Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95972235 0.09553744 -0.26420752 39.07093414
-0.07396939 0.99315174 0.09043310 -7.28703314
0.27103791 -0.06724740 0.96021677 -23.53165945
Axis -0.27038667 -0.91782581 -0.29066618
Axis point 103.47778140 0.00000000 135.13797870
Rotation angle (degrees) 16.95277212
Shift along axis 2.96382485
> close #7
> volume #1 level 0.127
> hide #!1 models
> volume #2 level 0.2119
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,-0.067254,-0.26525,-0.96183,404.94,0.33444,-0.91423,0.22874,235.99,-0.94001,-0.30629,0.1502,378.5
> view matrix models
> #3,-0.062041,-0.27434,-0.95963,405.16,0.30586,-0.92045,0.24337,239.46,-0.95005,-0.27841,0.14102,377.22
> view matrix models
> #3,-0.080997,-0.27474,-0.9581,408.29,0.28653,-0.9271,0.24163,244.29,-0.95464,-0.25496,0.15382,371.8
> view matrix models
> #3,-0.097933,-0.27408,-0.95671,410.91,0.27959,-0.93019,0.23786,246.7,-0.95511,-0.24419,0.16773,367.59
> undo
> view matrix models
> #3,-0.093936,-0.28928,-0.95262,412.03,0.28743,-0.92399,0.25224,241.72,-0.95318,-0.25012,0.16994,367.86
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.19,0.28616,-0.92153,0.26247,239.7,-0.95303,-0.24537,0.17756,365.67
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.02,0.76527,0.12677,0.63111,198.98,-0.078317,0.99147,-0.10419,210.72
> view matrix models
> #9,-0.63893,0.03031,0.76867,179.9,0.76527,0.12677,0.63111,199.21,-0.078317,0.99147,-0.10419,210.64
> view matrix models
> #9,-0.63893,0.03031,0.76867,179.76,0.76527,0.12677,0.63111,199.9,-0.078317,0.99147,-0.10419,210.02
> view matrix models
> #9,-0.63893,0.03031,0.76867,180,0.76527,0.12677,0.63111,200.37,-0.078317,0.99147,-0.10419,210.39
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.28,0.76527,0.12677,0.63111,200.62,-0.078317,0.99147,-0.10419,210.66
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.6138,0.057604,0.78735,180.24,0.78755,0.11393,0.60562,200.54,-0.054817,0.99182,-0.1153,210.59
> hide #!2 models
> view matrix models
> #9,-0.57468,0.068825,0.81548,180.27,0.81757,0.092677,0.56833,200.43,-0.036461,0.99331,-0.10953,210.59
> view matrix models
> #9,-0.55308,0.076775,0.82958,180.28,0.83069,0.12691,0.54207,200.21,-0.063663,0.98894,-0.13397,210.54
> view matrix models
> #9,-0.59939,0.13134,0.78961,180.01,0.79964,0.14277,0.58326,200.35,-0.036127,0.981,-0.1906,210.32
> view matrix models
> #9,-0.6287,0.16179,0.76063,179.83,0.77763,0.13788,0.61342,200.5,-0.0056352,0.97715,-0.2125,210.21
> view matrix models
> #9,-0.66075,0.22875,0.7149,179.49,0.74952,0.14988,0.64479,200.62,0.040346,0.96188,-0.27049,209.99
> view matrix models
> #9,-0.67709,0.24845,0.69269,179.36,0.73306,0.14512,0.6645,200.72,0.064571,0.95771,-0.28039,209.94
> show #!2 models
> show #!1 models
> hide #!1 models
> ~select #9
Nothing selected
> volume #2 level 0.1883
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.67709,0.24845,0.69269,178.01,0.73306,0.14512,0.6645,202.1,0.064571,0.95771,-0.28039,210.69
> view matrix models
> #9,-0.67709,0.24845,0.69269,178.34,0.73306,0.14512,0.6645,203.46,0.064571,0.95771,-0.28039,208.74
> ~select #9
Nothing selected
> hide #!2 models
> show #!2 models
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms
average map value = 0.1762, steps = 284
shifted from previous position = 2.13
rotated from previous position = 46.6 degrees
atoms outside contour = 1895, contour level = 0.18834
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.67425254 -0.64675933 -0.35649092 139.61136773
0.63282394 0.25716285 0.73034312 159.63361093
-0.38068004 -0.71803171 0.58267751 133.55311546
Axis -0.74936689 0.01251508 0.66203673
Axis point 0.00000000 205.05562824 -10.25332907
Rotation angle (degrees) 75.10511823
Shift along axis -14.20524073
> undo
> undo
> undo
> ~select #9
Nothing selected
> volume #2 level 0.2324
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms
average map value = 0.1762, steps = 284
shifted from previous position = 2.13
rotated from previous position = 46.6 degrees
atoms outside contour = 2433, contour level = 0.23244
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.67425254 -0.64675933 -0.35649092 139.61136773
0.63282394 0.25716285 0.73034312 159.63361093
-0.38068004 -0.71803171 0.58267751 133.55311546
Axis -0.74936689 0.01251508 0.66203673
Axis point 0.00000000 205.05562824 -10.25332907
Rotation angle (degrees) 75.10511823
Shift along axis -14.20524073
> ui mousemode right "rotate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.51095,-0.017684,0.85943,178.44,0.84026,0.20068,0.50368,202.45,-0.18138,0.9795,-0.087678,211.18
> view matrix models
> #9,-0.56127,0.054587,0.82583,178.14,0.82479,0.1196,0.55265,202.9,-0.068599,0.99132,-0.11215,210.93
> hide #!2 models
> show #!2 models
> volume #2 level 0.1785
> hide #!2 models
> view matrix models
> #9,-0.55438,-0.0074968,0.83223,178.35,0.81959,0.16891,0.54748,202.74,-0.14467,0.9856,-0.087495,211.12
> show #!2 models
> hide #!2 models
> view matrix models
> #9,-0.6081,0.00065434,0.79386,178.23,0.7807,0.18184,0.59786,202.93,-0.14397,0.98333,-0.11109,211.04
> view matrix models
> #9,-0.60898,-0.00026107,0.79319,178.23,0.7797,0.18341,0.59869,202.93,-0.14563,0.98304,-0.11149,211.04
> view matrix models
> #9,-0.56366,0.059523,0.82386,178.12,0.81918,0.1683,0.54829,202.74,-0.10602,0.98394,-0.14362,210.87
> view matrix models
> #9,-0.61089,0.11381,0.78349,177.85,0.79055,0.14142,0.59585,203.04,-0.042985,0.98339,-0.17637,210.68
> show #!2 models
> volume #2 level 0.1908
> view matrix models
> #9,-0.59527,0.088593,0.79863,177.97,0.80315,0.095932,0.588,203.13,-0.024521,0.99144,-0.12826,210.82
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.59527,0.088593,0.79863,180.49,0.80315,0.095932,0.588,202.55,-0.024521,0.99144,-0.12826,210.1
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.54746,0.12014,0.82816,180.46,0.83671,0.062088,0.54411,202.45,0.013951,0.99081,-0.13451,210.04
> view matrix models
> #9,-0.61653,0.1277,0.77691,180.31,0.78731,0.092096,0.60964,202.66,0.0063037,0.98753,-0.15732,209.97
> view matrix models
> #9,-0.62782,0.073433,0.77489,180.48,0.77517,-0.030986,0.63099,203.13,0.070346,0.99682,-0.03747,210.34
> view matrix models
> #9,-0.62087,0.053369,0.7821,180.56,0.78091,-0.045216,0.62301,203.14,0.068612,0.99755,-0.013603,210.43
> view matrix models
> #9,-0.5736,-0.023782,0.81879,180.89,0.81885,0.0096521,0.57392,202.74,-0.021552,0.99967,0.013938,210.62
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.5736,-0.023782,0.81879,180.02,0.81885,0.0096521,0.57392,202.98,-0.021552,0.99967,0.013938,210.7
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.57847,0.031132,0.81511,179.85,0.81555,0.041881,0.57717,202.9,-0.01617,0.99864,-0.049616,210.46
> view matrix models
> #9,-0.56603,-0.015391,0.82424,180.01,0.82431,0.0025727,0.56613,202.97,-0.010834,0.99988,0.011231,210.68
> view matrix models
> #9,-0.71029,0.24008,0.6617,178.75,0.68817,0.039154,0.72449,203.6,0.14803,0.96996,-0.19303,209.83
> view matrix models
> #9,-0.68393,0.22919,0.69261,178.88,0.71976,0.056987,0.69188,203.39,0.1191,0.97171,-0.20393,209.81
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.76,0.71976,0.056987,0.69188,203.72,0.1191,0.97171,-0.20393,209.9
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.24,0.71976,0.056987,0.69188,203.81,0.1191,0.97171,-0.20393,210.17
> view matrix models
> #9,-0.68393,0.22919,0.69261,176.83,0.71976,0.056987,0.69188,203.91,0.1191,0.97171,-0.20393,210.29
> view matrix models
> #9,-0.68393,0.22919,0.69261,176.71,0.71976,0.056987,0.69188,203.93,0.1191,0.97171,-0.20393,210.32
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.17,0.71976,0.056987,0.69188,203.92,0.1191,0.97171,-0.20393,210.31
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.48,0.71976,0.056987,0.69188,203.79,0.1191,0.97171,-0.20393,210.28
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.92,0.71976,0.056987,0.69188,203.73,0.1191,0.97171,-0.20393,210.27
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.96,0.71976,0.056987,0.69188,203.75,0.1191,0.97171,-0.20393,210.29
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.7,0.71976,0.056987,0.69188,203.84,0.1191,0.97171,-0.20393,210.22
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.64555,0.14914,0.74902,178.12,0.76365,0.11273,0.63571,203.41,0.010372,0.98237,-0.18667,210.37
> ~select #9
Nothing selected
> hide #!2 models
> show #!2 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.52,0.91486,0.1468,0.37614,202.16,-0.082923,0.98002,-0.18079,210.49
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.76,0.91486,0.1468,0.37614,202.52,-0.082923,0.98002,-0.18079,210.02
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.91,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.94
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.84,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.69
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.58,0.91486,0.1468,0.37614,202.13,-0.082923,0.98002,-0.18079,210.55
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.72,0.91486,0.1468,0.37614,203.01,-0.082923,0.98002,-0.18079,210.68
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.44867,0.076406,0.89043,178.88,0.88471,0.17889,0.43044,203.15,-0.1264,0.9809,-0.14786,210.85
> ~select #9
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
——— End of log from Thu Mar 3 21:24:07 2022 ———
opened ChimeraX session
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/C
Alignment identifier is 1
> select #3/B-C:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:1-36
582 atoms, 598 bonds, 72 residues, 1 model selected
> hide #!2 models
> hide #9 models
> select #3/B-C:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:1-31
486 atoms, 496 bonds, 62 residues, 1 model selected
> select #3/B-C:1-2
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B-C:1-28
436 atoms, 446 bonds, 56 residues, 1 model selected
> select #3/B-C:25
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B-C:1-25
374 atoms, 378 bonds, 50 residues, 1 model selected
> color sel orange
> select #3/B-C:32-33
42 atoms, 42 bonds, 4 residues, 1 model selected
> select #3/B-C:32-139
1726 atoms, 1764 bonds, 216 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-144
1794 atoms, 1834 bonds, 226 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-150
1900 atoms, 1944 bonds, 238 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-159
2042 atoms, 2088 bonds, 256 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-171
2246 atoms, 2300 bonds, 280 residues, 1 model selected
> select #3/B-C:23
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:23-171
2404 atoms, 2464 bonds, 298 residues, 1 model selected
> select #3/B-C:26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/B-C:26-171
2358 atoms, 2418 bonds, 292 residues, 1 model selected
> select #3/B-C:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B-C:26-172
2376 atoms, 2436 bonds, 294 residues, 1 model selected
> select #3/B-C:174
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/B-C:26-174
2416 atoms, 2476 bonds, 298 residues, 1 model selected
> color sel medium blue
> color sel blue
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> show #!1 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.2959
> volume #2 level 0.3364
> volume #2 level 0.1382
> ui mousemode right "map eraser"
> volume erase #2 center 237.19,212.38,256.03 radius 33.098
> volume #2 level 0.1382
> volume erase #2 center 169.45,251.87,161.34 radius 16.218
> volume erase #2 center 169.29,250.35,162.17 radius 16.218
> volume erase #2 center 178.55,248.01,162.61 radius 16.218
> volume erase #2 center 193.98,241.53,160.53 radius 16.218
> volume erase #2 center 199.47,236.96,159.26 radius 16.218
> volume erase #2 center 162.44,240.05,168.47 radius 10.426
> volume erase #2 center 192.43,185.48,150.8 radius 10.426
> volume erase #2 center 222.56,163.1,224.04 radius 10.426
> volume erase #2 center 210.8,157.36,204.71 radius 4.3027
> volume erase #2 center 213.21,164.78,209.75 radius 4.3027
> volume erase #2 center 213.74,163.67,210.79 radius 4.3027
> volume erase #2 center 140.42,146.88,222.98 radius 7.2815
> volume erase #2 center 143.97,147.47,221.25 radius 7.2815
> volume erase #2 center 148.25,145.4,219.55 radius 7.2815
> volume erase #2 center 152.8,142.67,217.68 radius 7.2815
> volume erase #2 center 152.46,140.9,223.5 radius 7.2815
> volume erase #2 center 139.51,151.13,215.18 radius 7.2815
> volume erase #2 center 146.44,146.78,211.4 radius 7.2815
> volume erase #2 center 152.32,144.56,208.69 radius 7.2815
> volume erase #2 center 146.84,150.8,208.72 radius 7.2815
> volume erase #2 center 152.17,153.98,201.44 radius 7.2815
> hide #!2 models
> show #!2 models
> volume #2 level 0.3838
> volume #2 level 0.2253
> volume #2 level 0.0986
> volume #2 level 0.01
> volume #2 level 0.001
> volume #2 level 0.1
> volume #2 level 0.1475
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> color #3-4 bypolymer
> undo
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Fit in Map"
> hide #3 models
> show #3 models
> show #5 models
> hide #5 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,413.97,0.28616,-0.92153,0.26247,239.58,-0.95303,-0.24537,0.17756,365.68
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.09,0.28616,-0.92153,0.26247,239.88,-0.95303,-0.24537,0.17756,365.5
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.1,0.28616,-0.92153,0.26247,239.98,-0.95303,-0.24537,0.17756,365.39
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.098121,-0.30274,-0.94801,414.12,0.28638,-0.9209,0.26444,239.49,-0.95308,-0.24554,0.17706,365.52
> view matrix models
> #3,-0.10399,-0.29321,-0.95038,413.98,0.28519,-0.92422,0.25393,242.13,-0.95281,-0.24463,0.17973,364.84
> view matrix models
> #3,-0.10804,-0.25387,-0.96119,410,0.28731,-0.93356,0.21428,250.39,-0.95173,-0.25301,0.1738,367.12
> view matrix models
> #3,-0.089326,-0.26965,-0.95881,408.94,0.27746,-0.93128,0.23606,247.86,-0.95658,-0.24494,0.15801,369.43
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.07054, steps = 76
shifted from previous position = 1.56
rotated from previous position = 7.95 degrees
atoms outside contour = 4416, contour level = 0.12697
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.01853403 0.20523285 0.97853769 -30.97334856
0.00646830 0.97866071 -0.20538117 45.38206352
-0.99980733 0.01013602 0.01681102 356.85899567
Axis 0.10776124 0.98919674 -0.09938471
Axis point 163.99516504 0.00000000 196.80902229
Rotation angle (degrees) 89.59876110
Shift along axis 6.08773536
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1044, steps = 92
shifted from previous position = 1.81
rotated from previous position = 8.09 degrees
atoms outside contour = 2312, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87188277 -0.47824853 0.10535086 355.37302112
0.20869056 -0.16823549 0.96340288 57.21596158
-0.44302225 0.86196009 0.24648757 74.93473678
Axis -0.11464921 0.61976358 0.77636889
Axis point 179.54922209 52.98960138 0.00000000
Rotation angle (degrees) 153.74256446
Shift along axis 52.89413028
> view matrix models
> #4,0.86605,0.44369,-0.23043,24.081,-0.15116,-0.20695,-0.9666,357.32,-0.47656,0.87196,-0.11216,122.76
> view matrix models
> #4,0.24178,-0.10097,-0.96506,327.04,0.9586,-0.12931,0.25369,-9.1181,-0.15041,-0.98645,0.065523,378.67
> view matrix models
> #4,0.29714,-0.29814,-0.9071,345.67,0.95329,0.14663,0.26408,-59.546,0.054273,-0.94319,0.32778,301.43
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 320
shifted from previous position = 4.37
rotated from previous position = 11.4 degrees
atoms outside contour = 2213, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22359030 0.19234587 0.95551582 13.46864170
-0.96386692 0.10200874 -0.24607887 369.19247060
-0.14480322 -0.97601092 0.16258766 360.07001914
Axis -0.41589505 0.62693129 -0.65877801
Axis point 62.48187352 351.98959539 0.00000000
Rotation angle (degrees) 118.65255170
Shift along axis -11.34943811
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #5 models
> show #!2 models
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.0621 degrees
atoms outside contour = 2215, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22386136 0.19222999 0.95547567 13.54489824
-0.96395914 0.10094242 -0.24615736 369.41500556
-0.14376685 -0.97614461 0.16270474 359.89902128
Axis -0.41608471 0.62655616 -0.65901510
Axis point 62.46779097 351.82779571 0.00000000
Rotation angle (degrees) 118.69239674
Shift along axis -11.35546781
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.25124,-0.17542,-0.9519,335.64,0.9404,0.27709,0.19714,-70.324,0.22917,-0.9447,0.23458,277.59
> view matrix models
> #4,0.25124,-0.17542,-0.9519,335.72,0.9404,0.27709,0.19714,-70.489,0.22917,-0.9447,0.23458,277.37
> view matrix models
> #4,0.25124,-0.17542,-0.9519,336.84,0.9404,0.27709,0.19714,-70.794,0.22917,-0.9447,0.23458,276.49
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 60
shifted from previous position = 2.03
rotated from previous position = 0.0879 degrees
atoms outside contour = 2217, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22340595 0.19254318 0.95551920 13.40638758
-0.96384599 0.10241826 -0.24599073 369.10197141
-0.14522645 -0.97592912 0.16270112 360.10914844
Axis -0.41580714 0.62703635 -0.65873351
Axis point 62.50395161 352.02889088 0.00000000
Rotation angle (degrees) 118.62946316
Shift along axis -11.35008346
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C
Alignment identifier is 4/C
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/B:1-228
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> color sel forest green
> hide #!2 models
> ui tool show "Color Actions"
> color sel forest green
> color sel #e0fff2ff
> color sel #defff1ff
> color sel #c2ffcdff
> color sel #79ff7dff
> color sel #00ff05ff
> color sel #00ff07ff
> color sel #00ff09ff
> color sel #00ff07ff
[Repeated 1 time(s)]
> color sel #00f707ff
> color sel #00f507ff
> color sel #00f407ff
> color sel #00f307ff
> color sel #00f107ff
> color sel #00eb07ff
> color sel #00e907ff
> color sel #00e707ff
> color sel #00e106ff
> color sel #00dd06ff
> color sel #00db06ff
> color sel #00d906ff
> color sel #00d806ff
[Repeated 1 time(s)]
> color sel #00d606ff
> color sel #00d006ff
> color sel #00c706ff
> color sel #00c205ff
> color sel #00b905ff
> color sel #00b305ff
> color sel #00ab05ff
> color sel #00a605ff
> color sel #009d04ff
> color sel #009a04ff
> color sel #009604ff
> color sel #009404ff
> color sel #009204ff
> color sel #009104ff
> color sel #008f04ff
> color sel #008e04ff
[Repeated 1 time(s)]
> color sel #008d04ff
> color sel #008a04ff
[Repeated 1 time(s)]
> color sel #008804ff
> color sel #008704ff
> color sel #008604ff
> color sel #008504ff
[Repeated 1 time(s)]
> color sel #008304ff
> color sel #008204ff
> color sel #007f04ff
> color sel #007903ff
> color sel #007303ff
> color sel #006f03ff
> color sel #006e03ff
> color sel #006d03ff
> color sel #006c03ff
> color sel #006803ff
> color sel #005f03ff
> color sel #005c03ff
[Repeated 1 time(s)]
> color sel #005d03ff
> color sel #005e03ff
[Repeated 1 time(s)]
> color sel #005f03ff
> color sel #006003ff
[Repeated 2 time(s)]
> color sel #006103ff
[Repeated 2 time(s)]
> color sel #006203ff
[Repeated 3 time(s)]
> color sel #006103ff
[Repeated 2 time(s)]
> color sel #006003ff
[Repeated 1 time(s)]
> color sel #005f03ff
[Repeated 1 time(s)]
> color sel #005e03ff
[Repeated 1 time(s)]
> color sel #005d03ff
[Repeated 1 time(s)]
> color sel #005b03ff
[Repeated 1 time(s)]
> color sel #005a03ff
[Repeated 1 time(s)]
> color sel #005c03ff
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> show #!2 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C1.png"
> width 854 height 684 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
> width 1167 height 801 supersample 3
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
> width 1167 height 801 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C3.png"
> width 1167 height 801 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J90_005_volume_map_sharp.mrc
Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
416,416,416, pixel 0.858, shown at level 0.0366, step 2, values float32
> hide #4 models
> hide #3 models
> volume #6 step 1
> volume #6 level 0.05781
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting simple
> volume #6 level 0.08608
> volume #6 level 0.1744
> volume #6 level 0.07548
> volume #6 level 0.06841
> volume #6 level 0.08255
> color #6 #bfb700 models transparency 0
> color #6 #bfb70039 models
> color #6 #bfb70028 models
> color #6 #fff40028 models
> color #6 #33300028 models
> color #6 #b4ac0028 models
> color #6 #b4ac00 models transparency 0
> color #6 #fff400 models transparency 0
> color #6 #f0e500 models transparency 0
> color #6 #f0e65a models transparency 0
> color #6 #c3bb49 models transparency 0
> color #6 #c3bb499a models
> color #6 #c3bb4941 models
> color #6 #c3bb4942 models
> color #6 #fffb00 models transparency 0
> color #6 #fffb0044 models
> color #6 #fffb0016 models
> color #6 #fffb0033 models
> color #6 #fffc79 models transparency 0
> color #6 #fffc7932 models
> color #6 #fffc7943 models
> color #6 #fffc794c models
> color #6 #fffc794d models
> select #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.022009,-0.94973,0.31229,283.41,-0.71721,-0.23262,-0.65689,470,0.69651,-0.20952,-0.68628,231.36
> view matrix models
> #6,0.48413,-0.86475,0.13353,218.33,-0.43491,-0.37024,-0.82084,473.48,0.75926,0.33932,-0.55533,99.971
> view matrix models
> #6,-0.32751,-0.77901,0.53468,275.33,-0.92972,0.16487,-0.32929,377.53,0.16837,-0.60495,-0.77826,413.98
> view matrix models
> #6,-0.2755,-0.92018,0.27814,339.29,-0.85315,0.10072,-0.51185,409.53,0.44298,-0.37831,-0.8128,331.15
> view matrix models
> #6,0.69873,-0.70402,0.127,152.52,0.37445,0.20866,-0.90346,241.09,0.60956,0.67883,0.40942,-115.9
> view matrix models
> #6,0.45295,-0.31947,0.83233,-3.9083,0.64601,-0.52579,-0.55337,251.33,0.61441,0.78834,-0.031778,-51.296
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.45295,-0.31947,0.83233,16.369,0.64601,-0.52579,-0.55337,269.43,0.61441,0.78834,-0.031778,-42.833
> view matrix models
> #6,0.45295,-0.31947,0.83233,16.57,0.64601,-0.52579,-0.55337,267.55,0.61441,0.78834,-0.031778,-43.336
> view matrix models
> #6,0.45295,-0.31947,0.83233,17.018,0.64601,-0.52579,-0.55337,268.42,0.61441,0.78834,-0.031778,-43.438
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.457,0.64601,-0.52579,-0.55337,265.98,0.61441,0.78834,-0.031778,-43.237
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.708,0.64601,-0.52579,-0.55337,267.25,0.61441,0.78834,-0.031778,-43.377
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.833,0.64601,-0.52579,-0.55337,266.18,0.61441,0.78834,-0.031778,-42.937
> view matrix models
> #6,0.45295,-0.31947,0.83233,14.199,0.64601,-0.52579,-0.55337,266.61,0.61441,0.78834,-0.031778,-44.947
> volume #2 color #b8b5af4b
> volume #2 color #b8b5af4d
> show #3 models
> hide #!2 models
> volume #6 level 0.2239
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.29246,-0.71165,0.63876,258.29,-0.85627,-0.10251,-0.50625,462.3,0.42576,-0.69501,-0.57939,354.66
> view matrix models
> #6,-0.47549,-0.59046,0.65212,268.57,-0.79255,-0.034193,-0.60885,458.81,0.3818,-0.80634,-0.45171,357.01
> view matrix models
> #6,-0.34414,-0.36794,0.86382,164.08,-0.77861,-0.40232,-0.48157,495.02,0.52473,-0.8383,-0.14803,276.41
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.34414,-0.36794,0.86382,151.79,-0.77861,-0.40232,-0.48157,494.89,0.52473,-0.8383,-0.14803,279.06
> view matrix models
> #6,-0.34414,-0.36794,0.86382,151.48,-0.77861,-0.40232,-0.48157,494.87,0.52473,-0.8383,-0.14803,277.43
> volume #6 level 0.1673
> view matrix models
> #6,-0.34414,-0.36794,0.86382,149.97,-0.77861,-0.40232,-0.48157,494.85,0.52473,-0.8383,-0.14803,278.57
> view matrix models
> #6,-0.34414,-0.36794,0.86382,150.29,-0.77861,-0.40232,-0.48157,492.94,0.52473,-0.8383,-0.14803,277.18
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.34656,-0.40224,0.84741,159.86,-0.77344,-0.38862,-0.50077,493.34,0.53075,-0.82896,-0.17642,279.97
> view matrix models
> #6,-0.31668,-0.43946,0.84059,162.15,-0.77551,-0.39032,-0.49622,493.13,0.54617,-0.80903,-0.2172,281.6
> view matrix models
> #6,-0.32094,-0.45467,0.83083,167.46,-0.7722,-0.38228,-0.5075,493.32,0.54836,-0.80445,-0.22841,282.58
> view matrix models
> #6,-0.20123,-0.51264,0.83469,154.78,0.96454,0.044877,0.2601,-48.467,-0.1708,0.85743,0.48543,-11.902
> view matrix models
> #6,-0.19126,-0.46003,0.86706,137.55,0.78245,0.46189,0.41766,-117.87,-0.59262,0.75831,0.27161,124.2
> view matrix models
> #6,-0.16309,-0.47088,0.86699,134.27,0.77568,0.48185,0.40761,-118.14,-0.6097,0.73898,0.28667,127.76
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.16309,-0.47088,0.86699,134.42,0.77568,0.48185,0.40761,-149.14,-0.6097,0.73898,0.28667,101.11
> view matrix models
> #3,0.001066,-0.23035,-0.97311,385.86,0.36811,-0.90469,0.21456,228.51,-0.92978,-0.35844,0.08383,403.03
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.043523,-0.55853,0.82834,135.17,0.777,0.50225,0.37948,-147.46,-0.62799,0.66014,0.41212,93.77
> view matrix models
> #6,-0.13478,-0.49296,0.85955,134.49,0.77638,0.48647,0.40073,-148.74,-0.61569,0.72134,0.31716,99.344
> view matrix models
> #6,0.96181,-0.16288,-0.21999,85.595,0.2594,0.79899,0.54252,-135.51,0.087404,-0.57887,0.81072,99.737
> show #4 models
> view matrix models
> #6,0.67607,-0.69317,-0.24988,235.71,0.28695,0.56004,-0.77719,157.01,0.67866,0.45373,0.57753,-142.42
> view matrix models
> #6,0.24716,-0.80723,0.536,181.65,0.88374,0.41465,0.21697,-120.33,-0.39739,0.42006,0.81586,14.664
> view matrix models
> #6,-0.091274,-0.52365,0.84703,134.26,0.8991,0.32235,0.29617,-122.53,-0.42813,0.7886,0.44139,29.149
> view matrix models
> #6,-0.11554,-0.4685,0.87587,123.56,0.69127,0.59529,0.40961,-153.69,-0.7133,0.65279,0.25508,141.19
> view matrix models
> #6,-0.046411,-0.35281,0.93454,79.438,0.59316,0.74302,0.30997,-141.93,-0.80374,0.56872,0.17479,187.94
> view matrix models
> #6,-0.069072,-0.35388,0.93274,84.134,0.6004,0.73194,0.32216,-143.71,-0.79671,0.58226,0.16191,186.8
> view matrix models
> #6,-0.057044,-0.36632,0.92874,84.856,0.64945,0.69291,0.31319,-144.21,-0.75826,0.62103,0.19838,165.95
> view matrix models
> #6,-0.079957,-0.35928,0.9298,87.636,0.65299,0.68589,0.32118,-145.19,-0.75313,0.63283,0.17976,166.58
> view matrix models
> #6,-0.1341,-0.37541,0.91711,102.83,0.65851,0.65782,0.36557,-149.96,-0.74053,0.65295,0.159,164.81
> view matrix models
> #6,-0.12427,-0.37199,0.91988,99.899,0.65174,0.66844,0.35836,-149.16,-0.74819,0.64406,0.15938,167.68
> view matrix models
> #6,-0.11498,-0.39854,0.90992,104.73,0.64766,0.66446,0.37287,-150.54,-0.7532,0.63219,0.18172,166.32
> view matrix models
> #6,0.0002274,-0.40749,0.91321,84.492,0.63579,0.70493,0.3144,-144.02,-0.77186,0.58054,0.25924,163.65
> volume #6 level 0.1497
> view matrix models
> #6,0.0046913,-0.41214,0.91111,84.898,0.66603,0.68091,0.30458,-143.4,-0.74591,0.60539,0.27769,151.16
> view matrix models
> #6,-0.048323,-0.43445,0.8994,100.5,0.7189,0.61,0.33328,-146.09,-0.69343,0.66268,0.28285,130.85
> view matrix models
> #6,-0.10978,-0.42931,0.89646,111.19,0.68648,0.6195,0.38074,-151.02,-0.71881,0.6572,0.22671,147.1
> view matrix models
> #6,-0.12181,-0.41902,0.89977,110.93,0.69056,0.61537,0.38006,-150.91,-0.71294,0.66764,0.2144,146.6
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.12181,-0.41902,0.89977,108.89,0.69056,0.61537,0.38006,-148.49,-0.71294,0.66764,0.2144,143.63
> view matrix models
> #6,-0.12181,-0.41902,0.89977,110.07,0.69056,0.61537,0.38006,-147.38,-0.71294,0.66764,0.2144,145.3
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,472.46,-0.072251,0.33944,-0.93785,289.57,0.80252,-0.53855,-0.25675,172.86
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,487.54,-0.072251,0.33944,-0.93785,305.54,0.80252,-0.53855,-0.25675,191.57
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,493,-0.072251,0.33944,-0.93785,306.92,0.80252,-0.53855,-0.25675,188.04
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,502.5,-0.072251,0.33944,-0.93785,311.18,0.80252,-0.53855,-0.25675,188.67
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,499.52,-0.072251,0.33944,-0.93785,313.18,0.80252,-0.53855,-0.25675,187.29
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.82421,-0.553,0.12194,435.21,-0.037209,-0.16199,-0.98609,402.96,0.56506,-0.81729,0.11294,207.26
> view matrix models
> #6,-0.44543,-0.86122,0.24473,397.17,-0.26729,-0.13296,-0.9544,433.08,0.85449,-0.49053,-0.17097,153.23
> view matrix models
> #6,-0.36539,-0.89648,0.25061,387.81,-0.30567,-0.13874,-0.94198,438.58,0.87924,-0.4208,-0.22333,146.76
> volume #6 level 0.2451
> view matrix models
> #6,-0.26247,-0.55243,0.79116,201.13,-0.8293,-0.29003,-0.47764,470,0.49332,-0.78148,-0.382,313.01
> view matrix models
> #6,-0.28569,-0.52355,0.80267,198.17,-0.82429,-0.29297,-0.48448,470.94,0.48881,-0.80004,-0.34786,310.26
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28569,-0.52355,0.80267,180.48,-0.82429,-0.29297,-0.48448,474.67,0.48881,-0.80004,-0.34786,307.45
> volume #6 level 0.1673
> view matrix models
> #6,-0.28569,-0.52355,0.80267,178.35,-0.82429,-0.29297,-0.48448,476.02,0.48881,-0.80004,-0.34786,306.81
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.14718,-0.54954,0.8224,153.6,-0.85753,-0.34346,-0.38298,471.17,0.49292,-0.7616,-0.4207,313.54
> view matrix models
> #6,-0.14519,-0.57785,0.80312,161.88,-0.8523,-0.33921,-0.39815,472.41,0.5025,-0.74231,-0.44325,312.81
> view matrix models
> #6,-0.14171,-0.61705,0.77406,173.68,-0.84479,-0.3322,-0.41948,473.96,0.51599,-0.71336,-0.47421,311.33
> view matrix models
> #6,-0.123,-0.64321,0.75574,178.33,-0.8848,-0.2738,-0.37704,462.95,0.44944,-0.71506,-0.53544,335.73
> view matrix models
> #6,0.10222,-0.64957,0.7534,138.55,-0.86358,-0.43386,-0.2569,463.46,0.49374,-0.62436,-0.6053,325.44
> view matrix models
> #6,0.10839,-0.64998,0.75218,137.72,-0.86646,-0.4327,-0.24905,462.27,0.48734,-0.62473,-0.61008,327.61
> view matrix models
> #6,-0.17656,-0.48355,0.85733,140.78,-0.84554,-0.37137,-0.38359,473.92,0.50387,-0.79263,-0.34329,301.87
> view matrix models
> #6,-0.23478,-0.43523,0.86917,140.8,-0.85004,-0.34178,-0.40076,472.95,0.47149,-0.83292,-0.28972,304.4
> view matrix models
> #6,-0.22867,-0.43704,0.86989,139.85,-0.85367,-0.33948,-0.39497,472.09,0.46792,-0.83292,-0.29546,306.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.22867,-0.43704,0.86989,137.64,-0.85367,-0.33948,-0.39497,471.42,0.46792,-0.83292,-0.29546,310.38
> view matrix models
> #6,-0.22867,-0.43704,0.86989,137.55,-0.85367,-0.33948,-0.39497,472.47,0.46792,-0.83292,-0.29546,308.95
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.25766,-0.4215,0.86945,140.27,-0.85126,-0.32669,-0.41064,472.85,0.45712,-0.84594,-0.27463,309.15
> view matrix models
> #6,-0.24131,-0.47116,0.8484,149.96,-0.84523,-0.32751,-0.42229,474.15,0.47682,-0.81899,-0.3192,309.52
> view matrix models
> #6,-0.22049,-0.52796,0.82015,161.46,-0.83815,-0.32752,-0.43617,475.54,0.4989,-0.78357,-0.37029,309.25
> view matrix models
> #6,-0.16435,-0.57156,0.80393,161.86,-0.87529,-0.29128,-0.38603,466.35,0.45481,-0.76712,-0.45241,330.43
> view matrix models
> #6,-0.18555,-0.55494,0.81094,161.51,-0.86165,-0.30484,-0.40575,470.03,0.47237,-0.77403,-0.4216,322.42
> view matrix models
> #6,-0.2448,-0.5224,0.8168,165.61,-0.85708,-0.27726,-0.4342,469.93,0.4533,-0.80636,-0.37987,323.42
> view matrix models
> #6,-0.1668,-0.4734,0.86491,133.46,-0.84447,-0.38422,-0.37316,474.3,0.50897,-0.79263,-0.33568,302.25
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.1668,-0.4734,0.86491,132.36,-0.84447,-0.38422,-0.37316,474.18,0.50897,-0.79263,-0.33568,304.38
> view matrix models
> #6,-0.1668,-0.4734,0.86491,132.99,-0.84447,-0.38422,-0.37316,474.25,0.50897,-0.79263,-0.33568,304.17
> view matrix models
> #6,-0.1668,-0.4734,0.86491,133.6,-0.84447,-0.38422,-0.37316,474.33,0.50897,-0.79263,-0.33568,303.95
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.32695,-0.44627,0.83303,164.48,-0.82463,-0.29585,-0.48214,476.54,0.46162,-0.84458,-0.27128,309.14
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.32695,-0.44627,0.83303,165.99,-0.82463,-0.29585,-0.48214,476.36,0.46162,-0.84458,-0.27128,308.97
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.94,-0.82463,-0.29585,-0.48214,479.3,0.46162,-0.84458,-0.27128,310.62
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.99,-0.82463,-0.29585,-0.48214,477.92,0.46162,-0.84458,-0.27128,311.73
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.29,-0.82463,-0.29585,-0.48214,478.59,0.46162,-0.84458,-0.27128,310.92
> volume #6 level 0.1249
> view matrix models
> #6,-0.32695,-0.44627,0.83303,165.96,-0.82463,-0.29585,-0.48214,479.04,0.46162,-0.84458,-0.27128,311.24
> show #!1 models
> hide #3 models
> hide #4 models
> select #1
2 models selected
> view matrix models
> #1,-0.99948,-0.025572,-0.01976,364.95,0.031105,-0.92707,-0.3736,414.45,-0.0087649,-0.37402,0.92738,76.793
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.93251,0.32395,-0.15963,316.09,0.35214,0.71758,-0.6009,105.04,-0.080113,-0.61656,-0.78322,444.34
> view matrix models
> #1,-0.92079,0.38867,0.032827,267.4,0.38993,0.91934,0.052624,-56.723,-0.009726,0.061257,-0.99807,349.94
> view matrix models
> #1,-0.87777,0.3565,0.32005,213.16,0.3764,0.92646,0.00035867,-46.06,-0.29638,0.12078,-0.9474,381.24
> view matrix models
> #1,-0.89237,0.44968,0.038176,250.47,0.16187,0.3979,-0.90304,251.08,-0.42127,-0.79967,-0.42786,473.18
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89237,0.44968,0.038176,252.64,0.16187,0.3979,-0.90304,250.64,-0.42127,-0.79967,-0.42786,471.5
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91313,0.40742,0.014419,268.22,0.16668,0.40537,-0.89883,247.68,-0.37205,-0.81834,-0.43806,467.9
> view matrix models
> #1,-0.86639,0.4978,-0.039456,253.56,0.25363,0.37062,-0.89348,237.39,-0.43015,-0.78411,-0.44736,473.86
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.86639,0.4978,-0.039456,247.82,0.25363,0.37062,-0.89348,237.47,-0.43015,-0.78411,-0.44736,473.22
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.87597,0.47955,-0.052144,255.09,0.30604,0.46893,-0.82852,198.74,-0.37286,-0.74171,-0.55753,475.49
> view matrix models
> #1,-0.88553,0.45898,0.071919,237.88,0.23094,0.5692,-0.7891,187.07,-0.40311,-0.68216,-0.61004,479.83
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.88553,0.45898,0.071919,232.83,0.23094,0.5692,-0.7891,186.52,-0.40311,-0.68216,-0.61004,479.89
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.93268,0.36026,0.017859,268.7,0.20808,0.57784,-0.78918,189.07,-0.29463,-0.73234,-0.6139,470.19
> view matrix models
> #1,-0.9521,0.2987,0.065475,274.48,0.12858,0.58532,-0.80054,204,-0.27744,-0.75378,-0.59569,467.63
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 125084 points
correlation = 0.7737, correlation about mean = 0.5148, overlap = 4611
steps = 324, shift = 10.7, angle = 12.5 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00018548 -0.96024693 0.27915190 304.64819825
0.47329448 0.24582180 0.84591014 -90.95034872
-0.88090425 0.13227795 0.45443398 232.87270604
Axis -0.36089737 0.58666245 0.72496915
Axis point 266.13823335 42.12806522 0.00000000
Rotation angle (degrees) 98.62488972
Shift along axis 5.52163959
> show #!2 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs"
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs" includeMaps true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J88_003_volume_map_sharp.mrc
Opened cryosparc_P35_J88_003_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.0322, step 2, values float32
> hide #!6 models
> hide #!1 models
> hide #!2 models
> volume #7 level 0.08768
> volume #7 level 0.03374
> volume #7 level 0.01342
> volume #7 level 0.05407
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J87_003_volume_map_sharp.mrc
Opened cryosparc_P35_J87_003_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.858, shown at level 0.0329, step 2, values float32
> close #7
> volume #8 level 0.07979
> volume #8 level 0.05868
> volume #8 level 0.0493
> volume #8 color #b2ffff76
> volume #8 color #b2ffff75
> show #3 models
> select #8
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-5.0701,0,1,0,25.403,0,0,1,13.725
> view matrix models #8,1,0,0,-2.4128,0,1,0,22.261,0,0,1,17.693
> view matrix models #8,1,0,0,13.637,0,1,0,15.538,0,0,1,17.629
> view matrix models #8,1,0,0,17.759,0,1,0,21.107,0,0,1,15.457
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.9437,0.30533,-0.12727,-1.7134,-0.30648,0.95181,0.01092,77.369,0.12448,0.028702,0.99181,-8.2592
> view matrix models
> #8,0.93379,0.13868,-0.32987,64.541,0.05145,0.86023,0.5073,-55.026,0.35412,-0.49068,0.79614,77.197
> view matrix models
> #8,0.93056,0.16968,-0.32446,58.857,0.023869,0.85614,0.5162,-51.428,0.36537,-0.48809,0.79263,75.552
> view matrix models
> #8,0.92836,0.172,-0.32949,59.73,0.0092364,0.87553,0.48308,-46.35,0.37157,-0.45151,0.81122,65.012
> view matrix models
> #8,0.90406,0.053265,-0.42407,100.79,0.15019,0.88934,0.43188,-62.499,0.40015,-0.45413,0.79602,63.521
> view matrix models
> #8,0.90236,0.062663,-0.42639,99.9,0.13798,0.8953,0.42357,-60.014,0.40829,-0.44104,0.79924,59.399
> view matrix models
> #8,0.95884,0.13052,-0.25215,47.832,0.14193,0.54884,0.82379,-74.184,0.24591,-0.82568,0.50772,203.41
> view matrix models
> #8,0.8439,0.43609,-0.31252,25.859,0.15414,0.36088,0.91979,-61.706,0.51389,-0.82438,0.23733,208.08
> view matrix models
> #8,0.72071,0.42588,-0.547,89.933,0.3615,0.44239,0.82074,-91.531,0.59152,-0.78925,0.16489,202.5
> view matrix models
> #8,0.88841,0.1882,-0.4187,79.584,0.16981,0.71266,0.68065,-80.646,0.42648,-0.6758,0.60117,131.75
> view matrix models
> #8,0.81278,0.18222,-0.55333,117.19,0.28518,0.70377,0.65067,-92.602,0.50799,-0.68666,0.52005,134.87
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.81278,0.18222,-0.55333,111.12,0.28518,0.70377,0.65067,-89.214,0.50799,-0.68666,0.52005,131.56
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.66641,0.31634,-0.67515,134.32,0.37078,0.645,0.6682,-96.429,0.64685,-0.69563,0.31254,147.74
> view matrix models
> #8,0.64719,0.35366,-0.67533,131.19,0.38471,0.61328,0.68984,-97.242,0.65814,-0.70627,0.26085,157
> view matrix models
> #8,0.58239,0.30728,-0.75259,163.52,0.46192,0.63672,0.61743,-100.78,0.66892,-0.70723,0.22888,161.16
> view matrix models
> #8,0.7541,0.27199,-0.59778,113.55,0.30905,0.65618,0.68842,-91.868,0.5795,-0.70388,0.41077,142.46
> view matrix models
> #8,0.61599,0.12295,-0.7781,193.77,0.49388,0.70924,0.50306,-97.665,0.61371,-0.69417,0.37616,141.46
> view matrix models
> #8,0.73698,0.11525,-0.66601,155.12,0.40454,0.71417,0.57123,-96.173,0.54148,-0.69041,0.47971,133.98
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.73698,0.11525,-0.66601,155.56,0.40454,0.71417,0.57123,-90.04,0.54148,-0.69041,0.47971,141.01
> view matrix models
> #8,0.73698,0.11525,-0.66601,154.44,0.40454,0.71417,0.57123,-89.633,0.54148,-0.69041,0.47971,140.1
> view matrix models
> #8,0.73698,0.11525,-0.66601,153.2,0.40454,0.71417,0.57123,-89.182,0.54148,-0.69041,0.47971,139.08
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.73974,0.19261,-0.64473,135.84,0.34001,0.71983,0.60517,-85.705,0.58066,-0.66689,0.467,130.99
> close #8
> volume #1 color #b2b2b280
[Repeated 1 time(s)]
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
Opened
011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
as #7, grid size 3838,3710,1, pixel 0.85,0.85,0.85, shown at step 1, values
float32
> close #7
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #4 models
> show #9 models
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/B:2-3
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/B:2-19
142 atoms, 143 bonds, 18 residues, 1 model selected
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B:1-27
211 atoms, 212 bonds, 27 residues, 1 model selected
> select #9/B:1-27
211 atoms, 212 bonds, 27 residues, 1 model selected
> select #9/B:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/B:1-30
232 atoms, 233 bonds, 30 residues, 1 model selected
> ui mousemode right "color key"
> key delete
> ui mousemode right "rotate selected models"
> color sel cornflower blue
> color sel #7a81ffff
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> select #9/B-C:1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:1-30
464 atoms, 466 bonds, 60 residues, 1 model selected
> color sel #0433ffff
> color sel #7a81ffff
> select #9/B-C:31-33
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #9/B-C:31-63
562 atoms, 570 bonds, 66 residues, 1 model selected
> color sel dim gray
> select #9/B-C:64-65
38 atoms, 40 bonds, 4 residues, 1 model selected
> select #9/B-C:64-85
402 atoms, 414 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:86
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:108-109
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-140
190 atoms, 192 bonds, 22 residues, 1 model selected
> select #9/B-C:130-201
1092 atoms, 1102 bonds, 144 residues, 1 model selected
> select #9/B-C:130-150
334 atoms, 336 bonds, 42 residues, 1 model selected
> select #9/B-C:88-151
1030 atoms, 1038 bonds, 128 residues, 1 model selected
> select #9/B-C:130-151
342 atoms, 344 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:2-149,151-206
3296 atoms, 3340 bonds, 408 residues, 1 model selected
> select #9/B-C:151
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #9/B-C:151-157
108 atoms, 110 bonds, 14 residues, 1 model selected
> select #9/B-C:152-153
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #9/B-C:152-172
318 atoms, 320 bonds, 42 residues, 1 model selected
> select #9/B-C:31-34
60 atoms, 60 bonds, 8 residues, 1 model selected
> select #9/B-C:31-63
562 atoms, 570 bonds, 66 residues, 1 model selected
> select #9/B-C:2-149,151-206
3296 atoms, 3340 bonds, 408 residues, 1 model selected
> select #9/B-C:53
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/B-C:53-63
186 atoms, 184 bonds, 22 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:64
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:64-85
402 atoms, 414 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:86-87
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> color sel dim gray
> select #9/B-C:108
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> select #9/B-C:107
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:108-109
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-149
326 atoms, 328 bonds, 40 residues, 1 model selected
> select #9/B-C:130-131
38 atoms, 40 bonds, 4 residues, 1 model selected
> select #9/B-C:130-150
334 atoms, 336 bonds, 42 residues, 1 model selected
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-151
342 atoms, 344 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:152-153
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #9/B-C:152-172
318 atoms, 320 bonds, 42 residues, 1 model selected
> color sel dim gray
> select #9/B-C:174
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/B-C:174-176
48 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/B-C:173
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:173-183
174 atoms, 174 bonds, 22 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:184
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:184-207
354 atoms, 354 bonds, 48 residues, 1 model selected
> color sel dim gray
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> show #!2 models
> show #4 models
> hide #4 models
> volume #2 level 0.1179
> show #4 models
> volume #2 level 0.13
> volume #2 level 0.14
> volume #2 level 0.15
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_D.png"
> width 1009 height 824 supersample 3 transparentBackground true
> show #!6 models
> hide #!2 models
> show #!2 models
Fit map cryosparc_P35_J90_005_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 114729 points
correlation = 0.672, correlation about mean = 0.08483, overlap = 3988
steps = 212, shift = 5.69, angle = 24.1 degrees
Position of cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.48667344 0.82476587 0.28794127 36.88441365
-0.86459172 -0.40757626 -0.29387534 426.86136408
-0.12502033 -0.39197297 0.91144230 73.88929120
Axis -0.05631763 0.23708030 -0.96985631
Axis point 142.84730785 210.89177337 0.00000000
Rotation angle (degrees) 119.43288522
Shift along axis 27.46118471
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #6 level 0.12
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08293, steps = 148
shifted from previous position = 4.12
rotated from previous position = 15.3 degrees
atoms outside contour = 4112, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.47334151 0.84962673 0.23255592 79.20387762
0.74805308 0.24829808 0.61543861 -93.30922995
0.46514990 0.46527681 -0.75309567 157.40236379
Axis -0.50919647 -0.78872280 -0.34443477
Axis point 62.66416490 -0.00000000 102.29599347
Rotation angle (degrees) 171.52083443
Shift along axis -20.95006494
> undo
[Repeated 2 time(s)]
> hide #!2 models
> log metadata #3
The model has no metadata
> log chains #3
Chain information for D2NS1.pdb #3
---
Chain | Description
B C | No description available
> ui mousemode right "rotate selected models"
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,-0.0085676,-0.30727,-0.95158,398.88,0.38479,-0.87936,0.28049,211.07,-0.92297,-0.36375,0.12577,388.55
> view matrix models
> #3,-0.13489,-0.29223,-0.94679,417.71,0.36981,-0.90133,0.22551,227.19,-0.91926,-0.31971,0.22965,361.99
> view matrix models
> #3,-0.071496,-0.30058,-0.95107,408.73,0.37829,-0.89045,0.25298,218.98,-0.92292,-0.34169,0.17737,375.64
> view matrix models
> #3,-0.18267,-0.34044,-0.92235,429.87,0.39852,-0.88325,0.24708,215.26,-0.89878,-0.32244,0.29702,346.84
> view matrix models
> #3,-0.40995,0.57223,-0.71028,278.61,-0.10972,-0.804,-0.58442,439.45,-0.90548,-0.16165,0.39238,304
> view matrix models
> #3,-0.46987,0.63995,-0.60802,259.54,-0.55045,-0.75089,-0.36493,468.93,-0.69009,0.16321,0.70508,155.79
> view matrix models
> #3,-0.65716,0.081263,-0.74936,411.59,-0.053676,-0.99669,-0.061013,368.75,-0.75184,0.0001281,0.65934,202.22
> view matrix models
> #3,-0.62292,-0.22233,0.75003,189.5,-0.068144,-0.9397,-0.33515,410.55,0.77931,-0.25988,0.5702,-7.4739
> view matrix models
> #3,0.31022,-0.41267,0.85643,38.43,-0.2398,-0.90571,-0.34955,437.59,0.91992,-0.096935,-0.37993,109.67
> view matrix models
> #3,0.14284,-0.48882,0.86061,79.927,-0.73689,-0.63302,-0.23725,459.16,0.66075,-0.60029,-0.45063,252.47
> view matrix models
> #3,0.069717,-0.45875,0.88582,83.239,-0.93425,-0.34135,-0.10325,420.96,0.34974,-0.82038,-0.45239,344.49
> view matrix models
> #3,-0.24695,0.22628,0.94224,13.705,-0.87659,-0.46663,-0.11768,434.45,0.41304,-0.85502,0.31359,202.72
> view matrix models
> #3,-0.099087,-0.011917,0.99501,18.348,-0.8839,-0.45823,-0.09351,430.02,0.45706,-0.88875,0.034872,250.31
> view matrix models
> #3,0.0096812,0.032947,0.99941,-9.1088,-0.93353,-0.3579,0.020842,401.51,0.35838,-0.93318,0.027292,276.48
> view matrix models
> #3,-0.060408,-0.021128,0.99795,12.57,-0.98054,-0.18582,-0.063289,395.83,0.18678,-0.98236,-0.0094914,321.48
> view matrix models
> #3,-0.14852,-0.072188,0.98627,38.731,-0.98683,-0.053816,-0.15254,390.64,0.064089,-0.99594,-0.063245,354.92
> view matrix models
> #3,-0.35842,-0.23162,0.90437,117.04,-0.92969,0.00036447,-0.36835,409.93,0.084987,-0.97281,-0.21546,374.47
> view matrix models
> #3,-0.16442,-0.085208,0.9827,44.354,-0.94873,-0.25901,-0.1812,423.54,0.26997,-0.96211,-0.038251,308.57
> view matrix models
> #3,-0.29929,0.026962,0.95378,54.365,-0.9175,-0.28257,-0.27991,439.6,0.26196,-0.95887,0.10931,283.15
> view matrix models
> #3,0.21447,0.471,0.85566,-93.169,0.97669,-0.095031,-0.1925,59.362,-0.0093522,0.877,-0.4804,127.25
> view matrix models
> #3,0.56515,0.56728,0.59899,-125.3,0.82406,-0.42253,-0.37735,174.2,0.03903,0.70687,-0.70627,187.59
> view matrix models
> #3,0.2047,0.3956,0.89532,-85.837,0.92678,0.21596,-0.30731,36.306,-0.31492,0.89267,-0.32243,150.21
> view matrix models
> #3,0.26975,0.34464,0.89914,-89.39,0.91144,0.20987,-0.35388,48.323,-0.31067,0.91497,-0.25751,134.15
> view matrix models
> #3,0.15293,0.16968,0.97356,-52.687,0.98145,0.089212,-0.16972,23.489,-0.11565,0.98145,-0.15289,70.037
> view matrix models
> #3,0.042216,0.087727,0.99525,-23.3,0.97412,0.21777,-0.060515,-16.293,-0.22204,0.97205,-0.076263,76.678
> view matrix models
> #3,0.035376,0.093709,0.99497,-23.053,0.9291,0.36366,-0.067284,-31.697,-0.36814,0.92681,-0.0742,109.61
> view matrix models
> #3,-0.74086,0.45839,0.49092,141.95,-0.6574,-0.34504,-0.66991,473.84,-0.13769,-0.81904,0.55697,250.17
> view matrix models
> #3,-0.12274,0.85219,0.50863,-36.128,-0.96225,-0.22764,0.1492,361.79,0.24294,-0.47111,0.84796,72.892
> view matrix models
> #3,-0.67677,0.0678,0.73307,153.21,-0.71984,-0.26966,-0.63962,466.75,0.15432,-0.96057,0.2313,280.63
> view matrix models
> #3,-0.31096,-0.28409,0.90697,117.06,-0.89867,-0.2227,-0.37788,443.68,0.30934,-0.93258,-0.18605,323.01
> view matrix models
> #3,-0.31328,-0.20485,0.9273,100.52,-0.94642,-0.013217,-0.32266,407.02,0.078354,-0.9787,-0.18974,372.05
> view matrix models
> #3,0.084796,0.15045,0.98497,-39.503,-0.99107,-0.089391,0.098974,352.56,0.10294,-0.98457,0.14152,309.7
> view matrix models
> #3,-0.17084,-0.018385,0.98513,33.815,-0.98351,0.06341,-0.16938,373.35,-0.059353,-0.99782,-0.028915,370.83
> view matrix models
> #3,-0.3307,0.24426,0.91158,30.874,-0.94057,-0.0062546,-0.33954,407.82,-0.077235,-0.96969,0.23181,322.8
> view matrix models
> #3,-0.4809,0.025548,0.8764,100.33,-0.81554,-0.38005,-0.43642,465.94,0.32193,-0.92461,0.2036,250.04
> view matrix models
> #3,-0.53944,-0.043921,0.84088,128.63,-0.79768,-0.29313,-0.52705,464.33,0.26964,-0.95506,0.12309,278.7
> view matrix models
> #3,-0.45493,0.037354,0.88974,91.401,-0.78489,-0.48882,-0.3808,468.93,0.4207,-0.87159,0.2517,215.19
> view matrix models
> #3,-0.42074,0.12675,0.89828,68.835,-0.79214,-0.53394,-0.29568,462.63,0.44215,-0.83597,0.32506,192.35
> view matrix models
> #3,-0.55645,0.18988,0.80889,98.012,-0.74741,-0.53968,-0.38746,472.08,0.36297,-0.82018,0.44222,182.75
> view matrix models
> #3,-0.56077,0.17343,0.8096,101.41,-0.75525,-0.50786,-0.41434,472.89,0.3393,-0.8438,0.41578,195.6
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.56077,0.17343,0.8096,97.107,-0.75525,-0.50786,-0.41434,471.77,0.3393,-0.8438,0.41578,196.64
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.31072,0.047476,0.94931,49.418,-0.82644,-0.50685,-0.24516,453.98,0.46952,-0.86073,0.19672,215.61
> view matrix models
> #3,-0.10594,-0.13924,0.98458,38.514,-0.92405,-0.35194,-0.1492,428.01,0.36729,-0.92561,-0.091386,295.82
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08181, steps = 140
shifted from previous position = 5.91
rotated from previous position = 5.33 degrees
atoms outside contour = 4112, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.96127167 0.06226622 -0.26847668 48.62307340
-0.22542895 0.73805618 -0.63596769 218.36928771
0.15855157 0.67186013 0.72350910 -87.31437189
Axis 0.93048244 -0.30381850 -0.20468696
Axis point 0.00000000 232.24708974 246.16405973
Rotation angle (degrees) 44.64955765
Shift along axis -3.22959992
> view matrix models
> #3,-0.2167,-0.046006,0.97515,46.998,-0.825,-0.52541,-0.20812,455.06,0.52193,-0.8496,0.075903,227.93
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08275, steps = 232
shifted from previous position = 0.39
rotated from previous position = 10.7 degrees
atoms outside contour = 4141, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.94687496 0.16521963 -0.27591724 34.87295901
-0.32111058 0.53311437 -0.78273693 296.77138746
0.01777194 0.82975393 0.55784641 -59.68855935
Axis 0.94317112 -0.17178339 -0.28446215
Axis point 0.00000000 208.08374987 254.78468856
Rotation angle (degrees) 58.74030833
Shift along axis -1.11009298
> view matrix models
> #3,-0.29357,0.29509,0.90925,14.248,-0.93223,-0.29887,-0.20399,435.37,0.21155,-0.90752,0.36283,240.41
> view matrix models
> #3,-0.024736,0.33337,0.94247,-45.387,-0.98041,-0.19235,0.042305,382.05,0.19538,-0.92297,0.3316,251.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.024736,0.33337,0.94247,-50.647,-0.98041,-0.19235,0.042305,380.65,0.19538,-0.92297,0.3316,252
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.07754, steps = 124
shifted from previous position = 0.984
rotated from previous position = 11.7 degrees
atoms outside contour = 4222, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.97038128 -0.18348442 -0.15714223 69.99792136
-0.04643502 0.49668363 -0.86668864 273.08312267
0.23707384 0.84831532 0.47345239 -88.46523910
Axis 0.97164206 -0.22334462 0.07764586
Axis point 0.00000000 220.43718489 187.11160518
Rotation angle (degrees) 61.94891347
Shift along axis 0.15231786
> view matrix models
> #3,-0.16161,0.20679,0.96495,-7.8987,-0.94599,-0.31092,-0.091808,418.86,0.28103,-0.92767,0.24587,240.27
> view matrix models
> #3,-0.16161,0.20679,0.96495,-7.6794,-0.94599,-0.31092,-0.091808,419.8,0.28103,-0.92767,0.24587,239.05
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.065282,0.14337,0.98751,-17.979,-0.96082,-0.2762,-0.023418,404.39,0.26939,-0.95035,0.15578,260.96
> view matrix models
> #3,0.11914,-0.22697,0.96659,15.581,-0.91769,-0.3968,0.019938,409.35,0.37901,-0.8894,-0.25556,304.72
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.082, steps = 232
shifted from previous position = 14.3
rotated from previous position = 15.8 degrees
atoms outside contour = 4100, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.93730079 0.13375954 -0.32183172 47.54908073
-0.32984053 0.63871002 -0.69516528 263.49850116
0.11257216 0.75773210 0.64278271 -75.44380421
Axis 0.91623198 -0.27394552 -0.29235734
Axis point -0.00000000 224.55289345 259.75440758
Rotation angle (degrees) 52.45410370
Shift along axis -6.56169478
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.018323,-0.060034,0.99803,13.026,-0.84305,-0.53571,-0.047702,432.04,0.53752,-0.84226,-0.040796,240.98
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.036597,-0.098259,0.99449,23.297,-0.80637,-0.58491,-0.087465,440.94,0.59028,-0.80513,-0.057828,228.49
> view matrix models
> #3,-0.027477,-0.10288,0.99431,22.501,-0.77374,-0.6276,-0.086317,442.18,0.63291,-0.77171,-0.062357,216.18
> view matrix models
> #3,-0.10002,-0.07995,0.99177,31.858,-0.93297,-0.33885,-0.12141,427.89,0.34577,-0.93744,-0.040699,290.69
> view matrix models
> #3,-0.10077,-0.089813,0.99085,33.811,-0.91689,-0.37822,-0.12753,432.77,0.38621,-0.92135,-0.044236,281.5
> view matrix models
> #3,-0.032685,-0.1875,0.98172,39.889,-0.92726,-0.36087,-0.099796,426.73,0.37298,-0.91357,-0.16207,303.51
> volume #2 level 0.1688
> hide #!2 models
[Repeated 1 time(s)]
> volume #6 level 0.1932
> view matrix models
> #3,-0.15943,5.3271e-05,0.98721,29.667,-0.88694,0.43911,-0.14326,292.88,-0.4335,-0.89843,-0.06996,426.39
> view matrix models
> #3,-0.23062,0.17059,0.95797,18.724,-0.93077,-0.3257,-0.16608,433.25,0.28369,-0.92996,0.23389,251.43
> view matrix models
> #3,-0.029625,-0.49902,0.86608,112.33,-0.48854,-0.74869,-0.44809,476.83,0.87204,-0.43639,-0.22161,146.12
> view matrix models
> #3,0.26982,-0.40253,0.87474,41.898,-0.5711,-0.79831,-0.1912,453.92,0.77527,-0.44797,-0.44528,204.93
> view matrix models
> #3,-0.10768,-0.15758,0.98162,48.065,-0.99351,0.053323,-0.10043,368.86,-0.036518,-0.98607,-0.1623,387.76
> view matrix models
> #3,-0.059748,-0.20275,0.97741,47.98,-0.99636,0.071795,-0.046014,356.56,-0.060844,-0.9766,-0.2063,398.29
> view matrix models
> #3,-0.2527,-0.028861,0.96711,54.512,-0.96729,-0.015262,-0.2532,403,0.022068,-0.99947,-0.02406,355.08
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/4o6b_DV2NS1.pdb
4o6b_DV2NS1.pdb title:
Dengue TYPE2 virus non-structural protein 1 (NS1) form 1 crystal [more
info...]
Chain information for 4o6b_DV2NS1.pdb #7
---
Chain | Description | UniProt
A | NS1 | POLG_DEN26
B | NS1 | POLG_DEN26
Non-standard residues in 4o6b_DV2NS1.pdb #7
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select #7
5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,195.73,0,1,0,55.756,0,0,1,0.30073
> view matrix models #7,1,0,0,24.836,0,1,0,111.9,0,0,1,93.148
> view matrix models #7,1,0,0,184.13,0,1,0,225.28,0,0,1,192.15
> view matrix models #7,1,0,0,151.84,0,1,0,239.37,0,0,1,213.11
> view matrix models #7,1,0,0,191.69,0,1,0,227.02,0,0,1,208.55
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.98804,-0.14623,0.048956,188.26,0.13002,0.61931,-0.7743,195.13,0.082905,0.77141,0.63092,223.81
> view matrix models
> #7,0.99657,-0.079109,0.024224,189.79,0.063222,0.5393,-0.83974,190.38,0.053367,0.83839,0.54245,223.38
> view matrix models
> #7,0.94783,-0.3073,0.084745,183.81,0.25252,0.5616,-0.78793,193.76,0.19454,0.76823,0.6099,223.91
> view matrix models
> #7,0.59074,0.041726,0.80578,211.73,0.76522,0.28771,-0.57591,194.2,-0.25586,0.95681,0.13803,214.25
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.59074,0.041726,0.80578,206.56,0.76522,0.28771,-0.57591,184.3,-0.25586,0.95681,0.13803,224.47
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69999,-0.017723,0.71393,202.96,0.67927,0.32512,-0.65794,182.71,-0.22045,0.94551,0.23962,227.06
> view matrix models
> #7,0.84135,0.059716,0.53718,201.67,0.50634,0.26057,-0.82202,175.1,-0.18906,0.96361,0.18899,226.5
> view matrix models
> #7,0.91878,0.00070031,0.39477,196.52,0.37034,0.34484,-0.86252,175.78,-0.13674,0.93866,0.31658,229.47
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_00_final_volume.mrc
Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.79, shown at level 0.235, step 1, values float32
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_01_final_volume.mrc
Opened cryosparc_P35_J141_class_01_final_volume.mrc as #10, grid size
128,128,128, pixel 2.79, shown at level 0.281, step 1, values float32
> select #10
2 models selected
> view matrix models
> #10,-0.079171,0.66364,0.74385,-61.635,-0.22432,-0.73892,0.63536,232.1,0.97129,-0.11656,0.20737,-7.2572
> view matrix models
> #10,-0.28893,0.313,0.90474,9.1948,-0.47663,-0.86662,0.1476,393.94,0.83026,-0.38858,0.39958,30.91
> ~select #10
Nothing selected
> select #8
2 models selected
> view matrix models
> #8,0.27556,0.9224,0.27065,-84.292,-0.27059,-0.19574,0.94258,80.02,0.92241,-0.33297,0.19565,46.409
> view matrix models
> #8,0.63638,0.51065,0.57815,-136.4,0.085328,0.6983,-0.7107,175.68,-0.76664,0.50161,0.40081,166.71
> view matrix models
> #8,-0.3692,-0.17702,0.91234,105.18,-0.32493,-0.89515,-0.30518,456,0.8707,-0.40912,0.27296,54.461
> view matrix models
> #8,-0.21183,0.1782,0.96092,3.7465,-0.32373,-0.94052,0.10305,384.86,0.92213,-0.28925,0.25692,26.817
> color #10 #ffb2b270 models
[Repeated 1 time(s)]
> color #8 #ffb2ff56 models
> color #8 #ffb2ff57 models
> hide #4 models
> hide #3 models
> hide #!8 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #!10 models
> show #!8 models
> view matrix models
> #8,0.27556,0.39667,0.87562,-107.73,0.79978,-0.59996,0.020098,134.95,0.53331,0.69477,-0.48257,65.706
> view matrix models
> #8,0.27366,0.52314,0.80712,-116.65,0.91914,-0.38945,-0.059223,90.987,0.28335,0.75806,-0.58742,120.4
> view matrix models
> #8,0.33758,0.53414,0.77507,-124.09,0.9382,-0.25771,-0.23103,97.287,0.076338,0.80516,-0.58813,149.98
> view matrix models
> #8,0.45264,0.48026,0.75131,-130.92,0.89015,-0.19384,-0.41237,129.79,-0.052411,0.85544,-0.51524,150.44
> view matrix models
> #8,0.65699,0.41807,0.62736,-133.2,0.73578,-0.1742,-0.65443,201.34,-0.16431,0.89156,-0.42206,146.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.65699,0.41807,0.62736,-126.9,0.73578,-0.1742,-0.65443,207.73,-0.16431,0.89156,-0.42206,145.93
> view matrix models
> #8,0.65699,0.41807,0.62736,-126.22,0.73578,-0.1742,-0.65443,209.21,-0.16431,0.89156,-0.42206,144.54
> view matrix models
> #8,0.65699,0.41807,0.62736,-124.37,0.73578,-0.1742,-0.65443,208.1,-0.16431,0.89156,-0.42206,144.61
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.53344,-0.037486,0.84501,-62.766,0.5106,-0.78219,-0.35703,299.99,0.67434,0.62191,-0.39811,34.754
> volume #8 level 0.8045
> view matrix models
> #8,0.52401,-0.054439,0.84997,-58.961,0.47038,-0.81345,-0.3421,310.02,0.71003,0.57907,-0.40065,36.512
> volume #8 level 0.3577
> show #!10 models
> hide #!8 models
> view matrix models
> #8,0.60764,0.020079,0.79396,-76.868,0.73022,-0.40725,-0.54857,228.31,0.31232,0.9131,-0.26212,18.911
> show #!8 models
> view matrix models
> #8,0.37572,0.11623,0.91941,-75.961,0.70308,-0.68208,-0.20109,215.44,0.60375,0.72198,-0.33799,14.583
Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
cryosparc_P35_J141_class_00_final_volume.mrc using 20957 points
correlation = 0.9488, correlation about mean = 0.6585, overlap = 4385
steps = 288, shift = 15.4, angle = 91.5 degrees
Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
cryosparc_P35_J141_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
0.99679931 0.07719696 -0.02077903 -9.05098271
-0.07875179 0.99291028 -0.08903553 30.04476737
0.01375844 0.09038694 0.99581168 -19.54599107
Axis 0.74691139 -0.14377477 -0.64919349
Axis point 0.00000000 219.63678499 322.55619772
Rotation angle (degrees) 6.89842857
Shift along axis 1.60916844
> volume #6 level 0.1566
> volume #6 level 0.1346
Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 20957 points
correlation = 0.7294, correlation about mean = 0.2901, overlap = 713.6
steps = 312, shift = 14.7, angle = 29.6 degrees
Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.81655312 0.57639109 -0.03184812 223.81505889
-0.57200743 -0.81530920 -0.08987989 441.91818039
-0.07777204 -0.05517435 0.99544327 24.62573349
Axis 0.03018293 0.03993939 -0.99874613
Axis point 182.23608880 186.02084504 0.00000000
Rotation angle (degrees) 144.90596060
Shift along axis -0.18951992
Fit map cryosparc_P35_J141_class_00_final_volume.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 13326 points
correlation = 0.7531, correlation about mean = 0.2446, overlap = 614.5
steps = 200, shift = 14.7, angle = 20.2 degrees
Position of cryosparc_P35_J141_class_00_final_volume.mrc (#8) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.51114495 0.85836696 -0.04401141 122.12595771
-0.83601173 -0.50841524 -0.20639360 453.44795134
-0.19953752 -0.06870298 0.97747873 53.02558896
Axis 0.08065933 0.09110739 -0.99256915
Axis point 191.43391939 194.60207731 0.00000000
Rotation angle (degrees) 121.40208746
Shift along axis -1.46850799
> volume #10 level 0.3562
> volume #8 level 0.2852
> volume #8 level 0.318
> hide #!7 models
> show #!7 models
> select #7
5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91878,0.00070031,0.39477,195.03,0.37034,0.34484,-0.86252,183.44,-0.13674,0.93866,0.31658,212.37
> view matrix models
> #7,0.91878,0.00070031,0.39477,207.4,0.37034,0.34484,-0.86252,186.87,-0.13674,0.93866,0.31658,221.02
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.73404,-0.62761,0.2594,182.53,-0.25829,-0.61129,-0.74807,155.21,0.62806,0.48212,-0.61082,186.96
> view matrix models
> #7,0.74989,-0.64446,0.14946,179.17,-0.33839,-0.56778,-0.75041,155.99,0.56846,0.51215,-0.64386,186.63
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.74989,-0.64446,0.14946,177.57,-0.33839,-0.56778,-0.75041,160.17,0.56846,0.51215,-0.64386,189.52
> view matrix models
> #7,0.74989,-0.64446,0.14946,178.16,-0.33839,-0.56778,-0.75041,160.58,0.56846,0.51215,-0.64386,182.7
> view matrix models
> #7,0.74989,-0.64446,0.14946,177.56,-0.33839,-0.56778,-0.75041,162.27,0.56846,0.51215,-0.64386,183.32
> view matrix models
> #7,0.74989,-0.64446,0.14946,179.58,-0.33839,-0.56778,-0.75041,162.74,0.56846,0.51215,-0.64386,180.3
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69567,-0.70398,0.14302,177.14,-0.33345,-0.49279,-0.80372,163.74,0.63628,0.51144,-0.57756,182.51
> view matrix models
> #7,0.76223,-0.64567,0.045974,176.86,-0.30995,-0.42641,-0.84977,164.78,0.56827,0.63347,-0.52515,187.33
> view matrix models
> #7,0.78877,-0.61274,0.04891,178.17,-0.30035,-0.4536,-0.83907,164.27,0.53632,0.64714,-0.54182,187.1
> view matrix models
> #7,0.6402,-0.76747,-0.033591,170.03,-0.27585,-0.18885,-0.94246,170.1,0.71697,0.61263,-0.33261,192.81
> view matrix models
> #7,0.62699,-0.77647,0.063022,172.23,-0.19611,-0.23561,-0.95186,168.91,0.75394,0.58444,-0.3,193.04
> view matrix models
> #7,0.75838,-0.62248,0.19333,181.51,-0.13362,-0.43878,-0.8886,164.56,0.63797,0.64807,-0.41594,191.18
> view matrix models
> #7,0.70141,-0.70676,0.092259,175.74,-0.28093,-0.39309,-0.87553,165.35,0.65506,0.58819,-0.47427,187.83
> view matrix models
> #7,0.69618,-0.71217,0.090246,175.48,-0.28016,-0.38529,-0.87924,165.51,0.66094,0.58683,-0.46775,188
> view matrix models
> #7,0.68522,-0.72338,0.084779,174.9,-0.27616,-0.36576,-0.88879,165.9,0.67395,0.58561,-0.4504,188.52
> view matrix models
> #7,0.74436,-0.66753,0.018223,175.3,-0.26396,-0.31919,-0.91019,166.9,0.61339,0.6727,-0.4138,191.85
> view matrix models
> #7,0.77161,-0.63604,-0.0079224,175.8,-0.26676,-0.31226,-0.91177,167.06,0.57745,0.70565,-0.41062,192.74
> view matrix models
> #7,0.73389,-0.66982,0.11293,177.69,-0.19652,-0.36852,-0.90861,165.83,0.65022,0.64462,-0.40208,191.52
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.73389,-0.66982,0.11293,176.82,-0.19652,-0.36852,-0.90861,164.33,0.65022,0.64462,-0.40208,195.23
> show #3 models
> hide #3 models
> show #!2 models
> show #3 models
> hide #!10 models
> hide #!7 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 5602 atoms
average map value = 0.1888, steps = 160
shifted from previous position = 4.81
rotated from previous position = 23.5 degrees
atoms outside contour = 2712, contour level = 0.1688
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.55420887 0.78282865 -0.28289899 176.19297958
-0.82333712 -0.46560234 0.32454654 303.63070097
0.12234590 0.41278781 0.90257282 -106.76939213
Axis 0.05319429 -0.24429289 -0.96824137
Axis point 171.19224328 117.42998509 0.00000000
Rotation angle (degrees) 123.96035927
Shift along axis 38.57618189
> close #10
> show #9 models
> hide #9 models
> show #!7 models
> view matrix models
> #7,0.73389,-0.66982,0.11293,170.79,-0.19652,-0.36852,-0.90861,155.22,0.65022,0.64462,-0.40208,205.07
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.90325,0.19269,0.38342,206.62,0.0001087,0.89341,-0.44925,208.99,-0.42912,0.40583,0.80695,222.37
> view matrix models
> #7,0.91285,-0.26756,0.30841,190.03,0.40807,0.57317,-0.7106,194.6,0.013357,0.77453,0.6324,232.47
> view matrix models
> #7,0.76546,-0.55709,0.32206,180.18,0.59967,0.43603,-0.67102,192.6,0.23339,0.70677,0.66784,232.76
> view matrix models
> #7,0.49342,-0.33249,0.80373,198.32,0.86883,0.23191,-0.43745,194.17,-0.040945,0.91415,0.4033,230.43
> view matrix models
> #7,0.61212,-0.26384,0.74546,199.76,0.7065,0.60592,-0.36567,206.88,-0.35521,0.7505,0.5573,227.19
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.61212,-0.26384,0.74546,192.13,0.7065,0.60592,-0.36567,204.9,-0.35521,0.7505,0.5573,229.56
Fit molecule 4o6b_DV2NS1.pdb (#7) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 5126 atoms
average map value = 0.1927, steps = 152
shifted from previous position = 14.6
rotated from previous position = 16.1 degrees
atoms outside contour = 2452, contour level = 0.1688
Position of 4o6b_DV2NS1.pdb (#7) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.34465485 -0.66063558 -0.66691350 125.14009286
0.80909618 0.56930074 -0.14580812 154.59882031
0.47600039 -0.48934370 0.73073000 156.62388255
Axis -0.18145322 -0.60367956 0.77630260
Axis point -61.23617800 251.69459436 0.00000000
Rotation angle (degrees) 71.19533318
Shift along axis 5.55230604
> close #7
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J130_004_volume_map_sharp.mrc
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.0371, step 2, values float32
> volume #7 level 0.09025
> lighting simple
> hide #3 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #3 models
> show #!1 models
> hide #!2 models
> hide #3 models
> select #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.24103,-0.29696,-0.92397,349.21,-0.038945,-0.95423,0.29653,285.57,-0.96974,-0.035487,-0.24156,398.71
> view matrix models
> #7,-0.24983,0.23805,-0.93857,346.61,-0.30202,0.90179,0.30911,13.804,0.91998,0.3607,-0.1534,-14.399
> view matrix models
> #7,-0.10249,0.16037,-0.98172,341.85,0.025379,0.98702,0.15858,-30.757,0.99441,-0.0086622,-0.10523,26.713
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.10249,0.16037,-0.98172,336.3,0.025379,0.98702,0.15858,-28.758,0.99441,-0.0086622,-0.10523,26.913
> view matrix models
> #7,-0.10249,0.16037,-0.98172,337.29,0.025379,0.98702,0.15858,-28.672,0.99441,-0.0086622,-0.10523,28.197
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.22211,-0.1265,-0.96678,404.24,-0.24639,0.96665,-0.069873,63.34,0.94338,0.22268,-0.24587,23.093
> view matrix models
> #7,-0.19183,0.047993,-0.98025,371.72,-0.43799,0.88964,0.12927,74.05,0.87827,0.45414,-0.14964,-22.192
> view matrix models
> #7,-0.34489,-0.073759,-0.93574,411.13,-0.53139,0.83711,0.12987,99.175,0.77374,0.54204,-0.32791,13.194
> view matrix models
> #7,-0.36324,0.1037,-0.92591,382.4,-0.38069,0.89052,0.24908,42.339,0.85037,0.44296,-0.284,8.7541
> view matrix models
> #7,-0.36165,0.10266,-0.92664,382.44,-0.38188,0.8904,0.24768,42.819,0.85051,0.44344,-0.28281,8.4329
> view matrix models
> #7,-0.35715,0.16036,-0.92018,370.68,-0.43075,0.84586,0.3146,46.881,0.82879,0.50872,-0.23302,-7.8271
> view matrix models
> #7,-0.37647,0.070708,-0.92373,389.93,-0.48903,0.83168,0.26297,68.754,0.78684,0.55073,-0.27853,0.54545
> view matrix models
> #7,-0.21108,0.96488,-0.15637,71.026,-0.41939,0.055099,0.90613,72.864,0.88292,0.25684,0.39304,-87.108
> view matrix models
> #7,-0.19093,-0.093424,0.97715,43.432,-0.59513,-0.78062,-0.19092,442.95,0.78062,-0.61798,0.093448,133.33
> view matrix models
> #7,-0.25485,0.0071755,0.96696,39.327,0.96698,0.0034538,0.25483,-43.217,-0.0015111,0.99997,-0.0078187,13.125
> view matrix models
> #7,-0.017228,0.34616,0.93802,-54.562,0.65851,0.70988,-0.24988,-18.615,-0.75238,0.61338,-0.24018,251.72
> view matrix models
> #7,0.28808,0.16888,0.9426,-78.558,0.64678,0.69156,-0.32157,-0.5571,-0.70617,0.7023,0.089997,169.14
> view matrix models
> #7,0.16326,0.14447,0.97595,-58.619,0.66325,0.71625,-0.21698,-26.446,-0.73037,0.68273,0.021113,189.08
Fit map cryosparc_P35_J130_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 19964 points
correlation = 0.8354, correlation about mean = 0.6739, overlap = 929.1
steps = 276, shift = 3.71, angle = 23.7 degrees
Position of cryosparc_P35_J130_004_volume_map_sharp.mrc (#7) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.08559775 -0.03414562 -0.99574450 347.85846819
0.92968539 -0.35664221 0.09214889 59.72132131
-0.35827099 -0.93361685 0.00121691 410.96755552
Axis -0.66385471 -0.41255988 0.62377181
Axis point 0.00000000 67.86622584 347.54047210
Rotation angle (degrees) 129.41358899
Shift along axis 0.78387399
> volume #1 level 0.09
> volume #7 level 0.09
> ~select #7
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs" includeMaps true
——— End of log from Fri Mar 11 18:14:28 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!7 models
> show #3 models
> show #4 models
> show #!8 models
> hide #!8 models
> close #8
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Sat Mar 12 14:58:51 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P39_J166_002_volume_map_sharp
> (1).mrc"
Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
416,416,416, pixel 0.85, shown at level 0.0339, step 2, values float32
> volume #6 level 0.05868
> volume #6 step 1
> ui mousemode right "translate selected models"
> show #!7 models
> hide #!7 models
> show #9 models
> hide #9 models
> select #6
2 models selected
> view matrix models #6,1,0,0,1.4767,0,1,0,-0.11126,0,0,1,17.894
> view matrix models #6,1,0,0,2.5835,0,1,0,15.467,0,0,1,19.701
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.077918,0.99542,-0.055373,-3.5895,-0.96552,0.089183,0.24459,303.08,0.24841,0.034406,0.96804,-24.193
> view matrix models
> #6,-0.62577,0.77732,-0.06471,158.15,-0.76968,-0.62881,-0.1104,452.92,-0.12651,-0.019279,0.99178,46.339
> view matrix models
> #6,-0.49195,0.83765,-0.23731,152.38,-0.80175,-0.32963,0.49855,307.08,0.33939,0.43553,0.83375,-88.641
> view matrix models
> #6,-0.43603,0.58765,-0.68157,258.71,-0.82618,0.03888,0.56206,236.26,0.3568,0.80818,0.46855,-97.873
> view matrix models
> #6,0.17544,0.72595,-0.66499,125.79,-0.86837,0.43236,0.24289,226.23,0.46384,0.53485,0.70625,-106.96
> view matrix models
> #6,-0.010663,0.39041,-0.92058,258.46,-0.28789,0.88046,0.37672,25.213,0.95761,0.26904,0.103,-47.908
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.010663,0.39041,-0.92058,281.12,-0.28789,0.88046,0.37672,26.602,0.95761,0.26904,0.103,-46.122
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.14635,0.34874,-0.92572,262.07,-0.39341,0.87913,0.26899,62.599,0.90764,0.32483,0.26586,-73.695
> view matrix models
> #6,0.12836,0.25158,-0.95929,287.7,-0.38687,0.90336,0.18515,70.814,0.91316,0.34735,0.21329,-70.077
> view matrix models
> #6,0.14119,0.15753,-0.97737,304.94,-0.41649,0.90509,0.085709,91.778,0.89811,0.39496,0.1934,-72.61
> view matrix models
> #6,0.16148,0.39933,-0.90248,246.79,-0.45122,0.84317,0.29235,75.141,0.87768,0.36001,0.31634,-82.878
> view matrix models
> #6,0.26156,0.1615,-0.95158,279.21,-0.12782,0.98301,0.1317,20.613,0.95669,0.087181,0.27776,-42.368
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.26156,0.1615,-0.95158,282.66,-0.12782,0.98301,0.1317,9.0483,0.95669,0.087181,0.27776,-38.201
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.13471,0.17399,-0.97549,306.32,-0.19051,0.97064,0.14682,19.629,0.9724,0.16606,0.1639,-36.307
> view matrix models
> #6,0.1878,0.10849,-0.9762,308.75,-0.44957,0.89315,0.012769,99.878,0.87328,0.43647,0.21651,-75.185
> view matrix models
> #6,0.28328,0.3407,-0.89648,238.47,-0.3572,0.905,0.23106,46.37,0.89003,0.25476,0.37807,-72.377
> volume #6 level 0.169
> volume #6 level 0.05336
> ui tool show "Fit in Map"
Fit map cryosparc_P39_J166_002_volume_map_sharp (1).mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 331401 points
correlation = 0.898, correlation about mean = 0.6711, overlap = 6198
steps = 152, shift = 5.34, angle = 16.7 degrees
Position of cryosparc_P39_J166_002_volume_map_sharp (1).mrc (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.92297785 -0.38455624 0.01511101 379.01804384
-0.38212566 0.91106400 -0.15473309 83.70405585
0.04573648 -0.14858952 -0.98784072 344.43723548
Axis 0.19609203 -0.97751177 0.07757998
Axis point 196.53062877 0.00000000 177.04366349
Rotation angle (degrees) 179.10242404
Shift along axis 19.22215351
> volume #6 level 0.05037
> volume #6 level 0.03372
> volume #6 level 0.02603
> volume #2 level 0.1649
> volume #2 level 0.1496
> show #9 models
> volume #6 color #bf9d9e
> volume #6 color #bf9d9e57
> volume #6 level 0.05379
> volume #6 level 0.06874
> volume #2 level 0.1649
> volume #2 level 0.17
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_E2.png"
> width 1326 height 850 supersample 3 transparentBackground true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32
> select #8
2 models selected
> view matrix models
> #8,0.93452,-0.21005,-0.2873,102.16,-0.33903,-0.27981,-0.8982,451.28,0.10828,0.93679,-0.3327,69.288
> view matrix models
> #8,-0.43794,-0.41147,0.79931,176.41,-0.88911,0.32976,-0.31738,334,-0.13299,-0.84967,-0.51026,455.34
> view matrix models
> #8,-0.13025,-0.70515,0.697,191.9,-0.98813,0.15007,-0.032822,329.17,-0.081457,-0.693,-0.71632,457.81
> close #8
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32
> color #8 #fff5c5 models transparency 0
> select #8
2 models selected
> view matrix models
> #8,-0.37477,-0.5067,0.77641,186,-0.92653,0.23447,-0.29422,352.81,-0.032965,-0.82963,-0.55734,442.95
> view matrix models
> #8,-0.40741,-0.58403,0.70209,219.21,-0.91262,0.28892,-0.28924,339.96,-0.033924,-0.75857,-0.6507,448.38
> view matrix models
> #8,-0.26337,-0.46915,0.84293,147.17,-0.95679,0.23865,-0.16612,333.34,-0.12323,-0.85026,-0.51174,453.98
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.26337,-0.46915,0.84293,164.19,-0.95679,0.23865,-0.16612,339.86,-0.12323,-0.85026,-0.51174,459.4
> color #8 #fff5c592 models
> color #8 #fff5c591 models
> view matrix models
> #8,-0.26337,-0.46915,0.84293,164.75,-0.95679,0.23865,-0.16612,339.53,-0.12323,-0.85026,-0.51174,460.75
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.30728,0.18959,0.93254,41.475,-0.40778,0.85919,-0.30905,161.27,-0.85982,-0.47524,-0.1867,465.45
> view matrix models
> #8,-0.48566,0.40603,0.77413,65.486,-0.39669,0.68678,-0.60908,245.69,-0.77896,-0.60289,-0.17248,470.53
> view matrix models
> #8,-0.49722,0.30467,0.81237,77.911,-0.61559,0.53594,-0.57777,304.85,-0.61141,-0.78737,-0.078928,455.12
> view matrix models
> #8,0.06302,-0.34884,0.93506,68.532,-0.69818,-0.6849,-0.20846,461.65,0.71314,-0.63971,-0.28672,233.22
> view matrix models
> #8,0.26213,-0.7558,0.60005,166.78,-0.96461,-0.18676,0.18614,348.34,-0.028616,-0.62761,-0.778,455.47
> view matrix models
> #8,-0.37994,0.023033,0.92472,84.739,-0.51716,0.82356,-0.233,172.57,-0.76693,-0.56676,-0.301,486.33
> view matrix models
> #8,0.19338,0.23275,0.95312,-58.871,-0.72187,0.69166,-0.022445,192.18,-0.66446,-0.68369,0.30177,374.89
> view matrix models
> #8,-0.21084,0.47884,0.85221,-10.689,-0.12039,0.85245,-0.50876,148.96,-0.97008,-0.20987,-0.12208,426.87
> view matrix models
> #8,-0.41196,0.43496,0.80069,42.367,-0.11525,0.84679,-0.51929,151.02,-0.90389,-0.30621,-0.29871,465.07
> view matrix models
> #8,-0.47775,0.38326,0.79049,64.945,-0.089881,0.87377,-0.47796,134.05,-0.87389,-0.29939,-0.38299,474.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.47775,0.38326,0.79049,62.298,-0.089881,0.87377,-0.47796,139.19,-0.87389,-0.29939,-0.38299,469.27
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> view matrix models
> #8,-0.62887,0.14228,0.76438,135.85,-0.3807,0.80086,-0.46227,200.57,-0.67794,-0.5817,-0.44947,495.91
> view matrix models
> #8,-0.68532,0.11195,0.71959,159.58,-0.34754,0.81805,-0.45826,190.94,-0.63997,-0.56414,-0.52172,499.72
> view matrix models
> #8,-0.62799,-0.10151,0.77157,176.61,-0.55751,0.75043,-0.35503,220.55,-0.54297,-0.65311,-0.52785,499.06
> ui tool show "Fit in Map"
Fit map cryosparc_P36_J32_002_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 89910 points
correlation = 0.5947, correlation about mean = 0.2353, overlap = 907.9
steps = 260, shift = 8.79, angle = 25 degrees
Position of cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.83017657 0.55542318 0.04808244 -106.08230735
-0.55722739 0.82397862 0.10274640 83.33490981
0.01744883 -0.11209051 0.99354477 -6.27353855
Axis -0.18951476 0.02702292 -0.98150594
Axis point 82.90354713 206.61275632 0.00000000
Rotation angle (degrees) 34.52792807
Shift along axis 28.51363138
> volume #8 level 0.03877
> volume #8 step 1
> volume #8 level 0.05098
> volume #8 level 0.08193
> volume #8 level 0.07541
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-23_NS1wt-Ab-Fab-
> ApoAI_hdl.cxs" includeMaps true
——— End of log from Thu Mar 24 12:02:48 2022 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> show #!1 models
> close #1
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!2 models
> show #!2 models
> rename #2 sNS1wt-Ab562.mrc
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!8 models
> volume #6 level 0.0595
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> close #6
> show #!7 models
> hide #!2 models
> show #!2 models
> close #7
> show #5 models
> show #!8 models
> hide #9 models
> show #9 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #5 models
> show #5 models
> hide #!8 models
> show #!8 models
> hide #9 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right select
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.911,-0.19028,-0.36588,158.81,-0.385,-0.71042,-0.58914,511.26,-0.14783,0.67757,-0.72045,241.26
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.033091,0.22459,0.97389,-84.329,0.17148,0.9587,-0.22691,18.38,-0.98463,0.17451,-0.006788,310.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.033091,0.22459,0.97389,-41.613,0.17148,0.9587,-0.22691,17.858,-0.98463,0.17451,-0.006788,323.69
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.027159,0.41704,0.90848,-51.291,0.63529,0.70888,-0.30642,2.4644,-0.77179,0.56883,-0.2842,279.48
> view matrix models
> #5,-0.080191,0.31482,0.94576,-31.96,0.72243,0.67208,-0.16247,-40.126,-0.68678,0.67022,-0.28133,245.19
> view matrix models
> #5,-0.13135,0.33964,0.93134,-24.234,0.71868,0.67973,-0.14652,-44.687,-0.68283,0.65008,-0.33337,260.62
> view matrix models
> #5,-0.11889,0.37005,0.92137,-29.677,0.7114,0.6791,-0.18095,-35.108,-0.69266,0.63395,-0.34399,267.86
> view matrix models
> #5,0.045939,0.59116,0.80525,-71.763,0.70283,0.55371,-0.44659,52.881,-0.70988,0.58646,-0.39004,290.63
> view matrix models
> #5,0.084841,0.56745,0.81902,-77.41,0.67501,0.57189,-0.46615,59,-0.73291,0.5924,-0.33452,280.32
> view matrix models
> #5,-0.13391,0.55975,0.81777,-37.622,0.55097,0.72796,-0.40805,37.78,-0.82371,0.39592,-0.40589,349.58
> view matrix models
> #5,-0.09912,0.51183,0.85335,-43.247,0.59183,0.71973,-0.36294,21.462,-0.79994,0.46907,-0.37425,324.33
> view matrix models
> #5,-0.11178,0.47533,0.87268,-38.868,0.59167,0.73739,-0.32585,9.3844,-0.79839,0.47992,-0.36367,319.53
> view matrix models
> #5,-0.22153,0.44542,0.86748,-12.986,0.53956,0.79699,-0.27144,-5.5629,-0.81228,0.40793,-0.41688,347.98
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.22153,0.44542,0.86748,-14.111,0.53956,0.79699,-0.27144,-5.3645,-0.81228,0.40793,-0.41688,348.49
> select add #8
3401 atoms, 3493 bonds, 442 residues, 3 models selected
> fitmap #5 inMap #8
Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
(#8) using 3401 atoms
average map value = 0.09851, steps = 108
shifted from previous position = 1.67
rotated from previous position = 17.3 degrees
atoms outside contour = 1366, contour level = 0.075413
Position of F562b.pdb (#5) relative to
cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.45238682 -0.88366144 -0.12036870 287.11798101
0.88783684 0.43349946 0.15435016 -99.22400613
-0.08421352 -0.17669374 0.98065662 40.64404116
Axis -0.18365545 -0.02005805 0.98278601
Axis point 227.81128239 181.49795933 0.00000000
Rotation angle (degrees) 64.32464577
Shift along axis -10.79614671
> fitmap #5 inMap #8
Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
(#8) using 3401 atoms
average map value = 0.09851, steps = 44
shifted from previous position = 0.00416
rotated from previous position = 0.0187 degrees
atoms outside contour = 1367, contour level = 0.075413
Position of F562b.pdb (#5) relative to
cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.45231009 -0.88373711 -0.12010123 287.08058767
0.88785087 0.43341968 0.15449342 -99.24674165
-0.08447733 -0.17651091 0.98066686 40.65823137
Axis -0.18362633 -0.01976254 0.98279744
Axis point 227.80088638 181.42728547 0.00000000
Rotation angle (degrees) 64.32929481
Shift along axis -10.79538196
> show #3 models
> hide #3 models
> show #3 models
> color #8 #d7fef991 models
> color #8 #c5fef791 models
> color #8 #c4fbfe91 models
> color #8 #c3fef791 models
> rename #8 sNS1wt-Fab562.mrc
> select subtract #5
2 models selected
> select subtract #8
Nothing selected
> show #4 models
> show #!2 models
> rename #4 F562a-FL.pdb
> show #9 models
> color #2 #c4a1924d models
[Repeated 1 time(s)]
> hide #!2 models
> hide #4 models
> ui mousemode right zoom
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM Maps_docked
> structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Sat Nov 19 10:30:44 2022 ———
opened ChimeraX session
> volume #8 color #dbfdf891
> volume #8 color #c5fdf891
> volume #8 color #c5fdf849
> volume #8 color #c5fdf84c
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> rename #3 eden2ns1.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/C
Alignment identifier is 1
> select #3/B-C:2
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B-C:2-75
1174 atoms, 1200 bonds, 148 residues, 1 model selected
> select #3/B-C:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B-C:172-178
118 atoms, 116 bonds, 14 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
not of the form 'name: value' or is missing initial tab
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Data line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr not of
the form: atomspec value
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Line 43 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
not of the form 'name: value' or is missing initial tab
> color #3/A-B dimgray
> hide #3 models
> show #3 models
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> color #3 dimgray
> ui tool show "Change Chain IDs"
> changechains C A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/1/)
> changechains C A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/1/)
> changechains sel C A
Chain IDs of 352 residues changed
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/A
Alignment identifier is 1
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
residues using match mode: any
> ui tool show "Show Sequence Viewer"
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
residues using match mode: any
> byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key true
> bluered noValueColor gray
Unknown command: byattribute relative_deuterium_uptake_NS1c_10min
#3/A-B:174-361 key true bluered noValueColor gray
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true bluered noValueColor gray
Expected a keyword
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
> ui mousemode right "color key"
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> key blue-white-red :-0.98 :-0.47 :1
> key blue-white-red :-2 :-0.47 :1
> key blue-white-red :-2 :0 :1
> hide #5 models
> hide #9 models
> hide #!8 models
> hide #8.1 models
> key pos 0.636108,0.370379 size 0.0013699,0.146465
> undo
> key pos 0.479592,0.196551 size 0.329083,0.0401247
> ui mousemode right zoom
> select subtract #3
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select #3/B,A:212-213
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:212-217
96 atoms, 96 bonds, 12 residues, 1 model selected
> select #3/B,A:216
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:212-216
74 atoms, 72 bonds, 10 residues, 1 model selected
> select #3/B,A:211
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:211-216
92 atoms, 90 bonds, 12 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 984
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor grey
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> ui tool show "Selection Inspector"
> toolshed show
> view sel
> key blue-white-red :-0.98 :-0.47 :1
> key blue-white-red :- :-0.47 :1
> key blue-white-red :-2 :-0.47 :1
> key colorTreatment distinct
> key colorTreatment blended
> attributes available
Unknown command: attributes available
> info attributes
Expected a models specifier or a keyword
> info resattr
resattr alt_loc
resattr alt_locs
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr custom_attrs
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr relative_deuterium_uptake_NS1c_10min
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr seq_conservation
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> select #3/B,A:181
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:181-198
268 atoms, 268 bonds, 36 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor grey
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> select #3/B,A:299-300
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B,A:299-301
50 atoms, 48 bonds, 6 residues, 1 model selected
> key red-white-blue :0.04 :-0.47 :-0.98
> key blue-white-red :-0.98 :-0.47 :0.04
> key red-white-blue :0.04 :-0.47 :-0.98
> key blue-white-red :-0.98 :-0.47 :0.04
> key blue-white-red :- :-0.47 :0.04
> key blue-white-red :-2 :-0.47 :0.04
> key blue-white-red :-2 :-0.47 :1
> key blue-white-red :-2 :0 :1
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2:1 noValueColor grey
Invalid "range" argument: Expected some numbers or 'full'
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 866
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> undo
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> select #3/B,A:175
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:175-178
60 atoms, 58 bonds, 8 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right zoom
> select #3/B,A:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:172-174
58 atoms, 56 bonds, 6 residues, 1 model selected
> select #3/B,A:174-175
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #3/B,A:174-178
82 atoms, 80 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #cbdbffff
> color sel #c1d2ffff
> color sel #c1d1ffff
> color sel #c2d2ffff
[Repeated 1 time(s)]
> color sel #c3d3ffff
> color sel #c4d3ffff
> color sel #c4d4ffff
> color sel #c4d5ffff
> color sel #c5d6ffff
> color sel #c5d5ffff
> color sel #c4d4ffff
> color sel #c4d3ffff
[Repeated 1 time(s)]
> color sel #c3d2ffff
> color sel #c3d1ffff
> color sel #c2d0ffff
[Repeated 1 time(s)]
> color sel #c1cfffff
> color sel #c1ceffff
> color sel #c1cdffff
> color sel #c0cdffff
> color sel #c0ccffff
> color sel #c1cdffff
[Repeated 1 time(s)]
> color sel #c1ceffff
> color sel #c2cfffff
> color sel #b8c2ffff
> color sel #aebdffff
> select #3/B,A:179
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:179-187
122 atoms, 120 bonds, 18 residues, 1 model selected
> color sel #c4cfffff
> select #3/B,A:188
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:188-198
174 atoms, 174 bonds, 22 residues, 1 model selected
> color sel #b1bbffff
> select #3/B,A:199
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #3/B,A:199-200
32 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #99b0ffff
> color sel #96baffff
> color sel #92b4ffff
> color sel #6a97ffff
> select #3/B,A:201-202
44 atoms, 46 bonds, 4 residues, 1 model selected
> select #3/B,A:201-211
192 atoms, 198 bonds, 22 residues, 1 model selected
> color sel #91acffff
> select #3/B,A:212
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:212-217
96 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #aabeffff
> color sel #bfcfffff
[Repeated 1 time(s)]
> color sel #bfceffff
> color sel #beceffff
> color sel #becdffff
> color sel #bdcdffff
> select #3/B,A:218
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:218-219
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #adc4ffff
> select #3/B,A:220
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:220-231
198 atoms, 206 bonds, 24 residues, 1 model selected
> color sel #88a5ffff
> color sel #83a2ffff
> color sel #7fa0ffff
> select #3/B,A:232
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B,A:232-240
142 atoms, 144 bonds, 18 residues, 1 model selected
> color sel #98b0ffff
> select #3/B,A:231
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:220-231
198 atoms, 206 bonds, 24 residues, 1 model selected
> color sel #8da3edff
> color sel #8da3ecff
[Repeated 1 time(s)]
> color sel #8ca2ecff
> color sel #8ca2ebff
> color sel #8ba1eaff
> color sel #8ba0e9ff
> color sel #889ee5ff
> color sel #869be0ff
> color sel #8397dcff
> color sel #8195d9ff
> color sel #8094d7ff
> color sel #7f93d6ff
> color sel #7f93d5ff
> color sel #7e92d4ff
> color sel #7d90d2ff
> color sel #7b8eceff
> color sel #798cccff
> color sel #788bc9ff
> color sel #778ac8ff
[Repeated 1 time(s)]
> color sel #7689c7ff
> color sel #7688c6ff
> color sel #7587c5ff
> color sel #7587c4ff
> color sel #7487c3ff
> color sel #7486c3ff
> color sel #7081bcff
> color sel #6878afff
> color sel #6272a5ff
> color sel #576592ff
> color sel #4c5880ff
> color sel #444f73ff
> color sel #414b6dff
> color sel #404a6cff
> color sel #404a6bff
> color sel #3f4969ff
> color sel #3d4666ff
> color sel #3b4463ff
> color sel #38415fff
> color sel #343c57ff
> color sel #2e364eff
> color sel #2c3249ff
> color sel #2b3148ff
> color sel #2a3146ff
[Repeated 1 time(s)]
> color sel #2a3147ff
> color sel #2c334bff
> color sel #2f364fff
> color sel #343c58ff
> color sel #3a4361ff
> color sel #404a6cff
> color sel #475277ff
> color sel #4d5981ff
> color sel #55638fff
> color sel #596796ff
> color sel #5d6b9cff
> color sel #606fa1ff
> color sel #6272a5ff
> color sel #6878afff
> color sel #6b7bb3ff
> color sel #7082bcff
> color sel #7284c0ff
> color sel #7486c3ff
> color sel #7587c5ff
> color sel #7688c6ff
> color sel #7689c6ff
> color sel #778ac8ff
> color sel #788ac9ff
> color sel #788bcaff
> color sel #798cccff
> color sel #7a8dcdff
> color sel #7b8eceff
> color sel #7c8fcfff
> color sel #7c90d0ff
> color sel #7d90d1ff
> color sel #7d91d2ff
> color sel #7e91d3ff
> color sel #7e92d4ff
> color sel #7f93d5ff
[Repeated 1 time(s)]
> color sel #7f93d6ff
> color sel #8094d7ff
> color sel #8296daff
> color sel #859ae0ff
> color sel #879ce2ff
> color sel #899ee5ff
> color sel #899ee6ff
[Repeated 1 time(s)]
> color sel #899fe6ff
> color sel #899fe7ff
> color sel #8aa0e8ff
> color sel #8ca2ebff
> color sel #8da3ecff
> color sel #8da3edff
> color sel #8da4edff
> color sel #8ea5efff
> color sel #90a6f1ff
> color sel #91a7f3ff
> color sel #92a9f5ff
> color sel #92a9f6ff
> color sel #94abf8ff
> color sel #95acfaff
[Repeated 1 time(s)]
> color sel #95adfbff
> color sel #96aefcff
> color sel #97affeff
> color sel #98b0ffff
[Repeated 1 time(s)]
> color sel #97affeff
> color sel #94abf9ff
> color sel #92a9f6ff
> color sel #92a8f4ff
> color sel #91a8f4ff
> color sel #91a7f3ff
> color sel #90a7f2ff
> color sel #91a7f3ff
> color sel #91a8f4ff
> color sel #92a9f5ff
> color sel #92a9f6ff
> color sel #93aaf7ff
> color sel #94abf8ff
> color sel #94abf9ff
> color sel #6492f9ff
> color sel #4f5af9ff
> color sel #505df9ff
> color sel #505ef9ff
> color sel #515ff9ff
[Repeated 1 time(s)]
> color sel #5260f9ff
> color sel #5362f9ff
> color sel #5363f9ff
[Repeated 1 time(s)]
> color sel #5465f9ff
> color sel #5567f9ff
> color sel #5667f9ff
> color sel #5668f9ff
> color sel #5568f9ff
> color sel #5569f9ff
[Repeated 1 time(s)]
> color sel #5469f9ff
[Repeated 2 time(s)]
> color sel #5369f9ff
> color sel #536af9ff
> color sel #546bf9ff
> color sel #546cf9ff
[Repeated 1 time(s)]
> color sel #556df9ff
> color sel #556ef9ff
> color sel #556ff9ff
> color sel #5670f9ff
[Repeated 2 time(s)]
> color sel #5671f9ff
> color sel #5772f9ff
> color sel #5672f9ff
> color sel #5671f9ff
[Repeated 1 time(s)]
> color sel #5570f9ff
> color sel #556ff9ff
> color sel #546ef9ff
[Repeated 1 time(s)]
> color sel #536df9ff
[Repeated 1 time(s)]
> color sel #526cf9ff
[Repeated 1 time(s)]
> color sel #526bf9ff
> color sel #516af9ff
> color sel #5169f9ff
> color sel #5069f9ff
> color sel #5068f9ff
> color sel #4f67f9ff
> color sel #4f66f9ff
> color sel #4f65f9ff
> color sel #5069f9ff
> color sel #516af9ff
[Repeated 1 time(s)]
> color sel #516bf9ff
> color sel #536cf9ff
> color sel #536df9ff
> color sel #546df9ff
> color sel #546ef9ff
> color sel #556ff9ff
> color sel #5670f9ff
[Repeated 1 time(s)]
> color sel #5770f9ff
> color sel #5771f9ff
> color sel #5872f9ff
[Repeated 2 time(s)]
> color sel #5972f9ff
> color sel #5973f9ff
> color sel #5a73f9ff
[Repeated 1 time(s)]
> color sel #5a74f9ff
> color sel #5b73f9ff
[Repeated 1 time(s)]
> color sel #5c74f9ff
[Repeated 2 time(s)]
> color sel #5d74f9ff
[Repeated 1 time(s)]
> color sel #5e73f9ff
> color sel #5e74f9ff
[Repeated 1 time(s)]
> select #3/B,A:241
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:241
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel #8897f9ff
> color sel #b4bff9ff
> color sel #becff9ff
> color sel #bdcff9ff
[Repeated 1 time(s)]
> color sel #bccff9ff
[Repeated 1 time(s)]
> color sel #bbcff9ff
[Repeated 2 time(s)]
> color sel #bbd0f9ff
> color sel #bbcff9ff
> color sel #bacff9ff
> color sel #bacef9ff
> color sel #b9cdf9ff
> color sel #b9ccf9ff
[Repeated 1 time(s)]
> color sel #b8cbf9ff
[Repeated 1 time(s)]
> color sel #b7caf9ff
[Repeated 1 time(s)]
> color sel #b7c9f9ff
> color sel #b5c8f9ff
> color sel #b5c7f9ff
> color sel #b5c6f9ff
> color sel #b4c6f9ff
[Repeated 1 time(s)]
> color sel #b3c5f9ff
> color sel #b3c4f9ff
> color sel #b2c4f9ff
> color sel #b2c3f9ff
> color sel #b1c2f9ff
> color sel #b1c1f9ff
> color sel #b0c1f9ff
> color sel #b0c0f9ff
> color sel #afbff9ff
[Repeated 1 time(s)]
> color sel #aebef9ff
> color sel #aebdf9ff
> select #3/B,A:242
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:242-247
102 atoms, 104 bonds, 12 residues, 1 model selected
> color sel #909df9ff
> select #3/B,A:248-249
18 atoms, 16 bonds, 4 residues, 1 model selected
> select #3/B,A:248-253
76 atoms, 76 bonds, 12 residues, 1 model selected
> color sel #9fabf9ff
> select #3/B,A:254-255
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #3/B,A:254-262
162 atoms, 170 bonds, 18 residues, 1 model selected
> color sel #92a1f9ff
> select #3/B,A:263-264
32 atoms, 30 bonds, 4 residues, 1 model selected
> select #3/B,A:263-265
42 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #acbbf9ff
[Repeated 1 time(s)]
> color sel #abbaf9ff
> color sel #abb9f9ff
> select #3/B,A:266-267
22 atoms, 22 bonds, 4 residues, 1 model selected
> select #3/B,A:266-267
22 atoms, 22 bonds, 4 residues, 1 model selected
> color sel #7a98f9ff
> color sel #6689f9ff
> color sel #698bf9ff
> color sel #698cf9ff
> color sel #6a8cf9ff
> color sel #6b8cf9ff
> color sel #6c8df9ff
> color sel #6c8ef9ff
> color sel #6d8ef9ff
> color sel #6e8ef9ff
> color sel #6e8ff9ff
> color sel #6f90f9ff
> color sel #6f8ff9ff
> color sel #6284f9ff
> select #3/B,A:268-269
48 atoms, 52 bonds, 4 residues, 1 model selected
> select #3/B,A:268-273
110 atoms, 114 bonds, 12 residues, 1 model selected
> color sel #86abf9ff
> select #3/B,A:274-275
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:274-275
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #5584f9ff
> color sel #5684f9ff
> color sel #5785f9ff
> color sel #5886f9ff
> color sel #5986f9ff
> color sel #5b87f9ff
> color sel #5c88f9ff
[Repeated 1 time(s)]
> color sel #5c89f9ff
> color sel #5d89f9ff
> color sel #5e8af9ff
> color sel #5e8bf9ff
> color sel #5f8bf9ff
> color sel #5f8cf9ff
> color sel #608df9ff
> color sel #618df9ff
> color sel #618ef9ff
[Repeated 1 time(s)]
> color sel #628ff9ff
> color sel #638ff9ff
> color sel #6390f9ff
> color sel #6592f9ff
> color sel #6994f9ff
> color sel #6a96f9ff
> color sel #6b96f9ff
> color sel #6c97f9ff
[Repeated 1 time(s)]
> select #3/B,A:276-277
38 atoms, 38 bonds, 4 residues, 1 model selected
> select #3/B,A:276-277
38 atoms, 38 bonds, 4 residues, 1 model selected
> color sel #89aef9ff
> select #3/B,A:278
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:278-285
118 atoms, 118 bonds, 16 residues, 1 model selected
> select #3/B,A:286-287
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:286-287
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:286
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:286-299
206 atoms, 206 bonds, 28 residues, 1 model selected
> color sel #7c9df9ff
> color sel #798df9ff
> select #3/B,A:300
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:300-309
136 atoms, 134 bonds, 20 residues, 1 model selected
> color sel #527af9ff
> color sel #3a5af9ff
> select #3/B,A:310
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:310
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel #526af9ff
> select #3/B,A:311
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B,A:311-333
378 atoms, 392 bonds, 46 residues, 1 model selected
> color sel #c6c6f3ff
> color sel #b6b4f3ff
> select #3/B,A:334-335
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:334-335
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #9c98f3ff
> select #3/B,A:336-337
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #3/B,A:336-341
106 atoms, 106 bonds, 12 residues, 1 model selected
> color sel #a7acf3ff
> select #3/B,A:341-342
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B,A:341-350
158 atoms, 156 bonds, 20 residues, 1 model selected
> color sel #6b69f3ff
> color sel #6b6af3ff
> color sel #6b6bf3ff
> color sel #6d6ef3ff
> color sel #6f70f3ff
> color sel #7273f3ff
> color sel #7274f3ff
> color sel #7375f3ff
> color sel #7476f3ff
> color sel #7477f3ff
> color sel #7578f3ff
> color sel #7579f3ff
> color sel #7679f3ff
> color sel #777af3ff
> color sel #787cf3ff
> color sel #777bf3ff
> color sel #777af3ff
> color sel #7679f3ff
> color sel #7072f3ff
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:300
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:300-309
136 atoms, 134 bonds, 20 residues, 1 model selected
> color sel #4c4ef3ff
> color sel #4242f3ff
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:1-2
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:1-171
2732 atoms, 2798 bonds, 342 residues, 1 model selected
> color sel #edeff3ff
> color sel #c7c9ccff
> color sel #c7c8ccff
> color sel #c2c4c7ff
> color sel #c1c2c6ff
> color sel #c0c2c5ff
> color sel #bfc0c4ff
> color sel #bdbec2ff
> color sel #bcbdc0ff
> color sel #babcbfff
> color sel #babbbeff
> color sel #b9bbbeff
> color sel #b9babeff
> color sel #b6b7bbff
> color sel #b2b3b6ff
> color sel #afb0b3ff
> color sel #abacafff
> color sel #a6a7abff
> color sel #a3a4a7ff
> color sel #a1a2a5ff
> color sel #9fa0a3ff
> color sel #9c9da0ff
> color sel #999a9cff
> color sel #96979aff
[Repeated 1 time(s)]
> color sel #949597ff
> color sel #919295ff
> color sel #8b8b8eff
> color sel #87888aff
> color sel #7e7f81ff
> color sel #727375ff
> color sel #68686aff
> color sel #616264ff
> color sel #59595bff
> color sel #545556ff
> color sel #4d4e4fff
> color sel #464748ff
> color sel #444446ff
> color sel #424244ff
> color sel #3f3f40ff
> color sel #3e3e3fff
> color sel #3c3d3eff
[Repeated 1 time(s)]
> color sel #414243ff
> color sel #4d4e4fff
> color sel #565658ff
> color sel #606162ff
> color sel #656668ff
> color sel #6a6b6dff
> color sel #717274ff
> color sel #737476ff
> color sel #78797bff
> color sel #7b7b7eff
> color sel #818285ff
> color sel #858689ff
> color sel #88898cff
> color sel #8b8c8eff
> color sel #8c8d90ff
> color sel #8f8f92ff
> color sel #919295ff
> color sel #959699ff
> color sel #9a9b9eff
> color sel #9e9fa2ff
> color sel #a1a2a5ff
> color sel #a5a6a9ff
> color sel #a7a8abff
> color sel #a8a9adff
> color sel #a9aaaeff
> color sel #aaabaeff
[Repeated 1 time(s)]
> color sel #adaeb1ff
> color sel #afb0b3ff
[Repeated 1 time(s)]
> color sel #b0b1b4ff
> color sel #b1b2b5ff
> color sel #b2b3b6ff
[Repeated 1 time(s)]
> color sel #b2b3b6fa
> color sel #b2b3b6f5
> color sel #b2b3b6f3
> color sel #b2b3b6ee
[Repeated 2 time(s)]
> color sel #b2b3b6ed
[Repeated 1 time(s)]
> color sel #b2b3b6eb
[Repeated 1 time(s)]
> color sel #b2b3b6ea
> color sel #b2b3b6e9
> color sel #b2b3b6e8
[Repeated 1 time(s)]
> color sel #b2b3b6e7
[Repeated 1 time(s)]
> color sel #b2b3b6e6
> color sel #b2b3b6e5
> color sel #b2b3b6e3
> color sel #b2b3b6e2
> color sel #b2b3b6e1
> color sel #b2b3b6e0
> color sel #b2b3b6df
[Repeated 1 time(s)]
> color sel #b2b3b6de
> color sel #b2b3b6dd
> color sel #b2b3b6dc
> color sel #b2b3b6db
> color sel #b2b3b6da
[Repeated 1 time(s)]
> color sel #b2b3b6d9
> color sel #b2b3b6d8
[Repeated 1 time(s)]
> color sel #b2b3b6d7
[Repeated 1 time(s)]
> color sel #b2b3b6d6
> color sel #b2b3b6d5
> color sel #b2b3b6d4
> color sel #b2b3b6d2
> color sel #b2b3b6d1
> color sel #b2b3b6d0
[Repeated 1 time(s)]
> color sel #b2b3b6cf
> color sel #b2b3b6cd
[Repeated 1 time(s)]
> color sel #b1b3b6cd
> color sel #b1b2b6cd
> color sel #b1b2b5cd
[Repeated 1 time(s)]
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:1-171
2732 atoms, 2798 bonds, 342 residues, 1 model selected
> color sel #b1b2b5cc
> color sel #b1b2b5c8
> color sel #b1b2b5c6
> color sel #b1b2b5c5
> color sel #b1b2b5c1
> color sel #b1b2b5be
> color sel #b1b2b5bb
> color sel #b1b2b5b7
> color sel #b1b2b5b5
> color sel #b1b2b5b1
> color sel #b1b2b5ad
> color sel #b1b2b5aa
> color sel #b1b2b5a7
> color sel #b1b2b5a4
> color sel #b1b2b5a0
> color sel #b1b2b599
> color sel #b1b2b592
> color sel #b1b2b58c
> color sel #b1b2b586
> color sel #b1b2b576
> color sel #b1b2b573
> color sel #b1b2b56e
> color sel #b1b2b56a
> color sel #b1b2b568
> color sel #b1b2b567
> color sel #b1b2b565
> color sel #b1b2b563
[Repeated 1 time(s)]
> color sel #b1b2b565
> color sel #b1b2b569
> color sel #b1b2b56c
> color sel #b1b2b572
> color sel #b1b2b575
> color sel #b1b2b57b
> color sel #b1b2b581
> color sel #b1b2b587
> color sel #b1b2b589
> color sel #b1b2b58a
[Repeated 1 time(s)]
> color sel #b1b2b58d
> color sel #b1b2b590
> color sel #b1b2b591
> color sel #b1b2b594
> color sel #b1b2b596
[Repeated 2 time(s)]
> color sel #b1b2b597
> color sel #b1b2b598
[Repeated 1 time(s)]
> color sel #b1b2b599
> color sel #b1b2b59a
> color sel #b1b2b59c
> color sel #b1b2b59d
> color sel #b1b2b59c
[Repeated 1 time(s)]
> color sel #b1b2b59b
[Repeated 1 time(s)]
> color sel #b1b2b59a
[Repeated 1 time(s)]
> color sel #b1b2b599
[Repeated 1 time(s)]
> color sel #b1b2b598
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/sNS1wt-Ab562_EM-HDX.cxs"
> includeMaps true
> show #!2 models
> color #2 #cfbabb4d models
> color #2 #c1acae4d models
> color #2 #c1acae2e models
> color #2 #c1acae34 models
> show #!8 models
> show #4 models
> select add #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.25081,-0.17578,-0.95194,337.54,0.94086,0.27565,0.19699,-69.227,0.22777,-0.94505,0.23452,277.17
> view matrix models
> #4,0.25081,-0.17578,-0.95194,337.61,0.94086,0.27565,0.19699,-68.962,0.22777,-0.94505,0.23452,277.21
> view matrix models
> #4,0.25081,-0.17578,-0.95194,338.3,0.94086,0.27565,0.19699,-67.778,0.22777,-0.94505,0.23452,276.56
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.28381,-0.20491,-0.93673,335.61,0.93973,0.25368,0.22923,-67.38,0.19066,-0.94534,0.26456,280.03
> view matrix models
> #4,0.29033,-0.1329,-0.94765,322.58,0.93808,0.23513,0.25442,-66.671,0.18901,-0.96284,0.19293,291.98
> view matrix models
> #4,0.35013,-0.063779,-0.93453,297.24,0.92612,0.17313,0.33516,-62.689,0.14042,-0.98283,0.11968,313.39
> view matrix models
> #4,0.28929,-0.083154,-0.95362,314.43,0.94763,0.16569,0.27303,-58.03,0.1353,-0.98267,0.12673,313.48
> view matrix models
> #4,0.29468,-0.086777,-0.95165,313.84,0.94725,0.15789,0.27892,-57.235,0.12605,-0.98364,0.12873,315.16
> view matrix models
> #4,0.36145,-0.11336,-0.92548,303.06,0.89859,0.30718,0.31332,-79.332,0.24877,-0.94488,0.21289,275.15
> hide #!2 models
> view matrix models
> #4,0.75588,-0.11899,-0.6438,196.83,0.49521,0.74715,0.44333,-99.072,0.42827,-0.65392,0.62368,140.02
> view matrix models
> #4,0.79244,-0.19913,-0.57652,196.6,0.59732,0.44467,0.66744,-89.678,0.12346,-0.87328,0.47133,255.09
> show #!2 models
> view matrix models
> #4,0.84088,0.043539,-0.53947,139,0.20748,0.89468,0.3956,-66.307,0.49988,-0.44458,0.74328,74.375
> view matrix models
> #4,0.61732,-0.23939,-0.7494,257.2,0.45462,0.88598,0.091476,-75.144,0.64205,-0.39716,0.65577,49.425
> view matrix models
> #4,0.38724,0.030398,-0.92148,271.6,0.61211,0.73893,0.28161,-100.4,0.68947,-0.6731,0.26753,136.6
> view matrix models
> #4,0.32928,0.15127,-0.93204,261.73,0.67479,0.65276,0.34434,-103.89,0.66048,-0.74231,0.11286,172.9
> view matrix models
> #4,0.83345,-0.16899,-0.52612,177.48,0.33798,0.90914,0.24338,-75.428,0.43719,-0.38066,0.81484,66.051
> view matrix models
> #4,0.73197,-0.15661,-0.6631,210.44,0.61773,0.56316,0.54888,-101.05,0.28747,-0.81137,0.50895,208.62
> view matrix models
> #4,0.70748,-0.11472,-0.69736,211.46,0.67078,0.41972,0.61146,-92.303,0.22255,-0.90037,0.3739,252.95
> view matrix models
> #4,0.50475,-0.22825,-0.83254,286.11,0.80219,0.4803,0.35468,-97.631,0.31892,-0.84689,0.42553,219.04
> view matrix models
> #4,0.43321,-0.14625,-0.88935,291.32,0.79138,0.53394,0.29769,-98.629,0.43133,-0.83278,0.34705,204.67
> view matrix models
> #4,0.39985,-0.22492,-0.88856,311.79,0.73762,0.65442,0.16627,-94.936,0.54409,-0.7219,0.42757,153.83
> hide #!8 models
> view matrix models
> #4,0.40534,-0.24527,-0.88065,313.53,0.76932,0.61189,0.18368,-95.2,0.49381,-0.75196,0.43671,167.65
> view matrix models
> #4,0.25068,-0.40305,-0.88017,371.18,0.81823,0.57411,-0.029862,-72.272,0.51736,-0.7127,0.47371,151.72
> view matrix models
> #4,0.3665,-0.39401,-0.84287,343.41,0.8386,0.5323,0.11581,-85.696,0.40303,-0.74927,0.5255,173.7
> view matrix models
> #4,0.48359,-0.37777,-0.78957,312.2,0.85036,0.41655,0.32152,-91.15,0.20743,-0.82691,0.52268,224.84
> view matrix models
> #4,0.44767,-0.35695,-0.81986,318.73,0.84619,0.46549,0.25939,-91.93,0.28905,-0.80988,0.51043,207.88
> show #5 models
> hide #4 models
> show #!8 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> ui tool show "Change Chain IDs"
> select #5/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C
1632 atoms, 1668 bonds, 214 residues, 1 model selected
> changechains sel C L
Chain IDs of 214 residues changed
> changechains sel C L
No residues specified have any of the 'from' chain IDs
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L
Alignment identifier is 5/L
> ui tool show "Change Chain IDs"
> select
> #5/B:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
837 atoms, 847 bonds, 101 residues, 1 model selected
> select #5/B:228
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel B H
Chain IDs of 228 residues changed
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/H:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'fab562_10min_relative_deuterium_uptake' to 1126
residues using match mode: any
> color byattribute fab562_10min_relative_deuterium_uptake #3/A-B:174-361 key
> true palette bluered range -2.0,1.0 noValueColor grey
All 'fab562_10min_relative_deuterium_uptake' values are None
> color byattribute fab562_10min_relative_deuterium_uptake #5 key true palette
> bluered range -2.0,1.0 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
3401 atoms, 442 residues, atom fab562_10min_relative_deuterium_uptake range
-1.18 to 0.73
> hide #!8 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> ui mousemode right zoom
> select #5/H:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/H:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select #5/H:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:5-14
71 atoms, 71 bonds, 10 residues, 1 model selected
> color sel #ddddffff
> color sel #aab4ffff
> color sel #8390ffff
> select #5/H:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:15-29
120 atoms, 124 bonds, 15 residues, 1 model selected
> color sel #ffe6e6ff
> color sel #ffe2ddff
> color sel #ffe1ddff
> color sel #ffe0dcff
[Repeated 2 time(s)]
> color sel #ffe0dbff
> color sel #ffdfdaff
[Repeated 1 time(s)]
> color sel #ffdedaff
> color sel #ffddd9ff
[Repeated 1 time(s)]
> color sel #ffdcd8ff
> select #5/H:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:30-35
43 atoms, 43 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #6f70ffff
> color sel #4449ffff
> color sel #1f28ffff
> color sel #1f29ffff
> color sel #202affff
> color sel #212cffff
> color sel #222cffff
> color sel #222dffff
> color sel #232effff
> color sel #242fffff
[Repeated 2 time(s)]
> color sel #2531ffff
> color sel #2631ffff
> color sel #2632ffff
> color sel #2732ffff
> color sel #2733ffff
> color sel #2935ffff
> color sel #2a35ffff
> color sel #2a36ffff
> color sel #2b37ffff
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:36-47
115 atoms, 120 bonds, 12 residues, 1 model selected
> color sel #ffcfe1ff
> color sel #ffdddeff
[Repeated 1 time(s)]
> color sel #ffdddfff
> color sel #ffdde2ff
> color sel #ffdde3ff
> color sel #ffdde5ff
> color sel #ffdde8ff
> color sel #ffdde9ff
> color sel #ffdceaff
[Repeated 1 time(s)]
> color sel #ffdce9ff
> color sel #ffdae7ff
> color sel #ffd9e4ff
> color sel #ffd8e2ff
> color sel #ffd7e0ff
> color sel #ffd7dfff
> color sel #ffd6dcff
> color sel #ffd5dbff
> color sel #ffd3daff
> color sel #ffd3d9ff
> color sel #ffd2d7ff
[Repeated 1 time(s)]
> color sel #ffd1d6ff
> color sel #ffd0d5ff
> select #5/H:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:48-61
120 atoms, 123 bonds, 14 residues, 1 model selected
> color sel #6277ffff
> select #5/H:62-63
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/H:62-72
91 atoms, 92 bonds, 11 residues, 1 model selected
> color sel #ff7f7fff
> color sel #ff9b9aff
> select #5/H:79-80
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/H:79-81
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/H:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:78-95
142 atoms, 144 bonds, 18 residues, 1 model selected
> color sel #a9b9ffff
> select #5/H:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:96-103
75 atoms, 78 bonds, 8 residues, 1 model selected
> color sel #8493ffff
> color sel #88a0ffff
> select #5/H:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:104-112
73 atoms, 78 bonds, 9 residues, 1 model selected
> color sel #8296ffff
> color sel #8297ffff
> color sel #8398ffff
> color sel #8499ffff
> color sel #849affff
> color sel #849bffff
> color sel #859cffff
> color sel #859dffff
[Repeated 1 time(s)]
> color sel #869effff
> color sel #869fffff
> color sel #87a0ffff
> color sel #88a1ffff
> color sel #88a2ffff
> color sel #89a3ffff
[Repeated 1 time(s)]
> color sel #8aa4ffff
> color sel #8aa5ffff
> select #5/H:113-114
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #5/H:113-120
65 atoms, 67 bonds, 8 residues, 1 model selected
> color sel #aab4ffff
> select #5/H:120-121
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:120-121
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #7e95ffff
> select #5/H:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:121-123
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #5/H:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:121-122
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel #eceeffff
> color sel #73747cff
[Repeated 1 time(s)]
> color sel #74747dff
> color sel #74757dff
[Repeated 1 time(s)]
> color sel #75757eff
[Repeated 1 time(s)]
> color sel #75767eff
> undo
[Repeated 1 time(s)]
> select #5/H:123-124
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/H:123-145
153 atoms, 157 bonds, 23 residues, 1 model selected
> color sel #6c6c7eff
> color sel #dad8feff
> color sel #d9d8fdff
[Repeated 1 time(s)]
> color sel #d8d7fcff
> color sel #d6d5f9ff
> color sel #d5d4f8ff
> color sel #d4d3f7ff
> color sel #d4d2f7ff
> color sel #d3d2f6ff
> color sel #d3d1f5ff
> color sel #d2d1f5ff
> color sel #d1d0f4ff
> color sel #cbcaecff
> color sel #c7c6e8ff
> color sel #c5c4e6ff
> color sel #b3c3e6ff
> color sel #b6bee6ff
> select #5/H:146-193
349 atoms, 358 bonds, 48 residues, 1 model selected
> select #5/H:146-156
79 atoms, 79 bonds, 11 residues, 1 model selected
> color sel #e6ced9ff
> color sel #e6bfbaff
> select #5/H:157-159
27 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/H:157-168
93 atoms, 97 bonds, 12 residues, 1 model selected
> color sel #e6b7aeff
> select #5/H:169-171
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #5/H:169-176
54 atoms, 54 bonds, 8 residues, 1 model selected
> color sel #c1c4e6ff
> select #5/H:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/H:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #e6d7dbff
> color sel #e6bfc0ff
> select #5/H:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:181-184
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #5/H:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #e6ced4ff
> select #5/H:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:181-186
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #e6c9cdff
> color sel #e6c2c5ff
[Repeated 1 time(s)]
> color sel #e6c3c5ff
> color sel #e6c3c6ff
> color sel #e6c4c7ff
[Repeated 1 time(s)]
> color sel #e6c5c8ff
> color sel #e6c5c7ff
> color sel #e6c5c8ff
> color sel #e6c6c8ff
[Repeated 1 time(s)]
> select #5/H:188
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:188-198
73 atoms, 73 bonds, 11 residues, 1 model selected
> color sel #b4b7e6ff
> select #5/H:199-200
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:199-208
75 atoms, 76 bonds, 10 residues, 1 model selected
> color sel #8999e6ff
> color sel #7b90e6ff
> color sel #7083e6ff
> select #5/H:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:209-212
34 atoms, 34 bonds, 4 residues, 1 model selected
> color sel #95a4e6ff
> color sel #b0b6e6ff
> select #5/H:213-214
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:213-223
86 atoms, 86 bonds, 11 residues, 1 model selected
> color sel #93a0e6ff
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-6
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #5/L:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:7-14
58 atoms, 58 bonds, 8 residues, 1 model selected
> color sel #9daae6ff
> select #5/L:15
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:15-21
47 atoms, 46 bonds, 7 residues, 1 model selected
> color sel #e6c2caff
> color sel #e6c3c3ff
> select #5/L:22-23
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> color sel #e6cdceff
> select #5/L:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> color sel #a5bbe6ff
> color sel #a5b6e6ff
> select #5/L:29-30
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/L:29-35
51 atoms, 51 bonds, 7 residues, 1 model selected
> color sel #c4c6e6ff
> color sel #d0d4e6ff
> select #5/L:36-37
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/L:36
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #c7cfe6ff
> select #5/L:37
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:37-38
26 atoms, 28 bonds, 2 residues, 1 model selected
> color sel #b2bde6ff
> color sel #abbae6ff
> color sel #abbbe6ff
> color sel #abbce6ff
> color sel #acbce6ff
> color sel #acbde6ff
> color sel #adbee6ff
[Repeated 1 time(s)]
> color sel #adbfe6ff
[Repeated 1 time(s)]
> color sel #adc0e6ff
> color sel #aec0e6ff
> color sel #aec1e6ff
> color sel #aec2e6ff
> color sel #afc2e6ff
> color sel #afc3e6ff
> color sel #afc2e6ff
> color sel #aec2e6ff
> color sel #aec1e6ff
> color sel #aec0e6ff
[Repeated 1 time(s)]
> color sel #aebfe6ff
> color sel #adbee6ff
> color sel #b0c3e6ff
[Repeated 1 time(s)]
> color sel #b0c2e6ff
> color sel #b0c1e6ff
[Repeated 2 time(s)]
> color sel #b0c0e6ff
[Repeated 2 time(s)]
> color sel #b0bfe6ff
[Repeated 1 time(s)]
> color sel #b1bfe6ff
[Repeated 2 time(s)]
> color sel #b1bee6ff
[Repeated 1 time(s)]
> color sel #b2bee6ff
> select #5/L:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:39-48
74 atoms, 74 bonds, 10 residues, 1 model selected
> color sel #abbbe6ff
> select #5/L:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #a1ace6ff
> color sel #a1ade6ff
> color sel #a0b1e6ff
> color sel #a1b1e6ff
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50-55
47 atoms, 47 bonds, 6 residues, 1 model selected
> color sel #6a88e6ff
> color sel #5b80e6ff
> color sel #5176e6ff
> color sel #426be6ff
> color sel #3b67e6ff
> color sel #315ae6ff
> select #5/L:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #3f64e6ff
> select #5/L:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #b3b7e6ff
> select #5/L:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:58-69
78 atoms, 79 bonds, 12 residues, 1 model selected
> color sel #b0b2e6ff
> select #5/L:70-71
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:70-73
34 atoms, 35 bonds, 4 residues, 1 model selected
> color sel #a9ace6ff
> select #5/L:74-75
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #9eaae6ff
> select #5/L:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:80-82
21 atoms, 20 bonds, 3 residues, 1 model selected
> color sel #d3cbe6ff
> color sel #e6ced1ff
> select #5/L:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:82-83
14 atoms, 13 bonds, 2 residues, 1 model selected
> volume #8 level 0.09283
> color sel #b7bbe6ff
> select #5/L:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:84-87
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #d9cce6ff
> color sel #e6d9e4ff
> color sel #e6d2d0ff
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98-100
19 atoms, 19 bonds, 3 residues, 1 model selected
> select #5/L:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #d0d1e6ff
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98-105
56 atoms, 56 bonds, 8 residues, 1 model selected
> color sel #a9aee6ff
> select #5/L:114-115
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/L:114-125
97 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #a8ace6ff
> select #5/L:128-129
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:128-131
22 atoms, 21 bonds, 4 residues, 1 model selected
> color sel #ccccffff
> select #5/L:132
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:132-137
44 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #ffeefaff
> color sel #ffe4e2ff
> color sel #ffe7ddff
> color sel #ffe7dcff
[Repeated 2 time(s)]
> color sel #ffe7dbff
[Repeated 1 time(s)]
> color sel #ffe8daff
> color sel #ffe7daff
> color sel #ffe3d2ff
> color sel #ffe1cdff
> color sel #ffe2cdff
> color sel #ffdbc2ff
> color sel #ffdac2ff
> color sel #ffd5c2ff
> select #5/L:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:138-146
79 atoms, 81 bonds, 9 residues, 1 model selected
> color sel #d0d6ffff
> color sel #c1c6ffff
> color sel #b1bdffff
> select #5/L:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:147-158
95 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #ff5b5bff
> color sel #ff484dff
> color sel #ff4347ff
> color sel #ff4247ff
> color sel #ff4146ff
> color sel #ff4145ff
> color sel #ff4045ff
> color sel #ff4044ff
> color sel #ff3f43ff
> color sel #ff3e43ff
> color sel #ff3e42ff
> color sel #ff3d42ff
> color sel #ff3c41ff
> color sel #ff3c40ff
> color sel #ff3b40ff
> color sel #ff3c40ff
[Repeated 2 time(s)]
> color sel #ff3d40ff
> color sel #ff3e40ff
[Repeated 1 time(s)]
> color sel #ff3e41ff
> color sel #ff3f41ff
> color sel #ff3f40ff
> color sel #ff4040ff
[Repeated 2 time(s)]
> color sel #ff3f3aff
> color sel #ff3e39ff
[Repeated 2 time(s)]
> color sel #ff3e38ff
[Repeated 1 time(s)]
> select #5/L:159-160
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:159-160
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:161-162
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:161-179
144 atoms, 144 bonds, 19 residues, 1 model selected
> select #5/L:180-181
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:180-182
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #5/L:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:183-204
176 atoms, 180 bonds, 22 residues, 1 model selected
> color sel #6f7bffff
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> show #!8 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> hide #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> color #8 #c5fdf81a models
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:111-271
1300 atoms, 1342 bonds, 161 residues, 1 model selected
> select #3/B:302
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:302-304
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #3/B:301-302
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:301-310
70 atoms, 69 bonds, 10 residues, 1 model selected
> hide #5 models
> show #5 models
> select add #5
3471 atoms, 3562 bonds, 452 residues, 2 models selected
> select subtract #5
70 atoms, 69 bonds, 10 residues, 1 model selected
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select #3/B:301
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:301-313
96 atoms, 97 bonds, 13 residues, 1 model selected
> select add #5
3497 atoms, 3590 bonds, 455 residues, 2 models selected
> select add #3
9003 atoms, 9237 bonds, 1146 residues, 2 models selected
> select subtract #3
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.5206,0.69023,0.71954,-0.076505,-64.572,-0.70121,0.63904,-0.31613,263.65
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.1095,0.69023,0.71954,-0.076505,-65.814,-0.70121,0.63904,-0.31613,263.22
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.2566,0.69023,0.71954,-0.076505,-65.556,-0.70121,0.63904,-0.31613,262.84
> view matrix models
> #5,-0.17857,0.27184,0.94563,-3.5932,0.69023,0.71954,-0.076505,-65.573,-0.70121,0.63904,-0.31613,263.6
> view matrix models
> #5,-0.17857,0.27184,0.94563,6.1172,0.69023,0.71954,-0.076505,-64.318,-0.70121,0.63904,-0.31613,265.1
> view matrix models
> #5,-0.17857,0.27184,0.94563,6.2366,0.69023,0.71954,-0.076505,-63.955,-0.70121,0.63904,-0.31613,264.58
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.50511,0.42112,0.75334,81.099,-0.58382,-0.80958,0.061111,408.82,0.63563,-0.40895,0.65478,-4.5259
> view matrix models
> #5,-0.71614,0.48271,0.50412,165.69,-0.55355,-0.83274,0.011012,419.78,0.42512,-0.27117,0.86356,-43.167
> view matrix models
> #5,-0.85245,0.30633,0.42367,241.3,-0.43531,-0.86468,-0.25067,467.41,0.28955,-0.39811,0.87044,2.3483
> view matrix models
> #5,-0.93915,0.14358,0.31205,313.16,-0.24014,-0.924,-0.29757,455.63,0.24561,-0.3544,0.90226,-5.6943
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.93915,0.14358,0.31205,310.36,-0.24014,-0.924,-0.29757,454.57,0.24561,-0.3544,0.90226,-10.513
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.92978,0.12057,0.3478,304.49,-0.25511,-0.89219,-0.3727,469.15,0.26537,-0.43526,0.86031,11.045
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.92978,0.12057,0.3478,301.55,-0.25511,-0.89219,-0.3727,465.8,0.26537,-0.43526,0.86031,10.049
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96388,-0.016383,0.26582,352.42,-0.11335,-0.87796,-0.46513,460.49,0.241,-0.47846,0.84439,26.097
> view matrix models
> #5,-0.91826,0.06169,0.39115,300.16,-0.36231,-0.52952,-0.76703,510.97,0.15981,-0.84605,0.50859,188.38
> view matrix models
> #5,-0.92676,0.077675,0.36753,304.3,-0.31305,-0.70047,-0.64136,504.23,0.20763,-0.70944,0.67349,115.46
> view matrix models
> #5,-0.9834,-0.04765,0.17507,383.22,-0.094665,-0.6884,-0.71913,482.5,0.15478,-0.72376,0.67247,127.55
> view matrix models
> #5,-0.95001,-0.19011,0.24767,386.58,-0.077458,-0.62494,-0.77682,481.46,0.30246,-0.75717,0.57898,130.31
> view matrix models
> #5,-0.94393,-0.018851,0.3296,334.23,-0.26473,-0.55329,-0.7898,503.83,0.19725,-0.83277,0.51728,177.33
> view matrix models
> #5,-0.84008,0.30007,0.45192,227.84,-0.54043,-0.53518,-0.64924,514.98,0.047043,-0.78964,0.61176,172.97
> view matrix models
> #5,-0.90734,0.12615,0.40102,283.95,-0.29751,-0.86665,-0.40051,475.05,0.29702,-0.48271,0.82388,22.022
> view matrix models
> #5,-0.89414,0.12288,0.43059,275.22,-0.30852,-0.866,-0.39353,475.19,0.32453,-0.48472,0.81224,20.379
> view matrix models
> #5,-0.89988,0.10062,0.42437,281.83,-0.22953,-0.93663,-0.26465,443.88,0.37085,-0.33556,0.86595,-28.153
> view matrix models
> #5,-0.91467,-0.052744,0.40075,318.49,-0.021786,-0.98358,-0.17917,396.11,0.40362,-0.17262,0.8985,-71.851
> view matrix models
> #5,-0.83178,-0.098166,0.54635,277.86,0.12592,-0.99195,0.013478,326.12,0.54063,0.080008,0.83745,-128.06
> view matrix models
> #5,-0.63629,-0.24728,0.73074,227.64,0.13032,-0.96808,-0.21411,375.09,0.76036,-0.041004,0.6482,-98.781
> view matrix models
> #5,-0.61952,-0.21214,0.75577,212.25,0.091718,-0.97576,-0.19871,379.56,0.7796,-0.05379,0.62396,-93.986
> view matrix models
> #5,-0.75135,-0.11146,0.65042,241.56,0.10086,-0.99345,-0.053733,346.75,0.65215,0.025229,0.75767,-118.3
> view matrix models
> #5,-0.66332,-0.23987,0.70885,236.18,0.33554,-0.94201,-0.0047814,284.72,0.6689,0.23468,0.70534,-147.64
> view matrix models
> #5,-0.7722,0.036461,0.63433,221.56,0.075095,-0.98612,0.1481,301.84,0.63093,0.162,0.75874,-140.25
> view matrix models
> #5,-0.77412,-0.056826,0.63048,240.13,0.10514,-0.99367,0.039532,323.85,0.62424,0.096891,0.7752,-130.92
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.64,0.13237,-0.98838,-0.074658,345.31,0.54779,0.010175,0.83655,-116.13
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.24,0.13237,-0.98838,-0.074658,345.43,0.54779,0.010175,0.83655,-116.45
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.21,0.13237,-0.98838,-0.074658,345.17,0.54779,0.010175,0.83655,-116.29
> select subtract #5
Nothing selected
> select #3/B:301
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:301-313
96 atoms, 97 bonds, 13 residues, 1 model selected
> select #3/B:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:300-310
77 atoms, 76 bonds, 11 residues, 1 model selected
> ui mousemode right "rotate selected models"
> select add #5
3478 atoms, 3569 bonds, 453 residues, 2 models selected
> select add #3
9003 atoms, 9237 bonds, 1146 residues, 2 models selected
> select subtract #3
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.57941,0.69777,0.4212,115.54,-0.37625,0.22943,-0.89766,403.45,-0.723,-0.67859,0.1296,400.92
> view matrix models
> #5,-0.42133,0.73627,0.52952,55.111,0.43201,0.67631,-0.59663,108.23,-0.7974,-0.022616,-0.60303,466.45
> view matrix models
> #5,-0.21413,0.8577,0.46743,11.295,0.513,0.50597,-0.69341,148.79,-0.83125,0.091314,-0.54835,438.17
> view matrix models
> #5,-0.1885,0.67264,0.71556,-17.862,0.29998,0.73323,-0.61023,123.87,-0.93514,0.09963,-0.33999,405.12
> log thumbnail
> view matrix models
> #5,-0.31715,0.77532,0.54617,25.775,0.1619,0.61171,-0.77434,209.51,-0.93445,-0.15716,-0.31953,447.8
> view matrix models
> #5,-0.32237,0.77028,0.55023,26.653,0.15917,0.61709,-0.77062,208.1,-0.93313,-0.16085,-0.32154,448.73
> view matrix models
> #5,-0.35979,0.63359,0.68492,26.481,0.1023,0.75644,-0.64601,162.47,-0.92741,-0.16236,-0.33698,451.69
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.22546,0.76745,0.60016,-1.5674,0.19788,0.63926,-0.7431,190.7,-0.95395,-0.048776,-0.29599,425.47
> view matrix models
> #5,0.070979,0.66168,0.74642,-68.315,0.16435,0.73032,-0.66304,160.57,-0.98385,0.16974,-0.056909,333.2
> view matrix models
> #5,0.11489,0.59902,0.79245,-75.277,0.39981,0.70238,-0.5889,107.15,-0.90937,0.38449,-0.1588,304.63
> view matrix models
> #5,0.18754,0.5726,0.7981,-84.357,0.35537,0.71792,-0.59858,114.3,-0.91572,0.39588,-0.068839,282.21
> view matrix models
> #5,0.12973,0.70112,0.70114,-75.082,0.32499,0.63799,-0.6981,158.11,-0.93678,0.31843,-0.14509,318.4
> view matrix models
> #5,0.012151,0.66827,0.74382,-58.685,0.27803,0.71228,-0.64448,139.73,-0.9605,0.21463,-0.17714,349.42
> view matrix models
> #5,0.087714,-0.77021,0.63174,221.89,0.82852,-0.29568,-0.47553,190.87,0.55305,0.56511,0.61219,-166.83
> view matrix models
> #5,-0.33436,-0.81985,0.46481,344.26,0.68971,-0.54897,-0.47216,261.24,0.64227,0.16271,0.74901,-140.21
> view matrix models
> #5,-0.44895,-0.57242,0.68614,265.59,0.52883,-0.78916,-0.31235,295.78,0.72027,0.22263,0.657,-143
> view matrix models
> #5,-0.4442,-0.59383,0.67086,272.37,0.54224,-0.77427,-0.32633,294.01,0.7132,0.21881,0.66593,-143.19
> view matrix models
> #5,-0.46401,-0.4815,0.74354,237.67,0.47306,-0.84435,-0.25157,301.26,0.74894,0.23501,0.61957,-141.38
> view matrix models
> #5,-0.44441,-0.50908,0.73711,240.91,0.50441,-0.8222,-0.26373,294.59,0.74031,0.25461,0.62218,-144.14
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.44441,-0.50908,0.73711,237.62,0.50441,-0.8222,-0.26373,296.55,0.74031,0.25461,0.62218,-146.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.60143,-0.49924,0.62373,290.1,0.509,-0.8412,-0.18249,279.94,0.61579,0.20772,0.76004,-149.35
> view matrix models
> #5,-0.74827,-0.24752,0.61549,270.87,0.3197,-0.94749,0.0076404,287.36,0.58128,0.20249,0.78811,-149.06
> view matrix models
> #5,-0.81926,-0.51039,0.26136,416.31,0.4815,-0.85984,-0.1698,285.16,0.31139,-0.013269,0.95019,-100.62
> view matrix models
> #5,-0.8197,-0.3099,0.48172,326.72,0.29937,-0.94878,-0.10096,316.98,0.48834,0.061452,0.87049,-126.31
> view matrix models
> #5,-0.74081,-0.34591,0.57581,297.29,0.14449,-0.91921,-0.3663,401.59,0.65599,-0.18816,0.73094,-75.929
> view matrix models
> #5,-0.81757,-0.07895,0.57039,262.37,-0.070004,-0.96958,-0.23455,416.9,0.57155,-0.23169,0.78718,-66.543
> view matrix models
> #5,-0.91951,-0.12462,0.37278,335.62,0.063486,-0.98304,-0.17204,381.3,0.3879,-0.13453,0.91183,-82.295
> view matrix models
> #5,-0.90793,0.0064486,0.41907,298.25,-0.059509,-0.99174,-0.11367,390.42,0.41488,-0.12814,0.90081,-85.551
> view matrix models
> #5,-0.91351,-0.073219,0.40017,318.51,-0.028011,-0.97001,-0.24143,411.31,0.40585,-0.23176,0.88407,-60.76
> view matrix models
> #5,-0.89133,0.0016103,0.45335,288.11,-0.071877,-0.98785,-0.13781,397.59,0.44762,-0.15542,0.88062,-81.377
> view matrix models
> #5,-0.88255,0.076297,0.46398,270.18,-0.18199,-0.96527,-0.18743,424.37,0.43356,-0.24986,0.86579,-57.872
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.90173,0.066834,0.42711,284.05,-0.16494,-0.96643,-0.197,423.89,0.3996,-0.24809,0.88248,-56.263
> view matrix models
> #5,-0.91899,-0.040079,0.39223,315.2,-0.062389,-0.9675,-0.24504,417.68,0.3893,-0.24966,0.88663,-55.168
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91899,-0.040079,0.39223,315,-0.062389,-0.9675,-0.24504,417.81,0.3893,-0.24966,0.88663,-53.939
> view matrix models
> #5,-0.91899,-0.040079,0.39223,318.19,-0.062389,-0.9675,-0.24504,417.19,0.3893,-0.24966,0.88663,-52.686
> view matrix models
> #5,-0.91899,-0.040079,0.39223,318.14,-0.062389,-0.9675,-0.24504,417.21,0.3893,-0.24966,0.88663,-52.699
> view matrix models
> #5,-0.91899,-0.040079,0.39223,317.71,-0.062389,-0.9675,-0.24504,417.12,0.3893,-0.24966,0.88663,-52.726
> view matrix models
> #5,-0.91899,-0.040079,0.39223,317.53,-0.062389,-0.9675,-0.24504,417.02,0.3893,-0.24966,0.88663,-52.524
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.94446,-0.024801,0.32768,334.49,-0.074776,-0.95477,-0.28779,426.99,0.31999,-0.29631,0.89989,-34.96
> view matrix models
> #5,-0.9387,-0.13701,0.31634,357.02,0.018467,-0.93629,-0.35073,422.31,0.34424,-0.32339,0.88143,-29.758
> view matrix models
> #5,-0.97606,-0.21236,0.047016,441.6,0.10357,-0.64388,-0.75808,450.17,0.19126,-0.73506,0.65046,128.25
> view matrix models
> #5,-0.97665,-0.2075,0.055729,438.73,0.092906,-0.64173,-0.76128,452.39,0.19373,-0.73832,0.64603,129.48
> view matrix models
> #5,-0.9734,-0.14293,0.17908,396.82,-0.057279,-0.60498,-0.79418,479.52,0.22185,-0.78331,0.5807,148.49
> view matrix models
> #5,-0.9046,-0.16174,0.39438,337.11,-0.12194,-0.78835,-0.60302,479.32,0.40844,-0.59359,0.69342,53.977
> view matrix models
> #5,-0.88062,-0.11723,0.45909,309.27,-0.22079,-0.75576,-0.61651,493.68,0.41923,-0.64427,0.63965,74.305
> view matrix models
> #5,-0.77365,-0.13721,0.61857,256.41,-0.084758,-0.94508,-0.31565,433.55,0.62792,-0.29663,0.71954,-45.551
> view matrix models
> #5,-0.73239,-0.017561,0.68065,212.25,-0.29602,-0.89204,-0.34153,466.62,0.61317,-0.45162,0.64812,2.7847
> view matrix models
> #5,-0.75559,0.045501,0.65347,211.04,-0.31215,-0.90204,-0.29812,460.96,0.57589,-0.42924,0.69578,-6.2267
> ui mousemode right select
> select clear
> volume #8 level 0.04382
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.81035,-0.039349,0.58462,252.71,-0.22376,-0.90134,-0.37083,462.75,0.54153,-0.43132,0.7216,-6.0096
> view matrix models
> #5,-0.75411,-0.09465,0.64989,237.66,-0.18462,-0.9191,-0.34808,453.83,0.63026,-0.38248,0.67563,-19.574
> view matrix models
> #5,-0.82045,-0.19006,0.5392,293.25,-0.01249,-0.93694,-0.34926,427.47,0.57158,-0.29329,0.76634,-47.509
> view matrix models
> #5,-0.8334,-0.14541,0.5332,288.65,-0.074442,-0.92644,-0.36901,441,0.54764,-0.34723,0.76127,-32.123
> view matrix models
> #5,-0.86676,-0.2008,0.45651,322.99,-0.01989,-0.90071,-0.43396,442.19,0.49833,-0.38522,0.77671,-20.166
> view matrix models
> #5,-0.91778,-0.012999,0.39688,311.19,-0.033872,-0.99326,-0.11086,384.91,0.39565,-0.11519,0.91115,-84.427
> view matrix models
> #5,-0.92008,-0.092652,0.38063,330.24,0.036985,-0.98783,-0.15106,381.14,0.38999,-0.12491,0.91231,-81.914
> view matrix models
> #5,-0.92081,-0.14037,0.36387,343.22,0.070303,-0.97744,-0.19917,384.86,0.38362,-0.15781,0.90991,-74.125
> view matrix models
> #5,-0.90137,-0.23742,0.36216,358.26,0.18937,-0.96821,-0.16341,353.92,0.38944,-0.078707,0.91768,-91.674
> view matrix models
> #5,-0.91318,-0.21739,0.34475,360.74,0.15071,-0.96603,-0.20993,371.32,0.37867,-0.13975,0.91492,-77.812
> view matrix models
> #5,-0.79261,-0.38378,0.47381,339.94,0.3287,-0.92343,-0.1981,329.62,0.51355,-0.0012739,0.85806,-113.45
> view matrix models
> #5,-0.82527,-0.3527,0.44105,347.65,0.32765,-0.93514,-0.13475,316.9,0.45997,0.033307,0.88731,-117.51
> view matrix models
> #5,-0.84093,-0.3241,0.43335,346.89,0.26592,-0.94495,-0.1907,342.78,0.4713,-0.045133,0.88082,-103.37
> view matrix models
> #5,-0.8011,-0.41235,0.43383,356.23,0.35913,-0.911,-0.20275,323.13,0.47883,-0.0066236,0.87788,-111.14
> view matrix models
> #5,-0.84269,-0.41546,0.34245,385.79,0.3308,-0.90136,-0.2795,344.54,0.4248,-0.12225,0.897,-84.819
> view matrix models
> #5,-0.79168,-0.41509,0.44827,351.66,0.24249,-0.88697,-0.39305,384.25,0.56075,-0.20247,0.80285,-71.174
> view matrix models
> #5,-0.80765,-0.39545,0.43739,353.39,0.27696,-0.90927,-0.31067,362.79,0.52056,-0.12977,0.8439,-87.449
> view matrix models
> #5,-0.80048,-0.3248,0.50372,323.24,0.18817,-0.93413,-0.3033,381.1,0.56905,-0.148,0.80887,-84.163
> view matrix models
> #5,-0.83802,-0.27227,0.47285,327.36,0.14615,-0.94695,-0.28624,386.73,0.5257,-0.17076,0.83336,-78.221
> view matrix models
> #5,-0.82968,-0.2976,0.47229,330.75,0.18414,-0.9446,-0.27172,376.23,0.52699,-0.13847,0.83852,-85.669
> volume #8 level 0.07251
> select subtract #5
Nothing selected
> ui tool show Rotamers
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/H:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> ui tool show "Model Loops"
> modeller refine 5/H:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: VWCNQFID77H03PPS
Modeller job (ID VWCNQFID77H03PPS) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 93, in
a.make()
File "/usr/lib64/python3.6/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
line 701, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> ui tool show "Side View"
> show #9 models
> hide #9 models
> show #9 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/H:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:89-116
230 atoms, 242 bonds, 28 residues, 1 model selected
> select #5/H:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/H:28-36
71 atoms, 73 bonds, 9 residues, 1 model selected
> select #5/H:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/H:28-35
59 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-35
55 atoms, 56 bonds, 7 residues, 1 model selected
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.78057,-0.25347,0.57136,290.43,0.14361,-0.96236,-0.23074,376.82,0.60834,-0.098055,0.78759,-95.206
> view matrix models
> #5,-0.70706,-0.3336,0.62352,280.11,0.24945,-0.94271,-0.22152,352.57,0.6617,-0.0010907,0.74977,-113.49
> view matrix models
> #5,-0.69694,-0.29889,0.65187,265.15,0.22036,-0.95428,-0.20196,355.12,0.68243,0.0028993,0.73094,-113.36
> view matrix models
> #5,-0.71926,-0.31911,0.61712,281.06,0.26188,-0.94728,-0.18461,342.47,0.6435,0.028824,0.7649,-119.48
> view matrix models
> #5,-0.73098,-0.35003,0.58579,296.3,0.27751,-0.93672,-0.21342,344.64,0.62342,0.0065603,0.78186,-115.89
> view matrix models
> #5,-0.744,-0.38717,0.54457,315.27,0.29793,-0.92173,-0.24828,346.61,0.59808,-0.022477,0.80112,-110.67
> view matrix models
> #5,-0.64878,-0.44583,0.6167,292.42,0.35923,-0.89386,-0.26827,335.52,0.67084,0.047487,0.74008,-121.79
> view matrix models
> #5,-0.62439,-0.46334,0.62884,288.54,0.36562,-0.88479,-0.2889,337.64,0.69026,0.049536,0.72187,-121.21
> view matrix models
> #5,-0.63478,-0.46697,0.61562,294.17,0.35225,-0.88401,-0.30733,344.2,0.68773,0.021768,0.72564,-116.52
> view matrix models
> #5,-0.61524,-0.38128,0.69001,257.16,0.33568,-0.91865,-0.20832,329.96,0.71331,0.10345,0.69318,-128.41
> view matrix models
> #5,-0.76581,-0.22867,0.60103,276.2,0.13893,-0.9714,-0.19256,370.23,0.62788,-0.063967,0.77568,-102.1
> view matrix models
> #5,-0.78982,-0.28243,0.54445,303.82,0.18289,-0.95574,-0.23046,368.69,0.58544,-0.082452,0.80651,-98.621
> view matrix models
> #5,-0.79292,-0.27196,0.54527,302.22,0.18011,-0.95949,-0.21664,366.58,0.5821,-0.073569,0.80978,-100.47
> view matrix models
> #5,-0.79401,-0.27238,0.54346,302.92,0.18004,-0.95926,-0.21773,366.81,0.58063,-0.075037,0.8107,-100.16
> view matrix models
> #5,-0.80028,-0.30121,0.51848,315.31,0.14171,-0.93519,-0.32456,394.44,0.58264,-0.18627,0.7911,-75.192
> view matrix models
> #5,-0.78732,-0.26873,0.55489,298.36,0.10956,-0.94667,-0.303,397.03,0.60673,-0.17777,0.77478,-77.078
> view matrix models
> #5,-0.77396,-0.26304,0.57601,289.95,0.10485,-0.95032,-0.29309,396.17,0.62449,-0.16645,0.76309,-79.488
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.77396,-0.26304,0.57601,289.63,0.10485,-0.95032,-0.29309,395.77,0.62449,-0.16645,0.76309,-79.465
> select subtract #5
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-35
55 atoms, 56 bonds, 7 residues, 1 model selected
> ui tool show "Model Loops"
[Repeated 2 time(s)]
> ui tool show "Modeller Comparative"
> select #5/H:56
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:56-62
58 atoms, 59 bonds, 7 residues, 1 model selected
> select #5/H:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:55-62
69 atoms, 70 bonds, 8 residues, 1 model selected
> select #5/H:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:55-58
35 atoms, 35 bonds, 4 residues, 1 model selected
> select #5/H:54-55
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #5/H:54-59
49 atoms, 49 bonds, 6 residues, 1 model selected
> select #5/H:55-56
23 atoms, 23 bonds, 2 residues, 1 model selected
> select #5/H:55-59
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #5/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:55-59
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #5/H:100-144
341 atoms, 356 bonds, 45 residues, 1 model selected
> select #5/H:100-112
113 atoms, 120 bonds, 13 residues, 1 model selected
> select #5/H:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:174-185
87 atoms, 89 bonds, 12 residues, 1 model selected
> select #5/H:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:102-107
54 atoms, 56 bonds, 6 residues, 1 model selected
> select #3/B:290-291
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:290-310
150 atoms, 150 bonds, 21 residues, 1 model selected
> select #3/B:290-315
193 atoms, 195 bonds, 26 residues, 1 model selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select #3/B:352
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B:341-352
91 atoms, 90 bonds, 12 residues, 1 model selected
> select
> #5/H:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
837 atoms, 847 bonds, 101 residues, 1 model selected
> select #5/H:127
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:127-130
27 atoms, 27 bonds, 4 residues, 1 model selected
> view matrix models
> #5,-0.77396,-0.26304,0.57601,280.18,0.10485,-0.95032,-0.29309,395.64,0.62449,-0.16645,0.76309,-74.626
> hide #!8 models
> show #!2 models
> hide #!2 models
> select #5/L:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:22-28
47 atoms, 46 bonds, 7 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-35
51 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/L:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50-54
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-55
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-56
47 atoms, 47 bonds, 6 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-62
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> show #!8 models
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> hide #!8 models
> hide #8.1 models
> select add #9
3416 atoms, 3463 bonds, 426 residues, 2 models selected
> select subtract #9
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.77396,-0.26304,0.57601,281.01,0.10485,-0.95032,-0.29309,395.7,0.62449,-0.16645,0.76309,-74.661
> view matrix models
> #5,-0.77396,-0.26304,0.57601,281.22,0.10485,-0.95032,-0.29309,395.6,0.62449,-0.16645,0.76309,-74.86
> view matrix models
> #5,-0.77396,-0.26304,0.57601,282.28,0.10485,-0.95032,-0.29309,396.27,0.62449,-0.16645,0.76309,-74.987
> view matrix models
> #5,-0.77396,-0.26304,0.57601,283.04,0.10485,-0.95032,-0.29309,396.66,0.62449,-0.16645,0.76309,-75.111
> view matrix models
> #5,-0.77396,-0.26304,0.57601,282.9,0.10485,-0.95032,-0.29309,397.32,0.62449,-0.16645,0.76309,-75.13
> view matrix models
> #5,-0.77396,-0.26304,0.57601,283.39,0.10485,-0.95032,-0.29309,397.2,0.62449,-0.16645,0.76309,-75.14
> view matrix models
> #5,-0.77396,-0.26304,0.57601,285.17,0.10485,-0.95032,-0.29309,397.62,0.62449,-0.16645,0.76309,-75.184
> view matrix models
> #5,-0.77396,-0.26304,0.57601,285.99,0.10485,-0.95032,-0.29309,397.56,0.62449,-0.16645,0.76309,-75.367
> view matrix models
> #5,-0.77396,-0.26304,0.57601,286.16,0.10485,-0.95032,-0.29309,397.36,0.62449,-0.16645,0.76309,-75.361
> select add #8.1
3401 atoms, 3493 bonds, 442 residues, 2 models selected
> show #8.1 models
> select subtract #5
1 model selected
> select add #8
2 models selected
> select subtract #8
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/L:66-68
14 atoms, 13 bonds, 3 residues, 1 model selected
> select #5/L:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:115-121
57 atoms, 60 bonds, 7 residues, 1 model selected
> select #5/L:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:102-106
41 atoms, 40 bonds, 5 residues, 1 model selected
> select #5/L:96
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:94-96
26 atoms, 27 bonds, 3 residues, 1 model selected
> select #5/L:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:75-77
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/L:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:80-81
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:94
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:93-94
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #5/L:91
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:91
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:92-93
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #5/L:92-93
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #5/L:92-97
56 atoms, 59 bonds, 6 residues, 1 model selected
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-100
750 atoms, 769 bonds, 100 residues, 1 model selected
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-111
834 atoms, 853 bonds, 111 residues, 1 model selected
> select #5/L:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:1-108
815 atoms, 834 bonds, 108 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-96
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-105
83 atoms, 85 bonds, 11 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-102
57 atoms, 59 bonds, 8 residues, 1 model selected
> select #5/L:93
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:93-101
70 atoms, 74 bonds, 9 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> ui mousemode right select
> select clear
> toolshed show
Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.0.1
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
Requirement already satisfied: ChimeraX-UI~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.24.3)
Requirement already satisfied: ChimeraX-Core~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.5)
Collecting openpyxl
Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 8.0 MB/s eta 0:00:00
Collecting seaborn
Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 18.8 MB/s eta 0:00:00
Collecting pandas
Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 8.1 MB/s eta 0:00:00
Collecting qtrangeslider
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0)
Collecting et-xmlfile
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: python-dateutil>=2.8.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2)
Requirement already satisfied: numpy>=1.20.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1)
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6)
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0.1)
Requirement already satisfied: pyparsing>=2.2.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9)
Requirement already satisfied: fonttools>=4.22.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(4.38.0)
Requirement already satisfied: packaging>=20.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3)
Requirement already satisfied: kiwisolver>=1.0.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4)
Requirement already satisfied: cycler>=0.10 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(0.11.0)
Requirement already satisfied: pillow>=6.2.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0)
Requirement already satisfied: six>=1.5 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)
Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
seaborn, ChimeraX-XMAS
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
\---
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
Installed ChimeraX-XMAS (1.1.2)
> toolshed install Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
Missing or invalid "bundleNames" argument: Expected a bundle name or a wheel
file name
> toolshed install /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-
> any.whl
bundle '/Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl'
already installed
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
——— End of log from Thu Mar 30 23:52:24 2023 ———
opened ChimeraX session
> select down
Nothing selected
> select down
Nothing selected
> ui tool show "Show Sequence Viewer"
> ui tool show "Change Chain IDs"
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-20
149 atoms, 151 bonds, 20 residues, 1 model selected
> select #3/B:1-20
149 atoms, 151 bonds, 20 residues, 1 model selected
> select #3/B:1-20,136-352
1872 atoms, 1920 bonds, 237 residues, 1 model selected
> select #3/B:1-20,136-352
1872 atoms, 1920 bonds, 237 residues, 1 model selected
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-180
1439 atoms, 1472 bonds, 180 residues, 1 model selected
> select #3/A
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/NS1chainA.pdb selectedOnly true relModel
> #8.1
> open /Users/alvinchew/Downloads/NS1chainA.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for NS1chainA.pdb #6
---
Chain | Description
A | No description available
> undo
> close #6
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> toolshed show
> xmas
Unknown command: xmas
> runscript xmas
Missing or invalid "scriptFile" argument: File 'xmas' does not exist
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-120
956 atoms, 977 bonds, 120 residues, 1 model selected
> select #3/A
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/NS1chainA.pdb models #3 selectedOnly true
> relModel #3
> open /Users/alvinchew/Downloads/NS1chainA.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for NS1chainA.pdb #6
---
Chain | Description
A | No description available
> close #6
> hide #3 models
> show #3 models
> save /Users/alvinchew/Downloads/D2NS1_A #3/A relModel #3/B
Cannot determine format for '/Users/alvinchew/Downloads/D2NS1_A'
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A relModel #3/B
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #6
---
Chain | Description
A B | No description available
> hide #3 models
> show #3 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> close #6
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A selectedOnly true relModel
> #3/B
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for D2NS1_A.pdb #6
---
Chain | Description
A | No description available
> hide #3 models
> select #3/B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:1-14
110 atoms, 111 bonds, 14 residues, 1 model selected
> show #3 models
> select add #8
110 atoms, 111 bonds, 14 residues, 5 models selected
> select subtract #8
110 atoms, 111 bonds, 14 residues, 1 model selected
> hide #!8 models
> hide #3 models
> show #3 models
> mmaker #6 to #3/A
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 eden2ns1.pdb, chain A (#3) with D2NS1_A.pdb, chain A (#6), sequence
alignment score = 1853.9
RMSD between 352 pruned atom pairs is 0.000 angstroms; (across all 352 pairs:
0.000)
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #6
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #7
---
Chain | Description
A | No description available
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true relModel
> #3/A
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #10
---
Chain | Description
B | No description available
> close #10
> save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #10
---
Chain | Description
B | No description available
> close #6
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> select #9/B-C:1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:1-8
114 atoms, 112 bonds, 16 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/C:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/C:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/C
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> save /Users/alvinchew/Downloads/ApoA1_Y.pdb #9/C selectedOnly true
> open /Users/alvinchew/Downloads/ApoA1_Y.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
ALA B 129 1 128
Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
1 20
Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
1 56
Chain information for ApoA1_Y.pdb #6
---
Chain | Description
C | No description available
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> save /Users/alvinchew/Downloads/ApoA1_X.pdb #9/B selectedOnly true
> open /Users/alvinchew/Downloads/ApoA1_X.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
ALA C 129 1 128
Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
1 20
Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
1 56
Chain information for ApoA1_X.pdb #11
---
Chain | Description
B | No description available
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #9 models
> hide #8.1 models
> hide #10 models
> hide #11 models
> select add #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> select subtract #9
Nothing selected
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #3 models
> show #3 models
> hide #7 models
> hide #6 models
> show #!8 models
> hide #!8 models
> show #8.1 models
> hide #8.1 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
[Repeated 1 time(s)]
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min.defattr attrName
> Fab_rDeutdelta_10min models #5
No known/registered attribute Fab_rDeutdelta_10min
> setattr #5 residues Fab_rDeutdelta_10min_color models create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color create true type color
Expected a keyword
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Cannot determine format for '/Users/alvinchew/Downloads/'
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
No known/registered attribute Fab_rDeutdelta_10min_color
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
No known/registered attribute Fab_rDeutdelta_10min_color
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type float
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Expected a number
> setattr #5 residues Fab_rDeutdelta_10min_color value create true
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type string
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
> save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Cannot determine format for '/Users/alvinchew/Downloads/'
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Saved attribute 'Fab_rDeutdelta_10min_color' of 442 residues using match mode:
1-to-1 to /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr
> ui tool show "Color Actions"
> close session
> open /Users/alvinchew/Downloads/ApoA1_X.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
ALA C 129 1 128
Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
1 20
Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
1 56
Chain information for ApoA1_X.pdb #1
---
Chain | Description
B | No description available
> open /Users/alvinchew/Downloads/ApoA1_Y.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
ALA B 129 1 128
Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
1 20
Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
1 56
Chain information for ApoA1_Y.pdb #2
---
Chain | Description
C | No description available
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #3
---
Chain | Description
B | No description available
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #4
---
Chain | Description
A | No description available
> color #2 #e0e6ecff
> color #2 #b1b6bbff
> color #1 #d7d0cbff
> color #3 #93a3e1ff
> color #3 #8a9ae1ff
> color #3 #969ae1ff
> color #3 #8496e1ff
> color #4 #b7d7ecff
> save /Users/alvinchew/Downloads/NS1-apoAI_monomers-forwint.cxs includeMaps
> true
——— End of log from Sat Apr 1 16:55:32 2023 ———
opened ChimeraX session
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy.txt
428 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 28 out of 33
Unique peptide pairs with pseudobonds: 28
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.tsv
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
> select subtract #5
Nothing selected
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
——— End of log from Mon Apr 3 15:19:20 2023 ———
opened ChimeraX session
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt
432 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 29 out of 29
Unique peptide pairs with pseudobonds: 26
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.tsv
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Please select pseudobonds
/Users/wintwintphoo/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
> color #1 #684bdfff
> undo
> select subtract #6
Nothing selected
> select add #5
102 pseudobonds, 1 model selected
> select subtract #5
Nothing selected
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt
432 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 29 out of 29
Unique peptide pairs with pseudobonds: 26
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS.txt
436 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 25 out of 25
Unique peptide pairs with pseudobonds: 20
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.tsv
> select subtract #7
Nothing selected
> close #7
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
[Repeated 1 time(s)]Pseudobonds are stored in
/Users/wintwintphoo/Downloads/20220215_denv_ns1_apoA1_xmas_xlinks_list.pb
> select subtract #8
195 pseudobonds, 2 models selected
> select add #8
275 pseudobonds, 3 models selected
> hide #8 models
> show #8 models
> hide #7 models
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
——— End of log from Mon Apr 3 16:43:31 2023 ———
opened ChimeraX session
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> select subtract #7
275 pseudobonds, 3 models selected
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab562.mrc"
Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
level 0.0324, step 2, values float32
> volume #9 step 1
> volume #9 color #b2b2b25f
> volume #9 color #b2b2b24d
> volume #9 color #aebfbb4d
> volume #9 color #96bdbf4d
> volume #9 color #b4e3e64d
> select subtract #5
173 pseudobonds, 2 models selected
> select subtract #6
80 pseudobonds, 1 model selected
> select subtract #8
Nothing selected
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.87886,-0.26868,-0.39424,454.61,-2.4853e-05,0.82637,-0.56313,136.08,0.47709,-0.4949,-0.72627,325.9
> view matrix models
> #9,-0.58078,0.6843,0.44094,79.244,0.37206,0.7049,-0.6039,98.706,-0.72406,-0.18668,-0.66399,474.16
> volume #9 level 0.08346
> view matrix models
> #9,-0.62302,0.6249,0.47048,91.383,0.37769,0.76704,-0.51866,70.685,-0.68498,-0.14544,-0.71389,469.61
> view matrix models
> #9,-0.59735,0.62471,0.5029,80.705,0.44544,0.7799,-0.43971,41.448,-0.6669,-0.038648,-0.74414,453.65
> view matrix models
> #9,-0.73179,-0.006901,0.6815,180.03,-0.57374,0.54594,-0.61055,294.56,-0.36785,-0.83779,-0.40347,474.63
> view matrix models
> #9,-0.79319,-0.093028,0.60182,221,-0.596,0.32149,-0.73582,361.32,-0.12503,-0.94233,-0.31045,432.17
> view matrix models
> #9,-0.58382,-0.31126,0.74985,193.7,-0.73407,0.59693,-0.32375,259.38,-0.34683,-0.73946,-0.57698,486.91
> view matrix models
> #9,-0.34202,-0.16644,0.92484,92.532,-0.84723,0.48035,-0.22687,281.13,-0.40649,-0.86114,-0.3053,466.79
> view matrix models
> #9,-0.55882,0.49146,0.66797,65.577,-0.45981,0.4867,-0.74277,309.92,-0.69014,-0.72222,-0.045999,443.36
> view matrix models
> #9,-0.54201,-0.3239,0.77544,183.64,-0.79241,0.50424,-0.34326,289.48,-0.27982,-0.80052,-0.52997,476.72
> view matrix models
> #9,-0.58956,-0.063726,0.80521,141.21,-0.57182,0.737,-0.36035,213.39,-0.57047,-0.67289,-0.47094,494.64
> view matrix models
> #9,-0.39155,-0.00207,0.92016,73.642,-0.67059,0.68539,-0.28381,225.21,-0.63008,-0.72818,-0.26975,476.42
> view matrix models
> #9,-0.28776,-0.19817,0.93698,86.145,-0.87695,0.44774,-0.17463,282.08,-0.38491,-0.87193,-0.30263,464.35
> view matrix models
> #9,-0.25456,-0.094965,0.96238,57.53,-0.75216,0.64493,-0.13531,218.34,-0.60782,-0.75832,-0.2356,471.22
> view matrix models
> #9,0.08179,0.053136,0.99523,-33.823,-0.83033,0.55594,0.038556,214.45,-0.55124,-0.82952,0.089591,411.62
> view matrix models
> #9,-0.066864,0.18014,0.98137,-26.974,-0.92402,0.35991,-0.12902,296.95,-0.37644,-0.91543,0.14239,385.61
> view matrix models
> #9,-0.1796,0.42981,0.88488,-32.014,-0.68511,0.59085,-0.42605,271.28,-0.70595,-0.68276,0.18835,394.65
> view matrix models
> #9,-0.38938,-0.35219,0.85108,147.19,-0.71886,0.6939,-0.041736,186.13,-0.57587,-0.62806,-0.52337,497.8
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.38938,-0.35219,0.85108,163.76,-0.71886,0.6939,-0.041736,188.56,-0.57587,-0.62806,-0.52337,496.31
> view matrix models
> #9,-0.38938,-0.35219,0.85108,168.86,-0.71886,0.6939,-0.041736,197.29,-0.57587,-0.62806,-0.52337,495.68
> view matrix models
> #9,-0.38938,-0.35219,0.85108,169.85,-0.71886,0.6939,-0.041736,197.13,-0.57587,-0.62806,-0.52337,494.81
> volume #9 level 0.09622
> volume #9 level 0.1218
> volume #9 level 0.1102
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.37051,-0.036777,0.9281,96.88,-0.68448,0.68625,-0.24606,231.42,-0.62786,-0.72644,-0.27943,474.52
> view matrix models
> #9,-0.31168,-0.049862,0.94888,84.726,-0.69125,0.69707,-0.19043,220.1,-0.65194,-0.71527,-0.25173,471.56
> view matrix models
> #9,-0.1857,-0.07265,0.97992,60.36,-0.66701,0.74162,-0.07142,185.28,-0.72154,-0.66687,-0.18618,462.98
> view matrix models
> #9,-0.23942,-0.0021906,0.97091,59.372,-0.51422,0.84851,-0.12489,149.75,-0.82356,-0.52917,-0.20428,460.62
> view matrix models
> #9,-0.22507,0.022971,0.97407,51.838,-0.51742,0.84429,-0.13947,153.84,-0.8256,-0.5354,-0.17814,457.06
> view matrix models
> #9,-0.22651,0.020133,0.9738,52.639,-0.51714,0.84474,-0.13775,153.38,-0.82538,-0.5348,-0.18093,457.45
> view matrix models
> #9,-0.21551,0.029869,0.97604,48.561,-0.50806,0.85017,-0.1382,150.91,-0.83393,-0.52567,-0.16805,454.92
> view matrix models
> #9,-0.26159,0.28099,0.92337,23.126,-0.7227,0.57709,-0.38035,282.89,-0.63974,-0.76682,0.052114,420.27
> view matrix models
> #9,-0.41669,0.2104,0.88436,70.441,-0.68255,0.57014,-0.45725,291.66,-0.60041,-0.79415,-0.093959,445.96
> view matrix models
> #9,-0.43816,0.2546,0.86209,70.827,-0.46829,0.75397,-0.46068,222.24,-0.76728,-0.60556,-0.21113,465.21
> view matrix models
> #9,-0.40829,0.25984,0.87509,62.119,-0.47771,0.75607,-0.44739,221.01,-0.77788,-0.6007,-0.18457,461.17
> view matrix models
> #9,-0.44661,0.14869,0.88229,86.897,-0.5092,0.76859,-0.38728,212.93,-0.7357,-0.62223,-0.26755,473.29
> view matrix models
> #9,-0.44407,0.15675,0.88217,85.065,-0.50686,0.76795,-0.3916,213.45,-0.73884,-0.62104,-0.26158,472.5
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.44407,0.15675,0.88217,83.534,-0.50686,0.76795,-0.3916,214.96,-0.73884,-0.62104,-0.26158,474.33
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.47173,0.10261,0.87575,99.098,-0.49372,0.79217,-0.35876,202.13,-0.73056,-0.60161,-0.32303,481.23
> view matrix models
> #9,-0.46188,0.17351,0.86981,86.145,-0.45527,0.79525,-0.40039,202.72,-0.76118,-0.58093,-0.28831,476.44
> view matrix models
> #9,-0.17678,0.17743,0.96813,15.981,-0.55919,0.79135,-0.24714,192.57,-0.80997,-0.58505,-0.040674,438.48
> view matrix models
> #9,-0.20822,0.22068,0.95286,16.964,-0.47946,0.8261,-0.2961,181.71,-0.8525,-0.51851,-0.066201,439.34
> view matrix models
> #9,-0.23313,0.22067,0.94708,22.5,-0.51218,0.80002,-0.31248,195.19,-0.82664,-0.55792,-0.073484,442.99
> view matrix models
> #9,-0.272,0.31817,0.90818,19.883,-0.43497,0.80119,-0.41096,200.1,-0.85838,-0.50681,-0.07953,440.9
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.272,0.31817,0.90818,20.776,-0.43497,0.80119,-0.41096,197.63,-0.85838,-0.50681,-0.07953,443.72
> view matrix models
> #9,-0.272,0.31817,0.90818,21.653,-0.43497,0.80119,-0.41096,197.64,-0.85838,-0.50681,-0.07953,444.39
> view matrix models
> #9,-0.272,0.31817,0.90818,21.578,-0.43497,0.80119,-0.41096,197.39,-0.85838,-0.50681,-0.07953,444.75
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.34138,0.16793,0.9248,56.875,-0.43348,0.8449,-0.31343,170.87,-0.834,-0.50788,-0.21564,466.63
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> combine #1-4
Remapping chain ID 'B' in D2NS1_B.pdb #3 to 'D'
> hide #10 models
> show #10 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #10 models
> show #10 models
> hide #5 models
> show #5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #2 models
> show #3 models
> show #4 models
> view matrix models
> #9,0.52951,-0.025333,0.84793,-49.614,-0.39781,0.87542,0.27457,46.784,-0.74925,-0.4827,0.45346,319.24
> undo
> select subtract #9
Nothing selected
> ui mousemode right zoom
> molmap #1-4 onGrid #9 sigmaFactor 6
Missing or invalid "resolution" argument: Expected a number
> molmap #1-4 resolution 8 onGrid #9
Missing or invalid "resolution" argument: Expected a number
> molmap #1-4 8 onGrid #9
Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0635,
step 1, values float32
> volume #11 level 0.03753
> mmaker #9 to #11
No 'to' model specified
> fitmap #9 to #11
Expected a keyword
> Fit #9 in map #11
Unknown command: Fit #9 in map #11
> fitmap #9 inMap map #11
Invalid "inMap" argument: invalid density map specifier
> fitmap #9 inMap #11
Fit map sNS1wt-Fab562.mrc in map map 8 using 131473 points
correlation = 0.6323, correlation about mean = 0.08876, overlap = 2834
steps = 292, shift = 12.1, angle = 16.9 degrees
Position of sNS1wt-Fab562.mrc (#9) relative to map 8 (#11) coordinates:
Matrix rotation and translation
0.96199493 -0.17308261 0.21120645 -4.02299000
0.19395657 0.97754937 -0.08232910 -24.62700524
-0.19221500 0.12016506 0.97396805 10.65384009
Axis 0.34805838 0.69342351 0.63088763
Axis point 91.81802475 0.00000000 16.19663836
Rotation angle (degrees) 16.91131195
Shift along axis -11.75580388
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs" includeMaps true
——— End of log from Wed Apr 19 14:11:57 2023 ———
opened ChimeraX session
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb
Chain information for F562a.pdb #12
---
Chain | Description
C | No description available
D | No description available
> color #12 #8b92d7ff
> color #12 #718dd7ff
> color #12 #7693d7ff
> color #12 #849ed7ff
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.59826,0.23414,-0.76633,188.86,-0.29309,-0.82615,-0.48122,476.1,-0.74578,0.5125,-0.42563,337.4
> view matrix models
> #12,0.8198,-0.22926,-0.52475,175.64,-0.56234,-0.49535,-0.66212,513.22,-0.10814,0.8379,-0.53501,149.05
> view matrix models
> #12,0.70505,-0.47588,-0.52578,246.35,-0.42704,-0.87682,0.22096,392.51,-0.56617,0.068741,-0.82142,443.24
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.70505,-0.47588,-0.52578,242.09,-0.42704,-0.87682,0.22096,378.11,-0.56617,0.068741,-0.82142,460.51
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.89785,-0.43928,-0.030063,102.58,-0.37117,-0.71836,-0.58838,480.03,0.23687,0.53943,-0.80803,185.85
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.89785,-0.43928,-0.030063,97.925,-0.37117,-0.71836,-0.58838,480.91,0.23687,0.53943,-0.80803,179.17
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.96357,-0.26121,-0.057389,55.865,-0.25517,-0.8337,-0.48973,456.47,0.080078,0.48653,-0.86998,236.41
> view matrix models
> #12,0.90596,-0.39388,-0.15525,110.13,-0.42323,-0.85213,-0.30783,467.19,-0.011043,0.34459,-0.93869,295.05
> view matrix models
> #12,0.89108,-0.41763,-0.17768,121.79,-0.45249,-0.84775,-0.2767,467.81,-0.035067,0.32696,-0.94439,304.83
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.89108,-0.41763,-0.17768,121.19,-0.45249,-0.84775,-0.2767,465.74,-0.035067,0.32696,-0.94439,307.63
> view matrix models
> #12,0.89108,-0.41763,-0.17768,120.89,-0.45249,-0.84775,-0.2767,466.02,-0.035067,0.32696,-0.94439,307.05
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.90549,-0.36137,-0.22248,115.49,-0.40743,-0.88694,-0.21757,451.86,-0.11871,0.28765,-0.95035,334.75
Must specify one map, got 0
> fitmap #12 inMap #9
Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms
average map value = 0.09851, steps = 92
shifted from previous position = 4.5
rotated from previous position = 18.4 degrees
atoms outside contour = 1988, contour level = 0.11015
Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates:
Matrix rotation and translation
-0.10510217 -0.15771336 0.98187577 53.64785327
-0.09250566 -0.98151278 -0.16755707 397.45943422
0.99014960 -0.10843968 0.08856975 -3.70781985
Axis 0.66871425 -0.09359056 0.73760562
Axis point 22.55285651 199.33929044 0.00000000
Rotation angle (degrees) 177.46657060
Shift along axis -4.05827537
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> select #12/C:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/C:1-18
131 atoms, 132 bonds, 18 residues, 1 model selected
> color #12 #d0d2dfff
> select #12/C:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/C:5-14
71 atoms, 71 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #cbd8ffff
> color sel #9fbcffff
> color sel #93abffff
> color sel #88a4ffff
> color sel #8484f7ff
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/C:15-35
163 atoms, 168 bonds, 21 residues, 1 model selected
> color sel #fdf2f2ff
> select #12/C:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/C:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #fae0e0ff
> select #12/C:22
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:22-35
112 atoms, 116 bonds, 14 residues, 1 model selected
> color sel #fbe8e7ff
> select #12/C:36-37
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #12/C:36-42
77 atoms, 81 bonds, 7 residues, 1 model selected
> select #12/C:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/C:30-35
43 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #3535f5ff
> select #12/C:36-37
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #12/C:36-47
115 atoms, 120 bonds, 12 residues, 1 model selected
> color sel #fbe8e7ff
> select #12/C:48-49
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #12/C:48-57
94 atoms, 97 bonds, 10 residues, 1 model selected
> select #12/C:58-59
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #12/C:58-61
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #f1f1feff
> select #12/C:62-63
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #12/C:62-73
99 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #fadfdfff
> select #12/C:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:79-94
126 atoms, 128 bonds, 16 residues, 1 model selected
> color sel #efeffeff
> select #12/C:95
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:95-103
82 atoms, 85 bonds, 9 residues, 1 model selected
> color sel #ddddfcff
> select #12/C:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:102-103
24 atoms, 25 bonds, 2 residues, 1 model selected
> color sel #c9d0ffff
> hide #!9 models
> select #12/C:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:104-105
18 atoms, 18 bonds, 2 residues, 1 model selected
> set bgColor white
> select #12/C:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:104-112
73 atoms, 78 bonds, 9 residues, 1 model selected
> color sel #d3d3fbff
> color sel #bec7feff
> select #12/C:113
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:113-120
65 atoms, 67 bonds, 8 residues, 1 model selected
> color sel #d3d9feff
> select #12/C:123
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:123-145
153 atoms, 157 bonds, 23 residues, 1 model selected
> color sel #f6f6feff
> color sel #e7e8ffff
> color sel #edf0ffff
> select #12/C:146
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:146-156
79 atoms, 79 bonds, 11 residues, 1 model selected
> color sel #fdf1f1ff
> select #12/C:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:157-168
93 atoms, 97 bonds, 12 residues, 1 model selected
> color sel #fbeae9ff
> select #12/C:169
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C:169-176
54 atoms, 54 bonds, 8 residues, 1 model selected
> color sel #f0f0feff
> select #12/C:177-178
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #12/C:177-179
23 atoms, 24 bonds, 3 residues, 1 model selected
> select #12/C:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:177-178
18 atoms, 19 bonds, 2 residues, 1 model selected
> color sel #ffe7efff
> color sel #fdf6ffff
> color sel #fff0ffff
> color sel #ffeffdff
> color sel #ffedfaff
> color sel #ffecf9ff
> color sel #ffecfaff
> color sel #ffebf9ff
> color sel #ffecfaff
> color sel #ffecfbff
> color sel #ffecfcff
> color sel #ffedfdff
> color sel #ffecfdff
> color sel #ffedfdff
> color sel #ffeaffff
> color sel #ffeafeff
> color sel #ffe9feff
> color sel #ffe8feff
> color sel #ffe8fdff
> color sel #ffe8fcff
> color sel #ffe8fbff
> color sel #ffe8faff
> color sel #ffe8f8ff
> color sel #ffe8f7ff
> color sel #ffe9f7ff
> color sel #ffe8f6ff
> color sel #ffe9f6ff
> color sel #ffe9f5ff
> color sel #ffeaf5ff
> color sel #ffeaf4ff
> color sel #ffebf4ff
> color sel #ffebf3ff
> color sel #ffecf2ff
> color sel #ffecf1ff
> color sel #ffecf0ff
> color sel #ffebefff
> color sel #ffebeeff
> color sel #ffeaedff
> color sel #ffe9ecff
> color sel #ffe8ebff
> color sel #ffe7ebff
> color sel #ffe6eaff
> color sel #ffe6e9ff
> select #12/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:181-187
53 atoms, 53 bonds, 7 residues, 1 model selected
> color sel #fff7fdff
> color sel #f9f3ffff
> select #12/C:188-189
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/C:188-198
73 atoms, 73 bonds, 11 residues, 1 model selected
> color sel #f4efffff
> select #12/C:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:200-208
69 atoms, 70 bonds, 9 residues, 1 model selected
> color sel #cdd3ffff
> color sel #8e8ef8ff
> color sel #9da0ffff
> color sel #9c9fffff
> color sel #9c9effff
> color sel #9b9effff
> color sel #9b9dffff
> color sel #9a9cffff
> color sel #9696f8ff
> select #12/C:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:209-213
41 atoms, 42 bonds, 5 residues, 1 model selected
> color sel #f1f1feff
> select #12/C:214-215
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/C:214-223
79 atoms, 78 bonds, 10 residues, 1 model selected
> color sel #b8b8faff
> select #12/C:224-225
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #12/C:224-228
36 atoms, 36 bonds, 5 residues, 1 model selected
> color sel #f8f6ffff
> color sel #dad8e0ff
> color sel #c5c3caff
> color sel #c4c3caff
> color sel #b5b4baff
> color sel #b4b3baff
> color sel dim gray
> select #12/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C:1-4
29 atoms, 28 bonds, 4 residues, 1 model selected
> color sel dim gray
> select #12/C:122
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:121-122
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel dim gray
> select #12/C:178-179
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/C:178-180
19 atoms, 19 bonds, 3 residues, 1 model selected
> color sel dim gray
> select #12/C:73-74
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #12/C:73-78
54 atoms, 54 bonds, 6 residues, 1 model selected
> color sel dim gray
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/D
Alignment identifier is 12/D
> select #12/D:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D
1632 atoms, 1668 bonds, 214 residues, 1 model selected
> color sel dim gray
> view matrix models
> #12,0.71436,-0.39661,-0.57653,226.88,-0.66803,-0.63185,-0.39307,496.97,-0.20839,0.66593,-0.71632,245.16
> undo
> ui mousemode right select
> select clear
> ui mousemode right zoom
> select #12/D:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/D:7-14
58 atoms, 58 bonds, 8 residues, 1 model selected
> color sel #e0e0fcff
> select #12/D:15
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:15-21
47 atoms, 46 bonds, 7 residues, 1 model selected
> color sel #fdf4f4ff
> color sel #ffefedff
> select #12/D:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> color sel #fff1f0ff
> color sel #fff2f0ff
> select #12/D:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> color sel #e0e0fcff
> select #12/D:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:29-36
61 atoms, 62 bonds, 8 residues, 1 model selected
> color sel #f9f9ffff
> select #12/D:37
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/D:37-38
26 atoms, 28 bonds, 2 residues, 1 model selected
> color sel #ededfdff
> select #12/D:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:39-48
74 atoms, 74 bonds, 10 residues, 1 model selected
> color sel #dcdcfcff
> select
> #12/D:7-10,13-17,22-28,35-40,47-50,64-69,72-77,86-92,102-107,114-118,129-137,144-150,153-155,159-163,175-182,191-198,205-210
797 atoms, 797 bonds, 102 residues, 1 model selected
> select #12/D:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #e4e4fdff
> select #12/D:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:50-56
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel #5c5cf6ff
> select #12/D:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:57-58
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:57-58
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #fdf6f6ff
> select #12/D:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:58-67
68 atoms, 69 bonds, 10 residues, 1 model selected
> color sel #efeffeff
> select #12/D:58-67
68 atoms, 69 bonds, 10 residues, 1 model selected
> select #12/D:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:58-69
78 atoms, 79 bonds, 12 residues, 1 model selected
> color sel #e8e8fdff
> select #12/D:70
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/D:70-73
34 atoms, 35 bonds, 4 residues, 1 model selected
> color sel #d8d8fcff
> select #12/D:74-75
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/D:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #f4f4feff
> select #12/D:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/D:80-81
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel #fff6f4ff
> select #12/D:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:82-84
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel #efeffeff
> select #12/D:85
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:85-87
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #12/D:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/D:84-87
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #ffdedeff
> color sel #ffe8e9ff
> select #12/D:88
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/D:88-97
96 atoms, 102 bonds, 10 residues, 1 model selected
> select #12/D:98
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/D:98-105
56 atoms, 56 bonds, 8 residues, 1 model selected
> color sel #d0d0fbff
> select #12/D:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:114-125
97 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #d6d6fcff
> select #12/D:128-129
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:128-131
22 atoms, 21 bonds, 4 residues, 1 model selected
> color sel #dfdffcff
> select #12/D:132-133
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/D:132-137
44 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #fbeae9ff
> color sel #ffeeeaff
> select #12/D:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:138-146
79 atoms, 81 bonds, 9 residues, 1 model selected
> color sel #c9c9fbff
> select #12/D:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:147-158
95 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #f7cbcaff
> select #12/D:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:161-179
144 atoms, 144 bonds, 19 residues, 1 model selected
> color sel #c9c9fbff
> select #12/D:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:183-204
176 atoms, 180 bonds, 22 residues, 1 model selected
> color sel #bbbbfaff
> select #12/D:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/D:205-213
72 atoms, 72 bonds, 9 residues, 1 model selected
> color sel #fbebffff
> color sel #f1eaffff
> color sel #f6eeffff
> color sel #f7eeffff
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #4/A #10/D #10/A
Alignment identifier is 1
> show #!9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> select #3/B:1-81 #4/A:1-81 #10/D,A:1-81
2576 atoms, 2632 bonds, 14 pseudobonds, 324 residues, 5 models selected
> select #3/B:1-275 #4/A:1-275 #10/D,A:1-275
8808 atoms, 9044 bonds, 154 pseudobonds, 1100 residues, 5 models selected
> select #3/B:276 #4/A:276 #10/D,A:276
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:276-352 #4/A:276-352 #10/D,A:276-352
2396 atoms, 2440 bonds, 1 pseudobond, 308 residues, 4 models selected
> select #3/B:101-352 #4/A:101-352 #10/D,A:101-352
8076 atoms, 8300 bonds, 31 pseudobonds, 1008 residues, 5 models selected
> select #3/B #4/A #10/D,A
11204 atoms, 11488 bonds, 155 pseudobonds, 1408 residues, 5 models selected
> select subtract #5
11204 atoms, 11488 bonds, 53 pseudobonds, 1408 residues, 4 models selected
> select subtract #4
8403 atoms, 8616 bonds, 21 pseudobonds, 1056 residues, 3 models selected
> select subtract #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select add #10
8936 atoms, 9124 bonds, 1118 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select add #4
5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected
> select add #5
5602 atoms, 5744 bonds, 144 pseudobonds, 704 residues, 4 models selected
> select subtract #5
5602 atoms, 5744 bonds, 42 pseudobonds, 704 residues, 3 models selected
> select add #7
5602 atoms, 5744 bonds, 97 pseudobonds, 704 residues, 3 models selected
> select subtract #7
5602 atoms, 5744 bonds, 704 residues, 2 models selected
> color sel dim gray
> select subtract #3
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> select subtract #4
Nothing selected
> select #3/B:175 #4/A:175 #10/D,A:175
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:175-178 #4/A:175-178 #10/D,A:175-178
120 atoms, 116 bonds, 16 residues, 3 models selected
> ui tool show "Color Actions"
> color sel #d8d8fcff
> select #3/B:180 #4/A:180 #10/D,A:180
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:180-185 #4/A:180-185 #10/D,A:180-185
180 atoms, 176 bonds, 24 residues, 3 models selected
> select #3/B:179 #4/A:179 #10/D,A:179
24 atoms, 20 bonds, 4 residues, 3 models selected
> select #3/B:179-186 #4/A:179-186 #10/D,A:179-186
224 atoms, 220 bonds, 32 residues, 3 models selected
> color sel #e5e3ffff
> select #3/B:187-188 #4/A:187-188 #10/D,A:187-188
52 atoms, 48 bonds, 8 residues, 3 models selected
> select #3/B:187-198 #4/A:187-198 #10/D,A:187-198
368 atoms, 368 bonds, 48 residues, 3 models selected
> color sel #dbdcffff
> select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
64 atoms, 64 bonds, 8 residues, 3 models selected
> select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
64 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #d2d5ffff
> select #3/B:201 #4/A:201 #10/D,A:201
56 atoms, 60 bonds, 4 residues, 3 models selected
> select #3/B:201-211 #4/A:201-211 #10/D,A:201-211
384 atoms, 396 bonds, 44 residues, 3 models selected
> color sel #d9dbffff
> select #3/B:212 #4/A:212 #10/D,A:212
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:212-217 #4/A:212-217 #10/D,A:212-217
192 atoms, 192 bonds, 24 residues, 3 models selected
> color sel #f7f5ffff
> select #3/B:218 #4/A:218 #10/D,A:218
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:218-220 #4/A:218-220 #10/D,A:218-220
96 atoms, 92 bonds, 12 residues, 3 models selected
> select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
68 atoms, 64 bonds, 8 residues, 3 models selected
> select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
68 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #c9d5ffff
> color sel #cad4ffff
> color sel #cbd4ffff
> color sel #ccd4ffff
> color sel #cdd3ffff
> color sel #ced3ffff
> color sel #cfd3ffff
> color sel #cfd2ffff
> color sel #d0d2ffff
> color sel #d1d2ffff
> color sel #d1d1ffff
> select #3/B:220 #4/A:220 #10/D,A:220
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:220-231 #4/A:220-231 #10/D,A:220-231
396 atoms, 412 bonds, 48 residues, 3 models selected
> color sel #c8c9ffff
> select #3/B:232-233 #4/A:232-233 #10/D,A:232-233
80 atoms, 84 bonds, 8 residues, 3 models selected
> select #3/B:232-240 #4/A:232-240 #10/D,A:232-240
284 atoms, 288 bonds, 36 residues, 3 models selected
> color sel #d4d6ffff
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:242 #4/A:242 #10/D,A:242
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> color sel #dddfffff
> select #3/B:242 #4/A:242 #10/D,A:242
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:242-247 #4/A:242-247 #10/D,A:242-247
204 atoms, 208 bonds, 24 residues, 3 models selected
> color sel #d3d6ffff
> select #3/B:248 #4/A:248 #10/D,A:248
20 atoms, 16 bonds, 4 residues, 3 models selected
> select #3/B:248-254 #4/A:248-254 #10/D,A:248-254
192 atoms, 196 bonds, 28 residues, 3 models selected
> select #3/B:254 #4/A:254 #10/D,A:254
40 atoms, 40 bonds, 4 residues, 3 models selected
> select #3/B:254 #4/A:254 #10/D,A:254
40 atoms, 40 bonds, 4 residues, 3 models selected
> select #3/B:253 #4/A:253 #10/D,A:253
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:248-253 #4/A:248-253 #10/D,A:248-253
152 atoms, 152 bonds, 24 residues, 3 models selected
> color sel #dedfffff
> color sel #e1e1ffff
> select #3/B:254-255 #4/A:254-255 #10/D,A:254-255
72 atoms, 72 bonds, 8 residues, 3 models selected
> select #3/B:254-262 #4/A:254-262 #10/D,A:254-262
324 atoms, 340 bonds, 36 residues, 3 models selected
> color sel #d6d6ffff
> select #3/B:263 #4/A:263 #10/D,A:263
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:263-265 #4/A:263-265 #10/D,A:263-265
84 atoms, 80 bonds, 12 residues, 3 models selected
> color sel #dad9ffff
> select #3/B:266 #4/A:266 #10/D,A:266
16 atoms, 12 bonds, 4 residues, 3 models selected
> select #3/B:266-267 #4/A:266-267 #10/D,A:266-267
44 atoms, 44 bonds, 8 residues, 3 models selected
> color sel #cfcfffff
> color sel #d0cfffff
> color sel #d0d0ffff
> color sel #cecbffff
> select #3/B:268-269 #4/A:268-269 #10/D,A:268-269
96 atoms, 104 bonds, 8 residues, 3 models selected
> select #3/B:268-273 #4/A:268-273 #10/D,A:268-273
220 atoms, 228 bonds, 24 residues, 3 models selected
> color sel #d3d1ffff
> select #3/B:274 #4/A:274 #10/D,A:274
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:274-275 #4/A:274-275 #10/D,A:274-275
68 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #c3c6ffff
> select #3/B:276 #4/A:276 #10/D,A:276
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:276-277 #4/A:276-277 #10/D,A:276-277
76 atoms, 76 bonds, 8 residues, 3 models selected
> color sel #d1d4ffff
> select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
76 atoms, 76 bonds, 8 residues, 3 models selected
> select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
76 atoms, 76 bonds, 8 residues, 3 models selected
> color sel #dddcffff
> select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
340 atoms, 340 bonds, 48 residues, 3 models selected
> select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
340 atoms, 340 bonds, 48 residues, 3 models selected
> select #3/B:287-300 #4/A:287-300 #10/D,A:287-300
412 atoms, 412 bonds, 56 residues, 3 models selected
> select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:287-299 #4/A:287-299 #10/D,A:287-299
384 atoms, 384 bonds, 52 residues, 3 models selected
> color sel #d3d2ffff
> color sel #cbccffff
> select #3/B:300 #4/A:300 #10/D,A:300
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:300-309 #4/A:300-309 #10/D,A:300-309
272 atoms, 268 bonds, 40 residues, 3 models selected
> color sel #bfc3ffff
> select #3/B:310 #4/A:310 #10/D,A:310
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:310 #4/A:310 #10/D,A:310
36 atoms, 32 bonds, 4 residues, 3 models selected
> color sel #c8ceffff
> select #3/B:311-312 #4/A:311-312 #10/D,A:311-312
80 atoms, 84 bonds, 8 residues, 3 models selected
> select #3/B:311-333 #4/A:311-333 #10/D,A:311-333
756 atoms, 784 bonds, 1 pseudobond, 92 residues, 4 models selected
> color (#3-4,10 & sel) #d2d3ffff
> select #3/B:334 #4/A:334 #10/D,A:334
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:334 #4/A:334 #10/D,A:334
36 atoms, 32 bonds, 4 residues, 3 models selected
> color sel #cbd5ffff
> color sel #cbceffff
> select #3/B:335 #4/A:335 #10/D,A:335
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:335-340 #4/A:335-340 #10/D,A:335-340
208 atoms, 208 bonds, 24 residues, 3 models selected
> color sel #ceceffff
> color sel #cfd1ffff
> select #3/B:341 #4/A:341 #10/D,A:341
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:341-349 #4/A:341-349 #10/D,A:341-349
288 atoms, 284 bonds, 36 residues, 3 models selected
> color sel #caceffff
> color sel #c8ccffff
> color sel #c3caffff
> color sel #bdcbffff
> select #3/B:350 #4/A:350 #10/D,A:350
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:350-352 #4/A:350-352 #10/D,A:350-352
76 atoms, 72 bonds, 12 residues, 3 models selected
> color sel #ffebf3ff
> color sel #ffe8efff
> select #3/B:301-302 #4/A:301-302 #10/D,A:301-302
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:301-310 #4/A:301-310 #10/D,A:301-310
280 atoms, 276 bonds, 40 residues, 3 models selected
> color sel #8c8cf7ff
> color sel #8587ffff
> color sel #8282ffff
> color sel #7c83ffff
> select add #3
3011 atoms, 3079 bonds, 45 pseudobonds, 382 residues, 5 models selected
> select add #4
5742 atoms, 5882 bonds, 90 pseudobonds, 724 residues, 5 models selected
> select subtract #3
2941 atoms, 3010 bonds, 45 pseudobonds, 372 residues, 4 models selected
> select subtract #4
140 atoms, 138 bonds, 20 residues, 1 model selected
> select add #12
3541 atoms, 3631 bonds, 462 residues, 2 models selected
> select add #10
12337 atoms, 12617 bonds, 1560 residues, 2 models selected
> select subtract #10
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.82562,-0.34186,-0.44887,168.94,-0.52138,-0.76634,-0.37535,482.82,-0.21567,0.54392,-0.81094,284.87
> view matrix models
> #12,0.82562,-0.34186,-0.44887,169.91,-0.52138,-0.76634,-0.37535,479.02,-0.21567,0.54392,-0.81094,283.58
> view matrix models
> #12,0.82562,-0.34186,-0.44887,170.32,-0.52138,-0.76634,-0.37535,480.41,-0.21567,0.54392,-0.81094,282.28
> view matrix models
> #12,0.82562,-0.34186,-0.44887,171.18,-0.52138,-0.76634,-0.37535,479.61,-0.21567,0.54392,-0.81094,282.22
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.94747,-0.06803,0.31253,-40.388,-0.27852,-0.65592,0.70156,212.57,0.15727,-0.75175,-0.64041,392.6
> view matrix models
> #12,0.65713,0.16685,-0.73508,171.79,0.09209,-0.98566,-0.1414,332.31,-0.74813,0.025227,-0.66307,473.05
> view matrix models
> #12,0.95731,-0.18789,-0.21965,72.476,-0.15301,-0.97411,0.16641,333.66,-0.24523,-0.1257,-0.96128,433.82
> view matrix models
> #12,0.96798,-0.24602,-0.049963,50.221,-0.17279,-0.7973,0.57833,234.35,-0.18211,-0.55117,-0.81427,467.97
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> show #!9 models
> fitmap #12 inMap #9
Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms
average map value = 0.09851, steps = 252
shifted from previous position = 4.87
rotated from previous position = 66.7 degrees
atoms outside contour = 1988, contour level = 0.11015
Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates:
Matrix rotation and translation
-0.10506635 -0.15760122 0.98189762 53.59780496
-0.09254653 -0.98152811 -0.16744470 397.44466486
0.99014960 -0.10846402 0.08854013 -3.70228919
Axis 0.66872859 -0.09356170 0.73759629
Axis point 22.53945284 199.32977295 0.00000000
Rotation angle (degrees) 177.47248714
Shift along axis -4.07401058
> volume #9 level 0.08287
> volume #9 level 0.06241
> hide #10 models
> show #10 models
> hide #10 models
> color #5 #7b137cff models
> color #5 #7c0e7cff models
> color #5 #fe1effff models
> color #5 #ee1cefff models
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> hide #7 models
> hide #4 models
> show #4 models
> hide #8 models
> show #8 models
> select add #2
5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected
> select subtract #2
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select add #2
5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected
> select subtract #2
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select add #1
3334 atoms, 3380 bonds, 58 pseudobonds, 414 residues, 4 models selected
> select add #3
6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected
> select add #4
8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#2,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#3,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#4,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#2,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#3,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#4,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#2,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#3,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#4,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#2,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#3,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#4,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#2,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#3,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#4,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#2,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#3,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#4,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#2,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#3,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#4,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#2,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#3,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#4,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#2,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#3,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#4,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#2,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#3,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#4,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#2,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#3,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#4,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#2,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#3,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#4,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#2,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#3,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#4,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#2,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#3,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#4,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#2,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#3,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#4,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> select subtract #1
7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected
> select subtract #2
5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected
> select subtract #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> select subtract #12
Nothing selected
> select #12/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> hide #!9 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs" includeMaps true
> show #!9 models
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select add #3
4468 atoms, 4562 bonds, 74 pseudobonds, 559 residues, 5 models selected
> select add #4
7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected
> select add #5
7269 atoms, 7434 bonds, 173 pseudobonds, 911 residues, 6 models selected
> select subtract #5
7269 atoms, 7434 bonds, 71 pseudobonds, 911 residues, 5 models selected
> select add #6
7269 atoms, 7434 bonds, 142 pseudobonds, 911 residues, 5 models selected
> select subtract #6
7269 atoms, 7434 bonds, 49 pseudobonds, 911 residues, 4 models selected
> select add #7
7269 atoms, 7434 bonds, 97 pseudobonds, 911 residues, 4 models selected
> select subtract #7
7269 atoms, 7434 bonds, 911 residues, 3 models selected
> select add #1
8936 atoms, 9124 bonds, 29 pseudobonds, 1118 residues, 6 models selected
> select subtract #2
7269 atoms, 7434 bonds, 29 pseudobonds, 911 residues, 5 models selected
> select add #2
8936 atoms, 9124 bonds, 58 pseudobonds, 1118 residues, 6 models selected
> select subtract #3
6135 atoms, 6252 bonds, 58 pseudobonds, 766 residues, 5 models selected
> select add #3
8936 atoms, 9124 bonds, 103 pseudobonds, 1118 residues, 7 models selected
> select subtract #4
6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected
> select add #4
8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#2,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#3,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#4,0.9833,0.18192,0.0055417,-36.253,-0.18172,0.983,-0.026391,41.588,-0.010249,0.024943,0.99964,-2.0695,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#2,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#3,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#4,0.9833,0.18192,0.0055417,-36.847,-0.18172,0.983,-0.026391,41.972,-0.010249,0.024943,0.99964,-2.0445,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> volume #9 level 0.07332
> volume #9 level 0.1102
> view matrix models
> #1,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#2,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#3,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#4,0.9833,0.18192,0.0055417,-36.452,-0.18172,0.983,-0.026391,42.252,-0.010249,0.024943,0.99964,-1.3599,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#2,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#3,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#4,0.9833,0.18192,0.0055417,-36.881,-0.18172,0.983,-0.026391,42.629,-0.010249,0.024943,0.99964,-1.3368,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#2,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#3,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#4,0.98119,0.19216,-0.018632,-33.726,-0.19238,0.98126,-0.010945,41.781,0.016179,0.014324,0.99977,-3.9218,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#2,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#3,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#4,0.98027,0.19654,-0.021274,-33.885,-0.19691,0.98027,-0.017135,43.973,0.017487,0.020986,0.99963,-5.3968,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#2,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#3,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#4,0.98134,0.18921,-0.034256,-30.12,-0.19038,0.98109,-0.034836,46.156,0.027017,0.040708,0.99881,-10.665,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#2,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#3,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#4,0.98224,0.18112,-0.048941,-25.843,-0.18399,0.98094,-0.062517,50.521,0.036685,0.070412,0.99684,-17.635,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#2,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#3,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#4,0.99655,0.077131,0.030705,-24.147,-0.074724,0.99453,-0.073036,31.058,-0.03617,0.070489,0.99686,-5.0238,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#2,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#3,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#4,0.98562,0.16498,-0.036586,-25.784,-0.16709,0.98381,-0.064738,47.47,0.025313,0.06992,0.99723,-15.64,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#2,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#3,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#4,0.98733,0.14574,-0.062757,-17.252,-0.15017,0.98598,-0.072746,45.698,0.051275,0.081248,0.99537,-21.942,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#2,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#3,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#4,0.98899,0.13015,-0.070408,-13.054,-0.13512,0.98828,-0.071057,42.311,0.060334,0.079788,0.99498,-23.16,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#2,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#3,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#4,0.98612,0.15567,-0.057673,-19.94,-0.1595,0.98477,-0.069167,46.847,0.046028,0.077406,0.99594,-20.407,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#2,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#3,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#4,0.97272,0.12606,-0.19474,14.958,-0.15151,0.98092,-0.12182,56.628,0.17567,0.148,0.97326,-52.111,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#2,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#3,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#4,0.97391,0.04287,-0.22284,36.17,-0.072834,0.98909,-0.12804,42.459,0.21492,0.14093,0.96641,-56.313,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#2,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#3,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#4,0.97437,0.073896,-0.21246,28.12,-0.1022,0.98682,-0.12546,47.556,0.20039,0.14395,0.96908,-54.857,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#2,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#3,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#4,0.99279,0.030411,-0.11595,14.123,-0.049395,0.98513,-0.16456,46.325,0.10922,0.1691,0.97953,-45.703,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#2,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#3,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#4,0.99322,0.026282,-0.11323,14.297,-0.042299,0.98904,-0.14147,39.767,0.10827,0.1453,0.98345,-41.768,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#2,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#3,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#4,0.98565,0.068261,-0.15439,15.736,-0.087789,0.98846,-0.12342,44.288,0.14419,0.13521,0.98027,-45.509,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#2,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#3,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#4,0.98793,0.057456,-0.14382,15.313,-0.075925,0.98907,-0.12641,42.682,0.13499,0.13581,0.9815,-44.253,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right select
> select clear
> select #12/D:25
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select add #9
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 5 models selected
> select subtract #9
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select add #9
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 5 models selected
> select subtract #9
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select clear
> select add #10
8936 atoms, 9124 bonds, 1118 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #10
8936 atoms, 9124 bonds, 1118 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select clear
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.82559,-0.34194,-0.44887,169.92,-0.52142,-0.76637,-0.37524,483.13,-0.21569,0.54384,-0.811,285.08
> view matrix models
> #12,0.82559,-0.34194,-0.44887,170.04,-0.52142,-0.76637,-0.37524,483.13,-0.21569,0.54384,-0.811,285.05
> view matrix models
> #12,0.82559,-0.34194,-0.44887,170.05,-0.52142,-0.76637,-0.37524,482.88,-0.21569,0.54384,-0.811,285.15
> view matrix models
> #12,0.82559,-0.34194,-0.44887,170.12,-0.52142,-0.76637,-0.37524,482.29,-0.21569,0.54384,-0.811,285.24
> view matrix models
> #12,0.82559,-0.34194,-0.44887,170.68,-0.52142,-0.76637,-0.37524,482.21,-0.21569,0.54384,-0.811,285.02
> view matrix models
> #12,0.82559,-0.34194,-0.44887,171.91,-0.52142,-0.76637,-0.37524,481.88,-0.21569,0.54384,-0.811,284.81
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.85565,-0.40349,-0.32413,153.63,-0.51632,-0.70873,-0.48074,489.16,-0.035744,0.5787,-0.81476,236.91
> view matrix models
> #12,0.86103,-0.44709,-0.24235,145.6,-0.49595,-0.84364,-0.20569,459.53,-0.11249,0.29729,-0.94814,328.19
> view matrix models
> #12,0.8588,-0.45952,-0.22652,145.52,-0.47641,-0.87891,-0.023255,428.91,-0.18841,0.12789,-0.97373,380.47
> view matrix models
> #12,0.86899,-0.46074,-0.18049,135.2,-0.46357,-0.88559,0.028727,417.87,-0.17308,0.058707,-0.98316,390.72
> view matrix models
> #12,0.65716,-0.59002,-0.46906,258.92,-0.69689,-0.71272,-0.079835,461.58,-0.2872,0.37935,-0.87955,342.79
> view matrix models
> #12,0.68636,-0.55214,-0.47334,246.12,-0.67684,-0.72309,-0.13797,468.95,-0.26609,0.41507,-0.87001,329.82
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.68636,-0.55214,-0.47334,247.09,-0.67684,-0.72309,-0.13797,468.4,-0.26609,0.41507,-0.87001,329.01
> view matrix models
> #12,0.68636,-0.55214,-0.47334,245.66,-0.67684,-0.72309,-0.13797,466.52,-0.26609,0.41507,-0.87001,329.78
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right select
> select clear
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> ui mousemode right "rotate selected models"
> select subtract #3
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #12,0.21516,0.9712,0.10233,-13.578,-0.81472,0.12074,0.56714,225.64,0.53845,-0.2054,0.81724,-48.675
> view matrix models
> #12,0.43037,0.90252,0.01538,-36.834,-0.77438,0.3604,0.52005,182.2,0.46381,-0.23572,0.854,-32.23
> view matrix models
> #12,0.29061,0.92832,-0.23189,35.263,-0.85384,0.36098,0.37503,226.45,0.43186,0.089009,0.89754,-89.643
> view matrix models
> #12,0.19232,0.92899,-0.31622,73.22,-0.85462,0.31693,0.41132,227.99,0.48233,0.19114,0.85488,-112.01
> view matrix models
> #12,0.16773,0.93259,-0.3196,78.977,-0.8501,0.30098,0.43213,226.06,0.49919,0.19921,0.84328,-115.36
> view matrix models
> #12,-0.012017,0.94523,-0.32618,120.28,-0.79463,0.18898,0.57693,207.14,0.60697,0.26612,0.74884,-135.87
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.21625,0.97297,0.080975,-10.373,-0.57946,0.061151,0.8127,137.29,0.78579,-0.22267,0.57703,-61.482
> view matrix models
> #12,0.38482,0.92257,0.027751,-31.819,-0.62434,0.23804,0.744,128.82,0.67979,-0.30363,0.66761,-38.228
> view matrix models
> #12,0.49592,0.83935,0.22263,-77.775,-0.58873,0.13653,0.79671,129.01,0.63832,-0.52617,0.56186,29.471
> view matrix models
> #12,0.53883,0.71851,0.43979,-104.96,-0.52134,-0.12567,0.84405,150.98,0.66172,-0.68407,0.30687,96.857
> view matrix models
> #12,0.58792,0.7378,0.33167,-100.83,-0.43616,-0.056188,0.89812,109.1,0.68127,-0.67268,0.28876,93.441
> view matrix models
> #12,0.68026,0.64643,0.34551,-108.94,-0.39716,-0.071108,0.91499,99.553,0.61604,-0.75965,0.20837,138.36
> view matrix models
> #12,0.69449,0.65973,0.28713,-104.32,-0.344,-0.046041,0.93784,78.561,0.63194,-0.75009,0.19497,135.3
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.69449,0.65973,0.28713,-102.08,-0.344,-0.046041,0.93784,78.11,0.63194,-0.75009,0.19497,133.54
> view matrix models
> #12,0.69449,0.65973,0.28713,-102.45,-0.344,-0.046041,0.93784,78.386,0.63194,-0.75009,0.19497,133.74
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.34284,0.899,0.27252,-59.156,-0.32401,-0.15913,0.93257,94.544,0.88175,-0.40802,0.23673,7.1605
> view matrix models
> #12,0.30177,0.93844,0.16811,-37.978,-0.40954,-0.031635,0.91174,95.91,0.86093,-0.34399,0.37479,-23.623
> view matrix models
> #12,0.34216,0.92298,0.17617,-46.197,-0.37936,-0.035844,0.92456,87.272,0.85966,-0.38318,0.33787,-9.8896
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.994,-0.31103,-0.012038,0.95032,62.414,0.86819,-0.41042,0.27895,3.3167
> select subtract #12
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> ui mousemode right zoom
> select add #2
4468 atoms, 4562 bonds, 74 pseudobonds, 559 residues, 5 models selected
> select add #1
6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected
> select add #4
8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#2,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#3,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#4,0.98793,0.057456,-0.14382,14.056,-0.075925,0.98907,-0.12641,42.661,0.13499,0.13581,0.9815,-43.601,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#2,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#3,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#4,0.98793,0.057456,-0.14382,13.827,-0.075925,0.98907,-0.12641,42.608,0.13499,0.13581,0.9815,-43.292,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> volume #9 level 0.1033
> view matrix models
> #1,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#2,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#3,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#4,0.98793,0.057456,-0.14382,13.882,-0.075925,0.98907,-0.12641,42.414,0.13499,0.13581,0.9815,-43.066,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#2,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#3,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#4,0.98793,0.057456,-0.14382,13.743,-0.075925,0.98907,-0.12641,41.91,0.13499,0.13581,0.9815,-42.398,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#2,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#3,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#4,0.98976,0.050761,-0.13341,12.648,-0.06712,0.99036,-0.12114,39.078,0.12598,0.12885,0.98363,-39.91,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#2,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#3,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#4,0.99033,0.070382,-0.11954,6.0597,-0.084892,0.98902,-0.12099,42.418,0.10971,0.12996,0.98543,-37.629,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#2,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#3,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#4,0.9884,0.078396,-0.1301,6.9535,-0.093646,0.98887,-0.11557,42.908,0.11959,0.12642,0.98474,-38.545,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#2,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#3,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#4,0.98395,0.11436,-0.13701,2.2264,-0.12871,0.98654,-0.10086,46.584,0.12364,0.11688,0.98542,-37.564,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#2,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#3,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#4,0.98197,0.14007,-0.12693,-4.3253,-0.15486,0.98119,-0.11524,55.01,0.10841,0.13282,0.98519,-37.901,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#2,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#3,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#4,0.98017,0.16776,-0.1055,-13.524,-0.17994,0.97645,-0.11899,61.028,0.083055,0.13561,0.98727,-34.425,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#2,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#3,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#4,0.98125,0.15735,-0.11134,-10.574,-0.17036,0.97817,-0.11902,59.039,0.090181,0.13575,0.98663,-35.565,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#2,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#3,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#4,0.98125,0.15735,-0.11134,-11.563,-0.17036,0.97817,-0.11902,59.058,0.090181,0.13575,0.98663,-35.488,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right select
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #12/D
Alignment identifier is 12/D
> ui tool show "Renumber Residues"
> renumber #12/D seqStart 229 relative false
214 residues renumbered
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/F562_1-442.pdb" models #12
> combine #3 #4
> rename #13 sNS1
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #8 models
> hide #!9 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/D2NS1.pdb" models #13
> select #12/D:229
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D
1632 atoms, 1668 bonds, 214 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #4/A
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> show #3 models
> show #4 models
> select clear
> ui mousemode right zoom
> show #2 models
> show #1 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> show #!9 models
> color #9 #b4e3e620 models
> color #9 #b4e3e61d models
> color #9 #b4e3e61a models
> color #9 #b4e3e60a models
> color #9 #b4e3e60b models
> color #9 #b4e3e60d models
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> hide #!9 models
> show #!9 models
> hide #8 models
> show #8 models
> hide #12 models
> show #12 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_top.png" width 978 height 807
> supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_side.png" width 978 height 807
> supersample 3
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/view_side.png" width 978 height 807
> supersample 3 transparentBackground true
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.42,-0.31103,-0.012038,0.95032,62.146,0.86819,-0.41042,0.27895,3.0647
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.326,-0.31103,-0.012038,0.95032,61.501,0.86819,-0.41042,0.27895,2.9386
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.268,-0.31103,-0.012038,0.95032,61.611,0.86819,-0.41042,0.27895,2.923
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.161,-0.31103,-0.012038,0.95032,61.629,0.86819,-0.41042,0.27895,2.8732
> view matrix models
> #12,0.38667,0.91182,0.1381,-47.025,-0.31103,-0.012038,0.95032,61.858,0.86819,-0.41042,0.27895,2.61
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.40207,0.90968,0.10404,-44.258,-0.30079,0.023902,0.95339,52.565,0.86479,-0.41462,0.28323,3.394
> view matrix models
> #12,0.43588,0.8998,0.019269,-35.504,-0.22748,0.089432,0.96967,20.855,0.87078,-0.42704,0.24367,11.163
> view matrix models
> #12,0.44682,0.88805,0.10825,-51.738,-0.30462,0.037257,0.95175,51.403,0.84116,-0.45824,0.28716,15.96
> view matrix models
> #12,0.4731,0.86918,0.14391,-60.908,-0.27044,-0.012188,0.96266,50.135,0.83848,-0.49435,0.22929,33.188
> select subtract #12
Nothing selected
> select #12/C:101-103
32 atoms, 33 bonds, 3 residues, 1 model selected
> select #12/C:101-105
50 atoms, 52 bonds, 5 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select #12/C:102-103
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #12/C:102-108
61 atoms, 64 bonds, 7 residues, 1 model selected
> select #12/C:102-105
42 atoms, 44 bonds, 4 residues, 1 model selected
> select #12/C:102-109
65 atoms, 68 bonds, 8 residues, 1 model selected
> color sel #3b3bffff
> select #12/C:15-30
126 atoms, 130 bonds, 16 residues, 1 model selected
> select #12/C:31-34
25 atoms, 24 bonds, 4 residues, 1 model selected
> select #12/C:35
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:30-35
43 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #5d62ffff
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.48862,0.86407,0.12095,-59.608,-0.26178,0.012952,0.96504,43.24,0.8323,-0.5032,0.23252,35.632
> view matrix models
> #12,0.54523,0.80683,0.2275,-81.692,-0.25523,-0.098725,0.96183,61.956,0.79849,-0.58248,0.1521,71.795
> view matrix models
> #12,0.56505,0.79487,0.22115,-83.133,-0.25139,-0.089428,0.96375,59.071,0.78583,-0.60016,0.14929,78.392
> view matrix models
> #12,0.61857,0.76623,0.17398,-82.364,-0.21294,-0.049666,0.9758,40.865,0.75633,-0.64065,0.13244,95.463
> view matrix models
> #12,0.61335,0.74396,0.26517,-93.325,-0.25312,-0.13287,0.95827,68.106,0.74815,-0.65488,0.10682,104.43
> ui mousemode right select
> select clear
> ui mousemode right zoom
> color #9 #e4ebc20d models
> color #9 #e7ebbd0d models
> color #9 #e9eb960d models
> color #9 #ebe98e0d models
> color #9 #ebe7900d models
> color #9 #ebe79017 models
> select add #5
102 pseudobonds, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs
Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
level 0.0624, step 1, values float32
Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375,
step 1, values float32
Log from Wed Apr 19 17:03:52 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs
Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
level 0.11, step 1, values float32
Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0375,
step 1, values float32
Log from Wed Apr 19 14:11:57 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_MS_Wint/XMAS
> files/NS1-apoAI_models-forwint_forAlvin.cxs"
Log from Mon Apr 3 16:43:31 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Log from Mon Apr 3 15:19:20 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint.cxs
Log from Sat Apr 1 16:55:32 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Thu Mar 30 23:52:24 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab-
> ApoAI_Ab562_compare.cxs"
Opened sNS1wt-Ab562.mrc as #2, grid size 352,352,352, pixel 0.85, shown at
level 0.17, step 1, values float32
Opened sNS1wt-Fab562.mrc as #8, grid size 416,416,416, pixel 0.85, shown at
level 0.0754, step 1, values float32
Log from Sat Nov 19 10:30:44 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-
> ApoAI_hdl.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.17, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
416,416,416, pixel 0.85, shown at level 0.0687, step 1, values float32
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0754, step 1, values float32
Log from Thu Mar 24 12:02:48 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
> Fab-ApoAI_hdl.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Log from Sat Mar 12 14:58:51 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-
> Fab-ApoAI_hdl_Compare-NS1ts.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.169, step 1, values float32
Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
416,416,416, pixel 0.858, shown at level 0.135, step 1, values float32
Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.79, shown at level 0.318, step 1, values float32
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.09, step 2, values float32
Log from Fri Mar 11 18:14:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-
> Fab-ApoAI_hdl.cxs
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.127, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.191, step 1, values float32
Log from Thu Mar 3 21:24:07 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
352,352,352, pixel 0.85, shown at level 0.0969, step 1, values float32
Log from Thu Mar 3 19:50:19 2022UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab5-DL.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.05, step 1, values float32
Log from Thu Mar 3 12:01:46 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\dahailuo\\\OneDrive - Nanyang Technological
> University\\\Temporal\\\202112_FlaviNS1\\\Data_EM_Alvin\\\20220302_D2NS1ts-
> Ab56-apoa1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:18:18 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220302_D2NS1ts-
> Ab56-apoa1.cxs" format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Wed Mar 2 00:08:07 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 22:03:06 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56-AA1.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Log from Tue Feb 22 21:54:19 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "D:\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\20220222_D2NS1-Ab56.cxs"
> format session
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.08, step 1, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.421, step 2, values float32
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 1, values float32
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at level 0.471, step 1, values float32
Log from Tue Feb 22 21:05:12 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J91_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J91_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0468, step 2, values float32
> surface dust #1 size 8.58
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #2, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.58
> close #2
> close #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J96_006_volume_map_sharp.mrc"
Opened cryosparc_P35_J96_006_volume_map_sharp.mrc as #1, grid size
416,416,416, pixel 0.858, shown at level 0.0481, step 2, values float32
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J20_004_volume_map_sharp.mrc"
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc as #2, grid size
352,352,352, pixel 0.85, shown at level 0.142, step 2, values float32
> surface dust #1 size 8.58
> surface dust #2 size 8.5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/D2NS1.pdb"
Summary of feedback from opening D:/OneDrive - Nanyang Technological
University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
sNS1-Fab56-2/D2NS1.pdb
---
warning | Ignored bad PDB record found on line 5732
END
Chain information for D2NS1.pdb #3
---
Chain | Description
B C | No description available
> hide #!2 models
> volume #1 level 0.07524
> volume #1 level 0.07
> volume #1 level 0.072
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.89628,-0.44038,-0.052381,101.61,0.096778,0.078954,0.99217,-38.919,-0.43279,-0.89433,0.11338,384.44
> view matrix models
> #3,0.99109,-0.12056,-0.056551,31.91,0.0080432,0.4781,-0.87827,242.8,0.13292,0.86999,0.47482,-76.088
> view matrix models
> #3,0.79841,-0.57175,0.18879,97.95,-0.1953,0.050686,0.97943,19.471,-0.56956,-0.81886,-0.071196,428.68
> view matrix models
> #3,0.82022,-0.53629,0.19907,86.322,-0.4792,-0.8342,-0.2729,441.29,0.31242,0.12845,-0.94122,269.29
> view matrix models
> #3,0.33094,0.34033,0.88014,-96.351,-0.87516,0.45954,0.15137,217.82,-0.35295,-0.82036,0.44993,298
> view matrix models
> #3,0.12486,-0.10929,0.98614,-3.3941,-0.98525,0.10355,0.13622,299.73,-0.117,-0.9886,-0.094748,381.83
> view matrix models
> #3,-0.013734,0.34293,0.93926,-46.701,0.87722,0.45496,-0.15328,-35.332,-0.47989,0.82183,-0.30707,179.08
> view matrix models
> #3,-0.024741,-0.048477,0.99852,10.486,0.22627,0.97263,0.052827,-44.605,-0.97375,0.22725,-0.013095,313.53
> view matrix models
> #3,0.22803,-0.14862,0.96224,-10.67,-0.86757,-0.4796,0.13152,377.92,0.44195,-0.86481,-0.23831,288.28
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.594,-0.90644,0.38234,-0.1794,295.23,-0.4125,-0.89262,0.18187,368.38
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.090598,0.23885,0.96682,-20.895,-0.90644,0.38234,-0.1794,305.2,-0.4125,-0.89262,0.18187,368.62
> view matrix models
> #3,-0.090598,0.23885,0.96682,-18.453,-0.90644,0.38234,-0.1794,307.34,-0.4125,-0.89262,0.18187,380.09
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 72
shifted from previous position = 2.04
rotated from previous position = 4.6 degrees
atoms outside contour = 3319, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06802577 0.24460859 0.96723274 -24.08767794
-0.87342564 0.45395004 -0.17623011 287.61942533
-0.48218273 -0.85679405 0.18276711 387.90605974
Axis -0.34848182 0.74217118 -0.57248788
Axis point 265.32854097 -0.00000000 317.95880744
Rotation angle (degrees) 102.45391693
Shift along axis -0.21455122
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 40
shifted from previous position = 0.0168
rotated from previous position = 0.017 degrees
atoms outside contour = 3323, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800908 0.24437415 0.96729317 -24.07786550
-0.87335170 0.45412951 -0.17613415 287.55836847
-0.48231900 -0.85676584 0.18253965 387.96533381
Axis -0.34851775 0.74227452 -0.57233199
Axis point 265.31869899 0.00000000 317.91033718
Rotation angle (degrees) 102.45483514
Shift along axis -0.20615891
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 44
shifted from previous position = 0.00415
rotated from previous position = 0.0128 degrees
atoms outside contour = 3322, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06778785 0.24439903 0.96730241 -24.12733834
-0.87337367 0.45415748 -0.17595301 287.52563608
-0.48231036 -0.85674392 0.18266531 387.93712068
Axis -0.34858450 0.74224338 -0.57233173
Axis point 265.33740374 0.00000000 317.91776063
Rotation angle (degrees) 102.44383763
Shift along axis -0.20430725
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09223, steps = 44
shifted from previous position = 0.0152
rotated from previous position = 0.013 degrees
atoms outside contour = 3321, contour level = 0.072
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06797653 0.24451862 0.96725895 -24.09141306
-0.87335854 0.45410159 -0.17617224 287.57257739
-0.48231121 -0.85673942 0.18268417 387.93432608
Axis -0.34847884 0.74224049 -0.57239982
Axis point 265.31882258 -0.00000000 317.92823841
Rotation angle (degrees) 102.45045928
Shift along axis -0.21017795
> transparency #1.1 50
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/F562a.pdb"
Chain information for F562a.pdb #4
---
Chain | Description
B | No description available
C | No description available
> ui tool show "Color Actions"
> color sel bychain
> color sel bychain
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> color sel bychain
> color sel bychain
> color sel bychain
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/7bsc_DEN2 NS1c.pdb"
7bsc_DEN2 NS1c.pdb title:
Complex structure of 1G5.3 fab bound to DENV2 NS1C [more info...]
Chain information for 7bsc_DEN2 NS1c.pdb #5
---
Chain | Description
A | non-structural protein 1
H | 1G5.3 fab heavy chain
L | 1G5.3 fab light chain
> mmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with 7bsc_DEN2 NS1c.pdb, chain A (#5),
sequence alignment score = 896.9
RMSD between 162 pruned atom pairs is 0.535 angstroms; (across all 177 pairs:
2.714)
> mmaker #4 to #5
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 7bsc_DEN2 NS1c.pdb, chain H (#5) with F562a.pdb, chain B (#4),
sequence alignment score = 1028.9
RMSD between 105 pruned atom pairs is 0.627 angstroms; (across all 215 pairs:
11.308)
> ~select #4
Nothing selected
> hide #!5 models
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #4,0.59089,-0.15644,-0.79144,253.32,0.26071,0.96541,0.0038114,-36.876,0.76347,-0.20859,0.61123,8.3612
> view matrix models
> #4,0.59089,-0.15644,-0.79144,249.54,0.26071,0.96541,0.0038114,-38.171,0.76347,-0.20859,0.61123,-6.5674
> view matrix models
> #4,0.59089,-0.15644,-0.79144,250.18,0.26071,0.96541,0.0038114,-52.258,0.76347,-0.20859,0.61123,-8.7931
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.08302, steps = 284
shifted from previous position = 3.86
rotated from previous position = 9.32 degrees
atoms outside contour = 2026, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.70756240 -0.18104725 -0.68306467 216.74116501
0.24257753 0.97011437 -0.00585274 -48.06381473
0.66371047 -0.16155497 0.73033445 -11.10097449
Axis -0.10961944 -0.94817357 0.29824565
Axis point 132.17662306 0.00000000 263.68811665
Rotation angle (degrees) 45.25073566
Shift along axis 18.50297639
> transparency #1.1 0
> view matrix models
> #4,0.70756,-0.18105,-0.68306,218.9,0.24258,0.97011,-0.0058527,-47.556,0.66371,-0.16155,0.73033,-11.137
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.60929,0.056492,-0.79093,206.86,0.79214,-0.088481,0.60389,-30.096,-0.035867,-0.99447,-0.09866,369.53
> view matrix models
> #4,0.13536,-0.077461,-0.98776,343.37,0.97999,0.15727,0.12197,-53.095,0.1459,-0.98451,0.097201,310.49
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 96
shifted from previous position = 8.35
rotated from previous position = 5.73 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18515527 -0.12030538 -0.97531746 334.84540290
0.98054878 0.08839233 0.17524520 -44.47549541
0.06512764 -0.98879392 0.13433160 327.48525231
Axis -0.60933659 -0.54463915 0.57626133
Axis point 0.00000000 23.05515362 346.04002443
Rotation angle (degrees) 107.22113422
Shift along axis 8.90662490
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 28
shifted from previous position = 0.017
rotated from previous position = 0.0169 degrees
atoms outside contour = 1608, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18543237 -0.12023134 -0.97527394 334.76776945
0.98049261 0.08847529 0.17551742 -44.49851310
0.06518495 -0.98879550 0.13429212 327.47372226
Axis -0.60944823 -0.54461805 0.57616320
Axis point 0.00000000 23.10963968 345.96113737
Rotation angle (degrees) 107.21151966
Shift along axis 8.88937821
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1078, steps = 44
shifted from previous position = 0.0205
rotated from previous position = 0.0218 degrees
atoms outside contour = 1604, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.18554107 -0.12011878 -0.97526714 334.73699226
0.98049338 0.08814571 0.17567888 -44.47566373
0.06486328 -0.98883862 0.13413032 327.56427605
Axis -0.60959315 -0.54447990 0.57614045
Axis point 0.00000000 23.17721063 345.92539580
Rotation angle (degrees) 107.22299700
Shift along axis 8.88575635
> transparency #1.1 50
> view matrix models
> #4,0.95986,-0.22484,0.16768,73.526,0.27579,0.64758,-0.71034,90.606,0.051126,0.72807,0.68359,-47.104
> view matrix models
> #4,0.75847,0.64831,0.066474,-35.582,0.26049,-0.20809,-0.94278,276.59,-0.59738,0.73239,-0.32671,193.1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09049, steps = 88
shifted from previous position = 2.42
rotated from previous position = 6.19 degrees
atoms outside contour = 1911, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72637414 0.68694818 -0.02197301 -24.03798979
0.18664733 -0.22792648 -0.95562142 294.38643021
-0.66147062 0.69003748 -0.29377694 209.53189487
Axis 0.89678670 0.34848835 -0.27263435
Axis point 0.00000000 72.78629578 205.81231454
Rotation angle (degrees) 113.43226483
Shift along axis 23.90769923
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0905, steps = 44
shifted from previous position = 0.0137
rotated from previous position = 0.0204 degrees
atoms outside contour = 1906, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72623985 0.68709241 -0.02190190 -24.03578291
0.18654834 -0.22764140 -0.95570869 294.36480593
-0.66164597 0.68998798 -0.29349821 209.53312556
Axis 0.89671635 0.34858730 -0.27273923
Axis point 0.00000000 72.74870511 205.83733915
Rotation angle (degrees) 113.41885466
Shift along axis 23.91065009
> view matrix models
> #4,0.4777,0.81916,-0.31746,33.473,0.28288,-0.48553,-0.82719,308.03,-0.83173,0.30535,-0.46366,331.51
> view matrix models
> #4,0.53443,0.7221,-0.43927,54.882,0.15416,-0.59427,-0.78935,347.48,-0.83104,0.35413,-0.42891,318.4
> view matrix models
> #4,0.55861,0.65321,-0.51116,71.372,0.070767,-0.65156,-0.75529,369.52,-0.82641,0.38574,-0.41019,309.57
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 104
shifted from previous position = 3.1
rotated from previous position = 2.07 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58731938 0.63730986 -0.49889086 69.51709433
0.06189895 -0.64996950 -0.75743526 371.85473470
-0.80698480 0.41397558 -0.42118849 304.38816914
Axis 0.87354940 0.22975311 -0.42909784
Axis point 0.00000000 108.25389938 250.40641939
Rotation angle (degrees) 137.89516888
Shift along axis 15.54909083
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 100
shifted from previous position = 0.0102
rotated from previous position = 0.0178 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58732049 0.63712467 -0.49912604 69.58840441
0.06165901 -0.65012663 -0.75731997 371.91413492
-0.80700236 0.41401391 -0.42111716 304.37603978
Axis 0.87355306 0.22960687 -0.42916866
Axis point 0.00000000 108.28874120 250.42594564
Rotation angle (degrees) 137.89878759
Shift along axis 15.55454641
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.0972, steps = 84
shifted from previous position = 0.011
rotated from previous position = 0.0172 degrees
atoms outside contour = 1844, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.58733885 0.63729229 -0.49889038 69.51578518
0.06188954 -0.64997620 -0.75743028 371.85701767
-0.80697135 0.41399213 -0.42119800 304.38350057
Axis 0.87355567 0.22974281 -0.42909059
Axis point 0.00000000 108.25696578 250.40359329
Rotation angle (degrees) 137.89502914
Shift along axis 15.54928904
> view matrix models
> #4,0.65819,-0.32045,-0.68124,252,0.74547,0.15105,0.6492,-68.256,-0.10513,-0.93515,0.3383,328.44
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.102, steps = 172
shifted from previous position = 4.22
rotated from previous position = 10.1 degrees
atoms outside contour = 1745, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62980729 -0.32213914 -0.70680207 259.21419516
0.77615676 0.29659722 0.55642680 -86.34491343
0.03038868 -0.89903085 0.43682956 282.25072430
Axis -0.74003611 -0.37482903 0.55843509
Axis point 0.00000000 121.16366768 309.58820660
Rotation angle (degrees) 79.53603811
Shift along axis -1.84457671
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0802
rotated from previous position = 0.389 degrees
atoms outside contour = 1748, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62493642 -0.32416938 -0.71018919 260.92042942
0.78000765 0.29690303 0.55085085 -86.37873091
0.03228835 -0.89819976 0.43840012 281.55642716
Axis -0.73657217 -0.37741145 0.56126823
Axis point 0.00000000 119.97837519 311.01534570
Rotation angle (degrees) 79.62326298
Shift along axis -1.55772605
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 44
shifted from previous position = 0.00561
rotated from previous position = 0.0322 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.62451536 -0.32441238 -0.71044858 261.07250560
0.78034368 0.29682398 0.55041736 -86.36985039
0.03231597 -0.89813815 0.43852428 281.52393140
Axis -0.73629476 -0.37754414 0.56154292
Axis point 0.00000000 119.89834457 311.14057931
Rotation angle (degrees) 79.63421202
Shift along axis -1.53011648
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 80
shifted from previous position = 0.189
rotated from previous position = 1.07 degrees
atoms outside contour = 1750, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61106207 -0.33151468 -0.71881930 265.86650256
0.79073980 0.29753498 0.53497991 -86.41685086
0.03652019 -0.89530496 0.44395419 279.51480621
Axis -0.72651910 -0.38367781 0.57005380
Axis point 0.00000000 116.77430340 315.34054751
Rotation angle (degrees) 79.84710044
Shift along axis -0.66238880
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.014
rotated from previous position = 0.0403 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61056528 -0.33194773 -0.71904155 266.05161554
0.79112724 0.29741686 0.53447255 -86.39981112
0.03643813 -0.89518374 0.44420530 279.47442312
Axis -0.72617579 -0.38373633 0.57045170
Axis point 0.00000000 116.70216550 315.50779421
Rotation angle (degrees) 79.85768786
Shift along axis -0.61883651
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 56
shifted from previous position = 0.00922
rotated from previous position = 0.0302 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61096453 -0.33178461 -0.71877766 265.91505542
0.79082389 0.29745317 0.53490111 -86.40973158
0.03633074 -0.89523215 0.44411653 279.51627475
Axis -0.72644097 -0.38355984 0.57023274
Axis point -0.00000000 116.79213793 315.39803173
Rotation angle (degrees) 79.84759520
Shift along axis -0.63895706
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 60
shifted from previous position = 0.0112
rotated from previous position = 0.0392 degrees
atoms outside contour = 1755, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61092141 -0.33119723 -0.71908514 265.86201413
0.79084444 0.29729954 0.53495614 -86.39268360
0.03660768 -0.89550063 0.44355214 279.58799940
Axis -0.72655505 -0.38383015 0.56990540
Axis point 0.00000000 116.72048670 315.29183470
Rotation angle (degrees) 79.86974659
Shift along axis -0.66456157
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0123
rotated from previous position = 0.0779 degrees
atoms outside contour = 1747, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61046660 -0.33218219 -0.71901706 266.11491018
0.79119095 0.29782655 0.53415002 -86.45092816
0.03670725 -0.89496053 0.44463270 279.33262127
Axis -0.72594735 -0.38388637 0.57064148
Axis point 0.00000000 116.64464322 315.61501173
Rotation angle (degrees) 79.83619740
Shift along axis -0.59930216
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 36
shifted from previous position = 0.00553
rotated from previous position = 0.0185 degrees
atoms outside contour = 1746, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61052405 -0.33197184 -0.71906543 266.07628678
0.79114928 0.29764543 0.53431266 -86.42628442
0.03664978 -0.89509882 0.44435898 279.40085187
Axis -0.72607396 -0.38386786 0.57049283
Axis point 0.00000000 116.66062451 315.54721201
Rotation angle (degrees) 79.84776315
Shift along axis -0.61860883
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1019, steps = 48
shifted from previous position = 0.0181
rotated from previous position = 0.0284 degrees
atoms outside contour = 1749, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.61082613 -0.33169276 -0.71893766 265.95113585
0.79091989 0.29755592 0.53470198 -86.43037190
0.03656738 -0.89523203 0.44409733 279.47798684
Axis -0.72633614 -0.38375939 0.57023200
Axis point -0.00000000 116.71858763 315.43181746
Rotation angle (degrees) 79.84919126
Shift along axis -0.63416214
> view matrix models
> #4,0.4439,-0.28201,-0.85054,303.77,0.88884,0.018251,0.45784,-44.907,-0.11359,-0.95924,0.25876,341.18
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 424
shifted from previous position = 2.2
rotated from previous position = 6.39 degrees
atoms outside contour = 1635, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47014986 -0.27680804 -0.83805515 296.29282889
0.88242695 0.12936746 0.45231266 -60.98673857
-0.01678672 -0.95217718 0.30508496 317.15529629
Axis -0.70304515 -0.41110215 0.58027799
Axis point 0.00000000 97.60706796 321.98215187
Rotation angle (degrees) 92.73398070
Shift along axis 0.80277942
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 44
shifted from previous position = 0.0281
rotated from previous position = 0.296 degrees
atoms outside contour = 1634, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47131282 -0.27849458 -0.83684228 296.21168106
0.88186020 0.13410185 0.45203904 -61.71403302
-0.01366832 -0.95102969 0.30879721 315.93242787
Axis -0.70218063 -0.41196614 0.58071186
Axis point 0.00000000 97.40904882 322.29816415
Rotation angle (degrees) 92.45840264
Shift along axis 0.89569574
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0165
rotated from previous position = 0.16 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47202347 -0.27915399 -0.83622180 296.12646474
0.88150690 0.13674791 0.45193539 -62.12511633
-0.01180798 -0.95045940 0.31062439 315.27843547
Axis -0.70176755 -0.41254208 0.58080232
Axis point 0.00000000 97.28028496 322.43137386
Rotation angle (degrees) 92.30976635
Shift along axis 0.93172962
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1055, steps = 40
shifted from previous position = 0.0221
rotated from previous position = 0.193 degrees
atoms outside contour = 1638, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.47308077 -0.28050864 -0.83517034 296.03384583
0.88096007 0.13964438 0.45211592 -62.58112928
-0.01019558 -0.94963907 0.31317998 314.52160203
Axis -0.70135897 -0.41277074 0.58113330
Axis point 0.00000000 97.26838533 322.61659552
Rotation angle (degrees) 92.12314752
Shift along axis 0.98464198
> transparency #1.1 0
> view matrix models
> #4,0.84021,-0.0035817,-0.54224,142.19,-0.39021,0.69038,-0.60919,201.03,0.37654,0.72344,0.57867,-93.731
> view matrix models
> #4,0.79315,-0.11192,-0.59866,177.39,0.50761,-0.42168,0.75135,74.2,-0.33653,-0.89981,-0.27764,436.47
> view matrix models
> #4,0.7358,0.3335,-0.58938,106.02,-0.64815,0.094684,-0.7556,375.07,-0.19619,0.93798,0.28583,9.2542
> view matrix models
> #4,0.79115,-0.59673,-0.13416,211.08,0.60994,0.75351,0.24535,-98.992,-0.045318,-0.27593,0.96011,122.12
> view matrix models
> #4,0.66555,-0.4336,-0.60749,260.88,0.69641,0.65352,0.29652,-103.07,0.26843,-0.62041,0.73691,152.31
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 416
shifted from previous position = 2.7
rotated from previous position = 17.5 degrees
atoms outside contour = 1774, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67732915 -0.28469604 -0.67836083 239.91883502
0.71088577 0.49065254 0.50388643 -103.74543128
0.18938499 -0.82353401 0.53471962 227.48787848
Axis -0.70890735 -0.46341865 0.53168931
Axis point 0.00000000 101.86597662 309.82596584
Rotation angle (degrees) 69.43005060
Shift along axis -1.04978373
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1, steps = 44
shifted from previous position = 0.00594
rotated from previous position = 0.0194 degrees
atoms outside contour = 1776, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67756361 -0.28454385 -0.67819052 239.83133941
0.71064745 0.49081816 0.50406126 -103.75597407
0.18944069 -0.82348792 0.53477088 227.46549023
Axis -0.70904026 -0.46339937 0.53152886
Axis point 0.00000000 101.90886125 309.76335536
Rotation angle (degrees) 69.41623953
Shift along axis -1.06514982
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.09997, steps = 40
shifted from previous position = 0.0133
rotated from previous position = 0.00996 degrees
atoms outside contour = 1778, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.67763562 -0.28462709 -0.67808363 239.81516361
0.71058849 0.49090368 0.50406111 -103.75178064
0.18940430 -0.82340817 0.53490655 227.43306000
Axis -0.70903930 -0.46335011 0.53157309
Axis point 0.00000000 101.93201901 309.76345143
Rotation angle (degrees) 69.40726713
Shift along axis -1.06768104
> view matrix models
> #4,0.67386,0.21665,-0.70638,152.68,-0.73712,0.13162,-0.66282,370.99,-0.050625,0.96733,0.2484,-19.457
> view matrix models
> #4,0.26977,0.74198,-0.61375,121.96,-0.64983,-0.33008,-0.68467,441.19,-0.7106,0.58353,0.39312,157.04
> view matrix models
> #4,0.83537,0.35405,-0.42048,63.612,-0.53507,0.34852,-0.76957,306.25,-0.12592,0.86786,0.48059,-14.673
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 108
shifted from previous position = 1.02
rotated from previous position = 11.1 degrees
atoms outside contour = 1639, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88907475 0.29063713 -0.35366111 56.95234558
-0.45699328 0.51877555 -0.72251581 256.52548266
-0.02651919 0.80399130 0.59404945 -35.16228912
Axis 0.88188843 -0.18899530 -0.43191847
Axis point 0.00000000 161.74872048 251.74241852
Rotation angle (degrees) 59.93713751
Shift along axis 16.93074519
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1062, steps = 44
shifted from previous position = 0.0122
rotated from previous position = 0.077 degrees
atoms outside contour = 1637, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88924092 0.29042756 -0.35341541 56.93133633
-0.45670512 0.51991995 -0.72187513 256.18534624
-0.02590471 0.80332752 0.59497383 -35.27785394
Axis 0.88179482 -0.18935008 -0.43195422
Axis point -0.00000000 161.74523741 251.76190662
Rotation angle (degrees) 59.86313127
Shift along axis 16.93146051
> view matrix models
> #4,0.83879,0.21495,-0.50022,97.467,-0.52296,0.062549,-0.85006,366.96,-0.15144,0.97462,0.16488,7.9202
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1097, steps = 264
shifted from previous position = 0.803
rotated from previous position = 13.4 degrees
atoms outside contour = 1566, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.90125965 0.23249395 -0.36561951 66.81826163
-0.42074684 0.26813163 -0.86664730 312.38684742
-0.10345610 0.93490749 0.33947732 -14.03685609
Axis 0.93143071 -0.13554240 -0.33773523
Axis point 0.00000000 165.03559591 224.93775063
Rotation angle (degrees) 75.25993272
Shift along axis 24.63566001
> view matrix models
> #4,0.85035,0.35218,-0.39099,57.593,-0.48265,0.22596,-0.84616,329.25,-0.20965,0.90825,0.36212,8.0544
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.85035,0.35218,-0.39099,60.231,-0.48265,0.22596,-0.84616,326.26,-0.20965,0.90825,0.36212,12.759
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 168
shifted from previous position = 2.33
rotated from previous position = 5.98 degrees
atoms outside contour = 1596, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88028089 0.25385290 -0.40082949 74.19694561
-0.45618497 0.22068248 -0.86208731 322.45385437
-0.13038732 0.94173137 0.31006645 -3.17418883
Axis 0.92158142 -0.13817047 -0.36276246
Axis point 0.00000000 162.85511452 230.82234394
Rotation angle (degrees) 78.14035717
Shift along axis 24.97640109
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.011
rotated from previous position = 0.0221 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88011312 0.25412437 -0.40102585 74.19170998
-0.45646647 0.22069435 -0.86193525 322.48434036
-0.13053461 0.94165537 0.31023525 -3.15440043
Axis 0.92146618 -0.13819573 -0.36304548
Axis point 0.00000000 162.86097718 230.89097488
Rotation angle (degrees) 78.13997962
Shift along axis 24.94438268
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1101, steps = 64
shifted from previous position = 0.00421
rotated from previous position = 0.0136 degrees
atoms outside contour = 1600, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88018838 0.25419012 -0.40081894 74.13944294
-0.45629950 0.22079847 -0.86199700 322.44263683
-0.13061091 0.94161321 0.31033107 -3.14778151
Axis 0.92150340 -0.13805512 -0.36300449
Axis point 0.00000000 162.82540766 230.87431985
Rotation angle (degrees) 78.13192347
Shift along axis 24.94755119
> view matrix models
> #4,0.88019,0.25419,-0.40082,73.448,-0.4563,0.2208,-0.862,321.07,-0.13061,0.94161,0.31033,-5.8994
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 160
shifted from previous position = 2.99
rotated from previous position = 8.44 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327534 0.17162879 -0.45599755 97.28727310
-0.48720393 0.31672140 -0.81383039 304.58441441
0.00474745 0.93286180 0.36020320 -32.68286674
Axis 0.90839597 -0.23961801 -0.34263678
Axis point 0.00000000 182.33141527 229.00675692
Rotation angle (degrees) 74.03202850
Shift along axis 26.58980844
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 80
shifted from previous position = 0.0187
rotated from previous position = 0.0503 degrees
atoms outside contour = 1606, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307788 0.17102576 -0.45660182 97.51562460
-0.48755025 0.31670719 -0.81362849 304.62173537
0.00545764 0.93297736 0.35989370 -32.78455753
Axis 0.90828067 -0.24028299 -0.34247673
Axis point 0.00000000 182.48861826 229.00019788
Rotation angle (degrees) 74.04755731
Shift along axis 26.60408358
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 64
shifted from previous position = 0.00983
rotated from previous position = 0.00562 degrees
atoms outside contour = 1605, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87308357 0.17093159 -0.45662622 97.52642834
-0.48753906 0.31671935 -0.81363046 304.61327140
0.00554721 0.93299049 0.35985828 -32.79571036
Axis 0.90828615 -0.24034163 -0.34242104
Axis point 0.00000000 182.49871036 228.98437979
Rotation angle (degrees) 74.04808080
Shift along axis 26.60059602
> ui mousemode right "rotate selected models"
> transparency #1.1 50
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.87308,0.17093,-0.45663,98.781,-0.48754,0.31672,-0.81363,307.95,0.0055472,0.93299,0.35986,-31.624
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 152
shifted from previous position = 1.66
rotated from previous position = 10.1 degrees
atoms outside contour = 1670, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85430945 0.22816829 -0.46700601 94.00588935
-0.50530889 0.15416741 -0.84905556 345.08239658
-0.12173045 0.96133847 0.24700214 -1.12292161
Axis 0.91267386 -0.17406375 -0.36976782
Axis point 0.00000000 176.18270876 236.27702715
Rotation angle (degrees) 82.66101368
Shift along axis 26.14560144
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1045, steps = 60
shifted from previous position = 0.00837
rotated from previous position = 0.0183 degrees
atoms outside contour = 1667, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.85416080 0.22824487 -0.46724044 94.04888675
-0.50553655 0.15397090 -0.84895570 345.14108146
-0.12182835 0.96135179 0.24690203 -1.09962552
Axis 0.91260386 -0.17412755 -0.36991051
Axis point 0.00000000 176.20594034 236.31033169
Rotation angle (degrees) 82.67387511
Shift along axis 26.13756946
> view matrix models
> #4,0.85416,0.22824,-0.46724,92.304,-0.50554,0.15397,-0.84896,343.85,-0.12183,0.96135,0.2469,-1.3966
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 132
shifted from previous position = 2.46
rotated from previous position = 10.1 degrees
atoms outside contour = 1603, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87327321 0.17148581 -0.45605541 97.32164807
-0.48720576 0.31684479 -0.81378127 304.55640572
0.00494684 0.93284619 0.36024093 -32.71905415
Axis 0.90838381 -0.23975747 -0.34257148
Axis point 0.00000000 182.35784967 228.99751317
Rotation angle (degrees) 74.02729082
Shift along axis 26.59434986
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0199
rotated from previous position = 0.0492 degrees
atoms outside contour = 1607, contour level = 0.072
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87291436 0.17135958 -0.45678926 97.50396396
-0.48784609 0.31650499 -0.81352984 304.69020219
0.00516995 0.93298473 0.35987885 -32.73221582
Axis 0.90818184 -0.24021727 -0.34278478
Axis point 0.00000000 182.47945606 229.06508608
Rotation angle (degrees) 74.05889597
Shift along axis 26.57958591
> volume #1 step 1
> volume #1 level 0.08
> volume #2 step 1
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 96
shifted from previous position = 0.0269
rotated from previous position = 0.0588 degrees
atoms outside contour = 1705, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87339018 0.17133657 -0.45588748 97.30726750
-0.48699588 0.31678456 -0.81393032 304.55388891
0.00496208 0.93289407 0.36011672 -32.71648369
Axis 0.90847710 -0.23967565 -0.34238127
Axis point 0.00000000 182.34480224 228.95151912
Rotation angle (degrees) 74.02930115
Shift along axis 26.60878416
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 60
shifted from previous position = 0.0234
rotated from previous position = 0.0504 degrees
atoms outside contour = 1711, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87307658 0.17097372 -0.45662380 97.51998587
-0.48755237 0.31664803 -0.81365025 304.63116274
0.00547621 0.93300698 0.35981662 -32.78056504
Axis 0.90828882 -0.24029916 -0.34244377
Axis point 0.00000000 182.49216804 228.98849803
Rotation angle (degrees) 74.05165523
Shift along axis 26.59919907
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 84
shifted from previous position = 0.0236
rotated from previous position = 0.0512 degrees
atoms outside contour = 1709, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87330072 0.17150987 -0.45599367 97.31366850
-0.48715626 0.31696366 -0.81376461 304.52650710
0.00496476 0.93280138 0.36035670 -32.73218629
Axis 0.90838730 -0.23974404 -0.34257162
Axis point 0.00000000 182.35082823 229.00016180
Rotation angle (degrees) 74.01947881
Shift along axis 26.60320358
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0146 degrees
atoms outside contour = 3383, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06781116 0.24433459 0.96731706 -24.10970616
-0.87336663 0.45417416 -0.17594486 287.52120019
-0.48231982 -0.85675345 0.18259559 387.95373087
Axis -0.34859656 0.74226213 -0.57230007
Axis point 265.34079550 0.00000000 317.90521257
Rotation angle (degrees) 102.44607735
Shift along axis -0.20528738
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.09224, steps = 40
shifted from previous position = 0.00617
rotated from previous position = 0.0174 degrees
atoms outside contour = 3388, contour level = 0.08
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.06800223 0.24456045 0.96724657 -24.09574276
-0.87334229 0.45411451 -0.17621946 287.57652794
-0.48233700 -0.85672063 0.18270418 387.93151574
Axis -0.34844475 0.74224675 -0.57241245
Axis point 265.30857487 0.00000000 317.93174566
Rotation angle (degrees) 102.45024724
Shift along axis -0.20805003
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.8783,0.21948,-0.42476,83.959,-0.47606,0.31931,-0.81939,302.68,-0.044211,0.92188,0.38494,-24.427
> view matrix models
> #4,0.88185,0.18737,-0.43271,90.075,-0.47057,0.40846,-0.78213,281.03,0.030198,0.89334,0.44837,-40.684
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 108
shifted from previous position = 0.192
rotated from previous position = 5.8 degrees
atoms outside contour = 1706, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87316782 0.17153805 -0.45623751 97.35347505
-0.48739404 0.31688450 -0.81365305 304.56284709
0.00500214 0.93282310 0.36029997 -32.73417130
Axis 0.90830421 -0.23988070 -0.34269623
Axis point 0.00000000 182.38522859 229.02890887
Rotation angle (degrees) 74.02748836
Shift along axis 26.58569939
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 100
shifted from previous position = 0.0157
rotated from previous position = 0.0308 degrees
atoms outside contour = 1714, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87319228 0.17106442 -0.45636852 97.46138911
-0.48734683 0.31669009 -0.81375701 304.60534678
0.00532251 0.93297608 0.35989904 -32.76360108
Axis 0.90836070 -0.24009506 -0.34239627
Axis point 0.00000000 182.44525999 228.97324319
Rotation angle (degrees) 74.04449916
Shift along axis 26.61399150
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1115, steps = 76
shifted from previous position = 0.0215
rotated from previous position = 0.0496 degrees
atoms outside contour = 1707, contour level = 0.08
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.87344661 0.17154945 -0.45569927 97.23463453
-0.48689717 0.31676739 -0.81399606 304.54231699
0.00471009 0.93286078 0.36020634 -32.68225206
Axis 0.90851141 -0.23945131 -0.34244721
Axis point 0.00000000 182.29150588 228.95203805
Rotation angle (degrees) 74.02546087
Shift along axis 26.60766517
> close #5
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb"
Chain information for F562b.pdb #5
---
Chain | Description
B | No description available
C | No description available
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,0.88246,-0.46571,0.066244,91.139,0.4452,0.87234,0.20206,-101.84,-0.15189,-0.14881,0.97713,59.494
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.88246,-0.46571,0.066244,31.321,0.4452,0.87234,0.20206,-110.9,-0.15189,-0.14881,0.97713,2.868
> view matrix models
> #5,0.88246,-0.46571,0.066244,29.937,0.4452,0.87234,0.20206,-111.7,-0.15189,-0.14881,0.97713,-4.3706
> view matrix models
> #5,0.91945,-0.24365,-0.30863,71.496,-0.34812,-0.86933,-0.35081,481.22,-0.18283,0.42999,-0.88413,336.53
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1014, steps = 252
shifted from previous position = 4.97
rotated from previous position = 12.4 degrees
atoms outside contour = 1810, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.96186420 -0.19777272 -0.18895294 31.32789418
-0.26901427 -0.80896731 -0.52268846 497.86596548
-0.04948323 0.55358635 -0.83132038 280.55853441
Axis 0.98957826 -0.12823509 -0.06550286
Axis point 0.00000000 209.55045747 214.71270936
Rotation angle (degrees) 147.05697484
Shift along axis -51.21986933
> view matrix models
> #5,0.96186,-0.19777,-0.18895,31.586,-0.26901,-0.80897,-0.52269,497.84,-0.049483,0.55359,-0.83132,280.45
> view matrix models
> #5,0.96186,-0.19777,-0.18895,30.409,-0.26901,-0.80897,-0.52269,498.49,-0.049483,0.55359,-0.83132,281.14
> view matrix models
> #5,0.88111,-0.30725,-0.35949,105.37,-0.46365,-0.71093,-0.52878,515.6,-0.093104,0.63259,-0.76887,259.2
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 3.4
rotated from previous position = 5.08 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88807867 -0.23238898 -0.39662534 101.69393944
-0.43540490 -0.70196949 -0.56361460 519.59851714
-0.14744106 0.67322671 -0.72458742 250.51818794
Axis 0.96785351 -0.19499177 -0.15886409
Axis point 0.00000000 224.56879044 228.99496698
Rotation angle (degrees) 140.28561169
Shift along axis -42.69094177
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0247
rotated from previous position = 0.0823 degrees
atoms outside contour = 1771, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88749875 -0.23316934 -0.39746451 102.13143422
-0.43663025 -0.70123937 -0.56357554 519.69347155
-0.14730923 0.67371761 -0.72415784 250.30786189
Axis 0.96767878 -0.19564479 -0.15912543
Axis point 0.00000000 224.69705024 229.03906748
Rotation angle (degrees) 140.25962425
Shift along axis -42.67524524
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0089
rotated from previous position = 0.0313 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88726809 -0.23348649 -0.39779316 102.30830437
-0.43710961 -0.70099140 -0.56351243 519.72597500
-0.14727705 0.67386581 -0.72402648 250.24321586
Axis 0.96761002 -0.19589960 -0.15923003
Axis point 0.00000000 224.74651301 229.05595353
Rotation angle (degrees) 140.25296234
Shift along axis -42.66580653
> view matrix models
> #5,0.90434,-0.19289,-0.38074,87.744,-0.3816,-0.76498,-0.51883,511.31,-0.19118,0.61449,-0.76541,278.75
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 100
shifted from previous position = 0.228
rotated from previous position = 5.49 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88741151 -0.23323538 -0.39762052 102.19303295
-0.43675670 -0.70132020 -0.56337694 519.68635289
-0.14745987 0.67361061 -0.72422672 250.37123988
Axis 0.96765550 -0.19569262 -0.15920817
Axis point 0.00000000 224.70331960 229.05340664
Rotation angle (degrees) 140.27024302
Shift along axis -42.67227987
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 80
shifted from previous position = 0.0119
rotated from previous position = 0.0244 degrees
atoms outside contour = 1769, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88757691 -0.23309386 -0.39733424 102.06718757
-0.43649500 -0.70124393 -0.56367462 519.68560309
-0.14723913 0.67373898 -0.72415222 250.29116827
Axis 0.96770087 -0.19558315 -0.15906683
Axis point 0.00000000 224.68268474 229.02792313
Rotation angle (degrees) 140.25607412
Shift along axis -42.68426633
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 64
shifted from previous position = 0.0443
rotated from previous position = 0.146 degrees
atoms outside contour = 1761, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88644690 -0.23468134 -0.39891925 102.92117215
-0.43878232 -0.70033958 -0.56302270 519.80857088
-0.14724801 0.67412844 -0.72378787 250.13865633
Axis 0.96736944 -0.19679007 -0.15959331
Axis point 0.00000000 224.90663730 229.11626097
Rotation angle (degrees) 140.24985998
Shift along axis -42.65082531
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.0509 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88682818 -0.23410569 -0.39840974 102.63155782
-0.43798841 -0.70069517 -0.56319841 519.75407402
-0.14731582 0.67395906 -0.72393179 250.21245718
Axis 0.96748195 -0.19636048 -0.15944037
Axis point 0.00000000 224.82302925 229.08819200
Rotation angle (degrees) 140.25515764
Shift along axis -42.65894548
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Average map value = 0.1109 for 3401 atoms, 1770 outside contour
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 40
shifted from previous position = 0.0277
rotated from previous position = 0.119 degrees
atoms outside contour = 1770, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88773516 -0.23286893 -0.39711253 101.94821925
-0.43614356 -0.70150514 -0.56362163 519.65415902
-0.14732651 0.67354481 -0.72431506 250.37946507
Axis 0.96774956 -0.19539029 -0.15900765
Axis point 0.00000000 224.64447067 229.01845950
Rotation angle (degrees) 140.26798555
Shift along axis -42.68728231
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1109, steps = 36
shifted from previous position = 0.0101
rotated from previous position = 0.0384 degrees
atoms outside contour = 1772, contour level = 0.08
Position of F562b.pdb (#5) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.88743039 -0.23323831 -0.39757668 102.17484111
-0.43673470 -0.70130263 -0.56341586 519.68061974
-0.14741140 0.67362788 -0.72422052 250.35767544
Axis 0.96766061 -0.19568838 -0.15918228
Axis point 0.00000000 224.69868010 229.04697101
Rotation angle (degrees) 140.26833165
Shift along axis -42.67739283
> ~select #5
Nothing selected
> show #!2 models
> select #2
2 models selected
> view matrix models
> #2,0.19536,0.75362,0.62761,-85.152,-0.79186,-0.25635,0.5543,213.6,0.57862,-0.60527,0.54668,70.661
> view matrix models
> #2,0.11282,0.94881,0.29501,-45.954,-0.85716,-0.057225,0.51186,202.13,0.50254,-0.31062,0.80683,-2.2981
> view matrix models
> #2,0.11282,0.94881,0.29501,-10.942,-0.85716,-0.057225,0.51186,230.24,0.50254,-0.31062,0.80683,26.411
> view matrix models
> #2,-0.3673,0.80202,0.47101,56.376,-0.91933,-0.38991,-0.052965,380.04,0.14117,-0.45246,0.88054,91.186
> view matrix models
> #2,-0.37949,0.87152,0.31056,74.515,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,198.78
> view matrix models
> #2,-0.37949,0.87152,0.31056,77.692,-0.81999,-0.16136,-0.54916,412.77,-0.42849,-0.46305,0.77587,195.9
> view matrix models
> #2,-0.4416,0.17153,0.88066,94.799,-0.84825,0.23999,-0.47209,346.93,-0.29232,-0.9555,0.039518,365.71
> view matrix models
> #2,-0.16701,0.27438,0.94701,26.293,-0.9691,-0.22254,-0.10643,372.5,0.18155,-0.93552,0.30307,245.76
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 816, shift = 17.1, angle = 92.5 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884246 0.36253629 0.90084502 32.04958536
-0.12095024 0.90936326 -0.39803210 133.21868643
-0.96349643 -0.20402438 -0.17334571 390.21884814
Axis 0.10022302 0.96310562 -0.24976572
Axis point 169.19260085 0.00000000 200.88498104
Rotation angle (degrees) 104.56110947
Shift along axis 34.05247827
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 0.000646, angle = 0.0027 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884389 0.36253338 0.90084582 32.04982504
-0.12099611 0.90935469 -0.39803771 133.22769414
-0.96349031 -0.20406771 -0.17332869 390.22127920
Axis 0.10020344 0.96310196 -0.24978768
Axis point 169.19590472 0.00000000 200.88843406
Rotation angle (degrees) 104.56090162
Shift along axis 34.05088824
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3616, correlation about mean = 0.238, overlap = 5797
steps = 40, shift = 2.75e-05, angle = 5.91e-05 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23884450 0.36253261 0.90084597 32.05002579
-0.12099600 0.90935500 -0.39803705 133.22750949
-0.96349017 -0.20406771 -0.17332945 390.22138385
Axis 0.10020311 0.96310210 -0.24978726
Axis point 169.19595961 -0.00000000 200.88835343
Rotation angle (degrees) 104.56093288
Shift along axis 34.05087684
> hide #!1 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24143,0.39089,0.88821,30.445,-0.11992,0.89625,-0.42703,139.68,-0.96298,-0.20961,-0.16951,390.31
> view matrix models
> #2,-0.24371,0.41583,0.87618,29.184,-0.11889,0.8838,-0.45252,145.47,-0.96253,-0.21445,-0.16596,390.36
> view matrix models
> #2,-0.23248,0.44368,0.86551,25.173,-0.098419,0.87459,-0.47477,147.23,-0.96761,-0.19556,-0.15966,387.41
> view matrix models
> #2,-0.015904,0.29362,0.95579,-1.8481,0.11672,0.94992,-0.28987,72.596,-0.99304,0.10695,-0.049378,329.9
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 434908 points
correlation = 0.3636, correlation about mean = 0.2345, overlap = 5800
steps = 160, shift = 4.43, angle = 14.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.23589350 0.38613188 0.89177153 30.30521757
0.14116968 0.92155092 -0.36168365 84.35973344
-0.96147045 0.04057228 -0.27189798 372.10342069
Axis 0.21036827 0.96919218 -0.12810818
Axis point 149.90554609 -0.00000000 183.31483684
Rotation angle (degrees) 107.04485499
Shift along axis 40.46655914
> transparency sel 50
> view matrix models
> #2,-0.32117,0.35848,0.87655,50.083,0.35637,0.9033,-0.23885,33.297,-0.87741,0.23567,-0.41786,354.8
> view matrix models
> #2,-0.25849,0.33315,0.90675,38.999,0.20781,0.93585,-0.2846,59.301,-0.9434,0.11486,-0.31114,365.02
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> show #3 models
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C E | No description available
D | No description available
F | No description available
> close #6
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1.pdb" models #3
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb" models #4
> relModel #1
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/F562b.pdb" models #5
> relModel #1
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
B | No description available
C | No description available
> close #6
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/D2NS1-F562.pdb"
Chain information for D2NS1-F562.pdb #6
---
Chain | Description
A B | No description available
C E | No description available
D F | No description available
> hide atoms
> show cartoons
> hide #3 models
> hide #5 models
> hide #4 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.0103
rotated from previous position = 0.00699 degrees
atoms outside contour = 6863, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00007640 -0.00005950 0.01644925
0.00007639 0.99999999 -0.00007418 0.00540007
0.00005950 0.00007417 1.00000000 -0.02042262
Axis 0.60809281 -0.48779755 0.62631995
Axis point -36.04322257 258.47150214 0.00000000
Rotation angle (degrees) 0.00698874
Shift along axis -0.00542257
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 12404 atoms
average map value = 0.1322, steps = 204
shifted from previous position = 3.17
rotated from previous position = 16.9 degrees
atoms outside contour = 7037, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.15126719 0.47107682 -0.86902521 263.21094843
0.40313494 0.83210747 0.38089281 -155.24920226
0.90255217 -0.29271785 -0.31577809 100.07490639
Axis -0.35517923 -0.93411153 -0.03582417
Axis point 121.90346818 0.00000000 160.98219047
Rotation angle (degrees) 108.50992410
Shift along axis 47.94790735
> show #3 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> hide #3 models
> ui mousemode right "map eraser"
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J59_004_volume_map_sharp
> (3).mrc"
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc as #8, grid size
352,352,352, pixel 0.85, shown at level 0.366, step 2, values float32
> close #7
> hide #!2 models
> surface dust #8 size 8.5
> select #8
2 models selected
> close #7
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,35.396,0,1,0,60.903,0,0,1,32.921
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.3457,-0.50036,0.79381,208.17,-0.017535,0.84927,0.52767,14.154,-0.93818,0.1685,-0.30237,329.15
> view matrix models
> #8,-0.51948,-0.14515,0.84206,178.05,0.63577,0.59277,0.49439,-45.989,-0.57091,0.79219,-0.21565,171.93
> view matrix models
> #8,-0.55842,-0.30769,0.77039,216.83,0.59819,0.49406,0.63093,-44.478,-0.57475,0.81316,-0.09184,152.9
> view matrix models
> #8,-0.55842,-0.30769,0.77039,191.12,0.59819,0.49406,0.63093,-46.563,-0.57475,0.81316,-0.09184,158.22
> show #6 models
> ~select #8
Nothing selected
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 168
shifted from previous position = 1.67
rotated from previous position = 11.8 degrees
atoms outside contour = 6854, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00007634 0.00003096 356.91445101
-0.00007636 -0.99999975 -0.00069729 357.06728170
0.00003091 -0.00069729 0.99999976 0.11956672
Axis -0.00001547 0.00034864 -0.99999994
Axis point 178.46403997 178.52684922 0.00000000
Rotation angle (degrees) 179.99562555
Shift along axis -0.00059852
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 40
shifted from previous position = 0.00373
rotated from previous position = 0.0435 degrees
atoms outside contour = 6861, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 0.00004453 0.00006393 356.91507698
-0.00004452 -1.00000000 0.00006135 356.92005524
0.00006393 0.00006135 1.00000000 -0.02104448
Axis -0.00003196 -0.00003068 -1.00000000
Axis point 178.46151168 178.45605515 0.00000000
Rotation angle (degrees) 179.99744898
Shift along axis -0.00131278
> select #8
2 models selected
> view matrix models
> #8,-0.55842,-0.30769,0.77039,144.53,0.59819,0.49406,0.63093,-60.652,-0.57475,0.81316,-0.09184,256.77
> view matrix models
> #8,-0.55842,-0.30769,0.77039,188.5,0.59819,0.49406,0.63093,-43.585,-0.57475,0.81316,-0.09184,207.1
> view matrix models
> #8,0.20416,-0.32979,0.92171,53.292,0.8306,0.55667,0.015197,-5.7187,-0.5181,0.76247,0.38758,141.12
> view matrix models
> #8,-0.17775,-0.55408,0.81327,158.88,0.42359,0.70287,0.57144,-38.275,-0.88824,0.44606,0.10977,280.75
> view matrix models
> #8,-0.44365,-0.53212,0.72113,209.28,0.54415,0.47941,0.68853,-40.877,-0.71209,0.69787,0.076868,222.08
> view matrix models
> #8,-0.44365,-0.53212,0.72113,201.21,0.54415,0.47941,0.68853,-58.258,-0.71209,0.69787,0.076868,191.6
> view matrix models
> #8,-0.44365,-0.53212,0.72113,198.44,0.54415,0.47941,0.68853,-54.781,-0.71209,0.69787,0.076868,186.46
> view matrix models
> #8,-0.078986,-0.30105,0.95033,78.334,0.99624,-0.057911,0.064456,35.555,0.03563,0.95185,0.30449,4.0251
> view matrix models
> #8,-0.078986,-0.30105,0.95033,83.821,0.99624,-0.057911,0.064456,34.166,0.03563,0.95185,0.30449,22.679
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.12,0.9291,0.27408,0.24829,-27.377,-0.34419,0.88644,0.30946,90.098
> view matrix models
> #8,-0.13528,-0.37298,0.91792,107.41,0.9291,0.27408,0.24829,-25.4,-0.34419,0.88644,0.30946,74.434
> view matrix models
> #8,0.021026,-0.64563,0.76336,142.78,0.95068,0.24925,0.18463,-16.653,-0.30947,0.72183,0.61903,50.881
> view matrix models
> #8,0.18242,-0.5728,0.79914,102.63,0.95907,0.28269,-0.016302,4.2907,-0.21658,0.76941,0.60092,32.168
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.51,0.95907,0.28269,-0.016302,-14.792,-0.21658,0.76941,0.60092,29.021
> view matrix models
> #8,0.18242,-0.5728,0.79914,103.75,0.95907,0.28269,-0.016302,-13.773,-0.21658,0.76941,0.60092,25.236
> view matrix models
> #8,0.19689,-0.59123,0.7821,106.42,0.95308,0.30251,-0.011255,-16.342,-0.22993,0.74762,0.62305,27.429
> view matrix models
> #8,0.16349,-0.53138,0.83121,96.478,0.91695,0.39269,0.070685,-34.591,-0.36397,0.75062,0.55145,57.366
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2099, correlation about mean = -0.0466, overlap = 1148
steps = 220, shift = 8.88, angle = 20.7 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.16970377 -0.22411591 0.95967322 38.04053966
0.82808228 0.56039048 -0.01556391 -26.95927500
-0.53430362 0.79732965 0.28068680 115.40605181
Axis 0.40645268 0.74699927 0.52610674
Axis point 84.17805896 0.00000000 56.92499809
Rotation angle (degrees) 89.69114416
Shift along axis 56.03902271
> hide #!8 models
> hide #7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> view matrix models
> #8,0.17985,-0.20944,0.96114,34.185,0.82577,0.56311,-0.031812,-24.805,-0.53457,0.7994,0.27422,116.02
> view matrix models
> #8,-0.19365,-0.33381,0.92253,114.87,-0.70512,-0.60645,-0.36745,423.6,0.68213,-0.72166,-0.11794,196.81
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 196, shift = 4.16, angle = 13 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07683115 -0.17561277 0.98145662 66.44166832
-0.66408769 -0.72522667 -0.18175198 411.16957530
0.74369650 -0.66573749 -0.06090228 170.05104945
Axis -0.66519466 0.32677996 -0.67136497
Axis point 7.75299271 239.88960504 0.00000000
Rotation angle (degrees) 158.66671698
Shift along axis -24.00098327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00106, angle = 0.00247 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07685176 -0.17562808 0.98145227 66.44848746
-0.66411122 -0.72519937 -0.18177500 411.17240045
0.74367337 -0.66576320 -0.06090373 170.05786271
Axis -0.66518608 0.32679973 -0.67136385
Axis point 7.75566835 239.89404572 0.00000000
Rotation angle (degrees) 158.66630362
Shift along axis -24.00027887
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 44, shift = 0.00214, angle = 0.00428 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680221 -0.17565442 0.98145143 66.44396733
-0.66407552 -0.72523465 -0.18176462 411.17025225
0.74371036 -0.66571781 -0.06094818 170.05404481
Axis -0.66520863 0.32678246 -0.67134991
Axis point 7.74491366 239.89221167 -0.00000000
Rotation angle (degrees) 158.66868085
Shift along axis -24.00164195
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select up
24808 atoms, 25460 bonds, 3176 residues, 11 models selected
> select down
2 models selected
> volume flip #8
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip as #9, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> hide #!9 models
> show #!9 models
> select #9
2 models selected
> view matrix models
> #9,0.04932,0.5784,-0.81426,225.85,0.77832,-0.53317,-0.33159,193.54,-0.62593,-0.6174,-0.47647,432.54
> view matrix models
> #9,0.49864,0.44515,-0.74377,167.72,0.18866,-0.89322,-0.40812,346.38,-0.84603,0.063187,-0.52938,372.95
> view matrix models
> #9,0.41566,0.19473,-0.88843,240.37,-0.83603,-0.30285,-0.45753,418.6,-0.35815,0.93293,0.036921,80.781
> view matrix models
> #9,0.18699,-0.28999,-0.93858,354,0.30934,-0.88945,0.33644,207.89,-0.93239,-0.35325,-0.076615,374.31
> view matrix models
> #9,0.12166,-0.27135,-0.95476,363.51,0.35041,-0.88823,0.29709,207.97,-0.92866,-0.37071,-0.01298,366.08
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.12166,-0.27135,-0.95476,343.55,0.35041,-0.88823,0.29709,204.63,-0.92866,-0.37071,-0.01298,384.14
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03988, overlap = 1580
steps = 48, shift = 0.0161, angle = 0.00778 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07667600 -0.17562499 0.98146657 66.40220937
-0.66405605 -0.72527845 -0.18166098 411.15872420
0.74374077 -0.66567786 -0.06101339 170.05477366
Axis -0.66525588 0.32674168 -0.67132294
Axis point 7.71835621 239.88762888 0.00000000
Rotation angle (degrees) 158.66732589
Shift along axis -23.99344049
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 84, shift = 0.0157, angle = 0.009 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07682622 -0.17562423 0.98145496 66.44206918
-0.66408132 -0.72523107 -0.18175771 411.17012882
0.74370270 -0.66572968 -0.06091201 170.05004664
Axis -0.66519758 0.32677973 -0.67136219
Axis point 7.75121505 239.88987802 0.00000000
Rotation angle (degrees) 158.66744100
Shift along axis -24.00021217
> view matrix models
> #9,0.12166,-0.27135,-0.95476,338.02,0.35041,-0.88823,0.29709,203.08,-0.92866,-0.37071,-0.01298,379.52
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.30016,-0.86169,-0.40914,310.95,-0.62921,-0.50123,0.59402,242.86,-0.71693,0.079138,-0.69264,391.26
> view matrix models
> #9,0.079463,-0.47579,-0.87596,361.79,-0.033015,-0.87952,0.47472,229.87,-0.99629,-0.0088031,-0.085597,347.7
> view matrix models
> #9,0.41919,-0.72698,-0.54387,295.14,-0.54116,-0.68106,0.49326,272.69,-0.729,0.087548,-0.6789,389.59
> view matrix models
> #9,-0.24911,-0.67335,-0.6961,410.62,-0.72999,-0.34178,0.59185,234.54,-0.63644,0.65558,-0.4064,247.91
> view matrix models
> #9,0.38176,-0.48586,-0.78626,304.1,-0.52937,-0.81227,0.24491,330.41,-0.75764,0.32273,-0.56729,341.04
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.000846, angle = 0.00177 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07680654 -0.17560484 0.98145997 66.43537485
-0.66409320 -0.72522729 -0.18172939 411.16781129
0.74369413 -0.66573891 -0.06091578 170.05270073
Axis -0.66520310 0.32677576 -0.67135865
Axis point 7.74972828 239.88942606 0.00000000
Rotation angle (degrees) 158.66589087
Shift along axis -23.99969612
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 54470 points
correlation = 0.2626, correlation about mean = -0.03989, overlap = 1580
steps = 40, shift = 0.00125, angle = 0.00125 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.07681767 -0.17562278 0.98145589 66.43984164
-0.66408848 -0.72522635 -0.18175040 411.16938528
0.74369719 -0.66573520 -0.06091887 170.05309874
Axis -0.66520021 0.32678120 -0.67135886
Axis point 7.74944501 239.89073787 0.00000000
Rotation angle (degrees) 158.66693629
Shift along axis -24.00002709
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 435032 points
correlation = 0.2522, correlation about mean = -0.0372, overlap = 1.179e+04
steps = 324, shift = 5.58, angle = 29.2 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc z flip (#9)
relative to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.07209466 -0.25700523 -0.96371709 344.01508219
-0.25749943 -0.93827144 0.23095609 315.15876008
-0.96358516 0.23150590 -0.13382306 321.33072132
Axis 0.73215596 -0.17567940 -0.65809148
Axis point 0.00000000 198.81231893 315.31278484
Rotation angle (degrees) 179.97848683
Shift along axis -14.95921604
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!8 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!2 models
> ~select #9
Nothing selected
> show #7 models
> hide #6 models
> hide #!1 models
> select #7
1 model selected
> view matrix models
> #7,0.28314,0.80804,0.51663,178.11,-0.89657,0.0317,0.44178,178.55,0.34059,-0.58828,0.73343,173.27
> view matrix models
> #7,-0.85167,0.44193,-0.28171,178.2,0.13709,-0.33096,-0.93363,178.47,-0.50584,-0.83376,0.22128,173.34
> view matrix models
> #7,-0.052894,0.17656,-0.98287,178.14,0.95344,0.30156,0.0028629,178.4,0.2969,-0.93695,-0.18429,173.28
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.052894,0.17656,-0.98287,123.75,0.95344,0.30156,0.0028629,168.98,0.2969,-0.93695,-0.18429,135.65
> view matrix models
> #7,-0.052894,0.17656,-0.98287,171.65,0.95344,0.30156,0.0028629,239.46,0.2969,-0.93695,-0.18429,240.81
> view matrix models
> #7,-0.052894,0.17656,-0.98287,168.29,0.95344,0.30156,0.0028629,214.9,0.2969,-0.93695,-0.18429,234.8
> transparency #2.1 0
> volume erase #2 center 168.29,214.9,234.8 radius 57.895
Opened cryosparc_P47_J20_004_volume_map_sharp.mrc copy as #10, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.31,0.95344,0.30156,0.0028629,232.11,0.2969,-0.93695,-0.18429,231.78
> volume erase #10 center 158.31,232.11,231.78 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,179.95,0.95344,0.30156,0.0028629,219.57,0.2969,-0.93695,-0.18429,237.28
> view matrix models
> #7,-0.052894,0.17656,-0.98287,196.31,0.95344,0.30156,0.0028629,220.25,0.2969,-0.93695,-0.18429,246.32
> volume erase #10 center 196.31,220.25,246.32 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,185.48,0.95344,0.30156,0.0028629,234.46,0.2969,-0.93695,-0.18429,244.14
> view matrix models
> #7,-0.052894,0.17656,-0.98287,151.71,0.95344,0.30156,0.0028629,160.15,0.2969,-0.93695,-0.18429,262.05
> view matrix models
> #7,-0.052894,0.17656,-0.98287,147.93,0.95344,0.30156,0.0028629,158.34,0.2969,-0.93695,-0.18429,267.59
> view matrix models
> #7,-0.052894,0.17656,-0.98287,139.18,0.95344,0.30156,0.0028629,153.5,0.2969,-0.93695,-0.18429,267
> volume erase #10 center 139.18,153.5,267 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,140,0.95344,0.30156,0.0028629,152.53,0.2969,-0.93695,-0.18429,263.01
> view matrix models
> #7,-0.052894,0.17656,-0.98287,156.67,0.95344,0.30156,0.0028629,178.21,0.2969,-0.93695,-0.18429,266.42
> volume erase #10 center 156.67,178.21,266.42 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,158.47,0.95344,0.30156,0.0028629,179.86,0.2969,-0.93695,-0.18429,260.63
> view matrix models
> #7,-0.052894,0.17656,-0.98287,146.27,0.95344,0.30156,0.0028629,179.75,0.2969,-0.93695,-0.18429,264.96
> view matrix models
> #7,-0.052894,0.17656,-0.98287,136.73,0.95344,0.30156,0.0028629,165.7,0.2969,-0.93695,-0.18429,256.45
> volume erase #10 center 136.73,165.7,256.45 radius 57.895
> view matrix models
> #7,-0.052894,0.17656,-0.98287,170.65,0.95344,0.30156,0.0028629,257.57,0.2969,-0.93695,-0.18429,281.54
> view matrix models
> #7,-0.052894,0.17656,-0.98287,198.12,0.95344,0.30156,0.0028629,237.97,0.2969,-0.93695,-0.18429,234.34
> volume erase #10 center 198.12,237.97,234.34 radius 57.895
> close #7
> show #!1 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1732, overlap = 5606
steps = 100, shift = 2.13, angle = 5.64 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26232817 0.42310640 0.86727444 32.84932501
0.23389320 0.89982892 -0.36824168 75.35914970
-0.93620401 0.10624943 -0.33501218 371.04180450
Axis 0.25313923 0.96214902 -0.10094453
Axis point 142.07695422 0.00000000 181.57625532
Rotation angle (degrees) 110.41122784
Shift along axis 43.36754334
> select #10
2 models selected
> view matrix models
> #10,-0.26233,0.42311,0.86727,32.251,0.23389,0.89983,-0.36824,72.484,-0.9362,0.10625,-0.33501,370.49
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.13878,0.40417,0.9041,8.8226,0.22067,0.9026,-0.36963,74.459,-0.96543,0.14821,-0.21445,349.11
> view matrix models
> #10,0.081829,0.24713,0.96552,-14.455,0.27881,0.92441,-0.26024,43.68,-0.95685,0.29049,0.0067426,290.35
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 252601 points
correlation = 0.4197, correlation about mean = 0.1733, overlap = 5606
steps = 228, shift = 2.88, angle = 23.2 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.26246485 0.42303734 0.86726677 32.87464761
0.23392580 0.89986112 -0.36814227 75.32527217
-0.93615756 0.10625167 -0.33514125 371.06459232
Axis 0.25309913 0.96216476 -0.10089498
Axis point 142.08264269 0.00000000 181.57434136
Rotation angle (degrees) 110.41836671
Shift along axis 43.35731307
> show #6 models
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> hide #!10 models
> show #!8 models
> hide #!1 models
> ~select #10
Nothing selected
> hide #6 models
> select #7
1 model selected
> view matrix models
> #7,0.92464,0.25458,-0.28325,178.06,0.04684,0.66208,0.74796,178.47,0.37795,-0.70486,0.60026,173.27
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.92464,0.25458,-0.28325,204.47,0.04684,0.66208,0.74796,168.78,0.37795,-0.70486,0.60026,117.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,205.35,0.04684,0.66208,0.74796,172.6,0.37795,-0.70486,0.60026,132.71
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.38,0.04684,0.66208,0.74796,170.72,0.37795,-0.70486,0.60026,135.25
> view matrix models
> #7,0.92464,0.25458,-0.28325,208.14,0.04684,0.66208,0.74796,169.1,0.37795,-0.70486,0.60026,122.9
> volume #8 level 0.8304
> view matrix models
> #7,0.92464,0.25458,-0.28325,209.46,0.04684,0.66208,0.74796,167.64,0.37795,-0.70486,0.60026,121.48
> volume erase #8 center 209.46,167.64,121.48 radius 64.178
Opened cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy as #11, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> view matrix models
> #7,0.92464,0.25458,-0.28325,202.68,0.04684,0.66208,0.74796,128.68,0.37795,-0.70486,0.60026,117.72
> volume erase #11 center 202.68,128.68,117.72 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,183.78,0.04684,0.66208,0.74796,136.58,0.37795,-0.70486,0.60026,112.38
> volume erase #11 center 183.78,136.58,112.38 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,262.78,0.04684,0.66208,0.74796,132.37,0.37795,-0.70486,0.60026,184.94
> view matrix models
> #7,0.92464,0.25458,-0.28325,269.47,0.04684,0.66208,0.74796,136.95,0.37795,-0.70486,0.60026,179.85
> view matrix models
> #7,0.92464,0.25458,-0.28325,267.59,0.04684,0.66208,0.74796,127.26,0.37795,-0.70486,0.60026,154.16
> view matrix models
> #7,0.92464,0.25458,-0.28325,261.44,0.04684,0.66208,0.74796,136.21,0.37795,-0.70486,0.60026,158.39
> volume erase #11 center 261.44,136.21,158.39 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,234.76,0.04684,0.66208,0.74796,204.63,0.37795,-0.70486,0.60026,115.7
> view matrix models
> #7,0.92464,0.25458,-0.28325,232.48,0.04684,0.66208,0.74796,207.24,0.37795,-0.70486,0.60026,119.09
> volume erase #11 center 232.48,207.24,119.09 radius 64.178
> view matrix models
> #7,0.92464,0.25458,-0.28325,211.86,0.04684,0.66208,0.74796,185.05,0.37795,-0.70486,0.60026,105.87
> view matrix models
> #7,0.92464,0.25458,-0.28325,195.04,0.04684,0.66208,0.74796,187.39,0.37795,-0.70486,0.60026,114.92
> view matrix models
> #7,0.92464,0.25458,-0.28325,201.04,0.04684,0.66208,0.74796,190.35,0.37795,-0.70486,0.60026,113.3
> volume erase #11 center 201.04,190.35,113.3 radius 64.178
> show #!1 models
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3648, correlation about mean = -0.1049, overlap = 2621
steps = 72, shift = 2.57, angle = 2.92 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05111081 -0.21510165 0.97525327 67.52834138
-0.64952035 -0.73462917 -0.19606954 411.11615250
0.75862440 -0.64346813 -0.10216541 168.35220279
Axis -0.67771084 0.32814528 -0.65804915
Axis point 0.00000000 241.21252430 -1.00026216
Rotation angle (degrees) 160.72632370
Shift along axis -21.64288928
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 40, shift = 0.0141, angle = 0.00956 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05107225 -0.21496635 0.97528512 67.48907810
-0.64946346 -0.73471119 -0.19595064 411.10839498
0.75867570 -0.64341970 -0.10208944 168.33302170
Axis -0.67772214 0.32806961 -0.65807524
Axis point 0.00000000 241.19521972 -0.99729201
Rotation angle (degrees) 160.72350203
Shift along axis -21.64246440
Correlation = 0.3649, Correlation about mean = -0.1049, Overlap = 2621
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 37423 points
correlation = 0.3649, correlation about mean = -0.1049, overlap = 2621
steps = 28, shift = 0.011, angle = 0.00422 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.05110002 -0.21502631 0.97527045 67.51163904
-0.64943800 -0.73471600 -0.19601698 411.10850225
0.75869563 -0.64339417 -0.10210226 168.32377829
Axis -0.67771626 0.32808172 -0.65807526
Axis point 0.00000000 241.19615320 -1.00289431
Rotation angle (degrees) 160.72744238
Shift along axis -21.64626553
> close #7
> volume #8 level 0.4211
> hide #!8 models
> volume #11 level 0.6377
> volume #11 level 0.4713
> show #!10 models
> hide #!10 models
> show #!10 models
> select #11
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.14971,0.63965,-0.75394,191.13,-0.95888,-0.2799,-0.047058,377.99,-0.24113,0.71589,0.65525,40.47
> view matrix models
> #11,-0.069022,0.30969,-0.94833,249.55,0.96027,0.27828,0.020987,-16.584,0.2704,-0.9092,-0.3166,311.78
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.069022,0.30969,-0.94833,292.24,0.96027,0.27828,0.020987,-16.748,0.2704,-0.9092,-0.3166,306.11
> view matrix models
> #11,-0.069022,0.30969,-0.94833,288.83,0.96027,0.27828,0.020987,-15.141,0.2704,-0.9092,-0.3166,305.54
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.12042,0.37081,-0.92087,284.98,0.89214,0.44729,0.063446,-33.276,0.43542,-0.8139,-0.38467,274.73
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3705, correlation about mean = -0.01342, overlap = 9885
steps = 84, shift = 3.3, angle = 7.24 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08967779 0.29999028 -0.94971770 295.49237204
0.84493489 0.52775912 0.08692132 -41.96570345
0.52729773 -0.79465472 -0.30080053 248.18221209
Axis -0.48858097 -0.81858128 0.30201543
Axis point 60.64458577 -0.00000000 223.51625228
Rotation angle (degrees) 115.55387500
Shift along axis -35.06475327
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 185886 points
correlation = 0.3706, correlation about mean = -0.01331, overlap = 9885
steps = 40, shift = 0.0143, angle = 0.0103 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc copy (#11) relative
to cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.08981970 0.29998685 -0.94970537 295.52003565
0.84486634 0.52788229 0.08683967 -41.94876855
0.52738342 -0.79457419 -0.30086302 248.17026594
Axis -0.48850161 -0.81863956 0.30198584
Axis point 60.66605513 0.00000000 223.51111811
Rotation angle (degrees) 115.55645450
Shift along axis -35.07718649
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
> close #9
> show #!2 models
> hide #!11 models
> ~select #11
Nothing selected
> show #6 models
> hide #!2 models
> show #!2 models
Fit map cryosparc_P47_J20_004_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 434908 points
correlation = 0.8681, correlation about mean = 0.7943, overlap = 2.493e+04
steps = 100, shift = 2.6, angle = 5.47 degrees
Position of cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.99999417 -0.00078818 -0.00332112 0.86833791
0.00079720 0.99999599 0.00271726 -0.70720618
0.00331897 -0.00271989 0.99999079 0.00769659
Axis -0.62300052 -0.76083593 0.18165636
Axis point -1.67706066 0.00000000 261.17922578
Rotation angle (degrees) 0.25002110
Shift along axis -0.00150896
> hide #!1 models
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 124
shifted from previous position = 2.69
rotated from previous position = 12.5 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25275147 -0.43670415 -0.86336907 353.51447381
-0.44938591 -0.84323715 0.29496333 308.88812835
-0.85683660 0.31343349 -0.40937812 323.84932290
Axis 0.79143097 -0.27991074 -0.54340316
Axis point 0.00000000 215.73050893 284.44415750
Rotation angle (degrees) 179.33140963
Shift along axis 17.34045325
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 12404 atoms
average map value = 0.1247, steps = 36
shifted from previous position = 0.00249
rotated from previous position = 0.00661 degrees
atoms outside contour = 7351, contour level = 0.14151
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.25279114 -0.43660663 -0.86340677 353.49888697
-0.44933375 -0.84329450 0.29487884 308.90364784
-0.85685225 0.31341505 -0.40935948 323.85331097
Axis 0.79144345 -0.27985911 -0.54341158
Axis point 0.00000000 215.71863017 284.44492018
Rotation angle (degrees) 179.32902903
Shift along axis 17.33923677
> transparency #2.1#10.1 50
> hide #!2 models
> show #!8 models
> select #8
2 models selected
> view matrix models
> #8,0.33902,0.03981,-0.93994,229.8,-0.92382,-0.17477,-0.34061,394.45,-0.17784,0.9838,-0.022475,72.918
> view matrix models
> #8,-0.19081,0.15972,-0.96855,298.63,-0.9771,-0.1256,0.17178,326.79,-0.094217,0.97914,0.18003,33.4
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.19081,0.15972,-0.96855,333.9,-0.9771,-0.1256,0.17178,339.76,-0.094217,0.97914,0.18003,31.589
> view matrix models
> #8,-0.19081,0.15972,-0.96855,336.31,-0.9771,-0.1256,0.17178,330.87,-0.094217,0.97914,0.18003,34.463
> view matrix models
> #8,-0.19081,0.15972,-0.96855,332.19,-0.9771,-0.1256,0.17178,338.81,-0.094217,0.97914,0.18003,28.17
> view matrix models
> #8,-0.19081,0.15972,-0.96855,344.81,-0.9771,-0.1256,0.17178,333.8,-0.094217,0.97914,0.18003,27.752
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,233.97,0.79273,0.40527,0.45534,-53.893,0.46395,-0.88565,-0.019473,233.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.39538,0.22669,-0.8901,225.01,0.79273,0.40527,0.45534,-60.792,0.46395,-0.88565,-0.019473,244.4
> view matrix models
> #8,0.39538,0.22669,-0.8901,226.27,0.79273,0.40527,0.45534,-67.659,0.46395,-0.88565,-0.019473,244.84
Fit map cryosparc_P47_J59_004_volume_map_sharp (3).mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 47154 points
correlation = 0.3601, correlation about mean = -0.01926, overlap = 2801
steps = 244, shift = 6.57, angle = 20.9 degrees
Position of cryosparc_P47_J59_004_volume_map_sharp (3).mrc (#8) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.50275518 0.77664634 0.37954926 71.44698114
0.77480667 0.59955666 -0.20051529 -35.12156246
-0.38329076 0.19326720 -0.90318100 318.59922133
Axis 0.45869577 0.88859079 -0.00214294
Axis point 85.22138435 0.00000000 150.24137730
Rotation angle (degrees) 154.58056842
Shift along axis 0.88099311
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:05:12 2022 ———
opened ChimeraX session
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!1 models
> show #!2 models
> close #11
> close #8
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202109_zvNS1/3_Structures/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
7.1/A 7.2/A 7.3/A 7.4/A 7.5/A 7.6/A 7.7/A 7.8/A 7.9/A 7.10/A 7.1/B 7.2/B 7.3/B
7.4/B 7.5/B 7.6/B 7.7/B 7.8/B 7.9/B 7.10/B | apolipoprotein A-I
> close #7.2-10
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!2 models
> hide #!1 models
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 352
shifted from previous position = 4.55
rotated from previous position = 50.7 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51892205 0.80965860 -0.27417668 164.22917225
-0.84272074 -0.43077092 0.32289035 300.54198392
0.14332362 0.39860929 0.90585262 -107.70830576
Axis 0.04438420 -0.24472630 -0.96857580
Axis point 169.29706156 116.85077370 0.00000000
Rotation angle (degrees) 121.46114137
Shift along axis 38.06231174
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 40
shifted from previous position = 0.00569
rotated from previous position = 0.00161 degrees
atoms outside contour = 2609, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894067 0.80965192 -0.27416117 164.23500046
-0.84270669 -0.43078495 0.32290828 300.54258112
0.14333881 0.39860769 0.90585092 -107.71085737
Axis 0.04437330 -0.24472913 -0.96857558
Axis point 169.29862447 116.85084764 0.00000000
Rotation angle (degrees) 121.46229524
Shift along axis 38.06223078
> show #4 models
> hide #!7 models
> hide #6 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 184
shifted from previous position = 2.68
rotated from previous position = 43.1 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696585 -0.97040692 -0.04644960 286.31819473
0.13996862 0.08141367 -0.98680321 234.14224375
0.96138231 0.22733718 0.15511878 -33.92541253
Axis 0.62926604 -0.52234025 0.57548668
Axis point 0.00000000 269.88096267 6.34604794
Rotation angle (degrees) 105.26304401
Shift along axis 38.34477607
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.0163
rotated from previous position = 0.0184 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699244 -0.97040417 -0.04637137 286.30251238
0.14028426 0.08141314 -0.98675843 234.09383454
0.96132975 0.22734912 0.15542673 -33.96007421
Axis 0.62921931 -0.52224780 0.57562166
Axis point 0.00000000 269.87054516 6.30278577
Rotation angle (degrees) 105.25312557
Shift along axis 38.34392482
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0177
rotated from previous position = 0.024 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23699037 -0.97040260 -0.04641486 286.30808679
0.13987427 0.08136006 -0.98682101 234.17141287
0.96139000 0.22737483 0.15501591 -33.91830894
Axis 0.62930653 -0.52233598 0.57544628
Axis point 0.00000000 269.87165306 6.36745226
Rotation angle (degrees) 105.26696289
Shift along axis 38.34122922
> show #3 models
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 44
shifted from previous position = 0.0174
rotated from previous position = 0.02 degrees
atoms outside contour = 1053, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23696878 -0.97040926 -0.04638578 286.31082660
0.14021616 0.08140780 -0.98676855 234.10798884
0.96134552 0.22732931 0.15535816 -33.95179699
Axis 0.62922296 -0.52227064 0.57559694
Axis point 0.00000000 269.87770153 6.30937551
Rotation angle (degrees) 105.25602295
Shift along axis 38.34306534
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0232 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23695180 -0.97040946 -0.04646826 286.32373425
0.13981736 0.08139458 -0.98682623 234.17404048
0.96140779 0.22733318 0.15496668 -33.91113966
Axis 0.62929239 -0.52237681 0.57542468
Axis point 0.00000000 269.88626156 6.36736238
Rotation angle (degrees) 105.26854490
Shift along axis 38.34095150
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 3401 atoms
average map value = 0.2415, steps = 40
shifted from previous position = 0.00386
rotated from previous position = 0.0076 degrees
atoms outside contour = 1055, contour level = 0.14151
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.23701158 -0.97039892 -0.04638334 286.30019564
0.13991374 0.08134082 -0.98681700 234.16833276
0.96137903 0.22739739 0.15505086 -33.92599735
Axis 0.62931286 -0.52231123 0.57546182
Axis point 0.00000000 269.86512738 6.36383820
Rotation angle (degrees) 105.26586629
Shift along axis 38.34052770
> show #!2 models
> show #6 models
> hide #!2 models
> hide #!10 models
> hide #6 models
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!2 models
> show #!1 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.4911, correlation about mean = 0.2779, overlap = 6002
steps = 1308, shift = 0.661, angle = 22 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27793747 -0.14035072 -0.95029069 409.92559615
0.39452131 0.88530641 -0.24614115 -49.02432671
0.87584454 -0.44332178 -0.19068848 109.24693947
Axis -0.10307165 -0.95457032 0.27959209
Axis point 169.03926821 0.00000000 207.85299225
Rotation angle (degrees) 106.95735055
Shift along axis 35.09003774
> show #!10 models
> hide #!2 models
> hide #!1 models
> show #!2 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00219
rotated from previous position = 0.0172 degrees
atoms outside contour = 2607, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51889139 0.80974271 -0.27398626 164.17754795
-0.84268736 -0.43067692 0.32310277 300.48501792
0.14363056 0.39854000 0.90583449 -107.74724207
Axis 0.04421738 -0.24478525 -0.96856853
Axis point 169.27126594 116.83993981 0.00000000
Rotation angle (degrees) 121.45756347
Shift along axis 38.06578928
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 44
shifted from previous position = 0.00282
rotated from previous position = 0.00397 degrees
atoms outside contour = 2606, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51894411 0.80971407 -0.27397106 164.19040191
-0.84265984 -0.43073928 0.32309143 300.49449446
0.14360158 0.39853079 0.90584314 -107.74009884
Axis 0.04422032 -0.24476870 -0.96857258
Axis point 169.27313448 116.84271119 0.00000000
Rotation angle (degrees) 121.46113819
Shift along axis 38.06301215
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14665,-0.10019,0.9841,42.803,-0.93066,-0.32317,-0.17158,431.35,0.33522,-0.94102,-0.045847,294.18
> view matrix models
> #3,-0.24212,-0.16715,0.95574,75.904,-0.91312,-0.29375,-0.2827,443.12,0.328,-0.94116,-0.081503,301.82
> view matrix models
> #3,-0.22781,0.0025001,0.9737,41.665,-0.95433,-0.19906,-0.22277,423.77,0.19327,-0.97998,0.047735,309.02
> view matrix models
> #3,-0.31679,-0.24249,0.91698,108.61,-0.87534,-0.29756,-0.38109,454.64,0.36527,-0.92339,-0.118,298.78
> view matrix models
> #3,-0.20831,0.16138,0.96466,13.134,-0.97765,-0.063166,-0.20055,401.06,0.028569,-0.98487,0.17093,316.86
> view matrix models
> #3,-0.18189,0.029376,0.98288,27.434,-0.97841,0.094327,-0.18388,371.75,-0.098114,-0.99511,0.011585,369.25
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.18189,0.029376,0.98288,26.801,-0.97841,0.094327,-0.18388,370.7,-0.098114,-0.99511,0.011585,365.44
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1754, steps = 220
shifted from previous position = 5.16
rotated from previous position = 26.4 degrees
atoms outside contour = 2605, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.51865164 0.80982057 -0.27420999 164.16314366
-0.84285174 -0.43044060 0.32298891 300.49787860
0.14353196 0.39863709 0.90580740 -107.73453379
Axis 0.04433389 -0.24481919 -0.96855463
Axis point 169.29026360 116.83700867 0.00000000
Rotation angle (degrees) 121.44248630
Shift along axis 38.05712471
> hide #!2 models
> view matrix models
> #3,-0.095949,-0.048917,0.99418,23.903,-0.93262,-0.34465,-0.10697,422.69,0.34788,-0.93745,-0.012552,284.37
> view matrix models
> #3,-0.095949,-0.048917,0.99418,24.499,-0.93262,-0.34465,-0.10697,420.51,0.34788,-0.93745,-0.012552,282.55
> ui mousemode right "map eraser"
> volume erase #10 center 197.01,182.51,231.59 radius 31.633
> volume erase #10 center 213.27,171.82,231.83 radius 31.633
> volume erase #10 center 199.27,226.74,192.59 radius 31.633
> volume erase #10 center 201.83,210.63,213.73 radius 31.633
> close #8
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 84
shifted from previous position = 4.01
rotated from previous position = 2.96 degrees
atoms outside contour = 2586, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47450864 0.83236882 -0.28636287 154.63058051
-0.86693279 -0.38553270 0.31589884 297.74905925
0.15254210 0.39815408 0.90454642 -108.87748698
Axis 0.04681588 -0.24980441 -0.96716391
Axis point 169.11832797 115.96117517 0.00000000
Rotation angle (degrees) 118.53838807
Shift along axis 38.16251411
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 48
shifted from previous position = 0.00277
rotated from previous position = 0.00477 degrees
atoms outside contour = 2584, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47448892 0.83239630 -0.28631566 154.61369255
-0.86692974 -0.38549828 0.31594921 297.73456104
0.15262076 0.39812996 0.90454377 -108.88430164
Axis 0.04677274 -0.24981834 -0.96716240
Axis point 169.11102884 115.95863363 0.00000000
Rotation angle (degrees) 118.53670909
Shift along axis 38.16095498
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
copy (#10) using 5602 atoms
average map value = 0.1735, steps = 60
shifted from previous position = 0.0162
rotated from previous position = 0.0207 degrees
atoms outside contour = 2591, contour level = 0.14151
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.47456944 0.83227118 -0.28654585 154.70120447
-0.86694397 -0.38562941 0.31575007 297.80757285
0.15228918 0.39826452 0.90454042 -108.84769154
Axis 0.04696579 -0.24977725 -0.96716366
Axis point 169.15292707 115.96995015 0.00000000
Rotation angle (degrees) 118.54372018
Shift along axis 38.15363917
> show #!2 models
> show #!7 models
> show #7.1 models
> select #7.1
5464 atoms, 5510 bonds, 334 residues, 1 model selected
> close #8
> close #8
> ui mousemode right "translate selected models"
> view matrix models #7.1,1,0,0,169.78,0,1,0,228.66,0,0,1,242.62
> view matrix models #7.1,1,0,0,141.19,0,1,0,179.49,0,0,1,253.16
> view matrix models #7.1,1,0,0,139.34,0,1,0,181.33,0,0,1,279.32
> view matrix models #7.1,1,0,0,140.66,0,1,0,199.74,0,0,1,261.78
> view matrix models #7.1,1,0,0,152.52,0,1,0,194.28,0,0,1,257.24
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.96441,0.048869,0.25985,165.75,0.098602,0.8454,-0.52495,167.67,-0.24533,0.53189,0.8105,246.45
> view matrix models
> #7.1,0.52404,0.070357,0.84878,205.22,0.25659,0.93724,-0.23611,177.31,-0.81212,0.34152,0.4731,245.12
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.96,0.25659,0.93724,-0.23611,166.4,-0.81212,0.34152,0.4731,253.15
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.06,0.25659,0.93724,-0.23611,172.5,-0.81212,0.34152,0.4731,255.75
> view matrix models
> #7.1,0.52404,0.070357,0.84878,220.15,0.25659,0.93724,-0.23611,172.23,-0.81212,0.34152,0.4731,250.53
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.93,0.25659,0.93724,-0.23611,169.22,-0.81212,0.34152,0.4731,253.47
> view matrix models
> #7.1,0.52404,0.070357,0.84878,218.24,0.25659,0.93724,-0.23611,170.23,-0.81212,0.34152,0.4731,253.64
> view matrix models
> #7.1,0.52404,0.070357,0.84878,216.82,0.25659,0.93724,-0.23611,165.96,-0.81212,0.34152,0.4731,248.26
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.73952,-0.17388,0.65029,205.07,0.14405,0.98456,0.099452,184.79,-0.65754,0.020126,0.75315,262.95
> view matrix models
> #7.1,0.73125,-0.084624,0.67684,205.42,0.062378,0.99641,0.057187,184.4,-0.67925,0.00040129,0.73391,262.74
> view matrix models
> #7.1,0.69799,-0.10334,0.70861,208.03,0.074484,0.99464,0.071682,184.87,-0.71222,0.0027467,0.70195,261.87
> view matrix models
> #7.1,0.63726,0.053079,0.76882,210.42,0.18684,0.95722,-0.22096,168.07,-0.74766,0.28445,0.60008,253.89
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,0.63726,0.053079,0.76882,208.69,0.18684,0.95722,-0.22096,171.97,-0.74766,0.28445,0.60008,254.92
> view matrix models
> #7.1,0.63726,0.053079,0.76882,209.09,0.18684,0.95722,-0.22096,174.45,-0.74766,0.28445,0.60008,259.11
> ui mousemode right "rotate selected models"
> view matrix models
> #7.1,0.62362,0.070465,0.77855,209.66,0.22628,0.93702,-0.26606,171.53,-0.74826,0.34209,0.5684,256.78
> view matrix models
> #7.1,0.61203,0.086506,0.78609,210.1,0.26096,0.91623,-0.30401,169.1,-0.74654,0.3912,0.53819,254.58
> ui mousemode right "rotate selected models"
> ~select #7.1
Nothing selected
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 21:54:19 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/2n5e.pdb"
2n5e.pdb title:
The 3D solution structure of discoidal high-density lipoprotein particles
[more info...]
Chain information for 2n5e.pdb
---
Chain | Description
8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.1/B 8.2/B 8.3/B
8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B | apolipoprotein A-I
> mmaker #8 to #7
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 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.1), sequence
alignment score = 889.9
RMSD between 167 pruned atom pairs is 0.000 angstroms; (across all 167 pairs:
0.000)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.2), sequence
alignment score = 889.9
RMSD between 99 pruned atom pairs is 0.967 angstroms; (across all 167 pairs:
2.405)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.3), sequence
alignment score = 882.7
RMSD between 146 pruned atom pairs is 0.614 angstroms; (across all 167 pairs:
6.590)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.4), sequence
alignment score = 879.1
RMSD between 90 pruned atom pairs is 0.877 angstroms; (across all 167 pairs:
6.733)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.5), sequence
alignment score = 886.3
RMSD between 83 pruned atom pairs is 0.781 angstroms; (across all 167 pairs:
7.288)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.6), sequence
alignment score = 889.9
RMSD between 150 pruned atom pairs is 0.625 angstroms; (across all 167 pairs:
4.094)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.7), sequence
alignment score = 886.3
RMSD between 150 pruned atom pairs is 0.628 angstroms; (across all 167 pairs:
2.428)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.8), sequence
alignment score = 882.7
RMSD between 114 pruned atom pairs is 1.220 angstroms; (across all 167 pairs:
8.487)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.9), sequence
alignment score = 886.3
RMSD between 137 pruned atom pairs is 0.954 angstroms; (across all 167 pairs:
7.152)
Matchmaker 2n5e.pdb, chain A (#7.1) with 2n5e.pdb, chain A (#8.10), sequence
alignment score = 886.3
RMSD between 149 pruned atom pairs is 0.855 angstroms; (across all 167 pairs:
1.629)
> close #7
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220222_D2NS1-Ab56-AA1.cxs"
> includeMaps true
——— End of log from Tue Feb 22 22:03:06 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb #7
---
Chain | Description
B C | No description available
> select #7
4272 atoms, 4342 bonds, 530 residues, 1 model selected
> view matrix models #7,1,0,0,155.3,0,1,0,-32.66,0,0,1,15.862
> view matrix models #7,1,0,0,227.55,0,1,0,182.45,0,0,1,257.42
> view matrix models #7,1,0,0,226.69,0,1,0,184.64,0,0,1,255.63
> view matrix models #7,1,0,0,204.58,0,1,0,234.23,0,0,1,235.65
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.55,-0.4966,0.03861,-0.86712,237.02,-0.54821,0.76058,0.34783,236.07
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.67294,0.6481,-0.35654,202.23,-0.4966,0.03861,-0.86712,223.37,-0.54821,0.76058,0.34783,214.9
> view matrix models
> #7,0.67294,0.6481,-0.35654,204.71,-0.4966,0.03861,-0.86712,212.44,-0.54821,0.76058,0.34783,207.19
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.77,-0.4966,0.03861,-0.86712,212.73,-0.54821,0.76058,0.34783,213.42
> view matrix models
> #7,0.67294,0.6481,-0.35654,168.7,-0.4966,0.03861,-0.86712,204.73,-0.54821,0.76058,0.34783,218.41
> view matrix models
> #7,0.67294,0.6481,-0.35654,169.65,-0.4966,0.03861,-0.86712,208.53,-0.54821,0.76058,0.34783,221.42
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.74751,0.56918,-0.34243,169.65,-0.52825,0.19685,-0.82595,208.32,-0.40271,0.7983,0.44782,221.09
> view matrix models
> #7,0.17157,-0.18647,-0.96736,171.99,0.92678,0.36358,0.094287,205.38,0.33413,-0.91271,0.23519,222.64
> view matrix models
> #7,-0.43014,-0.90269,-0.011358,172.47,-0.7035,0.32728,0.63086,206.67,-0.56575,0.27935,-0.77582,223.35
> view matrix models
> #7,-0.56096,-0.12743,-0.81798,172.58,-0.79405,0.36224,0.48812,206.9,0.2341,0.92333,-0.30439,221.07
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,172.56,-0.84174,0.37778,0.38568,207.05,0.27385,0.91443,-0.29802,221.03
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,175.91,-0.84174,0.37778,0.38568,203.89,0.27385,0.91443,-0.29802,211.39
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.08,-0.84174,0.37778,0.38568,206.07,0.27385,0.91443,-0.29802,215.64
> hide #!8 models
> view matrix models
> #7,-0.46527,-0.14524,-0.87317,174.65,-0.84174,0.37778,0.38568,206.88,0.27385,0.91443,-0.29802,212.06
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:08:07 2022 ———
opened ChimeraX session
> open "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb"
Chain information for ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb
#9
---
Chain | Description
B C | No description available
> mmaker #9 to #10
No 'to' model specified
> mmaker #9 to #7
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 ApoA1_e6bc4_unrelaxed_rank_1_model_4.pdb, chain B (#7) with
ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb, chain B (#9),
sequence alignment score = 1084.5
RMSD between 74 pruned atom pairs is 0.985 angstroms; (across all 207 pairs:
10.547)
> hide #7 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.52533,-0.58815,-0.61491,177.85,0.0047201,0.72466,-0.68909,201.87,0.85089,0.35909,0.38346,210.74
> view matrix models
> #9,0.45946,-0.88174,0.10689,181.58,0.8882,0.45638,-0.053134,204.22,-0.0019327,0.11935,0.99285,214.69
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.45946,-0.88174,0.10689,177.6,0.8882,0.45638,-0.053134,197.13,-0.0019327,0.11935,0.99285,218.41
> view matrix models
> #9,0.45946,-0.88174,0.10689,175.75,0.8882,0.45638,-0.053134,203.48,-0.0019327,0.11935,0.99285,218.85
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.69,0.8882,0.45638,-0.053134,196.29,-0.0019327,0.11935,0.99285,214.81
> view matrix models
> #9,0.45946,-0.88174,0.10689,169.27,0.8882,0.45638,-0.053134,199.29,-0.0019327,0.11935,0.99285,212.88
> view matrix models
> #9,0.45946,-0.88174,0.10689,173.56,0.8882,0.45638,-0.053134,203.27,-0.0019327,0.11935,0.99285,212.35
> view matrix models
> #9,0.45946,-0.88174,0.10689,176.72,0.8882,0.45638,-0.053134,202,-0.0019327,0.11935,0.99285,212.91
> view matrix models
> #9,0.45946,-0.88174,0.10689,172.24,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.78
> view matrix models
> #9,0.45946,-0.88174,0.10689,171.54,0.8882,0.45638,-0.053134,200.71,-0.0019327,0.11935,0.99285,209.45
> ui tool show "Fit in Map"
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) using 3334 atoms
average map value = 0.1014, steps = 288
shifted from previous position = 26.2
rotated from previous position = 35.6 degrees
atoms outside contour = 2236, contour level = 0.14151
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.15030095 -0.25689088 -0.95468145 159.80559539
0.91205850 0.40867945 0.03362089 142.63963221
0.38152180 -0.87577859 0.29572442 147.85545078
Axis -0.45590440 -0.66987165 0.58602316
Axis point -104.50370211 0.00000000 221.35941513
Rotation angle (degrees) 94.16607036
Shift along axis -81.75960077
> view matrix models
> #9,0.67727,-0.51922,0.52127,172.73,0.71543,0.63007,-0.30194,194.77,-0.17166,0.57742,0.7982,218.78
> view matrix models
> #9,0.67727,-0.51922,0.52127,173.99,0.71543,0.63007,-0.30194,197.51,-0.17166,0.57742,0.7982,212.36
> view matrix models
> #9,0.67727,-0.51922,0.52127,174.96,0.71543,0.63007,-0.30194,195,-0.17166,0.57742,0.7982,208.97
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.66193,-0.59819,0.45168,174.95,0.73725,0.62836,-0.24824,195.18,-0.13532,0.49732,0.85695,209.41
> view matrix models
> #9,0.64956,-0.67275,0.35424,174.82,0.71372,0.70012,0.020895,196.02,-0.26207,0.23925,0.93492,210.62
> save "D:/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220302_D2NS1ts-
> Ab56-apoa1.cxs" includeMaps true
——— End of log from Wed Mar 2 00:18:18 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #9 models
> hide #!10 models
> show #6 models
> hide #4 models
> hide #3 models
> ui tool show "Fit in Map"
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.07482, steps = 364
shifted from previous position = 2.61
rotated from previous position = 17.1 degrees
atoms outside contour = 8195, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99640848 0.07252019 0.04371456 331.26650068
-0.01695668 -0.67668277 0.73607941 166.80204366
0.08296151 0.73269451 0.67548215 -88.38561339
Axis -0.03462299 -0.40144391 -0.91522895
Axis point 169.54681270 98.35816249 0.00000000
Rotation angle (degrees) 177.19813771
Shift along axis 2.46197109
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.64956,-0.67275,0.35424,175.54,0.71372,0.70012,0.020895,189.47,-0.26207,0.23925,0.93492,190.81
> ~select #9
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,-0.99797,0.039575,0.049905,338.25,-0.014392,-0.90338,0.42859,266.52,0.062045,0.42701,0.90212,-62.663
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.99623,0.082033,0.028348,334.24,-0.086585,-0.91673,-0.39002,429.14,-0.006007,-0.391,0.92037,92.117
> view matrix models
> #6,-0.99623,0.082033,0.028348,335.42,-0.086585,-0.91673,-0.39002,430.38,-0.006007,-0.391,0.92037,88.929
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09493, steps = 84
shifted from previous position = 3.13
rotated from previous position = 3.82 degrees
atoms outside contour = 7003, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820989 0.05968746 0.00379835 345.43779112
-0.05973880 -0.99809742 -0.01525811 372.27574829
0.00288041 -0.01545771 0.99987637 1.80150722
Axis -0.00167123 0.00768605 -0.99996907
Axis point 178.28007958 180.98306790 0.00000000
Rotation angle (degrees) 176.57654715
Shift along axis 0.48257203
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.09495, steps = 48
shifted from previous position = 0.019
rotated from previous position = 0.00432 degrees
atoms outside contour = 7012, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99820895 0.05970074 0.00383565 345.40975009
-0.05975246 -0.99809759 -0.01519388 372.26991158
0.00292127 -0.01539585 0.99987721 1.78218185
Axis -0.00169079 0.00765450 -0.99996927
Axis point 178.26722509 180.97930211 0.00000000
Rotation angle (degrees) 176.57577490
Shift along axis 0.48339683
> set bgColor white
> lighting full
> ~select #6
Nothing selected
> hide #6 models
> show #6 models
> color #6 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> select #1
2 models selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> ~select #1
Nothing selected
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #4 models
> hide #6 models
> volume #2 color #a7a49f80
> volume #2 color #b8b5af80
> color #3-4 bychain
Color zone shortcut requires 1 displayed atomic model and 1 map, got 12 atomic
models, 1 maps.
> hide #4 models
> show #4 models
> hide #4 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select #2
2 models selected
> ~select #2
Nothing selected
Color zone shortcut requires 1 displayed atomic model and 1 map, got 11 atomic
models, 1 maps.
> show #4 models
> ui tool show "Segment Map"
> show #9 models
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.64956,-0.67275,0.35424,173.28,0.71372,0.70012,0.020895,203.74,-0.26207,0.23925,0.93492,217.24
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.42545,-0.83111,0.35811,174.01,0.88507,0.46469,0.026952,204.31,-0.18881,0.30548,0.93329,216.96
> view matrix models
> #9,0.36854,-0.89204,0.26163,173.89,0.89839,0.4141,0.14638,204.91,-0.23892,0.18109,0.954,217.47
> view matrix models
> #9,0.39748,-0.85333,0.3374,174.03,0.89601,0.44024,0.057848,204.49,-0.1979,0.27932,0.93958,217.07
> view matrix models
> #9,0.4249,-0.82293,0.37715,174.06,0.89397,0.44699,-0.03185,204.13,-0.14237,0.3507,0.9256,216.74
> view matrix models
> #9,0.30959,-0.88763,0.34097,174.24,0.94929,0.30918,-0.057041,204.4,-0.05479,0.34134,0.93834,216.73
> ~select #9
Nothing selected
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.30959,-0.88763,0.34097,171.78,0.94929,0.30918,-0.057041,200.45,-0.05479,0.34134,0.93834,215.77
> ~select #9
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode "C:\Users\dahailuo\OneDrive - Nanyang Technological
> University\Temporal\202112_FlaviNS1\Data_EM_Alvin\movie2.mp4"
Movie saved to \C:Users\\...\Data_EM_Alvin\movie2.mp4
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> mmaker #6 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 F562a.pdb, chain B (#4) with D2NS1-F562.pdb, chain C (#6), sequence
alignment score = 1200
RMSD between 228 pruned atom pairs is 0.000 angstroms; (across all 228 pairs:
0.000)
> hide #!2 models
> hide #9 models
> hide #3 models
> hide #4 models
> show #!2 models
> hide #6 models
> show #!1 models
> show #!10 models
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 48, shift = 0.0601, angle = 0.109 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27792284 -0.14164293 -0.95010322 410.09306464
0.39540197 0.88452622 -0.24752902 -48.83916554
0.87545196 -0.44446666 -0.18982414 109.38604242
Axis -0.10294301 -0.95425209 0.28072349
Axis point 169.05771360 0.00000000 208.04394464
Rotation angle (degrees) 106.95439226
Shift along axis 35.09589160
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2809, overlap = 5991
steps = 48, shift = 0.0078, angle = 0.0885 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27794843 -0.14312388 -0.94987377 410.31424613
0.39534589 0.88416435 -0.24890760 -48.51539453
0.87546917 -0.44471217 -0.18916865 109.30275225
Axis -0.10234637 -0.95410041 0.28145627
Axis point 169.16249688 0.00000000 208.15543264
Rotation angle (degrees) 106.94636481
Shift along axis 35.05832906
> hide #!2 models
> select #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.74046,0.62541,0.24616,-107.44,-0.65719,0.75044,0.070241,152.95,-0.1408,-0.21378,0.96668,70.267
> view matrix models
> #1,0.72193,-0.13867,0.67793,-42.597,0.2204,0.97477,-0.035306,-25.414,-0.65593,0.1749,0.73428,133.11
> view matrix models
> #1,0.74615,0.64297,-0.17276,-38.999,0.62682,-0.76589,-0.14322,231.4,-0.22441,-0.0014231,-0.97449,383.68
> view matrix models
> #1,0.80841,0.29993,0.50648,-106.59,0.51816,-0.77083,-0.37058,291.07,0.27926,0.56202,-0.77856,159.28
> view matrix models
> #1,0.96135,-0.23483,0.14371,24.411,0.25186,0.96097,-0.11451,-14.839,-0.11121,0.14628,0.98297,-2.0945
> view matrix models
> #1,0.99141,-0.075528,-0.10677,34.022,0.051461,0.97582,-0.21244,35.244,0.12024,0.20512,0.97132,-51.881
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 716, shift = 1.66, angle = 12.6 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
-0.27785362 -0.14026525 -0.95032783 409.88132947
0.39567157 0.88475643 -0.24627224 -49.16134094
0.87535212 -0.44444535 -0.19033380 109.50506725
Axis -0.10359229 -0.95434929 0.28015367
Axis point 168.94433960 0.00000000 207.96495201
Rotation angle (degrees) 106.96068830
Shift along axis 35.13479072
> show #!2 models
> hide #!2 models
> show #!2 models
> ~select #1
Nothing selected
> select #1
2 models selected
> view matrix models
> #1,0.9987,0.030982,-0.040533,2.2432,0.0036821,0.74864,0.66296,-67.414,0.050884,-0.66225,0.74755,154.04
> view matrix models
> #1,0.87306,0.20075,-0.44437,64.348,0.48063,-0.20061,0.85367,-16.172,0.082229,-0.95888,-0.27163,378
> view matrix models
> #1,0.83244,0.37492,-0.40802,34.215,0.55119,-0.48475,0.67912,52.19,0.056831,-0.79023,-0.61017,411.1
> view matrix models
> #1,0.68639,0.56283,-0.46053,35.845,0.69489,-0.69435,0.1871,149.22,-0.21447,-0.44844,-0.8677,443.15
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> view matrix models
> #1,0.82844,0.50873,-0.23428,-19.057,0.47101,-0.40647,0.7829,34.547,0.30305,-0.75893,-0.57635,355.71
> view matrix models
> #1,0.84453,-0.094928,-0.52703,136.53,-0.025459,-0.99017,0.13755,339.15,-0.5349,-0.10275,-0.83864,433.6
> view matrix models
> #1,0.97799,-0.18464,-0.097184,54.238,-0.1969,-0.66248,-0.72274,460.34,0.069068,0.72597,-0.68425,151.17
> view matrix models
> #1,0.97796,-0.19168,-0.082782,53.003,-0.16644,-0.47632,-0.86337,446.06,0.12606,0.85812,-0.49773,85.086
> view matrix models
> #1,0.99726,0.035713,-0.06472,5.846,-0.039623,-0.48086,-0.8759,426.41,-0.062402,0.87607,-0.47813,112.12
> view matrix models
> #1,-0.96752,0.24305,-0.069446,320.31,-0.20699,-0.60408,0.76957,193.12,0.14509,0.75896,0.63477,-96.862
> view matrix models
> #1,-0.85416,0.24266,-0.45992,367.81,-0.51768,-0.48048,0.70792,237.19,-0.049202,0.84277,0.53603,-60.033
> view matrix models
> #1,-0.98697,0.14048,-0.078425,343.64,-0.16057,-0.82904,0.53564,265.52,0.010232,0.54125,0.8408,-69.644
> view matrix models
> #1,-0.99016,0.10292,-0.094853,353.76,-0.13794,-0.83244,0.53668,261.91,-0.023726,0.54448,0.83844,-63.751
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99016,0.10292,-0.094853,357.93,-0.13794,-0.83244,0.53668,248.71,-0.023726,0.54448,0.83844,-68.308
> view matrix models
> #1,-0.99016,0.10292,-0.094853,358.29,-0.13794,-0.83244,0.53668,250.68,-0.023726,0.54448,0.83844,-68.894
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.9422,-0.030752,0.33364,299.34,0.13856,-0.9424,0.30443,261.21,0.30506,0.33307,0.89219,-99.156
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.5,0.28029,-0.94609,-0.16233,317.46,0.56574,0.026196,0.82416,-79.125
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.77548,-0.32284,0.54259,268.3,0.28029,-0.94609,-0.16233,334.8,0.56574,0.026196,0.82416,-67.645
> view matrix models
> #1,-0.77548,-0.32284,0.54259,265.58,0.28029,-0.94609,-0.16233,338.57,0.56574,0.026196,0.82416,-65.98
> view matrix models
> #1,-0.77548,-0.32284,0.54259,285.03,0.28029,-0.94609,-0.16233,352.61,0.56574,0.026196,0.82416,-59.271
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91194,-0.17978,0.36883,313.96,0.10929,-0.97286,-0.20397,395.12,0.39549,-0.1457,0.90684,-12.537
> view matrix models
> #1,-0.91113,-0.10679,0.39805,295.73,0.021642,-0.97691,-0.21254,412.97,0.41156,-0.18504,0.8924,-5.8812
> view matrix models
> #1,-0.99135,-0.088862,0.096564,359.09,0.037913,-0.89841,-0.43753,435.05,0.12563,-0.43008,0.894,88.599
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99135,-0.088862,0.096564,361.35,0.037913,-0.89841,-0.43753,415.99,0.12563,-0.43008,0.894,90.946
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.47,-0.013738,-0.97125,-0.23766,403.58,0.13986,-0.23721,0.96134,42.319
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99008,-0.020034,0.1391,341.46,-0.013738,-0.97125,-0.23766,399.55,0.13986,-0.23721,0.96134,42.616
> view matrix models
> #1,-0.99008,-0.020034,0.1391,338.93,-0.013738,-0.97125,-0.23766,400.44,0.13986,-0.23721,0.96134,32.494
> view matrix models
> #1,-0.99008,-0.020034,0.1391,335.49,-0.013738,-0.97125,-0.23766,400.28,0.13986,-0.23721,0.96134,33.65
> view matrix models
> #1,-0.99008,-0.020034,0.1391,333.14,-0.013738,-0.97125,-0.23766,400.18,0.13986,-0.23721,0.96134,33.756
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99347,-0.11227,0.020092,370.83,0.11149,-0.99309,-0.036498,346.87,0.024051,-0.03402,0.99913,11.612
> view matrix models
> #1,-0.99314,-0.11513,0.02023,371.26,0.11367,-0.99155,-0.06254,350.72,0.027259,-0.059812,0.99784,15.866
> view matrix models
> #1,-0.99502,-0.048682,0.086949,348.18,0.043004,-0.99689,-0.06602,364.89,0.089893,-0.061952,0.99402,5.7314
> view matrix models
> #1,-0.9999,-0.011841,0.0079016,356.17,0.012535,-0.99545,0.094484,342.25,0.0067469,0.094574,0.9955,-7.6193
> view matrix models
> #1,-0.99955,0.029264,0.006465,349.02,-0.028596,-0.99584,0.086513,351.05,0.0089699,0.086289,0.99623,-6.6648
> show #!2 models
> hide #!2 models
> view matrix models
> #1,-0.99431,-0.012476,0.10579,338.32,0.013343,-0.99988,0.0074894,357.98,0.10568,0.0088583,0.99436,-9.7821
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc copy using 255459 points
correlation = 0.493, correlation about mean = 0.2808, overlap = 5991
steps = 948, shift = 10.3, angle = 23.5 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc copy (#10) coordinates:
Matrix rotation and translation
0.27780939 0.13998726 -0.95038174 260.70800172
-0.39575740 -0.88479067 -0.24601119 407.82841194
-0.87532735 0.44446484 -0.19040216 263.31428797
Axis 0.78717074 -0.08556506 -0.61077070
Axis point 0.00000000 178.59809032 292.75645151
Rotation angle (degrees) 153.98663078
Shift along axis 9.50119898
> hide #!10 models
> show #6 models
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
12404 atoms, 12730 bonds, 1588 residues, 1 model selected
> view matrix models
> #6,0.80584,-0.033933,0.59116,-60.641,-0.18803,0.93202,0.30982,-22.728,-0.56149,-0.36082,0.74468,228.14
> view matrix models
> #6,0.84169,0.23741,0.48497,-96.336,-0.031206,0.91804,-0.39525,78.603,-0.53906,0.31754,0.78012,96.759
> view matrix models
> #6,0.95752,0.28708,0.027255,-43.538,-0.26323,0.90873,-0.32391,108.93,-0.11776,0.30298,0.94569,-5.8011
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.95752,0.28708,0.027255,-47.959,-0.26323,0.90873,-0.32391,118,-0.11776,0.30298,0.94569,-22.337
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99918,0.040001,0.0063686,-7.5857,-0.036305,0.95416,-0.29708,64.472,-0.01796,0.2966,0.95483,-40.695
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) using 12404 atoms
average map value = 0.1026, steps = 96
shifted from previous position = 4.3
rotated from previous position = 4.93 degrees
atoms outside contour = 6857, contour level = 0.08
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-1.00000000 -0.00003889 0.00000390 356.92132489
0.00003889 -0.99999983 -0.00059770 357.02795185
0.00000392 -0.00059770 0.99999983 0.10572384
Axis -0.00000446 -0.00030232 0.99999995
Axis point 178.45719114 178.51746241 0.00000000
Rotation angle (degrees) 179.99777155
Shift along axis -0.00380630
> ~select #6
Nothing selected
> interfaces #6 & ~solvent
7 buried areas: A B 2354, E F 2040, C D 2040, B C 1572, A F 1542, B D 1312, A
E 1190
> open "C:/Users/dahailuo/Downloads/cryosparc_P35_J100_005_volume_map_sharp
> (1).mrc"
Opened cryosparc_P35_J100_005_volume_map_sharp (1).mrc as #11, grid size
416,416,416, pixel 0.858, shown at level 0.0415, step 2, values float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1102+1920+23 (frame:
1936x1141+1912-8) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1920x1017+1920+23 (frame:
1936x1056+1912-8) margins: 8, 31, 8, 8 minimum size: 493x1102 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=509,1141 maxtrack=0,0)
> volume #11 step 1
> surface dust #1 size 8.58
> surface dust #11 size 8.58
> volume #11 level 0.045
> volume #11 level 0.05
Fit molecule D2NS1-F562.pdb (#6) to map
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) using 12404 atoms
average map value = 0.08442, steps = 152
shifted from previous position = 1.4
rotated from previous position = 4.71 degrees
atoms outside contour = 5898, contour level = 0.05
Position of D2NS1-F562.pdb (#6) relative to
cryosparc_P35_J100_005_volume_map_sharp (1).mrc (#11) coordinates:
Matrix rotation and translation
0.99897026 0.04182548 -0.01757995 -4.15590074
-0.04516063 0.95385198 -0.29686178 69.02604187
0.00435228 0.29735001 0.95475862 -45.20466997
Axis 0.98879513 -0.03649622 -0.14474879
Axis point 0.00000000 183.11150795 204.04343868
Rotation angle (degrees) 17.48599398
Shift along axis -0.08520266
> transparency #11.1 50
> show #3 models
> mmaker #3 to #6
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 D2NS1-F562.pdb, chain A (#6) with D2NS1.pdb, chain B (#3), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> hide #6 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 60
shifted from previous position = 1.1
rotated from previous position = 2.61 degrees
atoms outside contour = 3025, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14875593 -0.08639183 -0.98509297 342.36735832
0.98470147 -0.07847453 0.15557896 -15.12271804
-0.09074546 -0.99316577 0.07339661 361.18209695
Axis -0.63557683 -0.49482408 0.59261389
Axis point 0.00000000 37.80172615 346.76474569
Rotation angle (degrees) 115.35090835
Shift along axis 3.92385104
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07339, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.00688 degrees
atoms outside contour = 3021, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14885535 -0.08637602 -0.98507934 342.35458834
0.98468094 -0.07852972 0.15568097 -15.13336069
-0.09080510 -0.99316278 0.07336326 361.19655370
Axis -0.63562980 -0.49478213 0.59259210
Axis point 0.00000000 37.81870419 346.75288311
Rotation angle (degrees) 115.35056364
Shift along axis 3.91916090
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 5602 atoms
average map value = 0.07338, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.0195 degrees
atoms outside contour = 3027, contour level = 0.05
Position of D2NS1.pdb (#3) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.14869429 -0.08663603 -0.98508083 342.41395707
0.98471526 -0.07839157 0.15553350 -15.12882419
-0.09069683 -0.99315105 0.07365544 361.12491138
Axis -0.63549687 -0.49480794 0.59271311
Axis point 0.00000000 37.79183158 346.80910583
Rotation angle (degrees) 115.34202749
Shift along axis 3.92633355
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,0.052602,-0.042076,-0.99773,354.08,0.96197,-0.26603,0.061936,37.093,-0.26803,-0.96305,0.026482,395.65
> view matrix models
> #3,0.0070452,-0.012575,-0.9999,357.51,0.93425,-0.35645,0.011066,66.236,-0.35656,-0.93423,0.0092369,409.45
> view matrix models
> #3,-0.0058622,0.0073093,-0.99996,356.45,0.91272,-0.40851,-0.0083368,82.232,-0.40855,-0.91272,-0.0042765,417.39
> view matrix models
> #3,-0.020074,-0.027951,-0.99941,364.78,0.92365,-0.38315,-0.0078364,75.954,-0.3827,-0.92326,0.033508,407.88
> view matrix models
> #3,0.0017745,-0.041136,-0.99915,363.11,0.92163,-0.38766,0.017597,72.537,-0.38806,-0.92088,0.037224,407.76
> view matrix models
> #3,-0.017771,-0.12129,-0.99246,378.83,0.9086,-0.41622,0.034596,76.603,-0.41728,-0.90114,0.1176,395.26
> view matrix models
> #3,0.012861,-0.10916,-0.99394,371.67,0.88601,-0.45952,0.061933,82.986,-0.46349,-0.88144,0.09081,404.85
> view matrix models
> #3,0.012034,-0.092833,-0.99561,369.37,0.88338,-0.46553,0.054084,85.858,-0.46851,-0.88015,0.076405,408.08
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.56,0.88274,-0.46516,0.066341,83.724,-0.46934,-0.8796,0.077605,407.92
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.16,0.88274,-0.46516,0.066341,83.998,-0.46934,-0.8796,0.077605,407.23
> view matrix models
> #3,0.022255,-0.099641,-0.99477,368.06,0.88274,-0.46516,0.066341,83.639,-0.46934,-0.8796,0.077605,407.78
> view matrix models
> #3,0.022255,-0.099641,-0.99477,369.91,0.88274,-0.46516,0.066341,85.463,-0.46934,-0.8796,0.077605,407.43
> ~select #3
Nothing selected
> show #6 models
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker D2NS1.pdb, chain B (#3) with D2NS1-F562.pdb, chain A (#6), sequence
alignment score = 1871.9
RMSD between 352 pruned atom pairs is 0.023 angstroms; (across all 352 pairs:
0.023)
> show #4 models
> hide #4 models
> show #4 models
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 64
shifted from previous position = 1.84
rotated from previous position = 3.05 degrees
atoms outside contour = 1419, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82616267 0.51307542 -0.23282799 17.45941536
-0.12390784 -0.23766697 -0.96341127 357.00880636
-0.54963816 0.82478363 -0.13277751 149.37621508
Axis 0.92916660 0.16461820 -0.33098381
Axis point 0.00000000 112.71394709 221.40097809
Rotation angle (degrees) 105.79170262
Shift along axis 25.55174348
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1004, steps = 48
shifted from previous position = 0.011
rotated from previous position = 0.0276 degrees
atoms outside contour = 1418, contour level = 0.05
Position of F562a.pdb (#4) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.82596970 0.51342982 -0.23273140 17.41926576
-0.12364669 -0.23778983 -0.96341451 356.97717269
-0.54998689 0.82452765 -0.13292329 149.51361297
Axis 0.92909832 0.16486078 -0.33105473
Axis point 0.00000000 112.65571575 221.42366392
Rotation angle (degrees) 105.80544612
Shift along axis 25.53855668
> hide #6 models
> show #5 models
Fit molecule F562b.pdb (#5) to map cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) using 3401 atoms
average map value = 0.1083, steps = 76
shifted from previous position = 0.951
rotated from previous position = 3.36 degrees
atoms outside contour = 1258, contour level = 0.05
Position of F562b.pdb (#5) relative to cryosparc_P35_J100_005_volume_map_sharp
(1).mrc (#11) coordinates:
Matrix rotation and translation
0.91100184 -0.19027699 -0.36588295 82.97740999
-0.38499639 -0.71041595 -0.58914087 517.50161240
-0.14782913 0.67757202 -0.72044619 248.76959820
Axis 0.97438742 -0.16773248 -0.14978305
Axis point 0.00000000 219.97208546 227.46670853
Rotation angle (degrees) 139.45804049
Shift along axis -43.21115606
> color #3-5 bychain
> hide #!11 models
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-Fab56
> .cxs"
> save "C:/Users/dahailuo/OneDrive - Nanyang Technological
> University/Temporal/202112_FlaviNS1/Data_EM_Alvin/20220303_D2NS1ts-
> Fab5-DL.cxs" includeMaps true
——— End of log from Thu Mar 3 12:01:46 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #5
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #7 models
> hide #!8 models
> hide #9 models
> close #8
> show #9 models
> hide #9 models
> show #7 models
> show #9 models
> hide #7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:9-11
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B:1-207
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-86
208 atoms, 215 bonds, 23 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an
ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-
tuples-or ndarrays with different lengths or shapes) is deprecated. If you
meant to do this, you must specify 'dtype=object' when creating the ndarray
return array(a, dtype, copy=False, order=order)
> select #9/B:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/B:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel blue
> color sel cornflower blue
> select #9/B:151-152
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #9/B:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel cornflower blue
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> close #10
> close #11
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #3 models
> show #4 models
> show #5 models
> hide #5 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> hide #4 models
> show #4 models
> hide #4 models
> select #9/C:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/C:64
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:64-85
201 atoms, 207 bonds, 22 residues, 1 model selected
> color sel medium blue
> select #9/C:151
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/C:151-172
163 atoms, 164 bonds, 22 residues, 1 model selected
> color sel medium blue
> close #7
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> close #6
> show #4 models
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J142_005_volume_map_sharp.mrc"
Opened cryosparc_P47_J142_005_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0449, step 2, values float32
> volume #6 step 1
> volume #6 level 0.1656
> volume #6 level 0.06061
> close #6
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J128_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 0.85, shown at level 0.0566, step 2, values float32
> hide #!2 models
> hide #3 models
> hide #4 models
> hide #!6 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> show #!6 models
> volume #6 step 1
> volume #6 level 0.116
> open "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202109_zvNS1/3_Structures/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P47_J132_002_volume_map_sharp.mrc"
Opened cryosparc_P47_J132_002_volume_map_sharp.mrc as #7, grid size
360,360,360, pixel 0.85, shown at level 0.0558, step 2, values float32
> volume #7 step 1
> volume #7 level 0.189
> volume #6 level 0.148
> volume #6 level 0.1384
> volume #7 level 0.08193
> volume #7 level 0.04862
> volume #6 level 0.06462
> close #7
> volume #6 level 0.1336
> volume #6 level 0.1256
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #6
2 models selected
> view matrix models
> #6,-0.83996,0.011508,0.54253,184.02,0.50426,0.3859,0.77253,-105.68,-0.20047,0.92247,-0.32995,103.36
> view matrix models
> #6,0.1848,-0.18014,0.96613,-8.4193,0.46665,-0.84908,-0.24758,260.82,0.86492,0.4966,-0.072852,-31.125
> view matrix models
> #6,0.25195,-0.19005,0.94889,-14.067,0.4832,-0.82485,-0.29351,262.08,0.83847,0.53245,-0.11599,-25.726
> view matrix models
> #6,-0.035938,-0.13733,0.98987,13.939,0.38333,-0.91664,-0.11325,261.83,0.92291,0.37538,0.085583,-46.756
> view matrix models
> #6,0.1558,-0.53982,0.82724,75.077,-0.30263,-0.82328,-0.48024,409.8,0.94029,-0.17552,-0.29163,98.871
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.1558,-0.53982,0.82724,121.85,-0.30263,-0.82328,-0.48024,428.76,0.94029,-0.17552,-0.29163,116.7
> view matrix models
> #6,0.1558,-0.53982,0.82724,122.7,-0.30263,-0.82328,-0.48024,438.5,0.94029,-0.17552,-0.29163,113.43
> view matrix models
> #6,0.1558,-0.53982,0.82724,123.68,-0.30263,-0.82328,-0.48024,449.46,0.94029,-0.17552,-0.29163,118.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.15847,-0.55227,0.81847,126.67,-0.30396,-0.81597,-0.49173,450.39,0.93941,-0.17086,-0.29717,118.9
> view matrix models
> #6,0.31733,-0.49565,0.80848,95.704,-0.41983,-0.83787,-0.34888,447.71,0.85032,-0.22872,-0.47397,170.26
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.921,-0.41983,-0.83787,-0.34888,440.31,0.85032,-0.22872,-0.47397,180.5
> view matrix models
> #6,0.31733,-0.49565,0.80848,96.096,-0.41983,-0.83787,-0.34888,439.7,0.85032,-0.22872,-0.47397,180.02
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.946,-0.41983,-0.83787,-0.34888,439.56,0.85032,-0.22872,-0.47397,179.06
> view matrix models
> #6,0.31733,-0.49565,0.80848,94.851,-0.41983,-0.83787,-0.34888,439.42,0.85032,-0.22872,-0.47397,178.96
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.32806,-0.48111,0.81296,90.235,-0.37939,-0.85524,-0.35303,436.79,0.86512,-0.19262,-0.4631,169.31
> view matrix models
> #6,0.36269,-0.41122,0.83627,70.284,-0.30986,-0.89953,-0.30795,425.95,0.87889,-0.14743,-0.45367,158.62
> view matrix models
> #6,0.36637,-0.44198,0.8188,77.421,-0.35476,-0.87986,-0.31621,430.93,0.86019,-0.17462,-0.47915,169.85
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.762,-0.30034,-0.9051,-0.30097,424.26,0.88299,-0.1445,-0.44659,156.39
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.36072,-0.39988,0.8426,67.7,-0.30034,-0.9051,-0.30097,421.64,0.88299,-0.1445,-0.44659,155.81
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.281,-0.30034,-0.9051,-0.30097,420.24,0.88299,-0.1445,-0.44659,157.09
> view matrix models
> #6,0.36072,-0.39988,0.8426,69.528,-0.30034,-0.9051,-0.30097,421,0.88299,-0.1445,-0.44659,156.78
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36427,-0.41429,0.83407,72.656,-0.28999,-0.90154,-0.32115,422.2,0.88499,-0.12489,-0.44854,153.73
> view matrix models
> #6,0.35177,-0.40975,0.84164,72.569,-0.29057,-0.90249,-0.31793,421.91,0.88984,-0.13272,-0.43653,152.26
> view matrix models
> #6,0.3599,-0.44231,0.82148,79.767,-0.28748,-0.89021,-0.35338,425.33,0.8876,-0.10898,-0.44754,150.68
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.749,-0.29539,-0.89136,-0.34382,425.13,0.87766,-0.11101,-0.46626,155.55
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37744,-0.43949,0.8151,76.75,-0.29539,-0.89136,-0.34382,424.99,0.87766,-0.11101,-0.46626,155.59
> view matrix models
> #6,0.37744,-0.43949,0.8151,75.665,-0.29539,-0.89136,-0.34382,426.6,0.87766,-0.11101,-0.46626,156.42
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.299,-0.29539,-0.89136,-0.34382,425.99,0.87766,-0.11101,-0.46626,155.38
> view matrix models
> #6,0.37744,-0.43949,0.8151,77.803,-0.29539,-0.89136,-0.34382,426.26,0.87766,-0.11101,-0.46626,155.31
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.3964,-0.4154,0.81873,70.6,-0.31009,-0.89996,-0.30647,423.68,0.86412,-0.13239,-0.48555,163.85
> view matrix models
> #6,0.36188,-0.4339,0.82509,77.612,-0.3531,-0.88293,-0.30945,427.92,0.86276,-0.17936,-0.47273,169.32
> view matrix models
> #6,0.34333,-0.43629,0.83173,79.67,-0.33947,-0.88333,-0.32323,428.21,0.87572,-0.17137,-0.45138,162.63
> view matrix models
> #6,0.36882,-0.43654,0.82061,77.724,-0.34143,-0.88476,-0.31721,427.74,0.86452,-0.16319,-0.47537,166.95
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.88,-0.33111,-0.89091,-0.31088,426.13,0.86644,-0.15658,-0.47409,165.42
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.37369,-0.42634,0.82377,75.079,-0.33111,-0.89091,-0.31088,425.43,0.86644,-0.15658,-0.47409,165.61
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.521,-0.33111,-0.89091,-0.31088,425.67,0.86644,-0.15658,-0.47409,165.89
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.154,-0.33111,-0.89091,-0.31088,425.74,0.86644,-0.15658,-0.47409,166.14
> view matrix models
> #6,0.37369,-0.42634,0.82377,74.447,-0.33111,-0.89091,-0.31088,425.75,0.86644,-0.15658,-0.47409,166.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.5154,-0.37111,0.77242,53.045,-0.24207,-0.9277,-0.2842,413.84,0.82205,-0.040509,-0.56797,170.41
> view matrix models
> #6,0.49373,-0.37696,0.78367,55.354,-0.26058,-0.92389,-0.28024,415.36,0.82966,-0.065846,-0.55437,171.02
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ~select #6
Nothing selected
> vop resample #6 onGrid #2
Opened cryosparc_P47_J128_002_volume_map_sharp.mrc resampled as #7, grid size
352,352,352, pixel 0.85, shown at step 1, values float32
> close #6
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> volume #7 level 0.09689
Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 175454 points
correlation = 0.8828, correlation about mean = 0.547, overlap = 7225
steps = 168, shift = 7.84, angle = 17 degrees
Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95949380 0.09544158 -0.26507085 39.26017660
-0.07373087 0.99314477 0.09070403 -7.34539260
0.27191066 -0.06748605 0.95995324 -23.66014125
Axis -0.27050228 -0.91822900 -0.28928192
Axis point 103.77985456 0.00000000 135.28320696
Rotation angle (degrees) 17.00173416
Shift along axis 2.96923623
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_ac.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 698, in take_snapshot
'region browser': self.region_browser.state(),
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in state
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <dictcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/region_browser.py", line 1106, in <listcomp>
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]
ValueError: <chimerax.seq-view.region_browser.Region object at 0x7fda72179070>
is not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fda70167a90> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7fda721771c0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fda70167a90> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7fda721771c0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Thu Mar 3 19:50:19 2022 ———
opened ChimeraX session
> show #9 models
> hide #!7 models
> show #3 models
> show #!7 models
> volume #7 level 0.1304
> hide #9 models
> hide #!2 models
> select #7
2 models selected
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.047588,-0.1037,-0.99347,365.91,0.86244,-0.4975,0.093243,89.677,-0.50392,-0.86124,0.065763,412.54
> view matrix models
> #3,0.06743,-0.16738,-0.98358,371.36,0.85706,-0.49497,0.14299,81.335,-0.51078,-0.85264,0.11008,404.4
> view matrix models
> #3,0.096228,-0.19565,-0.97594,369.69,0.85361,-0.48807,0.18201,73.83,-0.51194,-0.85059,0.12005,402.49
> view matrix models
> #3,0.12326,-0.1737,-0.97705,361.44,0.80994,-0.55129,0.20019,88.903,-0.57341,-0.81603,0.072729,415.92
> view matrix models
> #3,0.16662,-0.22348,-0.96036,359.21,0.80001,-0.5387,0.26416,77.136,-0.57639,-0.81231,0.089027,412.91
> view matrix models
> #3,0.16293,-0.22083,-0.96161,359.64,0.8006,-0.54002,0.25966,78.055,-0.57663,-0.81217,0.088811,412.97
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.16293,-0.22083,-0.96161,359.93,0.8006,-0.54002,0.25966,80.609,-0.57663,-0.81217,0.088811,411.39
> view matrix models
> #3,0.16293,-0.22083,-0.96161,360.07,0.8006,-0.54002,0.25966,81.287,-0.57663,-0.81217,0.088811,412.29
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.17153,-0.1861,-0.96744,353.75,0.81713,-0.52169,0.24523,77.868,-0.55034,-0.83259,0.062584,415.78
> view matrix models
> #3,0.18128,-0.16143,-0.97009,348.36,0.82389,-0.51369,0.23944,76.368,-0.53698,-0.84265,0.03988,419.16
> view matrix models
> #3,0.15753,-0.14621,-0.97663,351.15,0.82063,-0.53075,0.21182,84.727,-0.54931,-0.83482,0.03638,420.64
> view matrix models
> #3,0.14559,-0.14302,-0.97895,353.12,0.82526,-0.52818,0.1999,85.606,-0.54566,-0.837,0.04113,419.52
> view matrix models
> #3,0.10891,-0.20392,-0.97291,368.74,0.80086,-0.56179,0.20739,94.212,-0.58886,-0.80175,0.10213,410.32
> view matrix models
> #3,7.5917e-05,-0.38124,-0.92448,409.06,0.76186,-0.5988,0.247,100.24,-0.64774,-0.70434,0.29041,370.76
> view matrix models
> #3,0.020851,-0.42125,-0.9067,408.97,0.8145,-0.51877,0.25975,75.255,-0.57979,-0.74392,0.33229,358
> view matrix models
> #3,0.0058992,-0.41587,-0.90941,411.17,0.80554,-0.53687,0.25074,81.477,-0.59251,-0.73405,0.33183,358.66
> view matrix models
> #3,0.010117,-0.39918,-0.91682,408.95,0.78121,-0.56916,0.25643,90.171,-0.62418,-0.71883,0.30608,366.25
> show #!2 models
> show #4 models
> hide #!2 models
> hide #4 models
> hide #!7 models
> show #!2 models
> volume #2 level 0.1739
> volume #2 level 0.2952
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> select #3/B:2,7,40,94,101,112-114,116,120,122,233
96 atoms, 87 bonds, 12 residues, 1 model selected
> color sel red
> color sel red
> volume #2 level 0.275
> volume #2 level 0.2628
> show #!7 models
> show #9 models
> hide #!7 models
> hide #!2 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,0.38721,-0.79412,0.46845,171.91,0.90831,0.41577,-0.04598,200.21,-0.15825,0.4433,0.88229,215.35
> view matrix models
> #9,-0.087483,-0.4123,0.90684,172.91,0.99343,0.031343,0.11009,201.89,-0.073812,0.91051,0.40685,212.01
> view matrix models
> #9,-0.28915,-0.67075,0.68299,173.05,0.95728,-0.20238,0.20652,203.01,-0.00030104,0.71353,0.70062,213.67
> view matrix models
> #9,-0.26136,-0.69506,0.66977,173.04,0.95462,-0.083484,0.28588,202.96,-0.14278,0.71409,0.68534,213.75
> view matrix models
> #9,-0.24903,-0.6779,0.69169,173.06,0.94836,-0.025801,0.31615,202.9,-0.19647,0.7347,0.64932,213.61
> view matrix models
> #9,-0.29521,-0.62627,0.72155,173.07,0.95342,-0.14413,0.26498,203.06,-0.061948,0.76617,0.63965,213.33
> view matrix models
> #9,-0.20952,-0.51342,0.83217,173.06,0.97542,-0.05031,0.21455,202.56,-0.068285,0.85666,0.51134,212.57
> view matrix models
> #9,0.10294,-0.34459,0.93309,172.61,0.93996,0.34057,0.022073,200.66,-0.32539,0.8748,0.35896,212.2
> view matrix models
> #9,-0.16022,-0.18462,0.96966,172.53,0.98145,0.074958,0.17644,202.03,-0.10526,0.97995,0.16919,210.92
> show #!2 models
> view matrix models
> #9,-0.15367,-0.25507,0.95464,172.68,0.9497,-0.30492,0.0714,202.82,0.27288,0.91759,0.28909,211.18
> view matrix models
> #9,-0.5038,0.50581,0.70024,169.74,0.53017,-0.45894,0.71295,206.18,0.68199,0.73043,-0.036959,210.08
> view matrix models
> #9,-0.57338,0.5803,0.57834,169.11,0.40927,-0.40864,0.81579,206.54,0.70974,0.70446,-0.0031917,210.27
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.57338,0.5803,0.57834,169.15,0.40927,-0.40864,0.81579,203.59,0.70974,0.70446,-0.0031917,212
> view matrix models
> #3,0.010117,-0.39918,-0.91682,409.31,0.78121,-0.56916,0.25643,90.718,-0.62418,-0.71883,0.30608,366.04
> view matrix models
> #3,0.010117,-0.39918,-0.91682,409.6,0.78121,-0.56916,0.25643,90.515,-0.62418,-0.71883,0.30608,366.16
> view matrix models
> #2,-0.25925,0.42088,0.86928,32.265,0.23342,0.90067,-0.36647,74.017,-0.93718,0.1079,-0.33174,370.87
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.61844,0.56215,0.54911,169.14,0.3784,-0.39939,0.83505,203.67,0.68873,0.72421,0.034284,212.11
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.61844,0.56215,0.54911,177.9,0.3784,-0.39939,0.83505,199.13,0.68873,0.72421,0.034284,214.65
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.4,0.3784,-0.39939,0.83505,196.45,0.68873,0.72421,0.034284,215.17
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.59,0.3784,-0.39939,0.83505,195.92,0.68873,0.72421,0.034284,215.89
> ui tool show "Fit in Map"
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 5602 atoms
average map value = 0.1891, steps = 236
shifted from previous position = 3.82
rotated from previous position = 35.5 degrees
atoms outside contour = 3840, contour level = 0.26284
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97831960 0.09903901 0.18188469 -62.54218727
0.12885075 -0.97864261 -0.16017526 308.84298175
0.16213651 0.18013858 -0.97018650 260.99607581
Axis 0.99452465 0.05771160 0.08712110
Axis point 0.00000000 144.84592078 146.67317576
Rotation angle (degrees) 170.14858369
Shift along axis -21.63765850
> view matrix models
> #9,-0.61844,0.56215,0.54911,178.56,0.3784,-0.39939,0.83505,195.48,0.68873,0.72421,0.034284,215.15
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.6283,0.53153,0.56808,178.73,0.62001,-0.098962,0.77833,194.1,0.46993,0.84124,-0.26738,213.86
> view matrix models
> #9,-0.75088,0.39219,0.53138,179.14,0.55722,-0.055683,0.82849,194.22,0.35452,0.9182,-0.17673,214.09
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.41,0.62601,-0.03822,0.77888,193.91,0.31059,0.92838,-0.20408,214
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.53,0.31059,0.92838,-0.20408,211.04
> view matrix models
> #9,-0.71529,0.36967,0.59305,179.34,0.62601,-0.03822,0.77888,198.99,0.31059,0.92838,-0.20408,210.24
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.97,0.76527,0.12677,0.63111,197.77,-0.078317,0.99147,-0.10419,210.83
> select #3/C:2,7,40,94,101,112-114,116,120,122,233
96 atoms, 87 bonds, 12 residues, 1 model selected
> color sel red
> show #4 models
Average map value = 0.2376 for 3401 atoms, 1878 outside contour
Fit molecule F562a.pdb (#4) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 3401 atoms
average map value = 0.2415, steps = 72
shifted from previous position = 1.54
rotated from previous position = 3.06 degrees
atoms outside contour = 1864, contour level = 0.26284
Position of F562a.pdb (#4) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.23699392 -0.97040420 -0.04636322 286.30117001
0.14025454 0.08139807 -0.98676390 234.10565599
0.96133372 0.22735440 0.15539445 -33.95669350
Axis 0.62922896 -0.52224902 0.57561001
Axis point 0.00000000 269.86990420 6.31008896
Rotation angle (degrees) 105.25448782
Shift along axis 38.34172327
Fit map cryosparc_P47_J128_002_volume_map_sharp.mrc resampled in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 81674 points
correlation = 0.9169, correlation about mean = 0.5151, overlap = 5213
steps = 48, shift = 1.14, angle = 0.0547 degrees
Position of cryosparc_P47_J128_002_volume_map_sharp.mrc resampled (#7)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.95972235 0.09553744 -0.26420752 39.07093414
-0.07396939 0.99315174 0.09043310 -7.28703314
0.27103791 -0.06724740 0.96021677 -23.53165945
Axis -0.27038667 -0.91782581 -0.29066618
Axis point 103.47778140 0.00000000 135.13797870
Rotation angle (degrees) 16.95277212
Shift along axis 2.96382485
> close #7
> volume #1 level 0.127
> hide #!1 models
> volume #2 level 0.2119
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,-0.067254,-0.26525,-0.96183,404.94,0.33444,-0.91423,0.22874,235.99,-0.94001,-0.30629,0.1502,378.5
> view matrix models
> #3,-0.062041,-0.27434,-0.95963,405.16,0.30586,-0.92045,0.24337,239.46,-0.95005,-0.27841,0.14102,377.22
> view matrix models
> #3,-0.080997,-0.27474,-0.9581,408.29,0.28653,-0.9271,0.24163,244.29,-0.95464,-0.25496,0.15382,371.8
> view matrix models
> #3,-0.097933,-0.27408,-0.95671,410.91,0.27959,-0.93019,0.23786,246.7,-0.95511,-0.24419,0.16773,367.59
> undo
> view matrix models
> #3,-0.093936,-0.28928,-0.95262,412.03,0.28743,-0.92399,0.25224,241.72,-0.95318,-0.25012,0.16994,367.86
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.19,0.28616,-0.92153,0.26247,239.7,-0.95303,-0.24537,0.17756,365.67
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.02,0.76527,0.12677,0.63111,198.98,-0.078317,0.99147,-0.10419,210.72
> view matrix models
> #9,-0.63893,0.03031,0.76867,179.9,0.76527,0.12677,0.63111,199.21,-0.078317,0.99147,-0.10419,210.64
> view matrix models
> #9,-0.63893,0.03031,0.76867,179.76,0.76527,0.12677,0.63111,199.9,-0.078317,0.99147,-0.10419,210.02
> view matrix models
> #9,-0.63893,0.03031,0.76867,180,0.76527,0.12677,0.63111,200.37,-0.078317,0.99147,-0.10419,210.39
> view matrix models
> #9,-0.63893,0.03031,0.76867,180.28,0.76527,0.12677,0.63111,200.62,-0.078317,0.99147,-0.10419,210.66
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.6138,0.057604,0.78735,180.24,0.78755,0.11393,0.60562,200.54,-0.054817,0.99182,-0.1153,210.59
> hide #!2 models
> view matrix models
> #9,-0.57468,0.068825,0.81548,180.27,0.81757,0.092677,0.56833,200.43,-0.036461,0.99331,-0.10953,210.59
> view matrix models
> #9,-0.55308,0.076775,0.82958,180.28,0.83069,0.12691,0.54207,200.21,-0.063663,0.98894,-0.13397,210.54
> view matrix models
> #9,-0.59939,0.13134,0.78961,180.01,0.79964,0.14277,0.58326,200.35,-0.036127,0.981,-0.1906,210.32
> view matrix models
> #9,-0.6287,0.16179,0.76063,179.83,0.77763,0.13788,0.61342,200.5,-0.0056352,0.97715,-0.2125,210.21
> view matrix models
> #9,-0.66075,0.22875,0.7149,179.49,0.74952,0.14988,0.64479,200.62,0.040346,0.96188,-0.27049,209.99
> view matrix models
> #9,-0.67709,0.24845,0.69269,179.36,0.73306,0.14512,0.6645,200.72,0.064571,0.95771,-0.28039,209.94
> show #!2 models
> show #!1 models
> hide #!1 models
> ~select #9
Nothing selected
> volume #2 level 0.1883
> ui mousemode right "translate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.67709,0.24845,0.69269,178.01,0.73306,0.14512,0.6645,202.1,0.064571,0.95771,-0.28039,210.69
> view matrix models
> #9,-0.67709,0.24845,0.69269,178.34,0.73306,0.14512,0.6645,203.46,0.064571,0.95771,-0.28039,208.74
> ~select #9
Nothing selected
> hide #!2 models
> show #!2 models
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms
average map value = 0.1762, steps = 284
shifted from previous position = 2.13
rotated from previous position = 46.6 degrees
atoms outside contour = 1895, contour level = 0.18834
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.67425254 -0.64675933 -0.35649092 139.61136773
0.63282394 0.25716285 0.73034312 159.63361093
-0.38068004 -0.71803171 0.58267751 133.55311546
Axis -0.74936689 0.01251508 0.66203673
Axis point 0.00000000 205.05562824 -10.25332907
Rotation angle (degrees) 75.10511823
Shift along axis -14.20524073
> undo
> undo
> undo
> ~select #9
Nothing selected
> volume #2 level 0.2324
Fit molecule ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9) to
map cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 3334 atoms
average map value = 0.1762, steps = 284
shifted from previous position = 2.13
rotated from previous position = 46.6 degrees
atoms outside contour = 2433, contour level = 0.23244
Position of ApoA1_truncated_dimer_70bf1_unrelaxed_rank_1_model_4.pdb (#9)
relative to cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.67425254 -0.64675933 -0.35649092 139.61136773
0.63282394 0.25716285 0.73034312 159.63361093
-0.38068004 -0.71803171 0.58267751 133.55311546
Axis -0.74936689 0.01251508 0.66203673
Axis point 0.00000000 205.05562824 -10.25332907
Rotation angle (degrees) 75.10511823
Shift along axis -14.20524073
> ui mousemode right "rotate selected models"
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.51095,-0.017684,0.85943,178.44,0.84026,0.20068,0.50368,202.45,-0.18138,0.9795,-0.087678,211.18
> view matrix models
> #9,-0.56127,0.054587,0.82583,178.14,0.82479,0.1196,0.55265,202.9,-0.068599,0.99132,-0.11215,210.93
> hide #!2 models
> show #!2 models
> volume #2 level 0.1785
> hide #!2 models
> view matrix models
> #9,-0.55438,-0.0074968,0.83223,178.35,0.81959,0.16891,0.54748,202.74,-0.14467,0.9856,-0.087495,211.12
> show #!2 models
> hide #!2 models
> view matrix models
> #9,-0.6081,0.00065434,0.79386,178.23,0.7807,0.18184,0.59786,202.93,-0.14397,0.98333,-0.11109,211.04
> view matrix models
> #9,-0.60898,-0.00026107,0.79319,178.23,0.7797,0.18341,0.59869,202.93,-0.14563,0.98304,-0.11149,211.04
> view matrix models
> #9,-0.56366,0.059523,0.82386,178.12,0.81918,0.1683,0.54829,202.74,-0.10602,0.98394,-0.14362,210.87
> view matrix models
> #9,-0.61089,0.11381,0.78349,177.85,0.79055,0.14142,0.59585,203.04,-0.042985,0.98339,-0.17637,210.68
> show #!2 models
> volume #2 level 0.1908
> view matrix models
> #9,-0.59527,0.088593,0.79863,177.97,0.80315,0.095932,0.588,203.13,-0.024521,0.99144,-0.12826,210.82
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.59527,0.088593,0.79863,180.49,0.80315,0.095932,0.588,202.55,-0.024521,0.99144,-0.12826,210.1
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.54746,0.12014,0.82816,180.46,0.83671,0.062088,0.54411,202.45,0.013951,0.99081,-0.13451,210.04
> view matrix models
> #9,-0.61653,0.1277,0.77691,180.31,0.78731,0.092096,0.60964,202.66,0.0063037,0.98753,-0.15732,209.97
> view matrix models
> #9,-0.62782,0.073433,0.77489,180.48,0.77517,-0.030986,0.63099,203.13,0.070346,0.99682,-0.03747,210.34
> view matrix models
> #9,-0.62087,0.053369,0.7821,180.56,0.78091,-0.045216,0.62301,203.14,0.068612,0.99755,-0.013603,210.43
> view matrix models
> #9,-0.5736,-0.023782,0.81879,180.89,0.81885,0.0096521,0.57392,202.74,-0.021552,0.99967,0.013938,210.62
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.5736,-0.023782,0.81879,180.02,0.81885,0.0096521,0.57392,202.98,-0.021552,0.99967,0.013938,210.7
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.57847,0.031132,0.81511,179.85,0.81555,0.041881,0.57717,202.9,-0.01617,0.99864,-0.049616,210.46
> view matrix models
> #9,-0.56603,-0.015391,0.82424,180.01,0.82431,0.0025727,0.56613,202.97,-0.010834,0.99988,0.011231,210.68
> view matrix models
> #9,-0.71029,0.24008,0.6617,178.75,0.68817,0.039154,0.72449,203.6,0.14803,0.96996,-0.19303,209.83
> view matrix models
> #9,-0.68393,0.22919,0.69261,178.88,0.71976,0.056987,0.69188,203.39,0.1191,0.97171,-0.20393,209.81
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.76,0.71976,0.056987,0.69188,203.72,0.1191,0.97171,-0.20393,209.9
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.24,0.71976,0.056987,0.69188,203.81,0.1191,0.97171,-0.20393,210.17
> view matrix models
> #9,-0.68393,0.22919,0.69261,176.83,0.71976,0.056987,0.69188,203.91,0.1191,0.97171,-0.20393,210.29
> view matrix models
> #9,-0.68393,0.22919,0.69261,176.71,0.71976,0.056987,0.69188,203.93,0.1191,0.97171,-0.20393,210.32
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.17,0.71976,0.056987,0.69188,203.92,0.1191,0.97171,-0.20393,210.31
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.48,0.71976,0.056987,0.69188,203.79,0.1191,0.97171,-0.20393,210.28
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.92,0.71976,0.056987,0.69188,203.73,0.1191,0.97171,-0.20393,210.27
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.96,0.71976,0.056987,0.69188,203.75,0.1191,0.97171,-0.20393,210.29
> view matrix models
> #9,-0.68393,0.22919,0.69261,177.7,0.71976,0.056987,0.69188,203.84,0.1191,0.97171,-0.20393,210.22
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.64555,0.14914,0.74902,178.12,0.76365,0.11273,0.63571,203.41,0.010372,0.98237,-0.18667,210.37
> ~select #9
Nothing selected
> hide #!2 models
> show #!2 models
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.52,0.91486,0.1468,0.37614,202.16,-0.082923,0.98002,-0.18079,210.49
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.76,0.91486,0.1468,0.37614,202.52,-0.082923,0.98002,-0.18079,210.02
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.91,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.94
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.84,0.91486,0.1468,0.37614,202.6,-0.082923,0.98002,-0.18079,209.69
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.58,0.91486,0.1468,0.37614,202.13,-0.082923,0.98002,-0.18079,210.55
> view matrix models
> #9,-0.39517,0.13421,0.90875,178.72,0.91486,0.1468,0.37614,203.01,-0.082923,0.98002,-0.18079,210.68
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.44867,0.076406,0.89043,178.88,0.88471,0.17889,0.43044,203.15,-0.1264,0.9809,-0.14786,210.85
> ~select #9
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
——— End of log from Thu Mar 3 21:24:07 2022 ———
opened ChimeraX session
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/C
Alignment identifier is 1
> select #3/B-C:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:1-36
582 atoms, 598 bonds, 72 residues, 1 model selected
> hide #!2 models
> hide #9 models
> select #3/B-C:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:1-31
486 atoms, 496 bonds, 62 residues, 1 model selected
> select #3/B-C:1-2
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B-C:1-28
436 atoms, 446 bonds, 56 residues, 1 model selected
> select #3/B-C:25
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B-C:1-25
374 atoms, 378 bonds, 50 residues, 1 model selected
> color sel orange
> select #3/B-C:32-33
42 atoms, 42 bonds, 4 residues, 1 model selected
> select #3/B-C:32-139
1726 atoms, 1764 bonds, 216 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-144
1794 atoms, 1834 bonds, 226 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-150
1900 atoms, 1944 bonds, 238 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-159
2042 atoms, 2088 bonds, 256 residues, 1 model selected
> select #3/B-C:32
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #3/B-C:32-171
2246 atoms, 2300 bonds, 280 residues, 1 model selected
> select #3/B-C:23
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B-C:23-171
2404 atoms, 2464 bonds, 298 residues, 1 model selected
> select #3/B-C:26
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/B-C:26-171
2358 atoms, 2418 bonds, 292 residues, 1 model selected
> select #3/B-C:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B-C:26-172
2376 atoms, 2436 bonds, 294 residues, 1 model selected
> select #3/B-C:174
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #3/B-C:26-174
2416 atoms, 2476 bonds, 298 residues, 1 model selected
> color sel medium blue
> color sel blue
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> show #!1 models
> show #!2 models
> hide #!1 models
> volume #2 level 0.2959
> volume #2 level 0.3364
> volume #2 level 0.1382
> ui mousemode right "map eraser"
> volume erase #2 center 237.19,212.38,256.03 radius 33.098
> volume #2 level 0.1382
> volume erase #2 center 169.45,251.87,161.34 radius 16.218
> volume erase #2 center 169.29,250.35,162.17 radius 16.218
> volume erase #2 center 178.55,248.01,162.61 radius 16.218
> volume erase #2 center 193.98,241.53,160.53 radius 16.218
> volume erase #2 center 199.47,236.96,159.26 radius 16.218
> volume erase #2 center 162.44,240.05,168.47 radius 10.426
> volume erase #2 center 192.43,185.48,150.8 radius 10.426
> volume erase #2 center 222.56,163.1,224.04 radius 10.426
> volume erase #2 center 210.8,157.36,204.71 radius 4.3027
> volume erase #2 center 213.21,164.78,209.75 radius 4.3027
> volume erase #2 center 213.74,163.67,210.79 radius 4.3027
> volume erase #2 center 140.42,146.88,222.98 radius 7.2815
> volume erase #2 center 143.97,147.47,221.25 radius 7.2815
> volume erase #2 center 148.25,145.4,219.55 radius 7.2815
> volume erase #2 center 152.8,142.67,217.68 radius 7.2815
> volume erase #2 center 152.46,140.9,223.5 radius 7.2815
> volume erase #2 center 139.51,151.13,215.18 radius 7.2815
> volume erase #2 center 146.44,146.78,211.4 radius 7.2815
> volume erase #2 center 152.32,144.56,208.69 radius 7.2815
> volume erase #2 center 146.84,150.8,208.72 radius 7.2815
> volume erase #2 center 152.17,153.98,201.44 radius 7.2815
> hide #!2 models
> show #!2 models
> volume #2 level 0.3838
> volume #2 level 0.2253
> volume #2 level 0.0986
> volume #2 level 0.01
> volume #2 level 0.001
> volume #2 level 0.1
> volume #2 level 0.1475
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> color #3-4 bypolymer
> undo
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Fit in Map"
> hide #3 models
> show #3 models
> show #5 models
> hide #5 models
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,413.97,0.28616,-0.92153,0.26247,239.58,-0.95303,-0.24537,0.17756,365.68
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.09,0.28616,-0.92153,0.26247,239.88,-0.95303,-0.24537,0.17756,365.5
> view matrix models
> #3,-0.099224,-0.30095,-0.94846,414.1,0.28616,-0.92153,0.26247,239.98,-0.95303,-0.24537,0.17756,365.39
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.098121,-0.30274,-0.94801,414.12,0.28638,-0.9209,0.26444,239.49,-0.95308,-0.24554,0.17706,365.52
> view matrix models
> #3,-0.10399,-0.29321,-0.95038,413.98,0.28519,-0.92422,0.25393,242.13,-0.95281,-0.24463,0.17973,364.84
> view matrix models
> #3,-0.10804,-0.25387,-0.96119,410,0.28731,-0.93356,0.21428,250.39,-0.95173,-0.25301,0.1738,367.12
> view matrix models
> #3,-0.089326,-0.26965,-0.95881,408.94,0.27746,-0.93128,0.23606,247.86,-0.95658,-0.24494,0.15801,369.43
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 5602 atoms
average map value = 0.07054, steps = 76
shifted from previous position = 1.56
rotated from previous position = 7.95 degrees
atoms outside contour = 4416, contour level = 0.12697
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.01853403 0.20523285 0.97853769 -30.97334856
0.00646830 0.97866071 -0.20538117 45.38206352
-0.99980733 0.01013602 0.01681102 356.85899567
Axis 0.10776124 0.98919674 -0.09938471
Axis point 163.99516504 0.00000000 196.80902229
Rotation angle (degrees) 89.59876110
Shift along axis 6.08773536
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1044, steps = 92
shifted from previous position = 1.81
rotated from previous position = 8.09 degrees
atoms outside contour = 2312, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.87188277 -0.47824853 0.10535086 355.37302112
0.20869056 -0.16823549 0.96340288 57.21596158
-0.44302225 0.86196009 0.24648757 74.93473678
Axis -0.11464921 0.61976358 0.77636889
Axis point 179.54922209 52.98960138 0.00000000
Rotation angle (degrees) 153.74256446
Shift along axis 52.89413028
> view matrix models
> #4,0.86605,0.44369,-0.23043,24.081,-0.15116,-0.20695,-0.9666,357.32,-0.47656,0.87196,-0.11216,122.76
> view matrix models
> #4,0.24178,-0.10097,-0.96506,327.04,0.9586,-0.12931,0.25369,-9.1181,-0.15041,-0.98645,0.065523,378.67
> view matrix models
> #4,0.29714,-0.29814,-0.9071,345.67,0.95329,0.14663,0.26408,-59.546,0.054273,-0.94319,0.32778,301.43
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 320
shifted from previous position = 4.37
rotated from previous position = 11.4 degrees
atoms outside contour = 2213, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22359030 0.19234587 0.95551582 13.46864170
-0.96386692 0.10200874 -0.24607887 369.19247060
-0.14480322 -0.97601092 0.16258766 360.07001914
Axis -0.41589505 0.62693129 -0.65877801
Axis point 62.48187352 351.98959539 0.00000000
Rotation angle (degrees) 118.65255170
Shift along axis -11.34943811
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #5 models
> hide #5 models
> show #!2 models
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.0621 degrees
atoms outside contour = 2215, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22386136 0.19222999 0.95547567 13.54489824
-0.96395914 0.10094242 -0.24615736 369.41500556
-0.14376685 -0.97614461 0.16270474 359.89902128
Axis -0.41608471 0.62655616 -0.65901510
Axis point 62.46779097 351.82779571 0.00000000
Rotation angle (degrees) 118.69239674
Shift along axis -11.35546781
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.25124,-0.17542,-0.9519,335.64,0.9404,0.27709,0.19714,-70.324,0.22917,-0.9447,0.23458,277.59
> view matrix models
> #4,0.25124,-0.17542,-0.9519,335.72,0.9404,0.27709,0.19714,-70.489,0.22917,-0.9447,0.23458,277.37
> view matrix models
> #4,0.25124,-0.17542,-0.9519,336.84,0.9404,0.27709,0.19714,-70.794,0.22917,-0.9447,0.23458,276.49
Fit molecule F562a.pdb (#4) to map cryosparc_P35_J96_006_volume_map_sharp.mrc
(#1) using 3401 atoms
average map value = 0.1127, steps = 60
shifted from previous position = 2.03
rotated from previous position = 0.0879 degrees
atoms outside contour = 2217, contour level = 0.12697
Position of F562a.pdb (#4) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.22340595 0.19254318 0.95551920 13.40638758
-0.96384599 0.10241826 -0.24599073 369.10197141
-0.14522645 -0.97592912 0.16270112 360.10914844
Axis -0.41580714 0.62703635 -0.65873351
Axis point 62.50395161 352.02889088 0.00000000
Rotation angle (degrees) 118.62946316
Shift along axis -11.35008346
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C
Alignment identifier is 4/C
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/B:1-228
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> color sel forest green
> hide #!2 models
> ui tool show "Color Actions"
> color sel forest green
> color sel #e0fff2ff
> color sel #defff1ff
> color sel #c2ffcdff
> color sel #79ff7dff
> color sel #00ff05ff
> color sel #00ff07ff
> color sel #00ff09ff
> color sel #00ff07ff
[Repeated 1 time(s)]
> color sel #00f707ff
> color sel #00f507ff
> color sel #00f407ff
> color sel #00f307ff
> color sel #00f107ff
> color sel #00eb07ff
> color sel #00e907ff
> color sel #00e707ff
> color sel #00e106ff
> color sel #00dd06ff
> color sel #00db06ff
> color sel #00d906ff
> color sel #00d806ff
[Repeated 1 time(s)]
> color sel #00d606ff
> color sel #00d006ff
> color sel #00c706ff
> color sel #00c205ff
> color sel #00b905ff
> color sel #00b305ff
> color sel #00ab05ff
> color sel #00a605ff
> color sel #009d04ff
> color sel #009a04ff
> color sel #009604ff
> color sel #009404ff
> color sel #009204ff
> color sel #009104ff
> color sel #008f04ff
> color sel #008e04ff
[Repeated 1 time(s)]
> color sel #008d04ff
> color sel #008a04ff
[Repeated 1 time(s)]
> color sel #008804ff
> color sel #008704ff
> color sel #008604ff
> color sel #008504ff
[Repeated 1 time(s)]
> color sel #008304ff
> color sel #008204ff
> color sel #007f04ff
> color sel #007903ff
> color sel #007303ff
> color sel #006f03ff
> color sel #006e03ff
> color sel #006d03ff
> color sel #006c03ff
> color sel #006803ff
> color sel #005f03ff
> color sel #005c03ff
[Repeated 1 time(s)]
> color sel #005d03ff
> color sel #005e03ff
[Repeated 1 time(s)]
> color sel #005f03ff
> color sel #006003ff
[Repeated 2 time(s)]
> color sel #006103ff
[Repeated 2 time(s)]
> color sel #006203ff
[Repeated 3 time(s)]
> color sel #006103ff
[Repeated 2 time(s)]
> color sel #006003ff
[Repeated 1 time(s)]
> color sel #005f03ff
[Repeated 1 time(s)]
> color sel #005e03ff
[Repeated 1 time(s)]
> color sel #005d03ff
[Repeated 1 time(s)]
> color sel #005b03ff
[Repeated 1 time(s)]
> color sel #005a03ff
[Repeated 1 time(s)]
> color sel #005c03ff
> select #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ~select #4
Nothing selected
> show #!2 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C1.png"
> width 854 height 684 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
> width 1167 height 801 supersample 3
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C2.png"
> width 1167 height 801 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig2_C3.png"
> width 1167 height 801 supersample 3 transparentBackground true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J90_005_volume_map_sharp.mrc
Opened cryosparc_P35_J90_005_volume_map_sharp.mrc as #6, grid size
416,416,416, pixel 0.858, shown at level 0.0366, step 2, values float32
> hide #4 models
> hide #3 models
> volume #6 step 1
> volume #6 level 0.05781
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting simple
> volume #6 level 0.08608
> volume #6 level 0.1744
> volume #6 level 0.07548
> volume #6 level 0.06841
> volume #6 level 0.08255
> color #6 #bfb700 models transparency 0
> color #6 #bfb70039 models
> color #6 #bfb70028 models
> color #6 #fff40028 models
> color #6 #33300028 models
> color #6 #b4ac0028 models
> color #6 #b4ac00 models transparency 0
> color #6 #fff400 models transparency 0
> color #6 #f0e500 models transparency 0
> color #6 #f0e65a models transparency 0
> color #6 #c3bb49 models transparency 0
> color #6 #c3bb499a models
> color #6 #c3bb4941 models
> color #6 #c3bb4942 models
> color #6 #fffb00 models transparency 0
> color #6 #fffb0044 models
> color #6 #fffb0016 models
> color #6 #fffb0033 models
> color #6 #fffc79 models transparency 0
> color #6 #fffc7932 models
> color #6 #fffc7943 models
> color #6 #fffc794c models
> color #6 #fffc794d models
> select #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.022009,-0.94973,0.31229,283.41,-0.71721,-0.23262,-0.65689,470,0.69651,-0.20952,-0.68628,231.36
> view matrix models
> #6,0.48413,-0.86475,0.13353,218.33,-0.43491,-0.37024,-0.82084,473.48,0.75926,0.33932,-0.55533,99.971
> view matrix models
> #6,-0.32751,-0.77901,0.53468,275.33,-0.92972,0.16487,-0.32929,377.53,0.16837,-0.60495,-0.77826,413.98
> view matrix models
> #6,-0.2755,-0.92018,0.27814,339.29,-0.85315,0.10072,-0.51185,409.53,0.44298,-0.37831,-0.8128,331.15
> view matrix models
> #6,0.69873,-0.70402,0.127,152.52,0.37445,0.20866,-0.90346,241.09,0.60956,0.67883,0.40942,-115.9
> view matrix models
> #6,0.45295,-0.31947,0.83233,-3.9083,0.64601,-0.52579,-0.55337,251.33,0.61441,0.78834,-0.031778,-51.296
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.45295,-0.31947,0.83233,16.369,0.64601,-0.52579,-0.55337,269.43,0.61441,0.78834,-0.031778,-42.833
> view matrix models
> #6,0.45295,-0.31947,0.83233,16.57,0.64601,-0.52579,-0.55337,267.55,0.61441,0.78834,-0.031778,-43.336
> view matrix models
> #6,0.45295,-0.31947,0.83233,17.018,0.64601,-0.52579,-0.55337,268.42,0.61441,0.78834,-0.031778,-43.438
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.457,0.64601,-0.52579,-0.55337,265.98,0.61441,0.78834,-0.031778,-43.237
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.708,0.64601,-0.52579,-0.55337,267.25,0.61441,0.78834,-0.031778,-43.377
> view matrix models
> #6,0.45295,-0.31947,0.83233,13.833,0.64601,-0.52579,-0.55337,266.18,0.61441,0.78834,-0.031778,-42.937
> view matrix models
> #6,0.45295,-0.31947,0.83233,14.199,0.64601,-0.52579,-0.55337,266.61,0.61441,0.78834,-0.031778,-44.947
> volume #2 color #b8b5af4b
> volume #2 color #b8b5af4d
> show #3 models
> hide #!2 models
> volume #6 level 0.2239
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.29246,-0.71165,0.63876,258.29,-0.85627,-0.10251,-0.50625,462.3,0.42576,-0.69501,-0.57939,354.66
> view matrix models
> #6,-0.47549,-0.59046,0.65212,268.57,-0.79255,-0.034193,-0.60885,458.81,0.3818,-0.80634,-0.45171,357.01
> view matrix models
> #6,-0.34414,-0.36794,0.86382,164.08,-0.77861,-0.40232,-0.48157,495.02,0.52473,-0.8383,-0.14803,276.41
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.34414,-0.36794,0.86382,151.79,-0.77861,-0.40232,-0.48157,494.89,0.52473,-0.8383,-0.14803,279.06
> view matrix models
> #6,-0.34414,-0.36794,0.86382,151.48,-0.77861,-0.40232,-0.48157,494.87,0.52473,-0.8383,-0.14803,277.43
> volume #6 level 0.1673
> view matrix models
> #6,-0.34414,-0.36794,0.86382,149.97,-0.77861,-0.40232,-0.48157,494.85,0.52473,-0.8383,-0.14803,278.57
> view matrix models
> #6,-0.34414,-0.36794,0.86382,150.29,-0.77861,-0.40232,-0.48157,492.94,0.52473,-0.8383,-0.14803,277.18
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.34656,-0.40224,0.84741,159.86,-0.77344,-0.38862,-0.50077,493.34,0.53075,-0.82896,-0.17642,279.97
> view matrix models
> #6,-0.31668,-0.43946,0.84059,162.15,-0.77551,-0.39032,-0.49622,493.13,0.54617,-0.80903,-0.2172,281.6
> view matrix models
> #6,-0.32094,-0.45467,0.83083,167.46,-0.7722,-0.38228,-0.5075,493.32,0.54836,-0.80445,-0.22841,282.58
> view matrix models
> #6,-0.20123,-0.51264,0.83469,154.78,0.96454,0.044877,0.2601,-48.467,-0.1708,0.85743,0.48543,-11.902
> view matrix models
> #6,-0.19126,-0.46003,0.86706,137.55,0.78245,0.46189,0.41766,-117.87,-0.59262,0.75831,0.27161,124.2
> view matrix models
> #6,-0.16309,-0.47088,0.86699,134.27,0.77568,0.48185,0.40761,-118.14,-0.6097,0.73898,0.28667,127.76
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.16309,-0.47088,0.86699,134.42,0.77568,0.48185,0.40761,-149.14,-0.6097,0.73898,0.28667,101.11
> view matrix models
> #3,0.001066,-0.23035,-0.97311,385.86,0.36811,-0.90469,0.21456,228.51,-0.92978,-0.35844,0.08383,403.03
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.043523,-0.55853,0.82834,135.17,0.777,0.50225,0.37948,-147.46,-0.62799,0.66014,0.41212,93.77
> view matrix models
> #6,-0.13478,-0.49296,0.85955,134.49,0.77638,0.48647,0.40073,-148.74,-0.61569,0.72134,0.31716,99.344
> view matrix models
> #6,0.96181,-0.16288,-0.21999,85.595,0.2594,0.79899,0.54252,-135.51,0.087404,-0.57887,0.81072,99.737
> show #4 models
> view matrix models
> #6,0.67607,-0.69317,-0.24988,235.71,0.28695,0.56004,-0.77719,157.01,0.67866,0.45373,0.57753,-142.42
> view matrix models
> #6,0.24716,-0.80723,0.536,181.65,0.88374,0.41465,0.21697,-120.33,-0.39739,0.42006,0.81586,14.664
> view matrix models
> #6,-0.091274,-0.52365,0.84703,134.26,0.8991,0.32235,0.29617,-122.53,-0.42813,0.7886,0.44139,29.149
> view matrix models
> #6,-0.11554,-0.4685,0.87587,123.56,0.69127,0.59529,0.40961,-153.69,-0.7133,0.65279,0.25508,141.19
> view matrix models
> #6,-0.046411,-0.35281,0.93454,79.438,0.59316,0.74302,0.30997,-141.93,-0.80374,0.56872,0.17479,187.94
> view matrix models
> #6,-0.069072,-0.35388,0.93274,84.134,0.6004,0.73194,0.32216,-143.71,-0.79671,0.58226,0.16191,186.8
> view matrix models
> #6,-0.057044,-0.36632,0.92874,84.856,0.64945,0.69291,0.31319,-144.21,-0.75826,0.62103,0.19838,165.95
> view matrix models
> #6,-0.079957,-0.35928,0.9298,87.636,0.65299,0.68589,0.32118,-145.19,-0.75313,0.63283,0.17976,166.58
> view matrix models
> #6,-0.1341,-0.37541,0.91711,102.83,0.65851,0.65782,0.36557,-149.96,-0.74053,0.65295,0.159,164.81
> view matrix models
> #6,-0.12427,-0.37199,0.91988,99.899,0.65174,0.66844,0.35836,-149.16,-0.74819,0.64406,0.15938,167.68
> view matrix models
> #6,-0.11498,-0.39854,0.90992,104.73,0.64766,0.66446,0.37287,-150.54,-0.7532,0.63219,0.18172,166.32
> view matrix models
> #6,0.0002274,-0.40749,0.91321,84.492,0.63579,0.70493,0.3144,-144.02,-0.77186,0.58054,0.25924,163.65
> volume #6 level 0.1497
> view matrix models
> #6,0.0046913,-0.41214,0.91111,84.898,0.66603,0.68091,0.30458,-143.4,-0.74591,0.60539,0.27769,151.16
> view matrix models
> #6,-0.048323,-0.43445,0.8994,100.5,0.7189,0.61,0.33328,-146.09,-0.69343,0.66268,0.28285,130.85
> view matrix models
> #6,-0.10978,-0.42931,0.89646,111.19,0.68648,0.6195,0.38074,-151.02,-0.71881,0.6572,0.22671,147.1
> view matrix models
> #6,-0.12181,-0.41902,0.89977,110.93,0.69056,0.61537,0.38006,-150.91,-0.71294,0.66764,0.2144,146.6
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.12181,-0.41902,0.89977,108.89,0.69056,0.61537,0.38006,-148.49,-0.71294,0.66764,0.2144,143.63
> view matrix models
> #6,-0.12181,-0.41902,0.89977,110.07,0.69056,0.61537,0.38006,-147.38,-0.71294,0.66764,0.2144,145.3
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,472.46,-0.072251,0.33944,-0.93785,289.57,0.80252,-0.53855,-0.25675,172.86
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,487.54,-0.072251,0.33944,-0.93785,305.54,0.80252,-0.53855,-0.25675,191.57
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,493,-0.072251,0.33944,-0.93785,306.92,0.80252,-0.53855,-0.25675,188.04
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,502.5,-0.072251,0.33944,-0.93785,311.18,0.80252,-0.53855,-0.25675,188.67
> view matrix models
> #6,-0.59223,-0.7712,-0.2335,499.52,-0.072251,0.33944,-0.93785,313.18,0.80252,-0.53855,-0.25675,187.29
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.82421,-0.553,0.12194,435.21,-0.037209,-0.16199,-0.98609,402.96,0.56506,-0.81729,0.11294,207.26
> view matrix models
> #6,-0.44543,-0.86122,0.24473,397.17,-0.26729,-0.13296,-0.9544,433.08,0.85449,-0.49053,-0.17097,153.23
> view matrix models
> #6,-0.36539,-0.89648,0.25061,387.81,-0.30567,-0.13874,-0.94198,438.58,0.87924,-0.4208,-0.22333,146.76
> volume #6 level 0.2451
> view matrix models
> #6,-0.26247,-0.55243,0.79116,201.13,-0.8293,-0.29003,-0.47764,470,0.49332,-0.78148,-0.382,313.01
> view matrix models
> #6,-0.28569,-0.52355,0.80267,198.17,-0.82429,-0.29297,-0.48448,470.94,0.48881,-0.80004,-0.34786,310.26
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.28569,-0.52355,0.80267,180.48,-0.82429,-0.29297,-0.48448,474.67,0.48881,-0.80004,-0.34786,307.45
> volume #6 level 0.1673
> view matrix models
> #6,-0.28569,-0.52355,0.80267,178.35,-0.82429,-0.29297,-0.48448,476.02,0.48881,-0.80004,-0.34786,306.81
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.14718,-0.54954,0.8224,153.6,-0.85753,-0.34346,-0.38298,471.17,0.49292,-0.7616,-0.4207,313.54
> view matrix models
> #6,-0.14519,-0.57785,0.80312,161.88,-0.8523,-0.33921,-0.39815,472.41,0.5025,-0.74231,-0.44325,312.81
> view matrix models
> #6,-0.14171,-0.61705,0.77406,173.68,-0.84479,-0.3322,-0.41948,473.96,0.51599,-0.71336,-0.47421,311.33
> view matrix models
> #6,-0.123,-0.64321,0.75574,178.33,-0.8848,-0.2738,-0.37704,462.95,0.44944,-0.71506,-0.53544,335.73
> view matrix models
> #6,0.10222,-0.64957,0.7534,138.55,-0.86358,-0.43386,-0.2569,463.46,0.49374,-0.62436,-0.6053,325.44
> view matrix models
> #6,0.10839,-0.64998,0.75218,137.72,-0.86646,-0.4327,-0.24905,462.27,0.48734,-0.62473,-0.61008,327.61
> view matrix models
> #6,-0.17656,-0.48355,0.85733,140.78,-0.84554,-0.37137,-0.38359,473.92,0.50387,-0.79263,-0.34329,301.87
> view matrix models
> #6,-0.23478,-0.43523,0.86917,140.8,-0.85004,-0.34178,-0.40076,472.95,0.47149,-0.83292,-0.28972,304.4
> view matrix models
> #6,-0.22867,-0.43704,0.86989,139.85,-0.85367,-0.33948,-0.39497,472.09,0.46792,-0.83292,-0.29546,306.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.22867,-0.43704,0.86989,137.64,-0.85367,-0.33948,-0.39497,471.42,0.46792,-0.83292,-0.29546,310.38
> view matrix models
> #6,-0.22867,-0.43704,0.86989,137.55,-0.85367,-0.33948,-0.39497,472.47,0.46792,-0.83292,-0.29546,308.95
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.25766,-0.4215,0.86945,140.27,-0.85126,-0.32669,-0.41064,472.85,0.45712,-0.84594,-0.27463,309.15
> view matrix models
> #6,-0.24131,-0.47116,0.8484,149.96,-0.84523,-0.32751,-0.42229,474.15,0.47682,-0.81899,-0.3192,309.52
> view matrix models
> #6,-0.22049,-0.52796,0.82015,161.46,-0.83815,-0.32752,-0.43617,475.54,0.4989,-0.78357,-0.37029,309.25
> view matrix models
> #6,-0.16435,-0.57156,0.80393,161.86,-0.87529,-0.29128,-0.38603,466.35,0.45481,-0.76712,-0.45241,330.43
> view matrix models
> #6,-0.18555,-0.55494,0.81094,161.51,-0.86165,-0.30484,-0.40575,470.03,0.47237,-0.77403,-0.4216,322.42
> view matrix models
> #6,-0.2448,-0.5224,0.8168,165.61,-0.85708,-0.27726,-0.4342,469.93,0.4533,-0.80636,-0.37987,323.42
> view matrix models
> #6,-0.1668,-0.4734,0.86491,133.46,-0.84447,-0.38422,-0.37316,474.3,0.50897,-0.79263,-0.33568,302.25
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.1668,-0.4734,0.86491,132.36,-0.84447,-0.38422,-0.37316,474.18,0.50897,-0.79263,-0.33568,304.38
> view matrix models
> #6,-0.1668,-0.4734,0.86491,132.99,-0.84447,-0.38422,-0.37316,474.25,0.50897,-0.79263,-0.33568,304.17
> view matrix models
> #6,-0.1668,-0.4734,0.86491,133.6,-0.84447,-0.38422,-0.37316,474.33,0.50897,-0.79263,-0.33568,303.95
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.32695,-0.44627,0.83303,164.48,-0.82463,-0.29585,-0.48214,476.54,0.46162,-0.84458,-0.27128,309.14
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.32695,-0.44627,0.83303,165.99,-0.82463,-0.29585,-0.48214,476.36,0.46162,-0.84458,-0.27128,308.97
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.94,-0.82463,-0.29585,-0.48214,479.3,0.46162,-0.84458,-0.27128,310.62
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.99,-0.82463,-0.29585,-0.48214,477.92,0.46162,-0.84458,-0.27128,311.73
> view matrix models
> #6,-0.32695,-0.44627,0.83303,166.29,-0.82463,-0.29585,-0.48214,478.59,0.46162,-0.84458,-0.27128,310.92
> volume #6 level 0.1249
> view matrix models
> #6,-0.32695,-0.44627,0.83303,165.96,-0.82463,-0.29585,-0.48214,479.04,0.46162,-0.84458,-0.27128,311.24
> show #!1 models
> hide #3 models
> hide #4 models
> select #1
2 models selected
> view matrix models
> #1,-0.99948,-0.025572,-0.01976,364.95,0.031105,-0.92707,-0.3736,414.45,-0.0087649,-0.37402,0.92738,76.793
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.93251,0.32395,-0.15963,316.09,0.35214,0.71758,-0.6009,105.04,-0.080113,-0.61656,-0.78322,444.34
> view matrix models
> #1,-0.92079,0.38867,0.032827,267.4,0.38993,0.91934,0.052624,-56.723,-0.009726,0.061257,-0.99807,349.94
> view matrix models
> #1,-0.87777,0.3565,0.32005,213.16,0.3764,0.92646,0.00035867,-46.06,-0.29638,0.12078,-0.9474,381.24
> view matrix models
> #1,-0.89237,0.44968,0.038176,250.47,0.16187,0.3979,-0.90304,251.08,-0.42127,-0.79967,-0.42786,473.18
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89237,0.44968,0.038176,252.64,0.16187,0.3979,-0.90304,250.64,-0.42127,-0.79967,-0.42786,471.5
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.91313,0.40742,0.014419,268.22,0.16668,0.40537,-0.89883,247.68,-0.37205,-0.81834,-0.43806,467.9
> view matrix models
> #1,-0.86639,0.4978,-0.039456,253.56,0.25363,0.37062,-0.89348,237.39,-0.43015,-0.78411,-0.44736,473.86
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.86639,0.4978,-0.039456,247.82,0.25363,0.37062,-0.89348,237.47,-0.43015,-0.78411,-0.44736,473.22
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.87597,0.47955,-0.052144,255.09,0.30604,0.46893,-0.82852,198.74,-0.37286,-0.74171,-0.55753,475.49
> view matrix models
> #1,-0.88553,0.45898,0.071919,237.88,0.23094,0.5692,-0.7891,187.07,-0.40311,-0.68216,-0.61004,479.83
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.88553,0.45898,0.071919,232.83,0.23094,0.5692,-0.7891,186.52,-0.40311,-0.68216,-0.61004,479.89
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.93268,0.36026,0.017859,268.7,0.20808,0.57784,-0.78918,189.07,-0.29463,-0.73234,-0.6139,470.19
> view matrix models
> #1,-0.9521,0.2987,0.065475,274.48,0.12858,0.58532,-0.80054,204,-0.27744,-0.75378,-0.59569,467.63
Fit map cryosparc_P35_J96_006_volume_map_sharp.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 125084 points
correlation = 0.7737, correlation about mean = 0.5148, overlap = 4611
steps = 324, shift = 10.7, angle = 12.5 degrees
Position of cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00018548 -0.96024693 0.27915190 304.64819825
0.47329448 0.24582180 0.84591014 -90.95034872
-0.88090425 0.13227795 0.45443398 232.87270604
Axis -0.36089737 0.58666245 0.72496915
Axis point 266.13823335 42.12806522 0.00000000
Rotation angle (degrees) 98.62488972
Shift along axis 5.52163959
> show #!2 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs"
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs" includeMaps true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J88_003_volume_map_sharp.mrc
Opened cryosparc_P35_J88_003_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.0322, step 2, values float32
> hide #!6 models
> hide #!1 models
> hide #!2 models
> volume #7 level 0.08768
> volume #7 level 0.03374
> volume #7 level 0.01342
> volume #7 level 0.05407
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-HDL/cryosparc_P35_J87_003_volume_map_sharp.mrc
Opened cryosparc_P35_J87_003_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.858, shown at level 0.0329, step 2, values float32
> close #7
> volume #8 level 0.07979
> volume #8 level 0.05868
> volume #8 level 0.0493
> volume #8 color #b2ffff76
> volume #8 color #b2ffff75
> show #3 models
> select #8
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-5.0701,0,1,0,25.403,0,0,1,13.725
> view matrix models #8,1,0,0,-2.4128,0,1,0,22.261,0,0,1,17.693
> view matrix models #8,1,0,0,13.637,0,1,0,15.538,0,0,1,17.629
> view matrix models #8,1,0,0,17.759,0,1,0,21.107,0,0,1,15.457
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.9437,0.30533,-0.12727,-1.7134,-0.30648,0.95181,0.01092,77.369,0.12448,0.028702,0.99181,-8.2592
> view matrix models
> #8,0.93379,0.13868,-0.32987,64.541,0.05145,0.86023,0.5073,-55.026,0.35412,-0.49068,0.79614,77.197
> view matrix models
> #8,0.93056,0.16968,-0.32446,58.857,0.023869,0.85614,0.5162,-51.428,0.36537,-0.48809,0.79263,75.552
> view matrix models
> #8,0.92836,0.172,-0.32949,59.73,0.0092364,0.87553,0.48308,-46.35,0.37157,-0.45151,0.81122,65.012
> view matrix models
> #8,0.90406,0.053265,-0.42407,100.79,0.15019,0.88934,0.43188,-62.499,0.40015,-0.45413,0.79602,63.521
> view matrix models
> #8,0.90236,0.062663,-0.42639,99.9,0.13798,0.8953,0.42357,-60.014,0.40829,-0.44104,0.79924,59.399
> view matrix models
> #8,0.95884,0.13052,-0.25215,47.832,0.14193,0.54884,0.82379,-74.184,0.24591,-0.82568,0.50772,203.41
> view matrix models
> #8,0.8439,0.43609,-0.31252,25.859,0.15414,0.36088,0.91979,-61.706,0.51389,-0.82438,0.23733,208.08
> view matrix models
> #8,0.72071,0.42588,-0.547,89.933,0.3615,0.44239,0.82074,-91.531,0.59152,-0.78925,0.16489,202.5
> view matrix models
> #8,0.88841,0.1882,-0.4187,79.584,0.16981,0.71266,0.68065,-80.646,0.42648,-0.6758,0.60117,131.75
> view matrix models
> #8,0.81278,0.18222,-0.55333,117.19,0.28518,0.70377,0.65067,-92.602,0.50799,-0.68666,0.52005,134.87
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.81278,0.18222,-0.55333,111.12,0.28518,0.70377,0.65067,-89.214,0.50799,-0.68666,0.52005,131.56
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.66641,0.31634,-0.67515,134.32,0.37078,0.645,0.6682,-96.429,0.64685,-0.69563,0.31254,147.74
> view matrix models
> #8,0.64719,0.35366,-0.67533,131.19,0.38471,0.61328,0.68984,-97.242,0.65814,-0.70627,0.26085,157
> view matrix models
> #8,0.58239,0.30728,-0.75259,163.52,0.46192,0.63672,0.61743,-100.78,0.66892,-0.70723,0.22888,161.16
> view matrix models
> #8,0.7541,0.27199,-0.59778,113.55,0.30905,0.65618,0.68842,-91.868,0.5795,-0.70388,0.41077,142.46
> view matrix models
> #8,0.61599,0.12295,-0.7781,193.77,0.49388,0.70924,0.50306,-97.665,0.61371,-0.69417,0.37616,141.46
> view matrix models
> #8,0.73698,0.11525,-0.66601,155.12,0.40454,0.71417,0.57123,-96.173,0.54148,-0.69041,0.47971,133.98
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.73698,0.11525,-0.66601,155.56,0.40454,0.71417,0.57123,-90.04,0.54148,-0.69041,0.47971,141.01
> view matrix models
> #8,0.73698,0.11525,-0.66601,154.44,0.40454,0.71417,0.57123,-89.633,0.54148,-0.69041,0.47971,140.1
> view matrix models
> #8,0.73698,0.11525,-0.66601,153.2,0.40454,0.71417,0.57123,-89.182,0.54148,-0.69041,0.47971,139.08
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.73974,0.19261,-0.64473,135.84,0.34001,0.71983,0.60517,-85.705,0.58066,-0.66689,0.467,130.99
> close #8
> volume #1 color #b2b2b280
[Repeated 1 time(s)]
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
Opened
011762271936024191787_FoilHole_12249383_Data_12248537_12248539_20211012_184153-341492_patch_aligned.mrc
as #7, grid size 3838,3710,1, pixel 0.85,0.85,0.85, shown at step 1, values
float32
> close #7
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #4 models
> show #9 models
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/B:2-3
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/B:2-19
142 atoms, 143 bonds, 18 residues, 1 model selected
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B:1-27
211 atoms, 212 bonds, 27 residues, 1 model selected
> select #9/B:1-27
211 atoms, 212 bonds, 27 residues, 1 model selected
> select #9/B:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #9/B:1-30
232 atoms, 233 bonds, 30 residues, 1 model selected
> ui mousemode right "color key"
> key delete
> ui mousemode right "rotate selected models"
> color sel cornflower blue
> color sel #7a81ffff
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> select #9/B-C:1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:1-30
464 atoms, 466 bonds, 60 residues, 1 model selected
> color sel #0433ffff
> color sel #7a81ffff
> select #9/B-C:31-33
42 atoms, 42 bonds, 6 residues, 1 model selected
> select #9/B-C:31-63
562 atoms, 570 bonds, 66 residues, 1 model selected
> color sel dim gray
> select #9/B-C:64-65
38 atoms, 40 bonds, 4 residues, 1 model selected
> select #9/B-C:64-85
402 atoms, 414 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:86
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:108-109
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-140
190 atoms, 192 bonds, 22 residues, 1 model selected
> select #9/B-C:130-201
1092 atoms, 1102 bonds, 144 residues, 1 model selected
> select #9/B-C:130-150
334 atoms, 336 bonds, 42 residues, 1 model selected
> select #9/B-C:88-151
1030 atoms, 1038 bonds, 128 residues, 1 model selected
> select #9/B-C:130-151
342 atoms, 344 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:2-149,151-206
3296 atoms, 3340 bonds, 408 residues, 1 model selected
> select #9/B-C:151
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #9/B-C:151-157
108 atoms, 110 bonds, 14 residues, 1 model selected
> select #9/B-C:152-153
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #9/B-C:152-172
318 atoms, 320 bonds, 42 residues, 1 model selected
> select #9/B-C:31-34
60 atoms, 60 bonds, 8 residues, 1 model selected
> select #9/B-C:31-63
562 atoms, 570 bonds, 66 residues, 1 model selected
> select #9/B-C:2-149,151-206
3296 atoms, 3340 bonds, 408 residues, 1 model selected
> select #9/B-C:53
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/B-C:53-63
186 atoms, 184 bonds, 22 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:64
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:64-85
402 atoms, 414 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:86-87
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> color sel dim gray
> select #9/B-C:108
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> select #9/B-C:107
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:86-107
358 atoms, 360 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:108-109
30 atoms, 30 bonds, 4 residues, 1 model selected
> select #9/B-C:108-129
360 atoms, 362 bonds, 44 residues, 1 model selected
> color sel dim gray
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-149
326 atoms, 328 bonds, 40 residues, 1 model selected
> select #9/B-C:130-131
38 atoms, 40 bonds, 4 residues, 1 model selected
> select #9/B-C:130-150
334 atoms, 336 bonds, 42 residues, 1 model selected
> select #9/B-C:130
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:130-151
342 atoms, 344 bonds, 44 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:152-153
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #9/B-C:152-172
318 atoms, 320 bonds, 42 residues, 1 model selected
> color sel dim gray
> select #9/B-C:174
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/B-C:174-176
48 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/B-C:173
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:173-183
174 atoms, 174 bonds, 22 residues, 1 model selected
> color sel #d783ffff
> color sel #7a81ffff
> select #9/B-C:184
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/B-C:184-207
354 atoms, 354 bonds, 48 residues, 1 model selected
> color sel dim gray
> select #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> ~select #9
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
> show #!2 models
> show #4 models
> hide #4 models
> volume #2 level 0.1179
> show #4 models
> volume #2 level 0.13
> volume #2 level 0.14
> volume #2 level 0.15
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_D.png"
> width 1009 height 824 supersample 3 transparentBackground true
> show #!6 models
> hide #!2 models
> show #!2 models
Fit map cryosparc_P35_J90_005_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 114729 points
correlation = 0.672, correlation about mean = 0.08483, overlap = 3988
steps = 212, shift = 5.69, angle = 24.1 degrees
Position of cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.48667344 0.82476587 0.28794127 36.88441365
-0.86459172 -0.40757626 -0.29387534 426.86136408
-0.12502033 -0.39197297 0.91144230 73.88929120
Axis -0.05631763 0.23708030 -0.96985631
Axis point 142.84730785 210.89177337 0.00000000
Rotation angle (degrees) 119.43288522
Shift along axis 27.46118471
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #6 level 0.12
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> ~select #3
Nothing selected
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08293, steps = 148
shifted from previous position = 4.12
rotated from previous position = 15.3 degrees
atoms outside contour = 4112, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.47334151 0.84962673 0.23255592 79.20387762
0.74805308 0.24829808 0.61543861 -93.30922995
0.46514990 0.46527681 -0.75309567 157.40236379
Axis -0.50919647 -0.78872280 -0.34443477
Axis point 62.66416490 -0.00000000 102.29599347
Rotation angle (degrees) 171.52083443
Shift along axis -20.95006494
> undo
[Repeated 2 time(s)]
> hide #!2 models
> log metadata #3
The model has no metadata
> log chains #3
Chain information for D2NS1.pdb #3
---
Chain | Description
B C | No description available
> ui mousemode right "rotate selected models"
> select #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> view matrix models
> #3,-0.0085676,-0.30727,-0.95158,398.88,0.38479,-0.87936,0.28049,211.07,-0.92297,-0.36375,0.12577,388.55
> view matrix models
> #3,-0.13489,-0.29223,-0.94679,417.71,0.36981,-0.90133,0.22551,227.19,-0.91926,-0.31971,0.22965,361.99
> view matrix models
> #3,-0.071496,-0.30058,-0.95107,408.73,0.37829,-0.89045,0.25298,218.98,-0.92292,-0.34169,0.17737,375.64
> view matrix models
> #3,-0.18267,-0.34044,-0.92235,429.87,0.39852,-0.88325,0.24708,215.26,-0.89878,-0.32244,0.29702,346.84
> view matrix models
> #3,-0.40995,0.57223,-0.71028,278.61,-0.10972,-0.804,-0.58442,439.45,-0.90548,-0.16165,0.39238,304
> view matrix models
> #3,-0.46987,0.63995,-0.60802,259.54,-0.55045,-0.75089,-0.36493,468.93,-0.69009,0.16321,0.70508,155.79
> view matrix models
> #3,-0.65716,0.081263,-0.74936,411.59,-0.053676,-0.99669,-0.061013,368.75,-0.75184,0.0001281,0.65934,202.22
> view matrix models
> #3,-0.62292,-0.22233,0.75003,189.5,-0.068144,-0.9397,-0.33515,410.55,0.77931,-0.25988,0.5702,-7.4739
> view matrix models
> #3,0.31022,-0.41267,0.85643,38.43,-0.2398,-0.90571,-0.34955,437.59,0.91992,-0.096935,-0.37993,109.67
> view matrix models
> #3,0.14284,-0.48882,0.86061,79.927,-0.73689,-0.63302,-0.23725,459.16,0.66075,-0.60029,-0.45063,252.47
> view matrix models
> #3,0.069717,-0.45875,0.88582,83.239,-0.93425,-0.34135,-0.10325,420.96,0.34974,-0.82038,-0.45239,344.49
> view matrix models
> #3,-0.24695,0.22628,0.94224,13.705,-0.87659,-0.46663,-0.11768,434.45,0.41304,-0.85502,0.31359,202.72
> view matrix models
> #3,-0.099087,-0.011917,0.99501,18.348,-0.8839,-0.45823,-0.09351,430.02,0.45706,-0.88875,0.034872,250.31
> view matrix models
> #3,0.0096812,0.032947,0.99941,-9.1088,-0.93353,-0.3579,0.020842,401.51,0.35838,-0.93318,0.027292,276.48
> view matrix models
> #3,-0.060408,-0.021128,0.99795,12.57,-0.98054,-0.18582,-0.063289,395.83,0.18678,-0.98236,-0.0094914,321.48
> view matrix models
> #3,-0.14852,-0.072188,0.98627,38.731,-0.98683,-0.053816,-0.15254,390.64,0.064089,-0.99594,-0.063245,354.92
> view matrix models
> #3,-0.35842,-0.23162,0.90437,117.04,-0.92969,0.00036447,-0.36835,409.93,0.084987,-0.97281,-0.21546,374.47
> view matrix models
> #3,-0.16442,-0.085208,0.9827,44.354,-0.94873,-0.25901,-0.1812,423.54,0.26997,-0.96211,-0.038251,308.57
> view matrix models
> #3,-0.29929,0.026962,0.95378,54.365,-0.9175,-0.28257,-0.27991,439.6,0.26196,-0.95887,0.10931,283.15
> view matrix models
> #3,0.21447,0.471,0.85566,-93.169,0.97669,-0.095031,-0.1925,59.362,-0.0093522,0.877,-0.4804,127.25
> view matrix models
> #3,0.56515,0.56728,0.59899,-125.3,0.82406,-0.42253,-0.37735,174.2,0.03903,0.70687,-0.70627,187.59
> view matrix models
> #3,0.2047,0.3956,0.89532,-85.837,0.92678,0.21596,-0.30731,36.306,-0.31492,0.89267,-0.32243,150.21
> view matrix models
> #3,0.26975,0.34464,0.89914,-89.39,0.91144,0.20987,-0.35388,48.323,-0.31067,0.91497,-0.25751,134.15
> view matrix models
> #3,0.15293,0.16968,0.97356,-52.687,0.98145,0.089212,-0.16972,23.489,-0.11565,0.98145,-0.15289,70.037
> view matrix models
> #3,0.042216,0.087727,0.99525,-23.3,0.97412,0.21777,-0.060515,-16.293,-0.22204,0.97205,-0.076263,76.678
> view matrix models
> #3,0.035376,0.093709,0.99497,-23.053,0.9291,0.36366,-0.067284,-31.697,-0.36814,0.92681,-0.0742,109.61
> view matrix models
> #3,-0.74086,0.45839,0.49092,141.95,-0.6574,-0.34504,-0.66991,473.84,-0.13769,-0.81904,0.55697,250.17
> view matrix models
> #3,-0.12274,0.85219,0.50863,-36.128,-0.96225,-0.22764,0.1492,361.79,0.24294,-0.47111,0.84796,72.892
> view matrix models
> #3,-0.67677,0.0678,0.73307,153.21,-0.71984,-0.26966,-0.63962,466.75,0.15432,-0.96057,0.2313,280.63
> view matrix models
> #3,-0.31096,-0.28409,0.90697,117.06,-0.89867,-0.2227,-0.37788,443.68,0.30934,-0.93258,-0.18605,323.01
> view matrix models
> #3,-0.31328,-0.20485,0.9273,100.52,-0.94642,-0.013217,-0.32266,407.02,0.078354,-0.9787,-0.18974,372.05
> view matrix models
> #3,0.084796,0.15045,0.98497,-39.503,-0.99107,-0.089391,0.098974,352.56,0.10294,-0.98457,0.14152,309.7
> view matrix models
> #3,-0.17084,-0.018385,0.98513,33.815,-0.98351,0.06341,-0.16938,373.35,-0.059353,-0.99782,-0.028915,370.83
> view matrix models
> #3,-0.3307,0.24426,0.91158,30.874,-0.94057,-0.0062546,-0.33954,407.82,-0.077235,-0.96969,0.23181,322.8
> view matrix models
> #3,-0.4809,0.025548,0.8764,100.33,-0.81554,-0.38005,-0.43642,465.94,0.32193,-0.92461,0.2036,250.04
> view matrix models
> #3,-0.53944,-0.043921,0.84088,128.63,-0.79768,-0.29313,-0.52705,464.33,0.26964,-0.95506,0.12309,278.7
> view matrix models
> #3,-0.45493,0.037354,0.88974,91.401,-0.78489,-0.48882,-0.3808,468.93,0.4207,-0.87159,0.2517,215.19
> view matrix models
> #3,-0.42074,0.12675,0.89828,68.835,-0.79214,-0.53394,-0.29568,462.63,0.44215,-0.83597,0.32506,192.35
> view matrix models
> #3,-0.55645,0.18988,0.80889,98.012,-0.74741,-0.53968,-0.38746,472.08,0.36297,-0.82018,0.44222,182.75
> view matrix models
> #3,-0.56077,0.17343,0.8096,101.41,-0.75525,-0.50786,-0.41434,472.89,0.3393,-0.8438,0.41578,195.6
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.56077,0.17343,0.8096,97.107,-0.75525,-0.50786,-0.41434,471.77,0.3393,-0.8438,0.41578,196.64
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.31072,0.047476,0.94931,49.418,-0.82644,-0.50685,-0.24516,453.98,0.46952,-0.86073,0.19672,215.61
> view matrix models
> #3,-0.10594,-0.13924,0.98458,38.514,-0.92405,-0.35194,-0.1492,428.01,0.36729,-0.92561,-0.091386,295.82
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08181, steps = 140
shifted from previous position = 5.91
rotated from previous position = 5.33 degrees
atoms outside contour = 4112, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.96127167 0.06226622 -0.26847668 48.62307340
-0.22542895 0.73805618 -0.63596769 218.36928771
0.15855157 0.67186013 0.72350910 -87.31437189
Axis 0.93048244 -0.30381850 -0.20468696
Axis point 0.00000000 232.24708974 246.16405973
Rotation angle (degrees) 44.64955765
Shift along axis -3.22959992
> view matrix models
> #3,-0.2167,-0.046006,0.97515,46.998,-0.825,-0.52541,-0.20812,455.06,0.52193,-0.8496,0.075903,227.93
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.08275, steps = 232
shifted from previous position = 0.39
rotated from previous position = 10.7 degrees
atoms outside contour = 4141, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.94687496 0.16521963 -0.27591724 34.87295901
-0.32111058 0.53311437 -0.78273693 296.77138746
0.01777194 0.82975393 0.55784641 -59.68855935
Axis 0.94317112 -0.17178339 -0.28446215
Axis point 0.00000000 208.08374987 254.78468856
Rotation angle (degrees) 58.74030833
Shift along axis -1.11009298
> view matrix models
> #3,-0.29357,0.29509,0.90925,14.248,-0.93223,-0.29887,-0.20399,435.37,0.21155,-0.90752,0.36283,240.41
> view matrix models
> #3,-0.024736,0.33337,0.94247,-45.387,-0.98041,-0.19235,0.042305,382.05,0.19538,-0.92297,0.3316,251.41
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.024736,0.33337,0.94247,-50.647,-0.98041,-0.19235,0.042305,380.65,0.19538,-0.92297,0.3316,252
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.07754, steps = 124
shifted from previous position = 0.984
rotated from previous position = 11.7 degrees
atoms outside contour = 4222, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.97038128 -0.18348442 -0.15714223 69.99792136
-0.04643502 0.49668363 -0.86668864 273.08312267
0.23707384 0.84831532 0.47345239 -88.46523910
Axis 0.97164206 -0.22334462 0.07764586
Axis point 0.00000000 220.43718489 187.11160518
Rotation angle (degrees) 61.94891347
Shift along axis 0.15231786
> view matrix models
> #3,-0.16161,0.20679,0.96495,-7.8987,-0.94599,-0.31092,-0.091808,418.86,0.28103,-0.92767,0.24587,240.27
> view matrix models
> #3,-0.16161,0.20679,0.96495,-7.6794,-0.94599,-0.31092,-0.091808,419.8,0.28103,-0.92767,0.24587,239.05
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.065282,0.14337,0.98751,-17.979,-0.96082,-0.2762,-0.023418,404.39,0.26939,-0.95035,0.15578,260.96
> view matrix models
> #3,0.11914,-0.22697,0.96659,15.581,-0.91769,-0.3968,0.019938,409.35,0.37901,-0.8894,-0.25556,304.72
Fit molecule D2NS1.pdb (#3) to map cryosparc_P35_J90_005_volume_map_sharp.mrc
(#6) using 5602 atoms
average map value = 0.082, steps = 232
shifted from previous position = 14.3
rotated from previous position = 15.8 degrees
atoms outside contour = 4100, contour level = 0.12
Position of D2NS1.pdb (#3) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.93730079 0.13375954 -0.32183172 47.54908073
-0.32984053 0.63871002 -0.69516528 263.49850116
0.11257216 0.75773210 0.64278271 -75.44380421
Axis 0.91623198 -0.27394552 -0.29235734
Axis point -0.00000000 224.55289345 259.75440758
Rotation angle (degrees) 52.45410370
Shift along axis -6.56169478
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.018323,-0.060034,0.99803,13.026,-0.84305,-0.53571,-0.047702,432.04,0.53752,-0.84226,-0.040796,240.98
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.036597,-0.098259,0.99449,23.297,-0.80637,-0.58491,-0.087465,440.94,0.59028,-0.80513,-0.057828,228.49
> view matrix models
> #3,-0.027477,-0.10288,0.99431,22.501,-0.77374,-0.6276,-0.086317,442.18,0.63291,-0.77171,-0.062357,216.18
> view matrix models
> #3,-0.10002,-0.07995,0.99177,31.858,-0.93297,-0.33885,-0.12141,427.89,0.34577,-0.93744,-0.040699,290.69
> view matrix models
> #3,-0.10077,-0.089813,0.99085,33.811,-0.91689,-0.37822,-0.12753,432.77,0.38621,-0.92135,-0.044236,281.5
> view matrix models
> #3,-0.032685,-0.1875,0.98172,39.889,-0.92726,-0.36087,-0.099796,426.73,0.37298,-0.91357,-0.16207,303.51
> volume #2 level 0.1688
> hide #!2 models
[Repeated 1 time(s)]
> volume #6 level 0.1932
> view matrix models
> #3,-0.15943,5.3271e-05,0.98721,29.667,-0.88694,0.43911,-0.14326,292.88,-0.4335,-0.89843,-0.06996,426.39
> view matrix models
> #3,-0.23062,0.17059,0.95797,18.724,-0.93077,-0.3257,-0.16608,433.25,0.28369,-0.92996,0.23389,251.43
> view matrix models
> #3,-0.029625,-0.49902,0.86608,112.33,-0.48854,-0.74869,-0.44809,476.83,0.87204,-0.43639,-0.22161,146.12
> view matrix models
> #3,0.26982,-0.40253,0.87474,41.898,-0.5711,-0.79831,-0.1912,453.92,0.77527,-0.44797,-0.44528,204.93
> view matrix models
> #3,-0.10768,-0.15758,0.98162,48.065,-0.99351,0.053323,-0.10043,368.86,-0.036518,-0.98607,-0.1623,387.76
> view matrix models
> #3,-0.059748,-0.20275,0.97741,47.98,-0.99636,0.071795,-0.046014,356.56,-0.060844,-0.9766,-0.2063,398.29
> view matrix models
> #3,-0.2527,-0.028861,0.96711,54.512,-0.96729,-0.015262,-0.2532,403,0.022068,-0.99947,-0.02406,355.08
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/4o6b_DV2NS1.pdb
4o6b_DV2NS1.pdb title:
Dengue TYPE2 virus non-structural protein 1 (NS1) form 1 crystal [more
info...]
Chain information for 4o6b_DV2NS1.pdb #7
---
Chain | Description | UniProt
A | NS1 | POLG_DEN26
B | NS1 | POLG_DEN26
Non-standard residues in 4o6b_DV2NS1.pdb #7
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select #7
5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,195.73,0,1,0,55.756,0,0,1,0.30073
> view matrix models #7,1,0,0,24.836,0,1,0,111.9,0,0,1,93.148
> view matrix models #7,1,0,0,184.13,0,1,0,225.28,0,0,1,192.15
> view matrix models #7,1,0,0,151.84,0,1,0,239.37,0,0,1,213.11
> view matrix models #7,1,0,0,191.69,0,1,0,227.02,0,0,1,208.55
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.98804,-0.14623,0.048956,188.26,0.13002,0.61931,-0.7743,195.13,0.082905,0.77141,0.63092,223.81
> view matrix models
> #7,0.99657,-0.079109,0.024224,189.79,0.063222,0.5393,-0.83974,190.38,0.053367,0.83839,0.54245,223.38
> view matrix models
> #7,0.94783,-0.3073,0.084745,183.81,0.25252,0.5616,-0.78793,193.76,0.19454,0.76823,0.6099,223.91
> view matrix models
> #7,0.59074,0.041726,0.80578,211.73,0.76522,0.28771,-0.57591,194.2,-0.25586,0.95681,0.13803,214.25
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.59074,0.041726,0.80578,206.56,0.76522,0.28771,-0.57591,184.3,-0.25586,0.95681,0.13803,224.47
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69999,-0.017723,0.71393,202.96,0.67927,0.32512,-0.65794,182.71,-0.22045,0.94551,0.23962,227.06
> view matrix models
> #7,0.84135,0.059716,0.53718,201.67,0.50634,0.26057,-0.82202,175.1,-0.18906,0.96361,0.18899,226.5
> view matrix models
> #7,0.91878,0.00070031,0.39477,196.52,0.37034,0.34484,-0.86252,175.78,-0.13674,0.93866,0.31658,229.47
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_00_final_volume.mrc
Opened cryosparc_P35_J141_class_00_final_volume.mrc as #8, grid size
128,128,128, pixel 2.79, shown at level 0.235, step 1, values float32
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/NS1ts-Fab-HDL/cryosparc_P35_J141_class_01_final_volume.mrc
Opened cryosparc_P35_J141_class_01_final_volume.mrc as #10, grid size
128,128,128, pixel 2.79, shown at level 0.281, step 1, values float32
> select #10
2 models selected
> view matrix models
> #10,-0.079171,0.66364,0.74385,-61.635,-0.22432,-0.73892,0.63536,232.1,0.97129,-0.11656,0.20737,-7.2572
> view matrix models
> #10,-0.28893,0.313,0.90474,9.1948,-0.47663,-0.86662,0.1476,393.94,0.83026,-0.38858,0.39958,30.91
> ~select #10
Nothing selected
> select #8
2 models selected
> view matrix models
> #8,0.27556,0.9224,0.27065,-84.292,-0.27059,-0.19574,0.94258,80.02,0.92241,-0.33297,0.19565,46.409
> view matrix models
> #8,0.63638,0.51065,0.57815,-136.4,0.085328,0.6983,-0.7107,175.68,-0.76664,0.50161,0.40081,166.71
> view matrix models
> #8,-0.3692,-0.17702,0.91234,105.18,-0.32493,-0.89515,-0.30518,456,0.8707,-0.40912,0.27296,54.461
> view matrix models
> #8,-0.21183,0.1782,0.96092,3.7465,-0.32373,-0.94052,0.10305,384.86,0.92213,-0.28925,0.25692,26.817
> color #10 #ffb2b270 models
[Repeated 1 time(s)]
> color #8 #ffb2ff56 models
> color #8 #ffb2ff57 models
> hide #4 models
> hide #3 models
> hide #!8 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #!10 models
> show #!8 models
> view matrix models
> #8,0.27556,0.39667,0.87562,-107.73,0.79978,-0.59996,0.020098,134.95,0.53331,0.69477,-0.48257,65.706
> view matrix models
> #8,0.27366,0.52314,0.80712,-116.65,0.91914,-0.38945,-0.059223,90.987,0.28335,0.75806,-0.58742,120.4
> view matrix models
> #8,0.33758,0.53414,0.77507,-124.09,0.9382,-0.25771,-0.23103,97.287,0.076338,0.80516,-0.58813,149.98
> view matrix models
> #8,0.45264,0.48026,0.75131,-130.92,0.89015,-0.19384,-0.41237,129.79,-0.052411,0.85544,-0.51524,150.44
> view matrix models
> #8,0.65699,0.41807,0.62736,-133.2,0.73578,-0.1742,-0.65443,201.34,-0.16431,0.89156,-0.42206,146.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.65699,0.41807,0.62736,-126.9,0.73578,-0.1742,-0.65443,207.73,-0.16431,0.89156,-0.42206,145.93
> view matrix models
> #8,0.65699,0.41807,0.62736,-126.22,0.73578,-0.1742,-0.65443,209.21,-0.16431,0.89156,-0.42206,144.54
> view matrix models
> #8,0.65699,0.41807,0.62736,-124.37,0.73578,-0.1742,-0.65443,208.1,-0.16431,0.89156,-0.42206,144.61
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.53344,-0.037486,0.84501,-62.766,0.5106,-0.78219,-0.35703,299.99,0.67434,0.62191,-0.39811,34.754
> volume #8 level 0.8045
> view matrix models
> #8,0.52401,-0.054439,0.84997,-58.961,0.47038,-0.81345,-0.3421,310.02,0.71003,0.57907,-0.40065,36.512
> volume #8 level 0.3577
> show #!10 models
> hide #!8 models
> view matrix models
> #8,0.60764,0.020079,0.79396,-76.868,0.73022,-0.40725,-0.54857,228.31,0.31232,0.9131,-0.26212,18.911
> show #!8 models
> view matrix models
> #8,0.37572,0.11623,0.91941,-75.961,0.70308,-0.68208,-0.20109,215.44,0.60375,0.72198,-0.33799,14.583
Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
cryosparc_P35_J141_class_00_final_volume.mrc using 20957 points
correlation = 0.9488, correlation about mean = 0.6585, overlap = 4385
steps = 288, shift = 15.4, angle = 91.5 degrees
Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
cryosparc_P35_J141_class_00_final_volume.mrc (#8) coordinates:
Matrix rotation and translation
0.99679931 0.07719696 -0.02077903 -9.05098271
-0.07875179 0.99291028 -0.08903553 30.04476737
0.01375844 0.09038694 0.99581168 -19.54599107
Axis 0.74691139 -0.14377477 -0.64919349
Axis point 0.00000000 219.63678499 322.55619772
Rotation angle (degrees) 6.89842857
Shift along axis 1.60916844
> volume #6 level 0.1566
> volume #6 level 0.1346
Fit map cryosparc_P35_J141_class_01_final_volume.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 20957 points
correlation = 0.7294, correlation about mean = 0.2901, overlap = 713.6
steps = 312, shift = 14.7, angle = 29.6 degrees
Position of cryosparc_P35_J141_class_01_final_volume.mrc (#10) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.81655312 0.57639109 -0.03184812 223.81505889
-0.57200743 -0.81530920 -0.08987989 441.91818039
-0.07777204 -0.05517435 0.99544327 24.62573349
Axis 0.03018293 0.03993939 -0.99874613
Axis point 182.23608880 186.02084504 0.00000000
Rotation angle (degrees) 144.90596060
Shift along axis -0.18951992
Fit map cryosparc_P35_J141_class_00_final_volume.mrc in map
cryosparc_P35_J90_005_volume_map_sharp.mrc using 13326 points
correlation = 0.7531, correlation about mean = 0.2446, overlap = 614.5
steps = 200, shift = 14.7, angle = 20.2 degrees
Position of cryosparc_P35_J141_class_00_final_volume.mrc (#8) relative to
cryosparc_P35_J90_005_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.51114495 0.85836696 -0.04401141 122.12595771
-0.83601173 -0.50841524 -0.20639360 453.44795134
-0.19953752 -0.06870298 0.97747873 53.02558896
Axis 0.08065933 0.09110739 -0.99256915
Axis point 191.43391939 194.60207731 0.00000000
Rotation angle (degrees) 121.40208746
Shift along axis -1.46850799
> volume #10 level 0.3562
> volume #8 level 0.2852
> volume #8 level 0.318
> hide #!7 models
> show #!7 models
> select #7
5126 atoms, 5257 bonds, 5 pseudobonds, 644 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91878,0.00070031,0.39477,195.03,0.37034,0.34484,-0.86252,183.44,-0.13674,0.93866,0.31658,212.37
> view matrix models
> #7,0.91878,0.00070031,0.39477,207.4,0.37034,0.34484,-0.86252,186.87,-0.13674,0.93866,0.31658,221.02
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.73404,-0.62761,0.2594,182.53,-0.25829,-0.61129,-0.74807,155.21,0.62806,0.48212,-0.61082,186.96
> view matrix models
> #7,0.74989,-0.64446,0.14946,179.17,-0.33839,-0.56778,-0.75041,155.99,0.56846,0.51215,-0.64386,186.63
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.74989,-0.64446,0.14946,177.57,-0.33839,-0.56778,-0.75041,160.17,0.56846,0.51215,-0.64386,189.52
> view matrix models
> #7,0.74989,-0.64446,0.14946,178.16,-0.33839,-0.56778,-0.75041,160.58,0.56846,0.51215,-0.64386,182.7
> view matrix models
> #7,0.74989,-0.64446,0.14946,177.56,-0.33839,-0.56778,-0.75041,162.27,0.56846,0.51215,-0.64386,183.32
> view matrix models
> #7,0.74989,-0.64446,0.14946,179.58,-0.33839,-0.56778,-0.75041,162.74,0.56846,0.51215,-0.64386,180.3
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.69567,-0.70398,0.14302,177.14,-0.33345,-0.49279,-0.80372,163.74,0.63628,0.51144,-0.57756,182.51
> view matrix models
> #7,0.76223,-0.64567,0.045974,176.86,-0.30995,-0.42641,-0.84977,164.78,0.56827,0.63347,-0.52515,187.33
> view matrix models
> #7,0.78877,-0.61274,0.04891,178.17,-0.30035,-0.4536,-0.83907,164.27,0.53632,0.64714,-0.54182,187.1
> view matrix models
> #7,0.6402,-0.76747,-0.033591,170.03,-0.27585,-0.18885,-0.94246,170.1,0.71697,0.61263,-0.33261,192.81
> view matrix models
> #7,0.62699,-0.77647,0.063022,172.23,-0.19611,-0.23561,-0.95186,168.91,0.75394,0.58444,-0.3,193.04
> view matrix models
> #7,0.75838,-0.62248,0.19333,181.51,-0.13362,-0.43878,-0.8886,164.56,0.63797,0.64807,-0.41594,191.18
> view matrix models
> #7,0.70141,-0.70676,0.092259,175.74,-0.28093,-0.39309,-0.87553,165.35,0.65506,0.58819,-0.47427,187.83
> view matrix models
> #7,0.69618,-0.71217,0.090246,175.48,-0.28016,-0.38529,-0.87924,165.51,0.66094,0.58683,-0.46775,188
> view matrix models
> #7,0.68522,-0.72338,0.084779,174.9,-0.27616,-0.36576,-0.88879,165.9,0.67395,0.58561,-0.4504,188.52
> view matrix models
> #7,0.74436,-0.66753,0.018223,175.3,-0.26396,-0.31919,-0.91019,166.9,0.61339,0.6727,-0.4138,191.85
> view matrix models
> #7,0.77161,-0.63604,-0.0079224,175.8,-0.26676,-0.31226,-0.91177,167.06,0.57745,0.70565,-0.41062,192.74
> view matrix models
> #7,0.73389,-0.66982,0.11293,177.69,-0.19652,-0.36852,-0.90861,165.83,0.65022,0.64462,-0.40208,191.52
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.73389,-0.66982,0.11293,176.82,-0.19652,-0.36852,-0.90861,164.33,0.65022,0.64462,-0.40208,195.23
> show #3 models
> hide #3 models
> show #!2 models
> show #3 models
> hide #!10 models
> hide #!7 models
Fit molecule D2NS1.pdb (#3) to map cryosparc_P47_J20_004_volume_map_sharp.mrc
(#2) using 5602 atoms
average map value = 0.1888, steps = 160
shifted from previous position = 4.81
rotated from previous position = 23.5 degrees
atoms outside contour = 2712, contour level = 0.1688
Position of D2NS1.pdb (#3) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.55420887 0.78282865 -0.28289899 176.19297958
-0.82333712 -0.46560234 0.32454654 303.63070097
0.12234590 0.41278781 0.90257282 -106.76939213
Axis 0.05319429 -0.24429289 -0.96824137
Axis point 171.19224328 117.42998509 0.00000000
Rotation angle (degrees) 123.96035927
Shift along axis 38.57618189
> close #10
> show #9 models
> hide #9 models
> show #!7 models
> view matrix models
> #7,0.73389,-0.66982,0.11293,170.79,-0.19652,-0.36852,-0.90861,155.22,0.65022,0.64462,-0.40208,205.07
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.90325,0.19269,0.38342,206.62,0.0001087,0.89341,-0.44925,208.99,-0.42912,0.40583,0.80695,222.37
> view matrix models
> #7,0.91285,-0.26756,0.30841,190.03,0.40807,0.57317,-0.7106,194.6,0.013357,0.77453,0.6324,232.47
> view matrix models
> #7,0.76546,-0.55709,0.32206,180.18,0.59967,0.43603,-0.67102,192.6,0.23339,0.70677,0.66784,232.76
> view matrix models
> #7,0.49342,-0.33249,0.80373,198.32,0.86883,0.23191,-0.43745,194.17,-0.040945,0.91415,0.4033,230.43
> view matrix models
> #7,0.61212,-0.26384,0.74546,199.76,0.7065,0.60592,-0.36567,206.88,-0.35521,0.7505,0.5573,227.19
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.61212,-0.26384,0.74546,192.13,0.7065,0.60592,-0.36567,204.9,-0.35521,0.7505,0.5573,229.56
Fit molecule 4o6b_DV2NS1.pdb (#7) to map
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) using 5126 atoms
average map value = 0.1927, steps = 152
shifted from previous position = 14.6
rotated from previous position = 16.1 degrees
atoms outside contour = 2452, contour level = 0.1688
Position of 4o6b_DV2NS1.pdb (#7) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.34465485 -0.66063558 -0.66691350 125.14009286
0.80909618 0.56930074 -0.14580812 154.59882031
0.47600039 -0.48934370 0.73073000 156.62388255
Axis -0.18145322 -0.60367956 0.77630260
Axis point -61.23617800 251.69459436 0.00000000
Rotation angle (degrees) 71.19533318
Shift along axis 5.55230604
> close #7
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/20220211_NUS-K3_gAU-
> sNS1-Fab56-2/cryosparc_P35_J130_004_volume_map_sharp.mrc
Opened cryosparc_P35_J130_004_volume_map_sharp.mrc as #7, grid size
416,416,416, pixel 0.858, shown at level 0.0371, step 2, values float32
> volume #7 level 0.09025
> lighting simple
> hide #3 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #3 models
> show #!1 models
> hide #!2 models
> hide #3 models
> select #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.24103,-0.29696,-0.92397,349.21,-0.038945,-0.95423,0.29653,285.57,-0.96974,-0.035487,-0.24156,398.71
> view matrix models
> #7,-0.24983,0.23805,-0.93857,346.61,-0.30202,0.90179,0.30911,13.804,0.91998,0.3607,-0.1534,-14.399
> view matrix models
> #7,-0.10249,0.16037,-0.98172,341.85,0.025379,0.98702,0.15858,-30.757,0.99441,-0.0086622,-0.10523,26.713
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.10249,0.16037,-0.98172,336.3,0.025379,0.98702,0.15858,-28.758,0.99441,-0.0086622,-0.10523,26.913
> view matrix models
> #7,-0.10249,0.16037,-0.98172,337.29,0.025379,0.98702,0.15858,-28.672,0.99441,-0.0086622,-0.10523,28.197
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.22211,-0.1265,-0.96678,404.24,-0.24639,0.96665,-0.069873,63.34,0.94338,0.22268,-0.24587,23.093
> view matrix models
> #7,-0.19183,0.047993,-0.98025,371.72,-0.43799,0.88964,0.12927,74.05,0.87827,0.45414,-0.14964,-22.192
> view matrix models
> #7,-0.34489,-0.073759,-0.93574,411.13,-0.53139,0.83711,0.12987,99.175,0.77374,0.54204,-0.32791,13.194
> view matrix models
> #7,-0.36324,0.1037,-0.92591,382.4,-0.38069,0.89052,0.24908,42.339,0.85037,0.44296,-0.284,8.7541
> view matrix models
> #7,-0.36165,0.10266,-0.92664,382.44,-0.38188,0.8904,0.24768,42.819,0.85051,0.44344,-0.28281,8.4329
> view matrix models
> #7,-0.35715,0.16036,-0.92018,370.68,-0.43075,0.84586,0.3146,46.881,0.82879,0.50872,-0.23302,-7.8271
> view matrix models
> #7,-0.37647,0.070708,-0.92373,389.93,-0.48903,0.83168,0.26297,68.754,0.78684,0.55073,-0.27853,0.54545
> view matrix models
> #7,-0.21108,0.96488,-0.15637,71.026,-0.41939,0.055099,0.90613,72.864,0.88292,0.25684,0.39304,-87.108
> view matrix models
> #7,-0.19093,-0.093424,0.97715,43.432,-0.59513,-0.78062,-0.19092,442.95,0.78062,-0.61798,0.093448,133.33
> view matrix models
> #7,-0.25485,0.0071755,0.96696,39.327,0.96698,0.0034538,0.25483,-43.217,-0.0015111,0.99997,-0.0078187,13.125
> view matrix models
> #7,-0.017228,0.34616,0.93802,-54.562,0.65851,0.70988,-0.24988,-18.615,-0.75238,0.61338,-0.24018,251.72
> view matrix models
> #7,0.28808,0.16888,0.9426,-78.558,0.64678,0.69156,-0.32157,-0.5571,-0.70617,0.7023,0.089997,169.14
> view matrix models
> #7,0.16326,0.14447,0.97595,-58.619,0.66325,0.71625,-0.21698,-26.446,-0.73037,0.68273,0.021113,189.08
Fit map cryosparc_P35_J130_004_volume_map_sharp.mrc in map
cryosparc_P35_J96_006_volume_map_sharp.mrc using 19964 points
correlation = 0.8354, correlation about mean = 0.6739, overlap = 929.1
steps = 276, shift = 3.71, angle = 23.7 degrees
Position of cryosparc_P35_J130_004_volume_map_sharp.mrc (#7) relative to
cryosparc_P35_J96_006_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.08559775 -0.03414562 -0.99574450 347.85846819
0.92968539 -0.35664221 0.09214889 59.72132131
-0.35827099 -0.93361685 0.00121691 410.96755552
Axis -0.66385471 -0.41255988 0.62377181
Axis point 0.00000000 67.86622584 347.54047210
Rotation angle (degrees) 129.41358899
Shift along axis 0.78387399
> volume #1 level 0.09
> volume #7 level 0.09
> ~select #7
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-10_NS1wt-Fab-ApoAI_hdl_Compare-
> NS1ts.cxs" includeMaps true
——— End of log from Fri Mar 11 18:14:28 2022 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!7 models
> show #3 models
> show #4 models
> show #!8 models
> hide #!8 models
> close #8
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #6
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_EM_Alvin/2022-03-03_NS1wt-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Sat Mar 12 14:58:51 2022 ———
opened ChimeraX session
> show #!1 models
> hide #!1 models
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/cryosparc_P39_J166_002_volume_map_sharp
> (1).mrc"
Opened cryosparc_P39_J166_002_volume_map_sharp (1).mrc as #6, grid size
416,416,416, pixel 0.85, shown at level 0.0339, step 2, values float32
> volume #6 level 0.05868
> volume #6 step 1
> ui mousemode right "translate selected models"
> show #!7 models
> hide #!7 models
> show #9 models
> hide #9 models
> select #6
2 models selected
> view matrix models #6,1,0,0,1.4767,0,1,0,-0.11126,0,0,1,17.894
> view matrix models #6,1,0,0,2.5835,0,1,0,15.467,0,0,1,19.701
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.077918,0.99542,-0.055373,-3.5895,-0.96552,0.089183,0.24459,303.08,0.24841,0.034406,0.96804,-24.193
> view matrix models
> #6,-0.62577,0.77732,-0.06471,158.15,-0.76968,-0.62881,-0.1104,452.92,-0.12651,-0.019279,0.99178,46.339
> view matrix models
> #6,-0.49195,0.83765,-0.23731,152.38,-0.80175,-0.32963,0.49855,307.08,0.33939,0.43553,0.83375,-88.641
> view matrix models
> #6,-0.43603,0.58765,-0.68157,258.71,-0.82618,0.03888,0.56206,236.26,0.3568,0.80818,0.46855,-97.873
> view matrix models
> #6,0.17544,0.72595,-0.66499,125.79,-0.86837,0.43236,0.24289,226.23,0.46384,0.53485,0.70625,-106.96
> view matrix models
> #6,-0.010663,0.39041,-0.92058,258.46,-0.28789,0.88046,0.37672,25.213,0.95761,0.26904,0.103,-47.908
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.010663,0.39041,-0.92058,281.12,-0.28789,0.88046,0.37672,26.602,0.95761,0.26904,0.103,-46.122
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.14635,0.34874,-0.92572,262.07,-0.39341,0.87913,0.26899,62.599,0.90764,0.32483,0.26586,-73.695
> view matrix models
> #6,0.12836,0.25158,-0.95929,287.7,-0.38687,0.90336,0.18515,70.814,0.91316,0.34735,0.21329,-70.077
> view matrix models
> #6,0.14119,0.15753,-0.97737,304.94,-0.41649,0.90509,0.085709,91.778,0.89811,0.39496,0.1934,-72.61
> view matrix models
> #6,0.16148,0.39933,-0.90248,246.79,-0.45122,0.84317,0.29235,75.141,0.87768,0.36001,0.31634,-82.878
> view matrix models
> #6,0.26156,0.1615,-0.95158,279.21,-0.12782,0.98301,0.1317,20.613,0.95669,0.087181,0.27776,-42.368
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.26156,0.1615,-0.95158,282.66,-0.12782,0.98301,0.1317,9.0483,0.95669,0.087181,0.27776,-38.201
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.13471,0.17399,-0.97549,306.32,-0.19051,0.97064,0.14682,19.629,0.9724,0.16606,0.1639,-36.307
> view matrix models
> #6,0.1878,0.10849,-0.9762,308.75,-0.44957,0.89315,0.012769,99.878,0.87328,0.43647,0.21651,-75.185
> view matrix models
> #6,0.28328,0.3407,-0.89648,238.47,-0.3572,0.905,0.23106,46.37,0.89003,0.25476,0.37807,-72.377
> volume #6 level 0.169
> volume #6 level 0.05336
> ui tool show "Fit in Map"
Fit map cryosparc_P39_J166_002_volume_map_sharp (1).mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 331401 points
correlation = 0.898, correlation about mean = 0.6711, overlap = 6198
steps = 152, shift = 5.34, angle = 16.7 degrees
Position of cryosparc_P39_J166_002_volume_map_sharp (1).mrc (#6) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.92297785 -0.38455624 0.01511101 379.01804384
-0.38212566 0.91106400 -0.15473309 83.70405585
0.04573648 -0.14858952 -0.98784072 344.43723548
Axis 0.19609203 -0.97751177 0.07757998
Axis point 196.53062877 0.00000000 177.04366349
Rotation angle (degrees) 179.10242404
Shift along axis 19.22215351
> volume #6 level 0.05037
> volume #6 level 0.03372
> volume #6 level 0.02603
> volume #2 level 0.1649
> volume #2 level 0.1496
> show #9 models
> volume #6 color #bf9d9e
> volume #6 color #bf9d9e57
> volume #6 level 0.05379
> volume #6 level 0.06874
> volume #2 level 0.1649
> volume #2 level 0.17
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/20211013_NTU-K2_EDEN2-Ab53/Fig4_E2.png"
> width 1326 height 850 supersample 3 transparentBackground true
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32
> select #8
2 models selected
> view matrix models
> #8,0.93452,-0.21005,-0.2873,102.16,-0.33903,-0.27981,-0.8982,451.28,0.10828,0.93679,-0.3327,69.288
> view matrix models
> #8,-0.43794,-0.41147,0.79931,176.41,-0.88911,0.32976,-0.31738,334,-0.13299,-0.84967,-0.51026,455.34
> view matrix models
> #8,-0.13025,-0.70515,0.697,191.9,-0.98813,0.15007,-0.032822,329.17,-0.081457,-0.693,-0.71632,457.81
> close #8
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_EM_Alvin/20220125_NTU-K2_NS1-WT_Fab/cryosparc_P36_J32_002_volume_map_sharp.mrc
Opened cryosparc_P36_J32_002_volume_map_sharp.mrc as #8, grid size
416,416,416, pixel 0.85, shown at level 0.0324, step 2, values float32
> color #8 #fff5c5 models transparency 0
> select #8
2 models selected
> view matrix models
> #8,-0.37477,-0.5067,0.77641,186,-0.92653,0.23447,-0.29422,352.81,-0.032965,-0.82963,-0.55734,442.95
> view matrix models
> #8,-0.40741,-0.58403,0.70209,219.21,-0.91262,0.28892,-0.28924,339.96,-0.033924,-0.75857,-0.6507,448.38
> view matrix models
> #8,-0.26337,-0.46915,0.84293,147.17,-0.95679,0.23865,-0.16612,333.34,-0.12323,-0.85026,-0.51174,453.98
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.26337,-0.46915,0.84293,164.19,-0.95679,0.23865,-0.16612,339.86,-0.12323,-0.85026,-0.51174,459.4
> color #8 #fff5c592 models
> color #8 #fff5c591 models
> view matrix models
> #8,-0.26337,-0.46915,0.84293,164.75,-0.95679,0.23865,-0.16612,339.53,-0.12323,-0.85026,-0.51174,460.75
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.30728,0.18959,0.93254,41.475,-0.40778,0.85919,-0.30905,161.27,-0.85982,-0.47524,-0.1867,465.45
> view matrix models
> #8,-0.48566,0.40603,0.77413,65.486,-0.39669,0.68678,-0.60908,245.69,-0.77896,-0.60289,-0.17248,470.53
> view matrix models
> #8,-0.49722,0.30467,0.81237,77.911,-0.61559,0.53594,-0.57777,304.85,-0.61141,-0.78737,-0.078928,455.12
> view matrix models
> #8,0.06302,-0.34884,0.93506,68.532,-0.69818,-0.6849,-0.20846,461.65,0.71314,-0.63971,-0.28672,233.22
> view matrix models
> #8,0.26213,-0.7558,0.60005,166.78,-0.96461,-0.18676,0.18614,348.34,-0.028616,-0.62761,-0.778,455.47
> view matrix models
> #8,-0.37994,0.023033,0.92472,84.739,-0.51716,0.82356,-0.233,172.57,-0.76693,-0.56676,-0.301,486.33
> view matrix models
> #8,0.19338,0.23275,0.95312,-58.871,-0.72187,0.69166,-0.022445,192.18,-0.66446,-0.68369,0.30177,374.89
> view matrix models
> #8,-0.21084,0.47884,0.85221,-10.689,-0.12039,0.85245,-0.50876,148.96,-0.97008,-0.20987,-0.12208,426.87
> view matrix models
> #8,-0.41196,0.43496,0.80069,42.367,-0.11525,0.84679,-0.51929,151.02,-0.90389,-0.30621,-0.29871,465.07
> view matrix models
> #8,-0.47775,0.38326,0.79049,64.945,-0.089881,0.87377,-0.47796,134.05,-0.87389,-0.29939,-0.38299,474.43
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.47775,0.38326,0.79049,62.298,-0.089881,0.87377,-0.47796,139.19,-0.87389,-0.29939,-0.38299,469.27
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> view matrix models
> #8,-0.62887,0.14228,0.76438,135.85,-0.3807,0.80086,-0.46227,200.57,-0.67794,-0.5817,-0.44947,495.91
> view matrix models
> #8,-0.68532,0.11195,0.71959,159.58,-0.34754,0.81805,-0.45826,190.94,-0.63997,-0.56414,-0.52172,499.72
> view matrix models
> #8,-0.62799,-0.10151,0.77157,176.61,-0.55751,0.75043,-0.35503,220.55,-0.54297,-0.65311,-0.52785,499.06
> ui tool show "Fit in Map"
Fit map cryosparc_P36_J32_002_volume_map_sharp.mrc in map
cryosparc_P47_J20_004_volume_map_sharp.mrc using 89910 points
correlation = 0.5947, correlation about mean = 0.2353, overlap = 907.9
steps = 260, shift = 8.79, angle = 25 degrees
Position of cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) relative to
cryosparc_P47_J20_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.83017657 0.55542318 0.04808244 -106.08230735
-0.55722739 0.82397862 0.10274640 83.33490981
0.01744883 -0.11209051 0.99354477 -6.27353855
Axis -0.18951476 0.02702292 -0.98150594
Axis point 82.90354713 206.61275632 0.00000000
Rotation angle (degrees) 34.52792807
Shift along axis 28.51363138
> volume #8 level 0.03877
> volume #8 step 1
> volume #8 level 0.05098
> volume #8 level 0.08193
> volume #8 level 0.07541
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_EM_Alvin/2022-03-23_NS1wt-Ab-Fab-
> ApoAI_hdl.cxs" includeMaps true
——— End of log from Thu Mar 24 12:02:48 2022 ———
opened ChimeraX session
> ui tool show "Volume Viewer"
> show #!1 models
> close #1
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!2 models
> show #!2 models
> rename #2 sNS1wt-Ab562.mrc
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!8 models
> volume #6 level 0.0595
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!2 models
> show #!2 models
> close #6
> show #!7 models
> hide #!2 models
> show #!2 models
> close #7
> show #5 models
> show #!8 models
> hide #9 models
> show #9 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #5 models
> show #5 models
> hide #!8 models
> show #!8 models
> hide #9 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right select
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.911,-0.19028,-0.36588,158.81,-0.385,-0.71042,-0.58914,511.26,-0.14783,0.67757,-0.72045,241.26
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.033091,0.22459,0.97389,-84.329,0.17148,0.9587,-0.22691,18.38,-0.98463,0.17451,-0.006788,310.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.033091,0.22459,0.97389,-41.613,0.17148,0.9587,-0.22691,17.858,-0.98463,0.17451,-0.006788,323.69
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.027159,0.41704,0.90848,-51.291,0.63529,0.70888,-0.30642,2.4644,-0.77179,0.56883,-0.2842,279.48
> view matrix models
> #5,-0.080191,0.31482,0.94576,-31.96,0.72243,0.67208,-0.16247,-40.126,-0.68678,0.67022,-0.28133,245.19
> view matrix models
> #5,-0.13135,0.33964,0.93134,-24.234,0.71868,0.67973,-0.14652,-44.687,-0.68283,0.65008,-0.33337,260.62
> view matrix models
> #5,-0.11889,0.37005,0.92137,-29.677,0.7114,0.6791,-0.18095,-35.108,-0.69266,0.63395,-0.34399,267.86
> view matrix models
> #5,0.045939,0.59116,0.80525,-71.763,0.70283,0.55371,-0.44659,52.881,-0.70988,0.58646,-0.39004,290.63
> view matrix models
> #5,0.084841,0.56745,0.81902,-77.41,0.67501,0.57189,-0.46615,59,-0.73291,0.5924,-0.33452,280.32
> view matrix models
> #5,-0.13391,0.55975,0.81777,-37.622,0.55097,0.72796,-0.40805,37.78,-0.82371,0.39592,-0.40589,349.58
> view matrix models
> #5,-0.09912,0.51183,0.85335,-43.247,0.59183,0.71973,-0.36294,21.462,-0.79994,0.46907,-0.37425,324.33
> view matrix models
> #5,-0.11178,0.47533,0.87268,-38.868,0.59167,0.73739,-0.32585,9.3844,-0.79839,0.47992,-0.36367,319.53
> view matrix models
> #5,-0.22153,0.44542,0.86748,-12.986,0.53956,0.79699,-0.27144,-5.5629,-0.81228,0.40793,-0.41688,347.98
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.22153,0.44542,0.86748,-14.111,0.53956,0.79699,-0.27144,-5.3645,-0.81228,0.40793,-0.41688,348.49
> select add #8
3401 atoms, 3493 bonds, 442 residues, 3 models selected
> fitmap #5 inMap #8
Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
(#8) using 3401 atoms
average map value = 0.09851, steps = 108
shifted from previous position = 1.67
rotated from previous position = 17.3 degrees
atoms outside contour = 1366, contour level = 0.075413
Position of F562b.pdb (#5) relative to
cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.45238682 -0.88366144 -0.12036870 287.11798101
0.88783684 0.43349946 0.15435016 -99.22400613
-0.08421352 -0.17669374 0.98065662 40.64404116
Axis -0.18365545 -0.02005805 0.98278601
Axis point 227.81128239 181.49795933 0.00000000
Rotation angle (degrees) 64.32464577
Shift along axis -10.79614671
> fitmap #5 inMap #8
Fit molecule F562b.pdb (#5) to map cryosparc_P36_J32_002_volume_map_sharp.mrc
(#8) using 3401 atoms
average map value = 0.09851, steps = 44
shifted from previous position = 0.00416
rotated from previous position = 0.0187 degrees
atoms outside contour = 1367, contour level = 0.075413
Position of F562b.pdb (#5) relative to
cryosparc_P36_J32_002_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.45231009 -0.88373711 -0.12010123 287.08058767
0.88785087 0.43341968 0.15449342 -99.24674165
-0.08447733 -0.17651091 0.98066686 40.65823137
Axis -0.18362633 -0.01976254 0.98279744
Axis point 227.80088638 181.42728547 0.00000000
Rotation angle (degrees) 64.32929481
Shift along axis -10.79538196
> show #3 models
> hide #3 models
> show #3 models
> color #8 #d7fef991 models
> color #8 #c5fef791 models
> color #8 #c4fbfe91 models
> color #8 #c3fef791 models
> rename #8 sNS1wt-Fab562.mrc
> select subtract #5
2 models selected
> select subtract #8
Nothing selected
> show #4 models
> show #!2 models
> rename #4 F562a-FL.pdb
> show #9 models
> color #2 #c4a1924d models
[Repeated 1 time(s)]
> hide #!2 models
> hide #4 models
> ui mousemode right zoom
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM Maps_docked
> structures/EDEN2 sNS1wt-Fab562/20220323_NS1wt-Ab-Fab-ApoAI_hdl.cxs"
> includeMaps true
——— End of log from Sat Nov 19 10:30:44 2022 ———
opened ChimeraX session
> volume #8 color #dbfdf891
> volume #8 color #c5fdf891
> volume #8 color #c5fdf849
> volume #8 color #c5fdf84c
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> rename #3 eden2ns1.pdb
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/C
Alignment identifier is 1
> select #3/B-C:2
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B-C:2-75
1174 atoms, 1200 bonds, 148 residues, 1 model selected
> select #3/B-C:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B-C:172-178
118 atoms, 116 bonds, 14 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
not of the form 'name: value' or is missing initial tab
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Data line 8 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr not of
the form: <tab> atomspec <tab> value
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Line 43 in eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr is either
not of the form 'name: value' or is missing initial tab
> color #3/A-B dimgray
> hide #3 models
> show #3 models
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> color #3 dimgray
> ui tool show "Change Chain IDs"
> changechains C A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/1/)
> changechains C A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/1/)
> changechains sel C A
Chain IDs of 352 residues changed
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #3/A
Alignment identifier is 1
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
residues using match mode: any
> ui tool show "Show Sequence Viewer"
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 1097
residues using match mode: any
> byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key true
> bluered noValueColor gray
Unknown command: byattribute relative_deuterium_uptake_NS1c_10min
#3/A-B:174-361 key true bluered noValueColor gray
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true bluered noValueColor gray
Expected a keyword
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
> ui mousemode right "color key"
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> key blue-white-red :-0.98 :-0.47 :1
> key blue-white-red :-2 :-0.47 :1
> key blue-white-red :-2 :0 :1
> hide #5 models
> hide #9 models
> hide #!8 models
> hide #8.1 models
> key pos 0.636108,0.370379 size 0.0013699,0.146465
> undo
> key pos 0.479592,0.196551 size 0.329083,0.0401247
> ui mousemode right zoom
> select subtract #3
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> select #3/B,A:212-213
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:212-217
96 atoms, 96 bonds, 12 residues, 1 model selected
> select #3/B,A:216
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:212-216
74 atoms, 72 bonds, 10 residues, 1 model selected
> select #3/B,A:211
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:211-216
92 atoms, 90 bonds, 12 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 984
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor gray
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor grey
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> ui tool show "Selection Inspector"
> toolshed show
> view sel
> key blue-white-red :-0.98 :-0.47 :1
> key blue-white-red :- :-0.47 :1
> key blue-white-red :-2 :-0.47 :1
> key colorTreatment distinct
> key colorTreatment blended
> attributes available
Unknown command: attributes available
> info attributes
Expected a models specifier or a keyword
> info resattr
resattr alt_loc
resattr alt_locs
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr custom_attrs
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr relative_deuterium_uptake_NS1c_10min
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr seq_conservation
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> select #3/B,A:181
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:181-198
268 atoms, 268 bonds, 36 residues, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered noValueColor grey
> key blue-white-red :-0.98 :-0.47 :0.04 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> select #3/B,A:299-300
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B,A:299-301
50 atoms, 48 bonds, 6 residues, 1 model selected
> key red-white-blue :0.04 :-0.47 :-0.98
> key blue-white-red :-0.98 :-0.47 :0.04
> key red-white-blue :0.04 :-0.47 :-0.98
> key blue-white-red :-0.98 :-0.47 :0.04
> key blue-white-red :- :-0.47 :0.04
> key blue-white-red :-2 :-0.47 :0.04
> key blue-white-red :-2 :-0.47 :1
> key blue-white-red :-2 :0 :1
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2:1 noValueColor grey
Invalid "range" argument: Expected some numbers or 'full'
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-0.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 834
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'relative_deuterium_uptake_NS1c_10min' to 866
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> undo
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/eden2ns1c_HDXMS_RelativeDchange_10min.defattr
---
note | Assigned attribute 'Relative_deuterium_uptake_NS1c_10min' to 2284
residues using match mode: any
> color byattribute relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom relative_deuterium_uptake_NS1c_10min range
-1.98 to 0.04
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> undo
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> color byattribute Relative_deuterium_uptake_NS1c_10min #3/A-B:174-361 key
> true palette bluered range -2,1 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
2834 atoms, 358 residues, atom Relative_deuterium_uptake_NS1c_10min range
-1.03 to 0
> select #3/B,A:175
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:175-178
60 atoms, 58 bonds, 8 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right zoom
> select #3/B,A:172
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:172-174
58 atoms, 56 bonds, 6 residues, 1 model selected
> select #3/B,A:174-175
40 atoms, 38 bonds, 4 residues, 1 model selected
> select #3/B,A:174-178
82 atoms, 80 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #cbdbffff
> color sel #c1d2ffff
> color sel #c1d1ffff
> color sel #c2d2ffff
[Repeated 1 time(s)]
> color sel #c3d3ffff
> color sel #c4d3ffff
> color sel #c4d4ffff
> color sel #c4d5ffff
> color sel #c5d6ffff
> color sel #c5d5ffff
> color sel #c4d4ffff
> color sel #c4d3ffff
[Repeated 1 time(s)]
> color sel #c3d2ffff
> color sel #c3d1ffff
> color sel #c2d0ffff
[Repeated 1 time(s)]
> color sel #c1cfffff
> color sel #c1ceffff
> color sel #c1cdffff
> color sel #c0cdffff
> color sel #c0ccffff
> color sel #c1cdffff
[Repeated 1 time(s)]
> color sel #c1ceffff
> color sel #c2cfffff
> color sel #b8c2ffff
> color sel #aebdffff
> select #3/B,A:179
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/B,A:179-187
122 atoms, 120 bonds, 18 residues, 1 model selected
> color sel #c4cfffff
> select #3/B,A:188
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:188-198
174 atoms, 174 bonds, 22 residues, 1 model selected
> color sel #b1bbffff
> select #3/B,A:199
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #3/B,A:199-200
32 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #99b0ffff
> color sel #96baffff
> color sel #92b4ffff
> color sel #6a97ffff
> select #3/B,A:201-202
44 atoms, 46 bonds, 4 residues, 1 model selected
> select #3/B,A:201-211
192 atoms, 198 bonds, 22 residues, 1 model selected
> color sel #91acffff
> select #3/B,A:212
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:212-217
96 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #aabeffff
> color sel #bfcfffff
[Repeated 1 time(s)]
> color sel #bfceffff
> color sel #beceffff
> color sel #becdffff
> color sel #bdcdffff
> select #3/B,A:218
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:218-219
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #adc4ffff
> select #3/B,A:220
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:220-231
198 atoms, 206 bonds, 24 residues, 1 model selected
> color sel #88a5ffff
> color sel #83a2ffff
> color sel #7fa0ffff
> select #3/B,A:232
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B,A:232-240
142 atoms, 144 bonds, 18 residues, 1 model selected
> color sel #98b0ffff
> select #3/B,A:231
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:220-231
198 atoms, 206 bonds, 24 residues, 1 model selected
> color sel #8da3edff
> color sel #8da3ecff
[Repeated 1 time(s)]
> color sel #8ca2ecff
> color sel #8ca2ebff
> color sel #8ba1eaff
> color sel #8ba0e9ff
> color sel #889ee5ff
> color sel #869be0ff
> color sel #8397dcff
> color sel #8195d9ff
> color sel #8094d7ff
> color sel #7f93d6ff
> color sel #7f93d5ff
> color sel #7e92d4ff
> color sel #7d90d2ff
> color sel #7b8eceff
> color sel #798cccff
> color sel #788bc9ff
> color sel #778ac8ff
[Repeated 1 time(s)]
> color sel #7689c7ff
> color sel #7688c6ff
> color sel #7587c5ff
> color sel #7587c4ff
> color sel #7487c3ff
> color sel #7486c3ff
> color sel #7081bcff
> color sel #6878afff
> color sel #6272a5ff
> color sel #576592ff
> color sel #4c5880ff
> color sel #444f73ff
> color sel #414b6dff
> color sel #404a6cff
> color sel #404a6bff
> color sel #3f4969ff
> color sel #3d4666ff
> color sel #3b4463ff
> color sel #38415fff
> color sel #343c57ff
> color sel #2e364eff
> color sel #2c3249ff
> color sel #2b3148ff
> color sel #2a3146ff
[Repeated 1 time(s)]
> color sel #2a3147ff
> color sel #2c334bff
> color sel #2f364fff
> color sel #343c58ff
> color sel #3a4361ff
> color sel #404a6cff
> color sel #475277ff
> color sel #4d5981ff
> color sel #55638fff
> color sel #596796ff
> color sel #5d6b9cff
> color sel #606fa1ff
> color sel #6272a5ff
> color sel #6878afff
> color sel #6b7bb3ff
> color sel #7082bcff
> color sel #7284c0ff
> color sel #7486c3ff
> color sel #7587c5ff
> color sel #7688c6ff
> color sel #7689c6ff
> color sel #778ac8ff
> color sel #788ac9ff
> color sel #788bcaff
> color sel #798cccff
> color sel #7a8dcdff
> color sel #7b8eceff
> color sel #7c8fcfff
> color sel #7c90d0ff
> color sel #7d90d1ff
> color sel #7d91d2ff
> color sel #7e91d3ff
> color sel #7e92d4ff
> color sel #7f93d5ff
[Repeated 1 time(s)]
> color sel #7f93d6ff
> color sel #8094d7ff
> color sel #8296daff
> color sel #859ae0ff
> color sel #879ce2ff
> color sel #899ee5ff
> color sel #899ee6ff
[Repeated 1 time(s)]
> color sel #899fe6ff
> color sel #899fe7ff
> color sel #8aa0e8ff
> color sel #8ca2ebff
> color sel #8da3ecff
> color sel #8da3edff
> color sel #8da4edff
> color sel #8ea5efff
> color sel #90a6f1ff
> color sel #91a7f3ff
> color sel #92a9f5ff
> color sel #92a9f6ff
> color sel #94abf8ff
> color sel #95acfaff
[Repeated 1 time(s)]
> color sel #95adfbff
> color sel #96aefcff
> color sel #97affeff
> color sel #98b0ffff
[Repeated 1 time(s)]
> color sel #97affeff
> color sel #94abf9ff
> color sel #92a9f6ff
> color sel #92a8f4ff
> color sel #91a8f4ff
> color sel #91a7f3ff
> color sel #90a7f2ff
> color sel #91a7f3ff
> color sel #91a8f4ff
> color sel #92a9f5ff
> color sel #92a9f6ff
> color sel #93aaf7ff
> color sel #94abf8ff
> color sel #94abf9ff
> color sel #6492f9ff
> color sel #4f5af9ff
> color sel #505df9ff
> color sel #505ef9ff
> color sel #515ff9ff
[Repeated 1 time(s)]
> color sel #5260f9ff
> color sel #5362f9ff
> color sel #5363f9ff
[Repeated 1 time(s)]
> color sel #5465f9ff
> color sel #5567f9ff
> color sel #5667f9ff
> color sel #5668f9ff
> color sel #5568f9ff
> color sel #5569f9ff
[Repeated 1 time(s)]
> color sel #5469f9ff
[Repeated 2 time(s)]
> color sel #5369f9ff
> color sel #536af9ff
> color sel #546bf9ff
> color sel #546cf9ff
[Repeated 1 time(s)]
> color sel #556df9ff
> color sel #556ef9ff
> color sel #556ff9ff
> color sel #5670f9ff
[Repeated 2 time(s)]
> color sel #5671f9ff
> color sel #5772f9ff
> color sel #5672f9ff
> color sel #5671f9ff
[Repeated 1 time(s)]
> color sel #5570f9ff
> color sel #556ff9ff
> color sel #546ef9ff
[Repeated 1 time(s)]
> color sel #536df9ff
[Repeated 1 time(s)]
> color sel #526cf9ff
[Repeated 1 time(s)]
> color sel #526bf9ff
> color sel #516af9ff
> color sel #5169f9ff
> color sel #5069f9ff
> color sel #5068f9ff
> color sel #4f67f9ff
> color sel #4f66f9ff
> color sel #4f65f9ff
> color sel #5069f9ff
> color sel #516af9ff
[Repeated 1 time(s)]
> color sel #516bf9ff
> color sel #536cf9ff
> color sel #536df9ff
> color sel #546df9ff
> color sel #546ef9ff
> color sel #556ff9ff
> color sel #5670f9ff
[Repeated 1 time(s)]
> color sel #5770f9ff
> color sel #5771f9ff
> color sel #5872f9ff
[Repeated 2 time(s)]
> color sel #5972f9ff
> color sel #5973f9ff
> color sel #5a73f9ff
[Repeated 1 time(s)]
> color sel #5a74f9ff
> color sel #5b73f9ff
[Repeated 1 time(s)]
> color sel #5c74f9ff
[Repeated 2 time(s)]
> color sel #5d74f9ff
[Repeated 1 time(s)]
> color sel #5e73f9ff
> color sel #5e74f9ff
[Repeated 1 time(s)]
> select #3/B,A:241
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:241
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel #8897f9ff
> color sel #b4bff9ff
> color sel #becff9ff
> color sel #bdcff9ff
[Repeated 1 time(s)]
> color sel #bccff9ff
[Repeated 1 time(s)]
> color sel #bbcff9ff
[Repeated 2 time(s)]
> color sel #bbd0f9ff
> color sel #bbcff9ff
> color sel #bacff9ff
> color sel #bacef9ff
> color sel #b9cdf9ff
> color sel #b9ccf9ff
[Repeated 1 time(s)]
> color sel #b8cbf9ff
[Repeated 1 time(s)]
> color sel #b7caf9ff
[Repeated 1 time(s)]
> color sel #b7c9f9ff
> color sel #b5c8f9ff
> color sel #b5c7f9ff
> color sel #b5c6f9ff
> color sel #b4c6f9ff
[Repeated 1 time(s)]
> color sel #b3c5f9ff
> color sel #b3c4f9ff
> color sel #b2c4f9ff
> color sel #b2c3f9ff
> color sel #b1c2f9ff
> color sel #b1c1f9ff
> color sel #b0c1f9ff
> color sel #b0c0f9ff
> color sel #afbff9ff
[Repeated 1 time(s)]
> color sel #aebef9ff
> color sel #aebdf9ff
> select #3/B,A:242
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:242-247
102 atoms, 104 bonds, 12 residues, 1 model selected
> color sel #909df9ff
> select #3/B,A:248-249
18 atoms, 16 bonds, 4 residues, 1 model selected
> select #3/B,A:248-253
76 atoms, 76 bonds, 12 residues, 1 model selected
> color sel #9fabf9ff
> select #3/B,A:254-255
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #3/B,A:254-262
162 atoms, 170 bonds, 18 residues, 1 model selected
> color sel #92a1f9ff
> select #3/B,A:263-264
32 atoms, 30 bonds, 4 residues, 1 model selected
> select #3/B,A:263-265
42 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #acbbf9ff
[Repeated 1 time(s)]
> color sel #abbaf9ff
> color sel #abb9f9ff
> select #3/B,A:266-267
22 atoms, 22 bonds, 4 residues, 1 model selected
> select #3/B,A:266-267
22 atoms, 22 bonds, 4 residues, 1 model selected
> color sel #7a98f9ff
> color sel #6689f9ff
> color sel #698bf9ff
> color sel #698cf9ff
> color sel #6a8cf9ff
> color sel #6b8cf9ff
> color sel #6c8df9ff
> color sel #6c8ef9ff
> color sel #6d8ef9ff
> color sel #6e8ef9ff
> color sel #6e8ff9ff
> color sel #6f90f9ff
> color sel #6f8ff9ff
> color sel #6284f9ff
> select #3/B,A:268-269
48 atoms, 52 bonds, 4 residues, 1 model selected
> select #3/B,A:268-273
110 atoms, 114 bonds, 12 residues, 1 model selected
> color sel #86abf9ff
> select #3/B,A:274-275
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:274-275
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #5584f9ff
> color sel #5684f9ff
> color sel #5785f9ff
> color sel #5886f9ff
> color sel #5986f9ff
> color sel #5b87f9ff
> color sel #5c88f9ff
[Repeated 1 time(s)]
> color sel #5c89f9ff
> color sel #5d89f9ff
> color sel #5e8af9ff
> color sel #5e8bf9ff
> color sel #5f8bf9ff
> color sel #5f8cf9ff
> color sel #608df9ff
> color sel #618df9ff
> color sel #618ef9ff
[Repeated 1 time(s)]
> color sel #628ff9ff
> color sel #638ff9ff
> color sel #6390f9ff
> color sel #6592f9ff
> color sel #6994f9ff
> color sel #6a96f9ff
> color sel #6b96f9ff
> color sel #6c97f9ff
[Repeated 1 time(s)]
> select #3/B,A:276-277
38 atoms, 38 bonds, 4 residues, 1 model selected
> select #3/B,A:276-277
38 atoms, 38 bonds, 4 residues, 1 model selected
> color sel #89aef9ff
> select #3/B,A:278
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:278-285
118 atoms, 118 bonds, 16 residues, 1 model selected
> select #3/B,A:286-287
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:286-287
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:286
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:286-299
206 atoms, 206 bonds, 28 residues, 1 model selected
> color sel #7c9df9ff
> color sel #798df9ff
> select #3/B,A:300
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:300-309
136 atoms, 134 bonds, 20 residues, 1 model selected
> color sel #527af9ff
> color sel #3a5af9ff
> select #3/B,A:310
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #3/B,A:310
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel #526af9ff
> select #3/B,A:311
28 atoms, 30 bonds, 2 residues, 1 model selected
> select #3/B,A:311-333
378 atoms, 392 bonds, 46 residues, 1 model selected
> color sel #c6c6f3ff
> color sel #b6b4f3ff
> select #3/B,A:334-335
34 atoms, 32 bonds, 4 residues, 1 model selected
> select #3/B,A:334-335
34 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #9c98f3ff
> select #3/B,A:336-337
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #3/B,A:336-341
106 atoms, 106 bonds, 12 residues, 1 model selected
> color sel #a7acf3ff
> select #3/B,A:341-342
36 atoms, 34 bonds, 4 residues, 1 model selected
> select #3/B,A:341-350
158 atoms, 156 bonds, 20 residues, 1 model selected
> color sel #6b69f3ff
> color sel #6b6af3ff
> color sel #6b6bf3ff
> color sel #6d6ef3ff
> color sel #6f70f3ff
> color sel #7273f3ff
> color sel #7274f3ff
> color sel #7375f3ff
> color sel #7476f3ff
> color sel #7477f3ff
> color sel #7578f3ff
> color sel #7579f3ff
> color sel #7679f3ff
> color sel #777af3ff
> color sel #787cf3ff
> color sel #777bf3ff
> color sel #777af3ff
> color sel #7679f3ff
> color sel #7072f3ff
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:300
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B,A:300-309
136 atoms, 134 bonds, 20 residues, 1 model selected
> color sel #4c4ef3ff
> color sel #4242f3ff
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:1-2
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #3/B,A:1-171
2732 atoms, 2798 bonds, 342 residues, 1 model selected
> color sel #edeff3ff
> color sel #c7c9ccff
> color sel #c7c8ccff
> color sel #c2c4c7ff
> color sel #c1c2c6ff
> color sel #c0c2c5ff
> color sel #bfc0c4ff
> color sel #bdbec2ff
> color sel #bcbdc0ff
> color sel #babcbfff
> color sel #babbbeff
> color sel #b9bbbeff
> color sel #b9babeff
> color sel #b6b7bbff
> color sel #b2b3b6ff
> color sel #afb0b3ff
> color sel #abacafff
> color sel #a6a7abff
> color sel #a3a4a7ff
> color sel #a1a2a5ff
> color sel #9fa0a3ff
> color sel #9c9da0ff
> color sel #999a9cff
> color sel #96979aff
[Repeated 1 time(s)]
> color sel #949597ff
> color sel #919295ff
> color sel #8b8b8eff
> color sel #87888aff
> color sel #7e7f81ff
> color sel #727375ff
> color sel #68686aff
> color sel #616264ff
> color sel #59595bff
> color sel #545556ff
> color sel #4d4e4fff
> color sel #464748ff
> color sel #444446ff
> color sel #424244ff
> color sel #3f3f40ff
> color sel #3e3e3fff
> color sel #3c3d3eff
[Repeated 1 time(s)]
> color sel #414243ff
> color sel #4d4e4fff
> color sel #565658ff
> color sel #606162ff
> color sel #656668ff
> color sel #6a6b6dff
> color sel #717274ff
> color sel #737476ff
> color sel #78797bff
> color sel #7b7b7eff
> color sel #818285ff
> color sel #858689ff
> color sel #88898cff
> color sel #8b8c8eff
> color sel #8c8d90ff
> color sel #8f8f92ff
> color sel #919295ff
> color sel #959699ff
> color sel #9a9b9eff
> color sel #9e9fa2ff
> color sel #a1a2a5ff
> color sel #a5a6a9ff
> color sel #a7a8abff
> color sel #a8a9adff
> color sel #a9aaaeff
> color sel #aaabaeff
[Repeated 1 time(s)]
> color sel #adaeb1ff
> color sel #afb0b3ff
[Repeated 1 time(s)]
> color sel #b0b1b4ff
> color sel #b1b2b5ff
> color sel #b2b3b6ff
[Repeated 1 time(s)]
> color sel #b2b3b6fa
> color sel #b2b3b6f5
> color sel #b2b3b6f3
> color sel #b2b3b6ee
[Repeated 2 time(s)]
> color sel #b2b3b6ed
[Repeated 1 time(s)]
> color sel #b2b3b6eb
[Repeated 1 time(s)]
> color sel #b2b3b6ea
> color sel #b2b3b6e9
> color sel #b2b3b6e8
[Repeated 1 time(s)]
> color sel #b2b3b6e7
[Repeated 1 time(s)]
> color sel #b2b3b6e6
> color sel #b2b3b6e5
> color sel #b2b3b6e3
> color sel #b2b3b6e2
> color sel #b2b3b6e1
> color sel #b2b3b6e0
> color sel #b2b3b6df
[Repeated 1 time(s)]
> color sel #b2b3b6de
> color sel #b2b3b6dd
> color sel #b2b3b6dc
> color sel #b2b3b6db
> color sel #b2b3b6da
[Repeated 1 time(s)]
> color sel #b2b3b6d9
> color sel #b2b3b6d8
[Repeated 1 time(s)]
> color sel #b2b3b6d7
[Repeated 1 time(s)]
> color sel #b2b3b6d6
> color sel #b2b3b6d5
> color sel #b2b3b6d4
> color sel #b2b3b6d2
> color sel #b2b3b6d1
> color sel #b2b3b6d0
[Repeated 1 time(s)]
> color sel #b2b3b6cf
> color sel #b2b3b6cd
[Repeated 1 time(s)]
> color sel #b1b3b6cd
> color sel #b1b2b6cd
> color sel #b1b2b5cd
[Repeated 1 time(s)]
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B,A:1
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/B,A:1-171
2732 atoms, 2798 bonds, 342 residues, 1 model selected
> color sel #b1b2b5cc
> color sel #b1b2b5c8
> color sel #b1b2b5c6
> color sel #b1b2b5c5
> color sel #b1b2b5c1
> color sel #b1b2b5be
> color sel #b1b2b5bb
> color sel #b1b2b5b7
> color sel #b1b2b5b5
> color sel #b1b2b5b1
> color sel #b1b2b5ad
> color sel #b1b2b5aa
> color sel #b1b2b5a7
> color sel #b1b2b5a4
> color sel #b1b2b5a0
> color sel #b1b2b599
> color sel #b1b2b592
> color sel #b1b2b58c
> color sel #b1b2b586
> color sel #b1b2b576
> color sel #b1b2b573
> color sel #b1b2b56e
> color sel #b1b2b56a
> color sel #b1b2b568
> color sel #b1b2b567
> color sel #b1b2b565
> color sel #b1b2b563
[Repeated 1 time(s)]
> color sel #b1b2b565
> color sel #b1b2b569
> color sel #b1b2b56c
> color sel #b1b2b572
> color sel #b1b2b575
> color sel #b1b2b57b
> color sel #b1b2b581
> color sel #b1b2b587
> color sel #b1b2b589
> color sel #b1b2b58a
[Repeated 1 time(s)]
> color sel #b1b2b58d
> color sel #b1b2b590
> color sel #b1b2b591
> color sel #b1b2b594
> color sel #b1b2b596
[Repeated 2 time(s)]
> color sel #b1b2b597
> color sel #b1b2b598
[Repeated 1 time(s)]
> color sel #b1b2b599
> color sel #b1b2b59a
> color sel #b1b2b59c
> color sel #b1b2b59d
> color sel #b1b2b59c
[Repeated 1 time(s)]
> color sel #b1b2b59b
[Repeated 1 time(s)]
> color sel #b1b2b59a
[Repeated 1 time(s)]
> color sel #b1b2b599
[Repeated 1 time(s)]
> color sel #b1b2b598
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/sNS1wt-Ab562_EM-HDX.cxs"
> includeMaps true
> show #!2 models
> color #2 #cfbabb4d models
> color #2 #c1acae4d models
> color #2 #c1acae2e models
> color #2 #c1acae34 models
> show #!8 models
> show #4 models
> select add #4
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.25081,-0.17578,-0.95194,337.54,0.94086,0.27565,0.19699,-69.227,0.22777,-0.94505,0.23452,277.17
> view matrix models
> #4,0.25081,-0.17578,-0.95194,337.61,0.94086,0.27565,0.19699,-68.962,0.22777,-0.94505,0.23452,277.21
> view matrix models
> #4,0.25081,-0.17578,-0.95194,338.3,0.94086,0.27565,0.19699,-67.778,0.22777,-0.94505,0.23452,276.56
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.28381,-0.20491,-0.93673,335.61,0.93973,0.25368,0.22923,-67.38,0.19066,-0.94534,0.26456,280.03
> view matrix models
> #4,0.29033,-0.1329,-0.94765,322.58,0.93808,0.23513,0.25442,-66.671,0.18901,-0.96284,0.19293,291.98
> view matrix models
> #4,0.35013,-0.063779,-0.93453,297.24,0.92612,0.17313,0.33516,-62.689,0.14042,-0.98283,0.11968,313.39
> view matrix models
> #4,0.28929,-0.083154,-0.95362,314.43,0.94763,0.16569,0.27303,-58.03,0.1353,-0.98267,0.12673,313.48
> view matrix models
> #4,0.29468,-0.086777,-0.95165,313.84,0.94725,0.15789,0.27892,-57.235,0.12605,-0.98364,0.12873,315.16
> view matrix models
> #4,0.36145,-0.11336,-0.92548,303.06,0.89859,0.30718,0.31332,-79.332,0.24877,-0.94488,0.21289,275.15
> hide #!2 models
> view matrix models
> #4,0.75588,-0.11899,-0.6438,196.83,0.49521,0.74715,0.44333,-99.072,0.42827,-0.65392,0.62368,140.02
> view matrix models
> #4,0.79244,-0.19913,-0.57652,196.6,0.59732,0.44467,0.66744,-89.678,0.12346,-0.87328,0.47133,255.09
> show #!2 models
> view matrix models
> #4,0.84088,0.043539,-0.53947,139,0.20748,0.89468,0.3956,-66.307,0.49988,-0.44458,0.74328,74.375
> view matrix models
> #4,0.61732,-0.23939,-0.7494,257.2,0.45462,0.88598,0.091476,-75.144,0.64205,-0.39716,0.65577,49.425
> view matrix models
> #4,0.38724,0.030398,-0.92148,271.6,0.61211,0.73893,0.28161,-100.4,0.68947,-0.6731,0.26753,136.6
> view matrix models
> #4,0.32928,0.15127,-0.93204,261.73,0.67479,0.65276,0.34434,-103.89,0.66048,-0.74231,0.11286,172.9
> view matrix models
> #4,0.83345,-0.16899,-0.52612,177.48,0.33798,0.90914,0.24338,-75.428,0.43719,-0.38066,0.81484,66.051
> view matrix models
> #4,0.73197,-0.15661,-0.6631,210.44,0.61773,0.56316,0.54888,-101.05,0.28747,-0.81137,0.50895,208.62
> view matrix models
> #4,0.70748,-0.11472,-0.69736,211.46,0.67078,0.41972,0.61146,-92.303,0.22255,-0.90037,0.3739,252.95
> view matrix models
> #4,0.50475,-0.22825,-0.83254,286.11,0.80219,0.4803,0.35468,-97.631,0.31892,-0.84689,0.42553,219.04
> view matrix models
> #4,0.43321,-0.14625,-0.88935,291.32,0.79138,0.53394,0.29769,-98.629,0.43133,-0.83278,0.34705,204.67
> view matrix models
> #4,0.39985,-0.22492,-0.88856,311.79,0.73762,0.65442,0.16627,-94.936,0.54409,-0.7219,0.42757,153.83
> hide #!8 models
> view matrix models
> #4,0.40534,-0.24527,-0.88065,313.53,0.76932,0.61189,0.18368,-95.2,0.49381,-0.75196,0.43671,167.65
> view matrix models
> #4,0.25068,-0.40305,-0.88017,371.18,0.81823,0.57411,-0.029862,-72.272,0.51736,-0.7127,0.47371,151.72
> view matrix models
> #4,0.3665,-0.39401,-0.84287,343.41,0.8386,0.5323,0.11581,-85.696,0.40303,-0.74927,0.5255,173.7
> view matrix models
> #4,0.48359,-0.37777,-0.78957,312.2,0.85036,0.41655,0.32152,-91.15,0.20743,-0.82691,0.52268,224.84
> view matrix models
> #4,0.44767,-0.35695,-0.81986,318.73,0.84619,0.46549,0.25939,-91.93,0.28905,-0.80988,0.51043,207.88
> show #5 models
> hide #4 models
> show #!8 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> sequence chain #5/C
Alignment identifier is 5/C
> ui tool show "Change Chain IDs"
> select #5/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/C
1632 atoms, 1668 bonds, 214 residues, 1 model selected
> changechains sel C L
Chain IDs of 214 residues changed
> changechains sel C L
No residues specified have any of the 'from' chain IDs
> ui tool show "Show Sequence Viewer"
> sequence chain #5/L
Alignment identifier is 5/L
> ui tool show "Change Chain IDs"
> select
> #5/B:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
837 atoms, 847 bonds, 101 residues, 1 model selected
> select #5/B:228
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel B H
Chain IDs of 228 residues changed
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/H:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
Summary of feedback from opening
/Users/alvinchew/Library/CloudStorage/OneDrive-
NanyangTechnologicalUniversity/202112_FlaviNS1/Data_HDXMS_Nikhil/Fab562_HDXMS_RelativeDchange_10min_recolored.defattr
---
note | Assigned attribute 'fab562_10min_relative_deuterium_uptake' to 1126
residues using match mode: any
> color byattribute fab562_10min_relative_deuterium_uptake #3/A-B:174-361 key
> true palette bluered range -2.0,1.0 noValueColor grey
All 'fab562_10min_relative_deuterium_uptake' values are None
> color byattribute fab562_10min_relative_deuterium_uptake #5 key true palette
> bluered range -2.0,1.0 noValueColor grey
> key blue-white-red :-2.0 :-0.5 :1.0 showTool true
3401 atoms, 442 residues, atom fab562_10min_relative_deuterium_uptake range
-1.18 to 0.73
> hide #!8 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> ui mousemode right zoom
> select #5/H:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/H:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select #5/H:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:5-14
71 atoms, 71 bonds, 10 residues, 1 model selected
> color sel #ddddffff
> color sel #aab4ffff
> color sel #8390ffff
> select #5/H:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:15-29
120 atoms, 124 bonds, 15 residues, 1 model selected
> color sel #ffe6e6ff
> color sel #ffe2ddff
> color sel #ffe1ddff
> color sel #ffe0dcff
[Repeated 2 time(s)]
> color sel #ffe0dbff
> color sel #ffdfdaff
[Repeated 1 time(s)]
> color sel #ffdedaff
> color sel #ffddd9ff
[Repeated 1 time(s)]
> color sel #ffdcd8ff
> select #5/H:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:30-35
43 atoms, 43 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #6f70ffff
> color sel #4449ffff
> color sel #1f28ffff
> color sel #1f29ffff
> color sel #202affff
> color sel #212cffff
> color sel #222cffff
> color sel #222dffff
> color sel #232effff
> color sel #242fffff
[Repeated 2 time(s)]
> color sel #2531ffff
> color sel #2631ffff
> color sel #2632ffff
> color sel #2732ffff
> color sel #2733ffff
> color sel #2935ffff
> color sel #2a35ffff
> color sel #2a36ffff
> color sel #2b37ffff
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:36-47
115 atoms, 120 bonds, 12 residues, 1 model selected
> color sel #ffcfe1ff
> color sel #ffdddeff
[Repeated 1 time(s)]
> color sel #ffdddfff
> color sel #ffdde2ff
> color sel #ffdde3ff
> color sel #ffdde5ff
> color sel #ffdde8ff
> color sel #ffdde9ff
> color sel #ffdceaff
[Repeated 1 time(s)]
> color sel #ffdce9ff
> color sel #ffdae7ff
> color sel #ffd9e4ff
> color sel #ffd8e2ff
> color sel #ffd7e0ff
> color sel #ffd7dfff
> color sel #ffd6dcff
> color sel #ffd5dbff
> color sel #ffd3daff
> color sel #ffd3d9ff
> color sel #ffd2d7ff
[Repeated 1 time(s)]
> color sel #ffd1d6ff
> color sel #ffd0d5ff
> select #5/H:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:48-61
120 atoms, 123 bonds, 14 residues, 1 model selected
> color sel #6277ffff
> select #5/H:62-63
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/H:62-72
91 atoms, 92 bonds, 11 residues, 1 model selected
> color sel #ff7f7fff
> color sel #ff9b9aff
> select #5/H:79-80
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/H:79-81
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/H:78
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/H:78-95
142 atoms, 144 bonds, 18 residues, 1 model selected
> color sel #a9b9ffff
> select #5/H:96
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:96-103
75 atoms, 78 bonds, 8 residues, 1 model selected
> color sel #8493ffff
> color sel #88a0ffff
> select #5/H:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:104-112
73 atoms, 78 bonds, 9 residues, 1 model selected
> color sel #8296ffff
> color sel #8297ffff
> color sel #8398ffff
> color sel #8499ffff
> color sel #849affff
> color sel #849bffff
> color sel #859cffff
> color sel #859dffff
[Repeated 1 time(s)]
> color sel #869effff
> color sel #869fffff
> color sel #87a0ffff
> color sel #88a1ffff
> color sel #88a2ffff
> color sel #89a3ffff
[Repeated 1 time(s)]
> color sel #8aa4ffff
> color sel #8aa5ffff
> select #5/H:113-114
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #5/H:113-120
65 atoms, 67 bonds, 8 residues, 1 model selected
> color sel #aab4ffff
> select #5/H:120-121
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:120-121
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:120
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #7e95ffff
> select #5/H:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:121-123
25 atoms, 25 bonds, 3 residues, 1 model selected
> select #5/H:121
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:121-122
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel #eceeffff
> color sel #73747cff
[Repeated 1 time(s)]
> color sel #74747dff
> color sel #74757dff
[Repeated 1 time(s)]
> color sel #75757eff
[Repeated 1 time(s)]
> color sel #75767eff
> undo
[Repeated 1 time(s)]
> select #5/H:123-124
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/H:123-145
153 atoms, 157 bonds, 23 residues, 1 model selected
> color sel #6c6c7eff
> color sel #dad8feff
> color sel #d9d8fdff
[Repeated 1 time(s)]
> color sel #d8d7fcff
> color sel #d6d5f9ff
> color sel #d5d4f8ff
> color sel #d4d3f7ff
> color sel #d4d2f7ff
> color sel #d3d2f6ff
> color sel #d3d1f5ff
> color sel #d2d1f5ff
> color sel #d1d0f4ff
> color sel #cbcaecff
> color sel #c7c6e8ff
> color sel #c5c4e6ff
> color sel #b3c3e6ff
> color sel #b6bee6ff
> select #5/H:146-193
349 atoms, 358 bonds, 48 residues, 1 model selected
> select #5/H:146-156
79 atoms, 79 bonds, 11 residues, 1 model selected
> color sel #e6ced9ff
> color sel #e6bfbaff
> select #5/H:157-159
27 atoms, 28 bonds, 3 residues, 1 model selected
> select #5/H:157-168
93 atoms, 97 bonds, 12 residues, 1 model selected
> color sel #e6b7aeff
> select #5/H:169-171
20 atoms, 19 bonds, 3 residues, 1 model selected
> select #5/H:169-176
54 atoms, 54 bonds, 8 residues, 1 model selected
> color sel #c1c4e6ff
> select #5/H:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/H:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel #e6d7dbff
> color sel #e6bfc0ff
> select #5/H:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:181-184
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #5/H:180
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #e6ced4ff
> select #5/H:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:181-186
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #e6c9cdff
> color sel #e6c2c5ff
[Repeated 1 time(s)]
> color sel #e6c3c5ff
> color sel #e6c3c6ff
> color sel #e6c4c7ff
[Repeated 1 time(s)]
> color sel #e6c5c8ff
> color sel #e6c5c7ff
> color sel #e6c5c8ff
> color sel #e6c6c8ff
[Repeated 1 time(s)]
> select #5/H:188
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:188-198
73 atoms, 73 bonds, 11 residues, 1 model selected
> color sel #b4b7e6ff
> select #5/H:199-200
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:199-208
75 atoms, 76 bonds, 10 residues, 1 model selected
> color sel #8999e6ff
> color sel #7b90e6ff
> color sel #7083e6ff
> select #5/H:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:209-212
34 atoms, 34 bonds, 4 residues, 1 model selected
> color sel #95a4e6ff
> color sel #b0b6e6ff
> select #5/H:213-214
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/H:213-223
86 atoms, 86 bonds, 11 residues, 1 model selected
> color sel #93a0e6ff
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-6
45 atoms, 44 bonds, 6 residues, 1 model selected
> select #5/L:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:7-14
58 atoms, 58 bonds, 8 residues, 1 model selected
> color sel #9daae6ff
> select #5/L:15
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:15-21
47 atoms, 46 bonds, 7 residues, 1 model selected
> color sel #e6c2caff
> color sel #e6c3c3ff
> select #5/L:22-23
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> color sel #e6cdceff
> select #5/L:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> color sel #a5bbe6ff
> color sel #a5b6e6ff
> select #5/L:29-30
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #5/L:29-35
51 atoms, 51 bonds, 7 residues, 1 model selected
> color sel #c4c6e6ff
> color sel #d0d4e6ff
> select #5/L:36-37
24 atoms, 26 bonds, 2 residues, 1 model selected
> select #5/L:36
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel #c7cfe6ff
> select #5/L:37
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:37-38
26 atoms, 28 bonds, 2 residues, 1 model selected
> color sel #b2bde6ff
> color sel #abbae6ff
> color sel #abbbe6ff
> color sel #abbce6ff
> color sel #acbce6ff
> color sel #acbde6ff
> color sel #adbee6ff
[Repeated 1 time(s)]
> color sel #adbfe6ff
[Repeated 1 time(s)]
> color sel #adc0e6ff
> color sel #aec0e6ff
> color sel #aec1e6ff
> color sel #aec2e6ff
> color sel #afc2e6ff
> color sel #afc3e6ff
> color sel #afc2e6ff
> color sel #aec2e6ff
> color sel #aec1e6ff
> color sel #aec0e6ff
[Repeated 1 time(s)]
> color sel #aebfe6ff
> color sel #adbee6ff
> color sel #b0c3e6ff
[Repeated 1 time(s)]
> color sel #b0c2e6ff
> color sel #b0c1e6ff
[Repeated 2 time(s)]
> color sel #b0c0e6ff
[Repeated 2 time(s)]
> color sel #b0bfe6ff
[Repeated 1 time(s)]
> color sel #b1bfe6ff
[Repeated 2 time(s)]
> color sel #b1bee6ff
[Repeated 1 time(s)]
> color sel #b2bee6ff
> select #5/L:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:39-48
74 atoms, 74 bonds, 10 residues, 1 model selected
> color sel #abbbe6ff
> select #5/L:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #a1ace6ff
> color sel #a1ade6ff
> color sel #a0b1e6ff
> color sel #a1b1e6ff
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50-55
47 atoms, 47 bonds, 6 residues, 1 model selected
> color sel #6a88e6ff
> color sel #5b80e6ff
> color sel #5176e6ff
> color sel #426be6ff
> color sel #3b67e6ff
> color sel #315ae6ff
> select #5/L:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:56
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #3f64e6ff
> select #5/L:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #b3b7e6ff
> select #5/L:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:58-69
78 atoms, 79 bonds, 12 residues, 1 model selected
> color sel #b0b2e6ff
> select #5/L:70-71
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:70-73
34 atoms, 35 bonds, 4 residues, 1 model selected
> color sel #a9ace6ff
> select #5/L:74-75
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #9eaae6ff
> select #5/L:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:80-82
21 atoms, 20 bonds, 3 residues, 1 model selected
> color sel #d3cbe6ff
> color sel #e6ced1ff
> select #5/L:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:82-83
14 atoms, 13 bonds, 2 residues, 1 model selected
> volume #8 level 0.09283
> color sel #b7bbe6ff
> select #5/L:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:84-87
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #d9cce6ff
> color sel #e6d9e4ff
> color sel #e6d2d0ff
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98-100
19 atoms, 19 bonds, 3 residues, 1 model selected
> select #5/L:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:97
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel #d0d1e6ff
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98-105
56 atoms, 56 bonds, 8 residues, 1 model selected
> color sel #a9aee6ff
> select #5/L:114-115
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/L:114-125
97 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #a8ace6ff
> select #5/L:128-129
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #5/L:128-131
22 atoms, 21 bonds, 4 residues, 1 model selected
> color sel #ccccffff
> select #5/L:132
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:132-137
44 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #ffeefaff
> color sel #ffe4e2ff
> color sel #ffe7ddff
> color sel #ffe7dcff
[Repeated 2 time(s)]
> color sel #ffe7dbff
[Repeated 1 time(s)]
> color sel #ffe8daff
> color sel #ffe7daff
> color sel #ffe3d2ff
> color sel #ffe1cdff
> color sel #ffe2cdff
> color sel #ffdbc2ff
> color sel #ffdac2ff
> color sel #ffd5c2ff
> select #5/L:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:138-146
79 atoms, 81 bonds, 9 residues, 1 model selected
> color sel #d0d6ffff
> color sel #c1c6ffff
> color sel #b1bdffff
> select #5/L:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:147-158
95 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #ff5b5bff
> color sel #ff484dff
> color sel #ff4347ff
> color sel #ff4247ff
> color sel #ff4146ff
> color sel #ff4145ff
> color sel #ff4045ff
> color sel #ff4044ff
> color sel #ff3f43ff
> color sel #ff3e43ff
> color sel #ff3e42ff
> color sel #ff3d42ff
> color sel #ff3c41ff
> color sel #ff3c40ff
> color sel #ff3b40ff
> color sel #ff3c40ff
[Repeated 2 time(s)]
> color sel #ff3d40ff
> color sel #ff3e40ff
[Repeated 1 time(s)]
> color sel #ff3e41ff
> color sel #ff3f41ff
> color sel #ff3f40ff
> color sel #ff4040ff
[Repeated 2 time(s)]
> color sel #ff3f3aff
> color sel #ff3e39ff
[Repeated 2 time(s)]
> color sel #ff3e38ff
[Repeated 1 time(s)]
> select #5/L:159-160
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:159-160
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:161-162
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:161-179
144 atoms, 144 bonds, 19 residues, 1 model selected
> select #5/L:180-181
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/L:180-182
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #5/L:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:183-204
176 atoms, 180 bonds, 22 residues, 1 model selected
> color sel #6f7bffff
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> show #!8 models
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> hide #!8 models
> select add #8
2 models selected
> select subtract #8
Nothing selected
> color #8 #c5fdf81a models
> show #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B
Alignment identifier is 3/B
> select #3/B:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:111-271
1300 atoms, 1342 bonds, 161 residues, 1 model selected
> select #3/B:302
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:302-304
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #3/B:301-302
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:301-310
70 atoms, 69 bonds, 10 residues, 1 model selected
> hide #5 models
> show #5 models
> select add #5
3471 atoms, 3562 bonds, 452 residues, 2 models selected
> select subtract #5
70 atoms, 69 bonds, 10 residues, 1 model selected
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select #3/B:301
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:301-313
96 atoms, 97 bonds, 13 residues, 1 model selected
> select add #5
3497 atoms, 3590 bonds, 455 residues, 2 models selected
> select add #3
9003 atoms, 9237 bonds, 1146 residues, 2 models selected
> select subtract #3
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.5206,0.69023,0.71954,-0.076505,-64.572,-0.70121,0.63904,-0.31613,263.65
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.1095,0.69023,0.71954,-0.076505,-65.814,-0.70121,0.63904,-0.31613,263.22
> view matrix models
> #5,-0.17857,0.27184,0.94563,-4.2566,0.69023,0.71954,-0.076505,-65.556,-0.70121,0.63904,-0.31613,262.84
> view matrix models
> #5,-0.17857,0.27184,0.94563,-3.5932,0.69023,0.71954,-0.076505,-65.573,-0.70121,0.63904,-0.31613,263.6
> view matrix models
> #5,-0.17857,0.27184,0.94563,6.1172,0.69023,0.71954,-0.076505,-64.318,-0.70121,0.63904,-0.31613,265.1
> view matrix models
> #5,-0.17857,0.27184,0.94563,6.2366,0.69023,0.71954,-0.076505,-63.955,-0.70121,0.63904,-0.31613,264.58
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.50511,0.42112,0.75334,81.099,-0.58382,-0.80958,0.061111,408.82,0.63563,-0.40895,0.65478,-4.5259
> view matrix models
> #5,-0.71614,0.48271,0.50412,165.69,-0.55355,-0.83274,0.011012,419.78,0.42512,-0.27117,0.86356,-43.167
> view matrix models
> #5,-0.85245,0.30633,0.42367,241.3,-0.43531,-0.86468,-0.25067,467.41,0.28955,-0.39811,0.87044,2.3483
> view matrix models
> #5,-0.93915,0.14358,0.31205,313.16,-0.24014,-0.924,-0.29757,455.63,0.24561,-0.3544,0.90226,-5.6943
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.93915,0.14358,0.31205,310.36,-0.24014,-0.924,-0.29757,454.57,0.24561,-0.3544,0.90226,-10.513
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.92978,0.12057,0.3478,304.49,-0.25511,-0.89219,-0.3727,469.15,0.26537,-0.43526,0.86031,11.045
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.92978,0.12057,0.3478,301.55,-0.25511,-0.89219,-0.3727,465.8,0.26537,-0.43526,0.86031,10.049
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96388,-0.016383,0.26582,352.42,-0.11335,-0.87796,-0.46513,460.49,0.241,-0.47846,0.84439,26.097
> view matrix models
> #5,-0.91826,0.06169,0.39115,300.16,-0.36231,-0.52952,-0.76703,510.97,0.15981,-0.84605,0.50859,188.38
> view matrix models
> #5,-0.92676,0.077675,0.36753,304.3,-0.31305,-0.70047,-0.64136,504.23,0.20763,-0.70944,0.67349,115.46
> view matrix models
> #5,-0.9834,-0.04765,0.17507,383.22,-0.094665,-0.6884,-0.71913,482.5,0.15478,-0.72376,0.67247,127.55
> view matrix models
> #5,-0.95001,-0.19011,0.24767,386.58,-0.077458,-0.62494,-0.77682,481.46,0.30246,-0.75717,0.57898,130.31
> view matrix models
> #5,-0.94393,-0.018851,0.3296,334.23,-0.26473,-0.55329,-0.7898,503.83,0.19725,-0.83277,0.51728,177.33
> view matrix models
> #5,-0.84008,0.30007,0.45192,227.84,-0.54043,-0.53518,-0.64924,514.98,0.047043,-0.78964,0.61176,172.97
> view matrix models
> #5,-0.90734,0.12615,0.40102,283.95,-0.29751,-0.86665,-0.40051,475.05,0.29702,-0.48271,0.82388,22.022
> view matrix models
> #5,-0.89414,0.12288,0.43059,275.22,-0.30852,-0.866,-0.39353,475.19,0.32453,-0.48472,0.81224,20.379
> view matrix models
> #5,-0.89988,0.10062,0.42437,281.83,-0.22953,-0.93663,-0.26465,443.88,0.37085,-0.33556,0.86595,-28.153
> view matrix models
> #5,-0.91467,-0.052744,0.40075,318.49,-0.021786,-0.98358,-0.17917,396.11,0.40362,-0.17262,0.8985,-71.851
> view matrix models
> #5,-0.83178,-0.098166,0.54635,277.86,0.12592,-0.99195,0.013478,326.12,0.54063,0.080008,0.83745,-128.06
> view matrix models
> #5,-0.63629,-0.24728,0.73074,227.64,0.13032,-0.96808,-0.21411,375.09,0.76036,-0.041004,0.6482,-98.781
> view matrix models
> #5,-0.61952,-0.21214,0.75577,212.25,0.091718,-0.97576,-0.19871,379.56,0.7796,-0.05379,0.62396,-93.986
> view matrix models
> #5,-0.75135,-0.11146,0.65042,241.56,0.10086,-0.99345,-0.053733,346.75,0.65215,0.025229,0.75767,-118.3
> view matrix models
> #5,-0.66332,-0.23987,0.70885,236.18,0.33554,-0.94201,-0.0047814,284.72,0.6689,0.23468,0.70534,-147.64
> view matrix models
> #5,-0.7722,0.036461,0.63433,221.56,0.075095,-0.98612,0.1481,301.84,0.63093,0.162,0.75874,-140.25
> view matrix models
> #5,-0.77412,-0.056826,0.63048,240.13,0.10514,-0.99367,0.039532,323.85,0.62424,0.096891,0.7752,-130.92
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.64,0.13237,-0.98838,-0.074658,345.31,0.54779,0.010175,0.83655,-116.13
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.24,0.13237,-0.98838,-0.074658,345.43,0.54779,0.010175,0.83655,-116.45
> view matrix models
> #5,-0.82608,-0.15163,0.54277,287.21,0.13237,-0.98838,-0.074658,345.17,0.54779,0.010175,0.83655,-116.29
> select subtract #5
Nothing selected
> select #3/B:301
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:301-313
96 atoms, 97 bonds, 13 residues, 1 model selected
> select #3/B:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:300-310
77 atoms, 76 bonds, 11 residues, 1 model selected
> ui mousemode right "rotate selected models"
> select add #5
3478 atoms, 3569 bonds, 453 residues, 2 models selected
> select add #3
9003 atoms, 9237 bonds, 1146 residues, 2 models selected
> select subtract #3
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.57941,0.69777,0.4212,115.54,-0.37625,0.22943,-0.89766,403.45,-0.723,-0.67859,0.1296,400.92
> view matrix models
> #5,-0.42133,0.73627,0.52952,55.111,0.43201,0.67631,-0.59663,108.23,-0.7974,-0.022616,-0.60303,466.45
> view matrix models
> #5,-0.21413,0.8577,0.46743,11.295,0.513,0.50597,-0.69341,148.79,-0.83125,0.091314,-0.54835,438.17
> view matrix models
> #5,-0.1885,0.67264,0.71556,-17.862,0.29998,0.73323,-0.61023,123.87,-0.93514,0.09963,-0.33999,405.12
> log thumbnail
> view matrix models
> #5,-0.31715,0.77532,0.54617,25.775,0.1619,0.61171,-0.77434,209.51,-0.93445,-0.15716,-0.31953,447.8
> view matrix models
> #5,-0.32237,0.77028,0.55023,26.653,0.15917,0.61709,-0.77062,208.1,-0.93313,-0.16085,-0.32154,448.73
> view matrix models
> #5,-0.35979,0.63359,0.68492,26.481,0.1023,0.75644,-0.64601,162.47,-0.92741,-0.16236,-0.33698,451.69
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.22546,0.76745,0.60016,-1.5674,0.19788,0.63926,-0.7431,190.7,-0.95395,-0.048776,-0.29599,425.47
> view matrix models
> #5,0.070979,0.66168,0.74642,-68.315,0.16435,0.73032,-0.66304,160.57,-0.98385,0.16974,-0.056909,333.2
> view matrix models
> #5,0.11489,0.59902,0.79245,-75.277,0.39981,0.70238,-0.5889,107.15,-0.90937,0.38449,-0.1588,304.63
> view matrix models
> #5,0.18754,0.5726,0.7981,-84.357,0.35537,0.71792,-0.59858,114.3,-0.91572,0.39588,-0.068839,282.21
> view matrix models
> #5,0.12973,0.70112,0.70114,-75.082,0.32499,0.63799,-0.6981,158.11,-0.93678,0.31843,-0.14509,318.4
> view matrix models
> #5,0.012151,0.66827,0.74382,-58.685,0.27803,0.71228,-0.64448,139.73,-0.9605,0.21463,-0.17714,349.42
> view matrix models
> #5,0.087714,-0.77021,0.63174,221.89,0.82852,-0.29568,-0.47553,190.87,0.55305,0.56511,0.61219,-166.83
> view matrix models
> #5,-0.33436,-0.81985,0.46481,344.26,0.68971,-0.54897,-0.47216,261.24,0.64227,0.16271,0.74901,-140.21
> view matrix models
> #5,-0.44895,-0.57242,0.68614,265.59,0.52883,-0.78916,-0.31235,295.78,0.72027,0.22263,0.657,-143
> view matrix models
> #5,-0.4442,-0.59383,0.67086,272.37,0.54224,-0.77427,-0.32633,294.01,0.7132,0.21881,0.66593,-143.19
> view matrix models
> #5,-0.46401,-0.4815,0.74354,237.67,0.47306,-0.84435,-0.25157,301.26,0.74894,0.23501,0.61957,-141.38
> view matrix models
> #5,-0.44441,-0.50908,0.73711,240.91,0.50441,-0.8222,-0.26373,294.59,0.74031,0.25461,0.62218,-144.14
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.44441,-0.50908,0.73711,237.62,0.50441,-0.8222,-0.26373,296.55,0.74031,0.25461,0.62218,-146.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.60143,-0.49924,0.62373,290.1,0.509,-0.8412,-0.18249,279.94,0.61579,0.20772,0.76004,-149.35
> view matrix models
> #5,-0.74827,-0.24752,0.61549,270.87,0.3197,-0.94749,0.0076404,287.36,0.58128,0.20249,0.78811,-149.06
> view matrix models
> #5,-0.81926,-0.51039,0.26136,416.31,0.4815,-0.85984,-0.1698,285.16,0.31139,-0.013269,0.95019,-100.62
> view matrix models
> #5,-0.8197,-0.3099,0.48172,326.72,0.29937,-0.94878,-0.10096,316.98,0.48834,0.061452,0.87049,-126.31
> view matrix models
> #5,-0.74081,-0.34591,0.57581,297.29,0.14449,-0.91921,-0.3663,401.59,0.65599,-0.18816,0.73094,-75.929
> view matrix models
> #5,-0.81757,-0.07895,0.57039,262.37,-0.070004,-0.96958,-0.23455,416.9,0.57155,-0.23169,0.78718,-66.543
> view matrix models
> #5,-0.91951,-0.12462,0.37278,335.62,0.063486,-0.98304,-0.17204,381.3,0.3879,-0.13453,0.91183,-82.295
> view matrix models
> #5,-0.90793,0.0064486,0.41907,298.25,-0.059509,-0.99174,-0.11367,390.42,0.41488,-0.12814,0.90081,-85.551
> view matrix models
> #5,-0.91351,-0.073219,0.40017,318.51,-0.028011,-0.97001,-0.24143,411.31,0.40585,-0.23176,0.88407,-60.76
> view matrix models
> #5,-0.89133,0.0016103,0.45335,288.11,-0.071877,-0.98785,-0.13781,397.59,0.44762,-0.15542,0.88062,-81.377
> view matrix models
> #5,-0.88255,0.076297,0.46398,270.18,-0.18199,-0.96527,-0.18743,424.37,0.43356,-0.24986,0.86579,-57.872
> ui mousemode right select
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.90173,0.066834,0.42711,284.05,-0.16494,-0.96643,-0.197,423.89,0.3996,-0.24809,0.88248,-56.263
> view matrix models
> #5,-0.91899,-0.040079,0.39223,315.2,-0.062389,-0.9675,-0.24504,417.68,0.3893,-0.24966,0.88663,-55.168
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91899,-0.040079,0.39223,315,-0.062389,-0.9675,-0.24504,417.81,0.3893,-0.24966,0.88663,-53.939
> view matrix models
> #5,-0.91899,-0.040079,0.39223,318.19,-0.062389,-0.9675,-0.24504,417.19,0.3893,-0.24966,0.88663,-52.686
> view matrix models
> #5,-0.91899,-0.040079,0.39223,318.14,-0.062389,-0.9675,-0.24504,417.21,0.3893,-0.24966,0.88663,-52.699
> view matrix models
> #5,-0.91899,-0.040079,0.39223,317.71,-0.062389,-0.9675,-0.24504,417.12,0.3893,-0.24966,0.88663,-52.726
> view matrix models
> #5,-0.91899,-0.040079,0.39223,317.53,-0.062389,-0.9675,-0.24504,417.02,0.3893,-0.24966,0.88663,-52.524
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.94446,-0.024801,0.32768,334.49,-0.074776,-0.95477,-0.28779,426.99,0.31999,-0.29631,0.89989,-34.96
> view matrix models
> #5,-0.9387,-0.13701,0.31634,357.02,0.018467,-0.93629,-0.35073,422.31,0.34424,-0.32339,0.88143,-29.758
> view matrix models
> #5,-0.97606,-0.21236,0.047016,441.6,0.10357,-0.64388,-0.75808,450.17,0.19126,-0.73506,0.65046,128.25
> view matrix models
> #5,-0.97665,-0.2075,0.055729,438.73,0.092906,-0.64173,-0.76128,452.39,0.19373,-0.73832,0.64603,129.48
> view matrix models
> #5,-0.9734,-0.14293,0.17908,396.82,-0.057279,-0.60498,-0.79418,479.52,0.22185,-0.78331,0.5807,148.49
> view matrix models
> #5,-0.9046,-0.16174,0.39438,337.11,-0.12194,-0.78835,-0.60302,479.32,0.40844,-0.59359,0.69342,53.977
> view matrix models
> #5,-0.88062,-0.11723,0.45909,309.27,-0.22079,-0.75576,-0.61651,493.68,0.41923,-0.64427,0.63965,74.305
> view matrix models
> #5,-0.77365,-0.13721,0.61857,256.41,-0.084758,-0.94508,-0.31565,433.55,0.62792,-0.29663,0.71954,-45.551
> view matrix models
> #5,-0.73239,-0.017561,0.68065,212.25,-0.29602,-0.89204,-0.34153,466.62,0.61317,-0.45162,0.64812,2.7847
> view matrix models
> #5,-0.75559,0.045501,0.65347,211.04,-0.31215,-0.90204,-0.29812,460.96,0.57589,-0.42924,0.69578,-6.2267
> ui mousemode right select
> select clear
> volume #8 level 0.04382
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.81035,-0.039349,0.58462,252.71,-0.22376,-0.90134,-0.37083,462.75,0.54153,-0.43132,0.7216,-6.0096
> view matrix models
> #5,-0.75411,-0.09465,0.64989,237.66,-0.18462,-0.9191,-0.34808,453.83,0.63026,-0.38248,0.67563,-19.574
> view matrix models
> #5,-0.82045,-0.19006,0.5392,293.25,-0.01249,-0.93694,-0.34926,427.47,0.57158,-0.29329,0.76634,-47.509
> view matrix models
> #5,-0.8334,-0.14541,0.5332,288.65,-0.074442,-0.92644,-0.36901,441,0.54764,-0.34723,0.76127,-32.123
> view matrix models
> #5,-0.86676,-0.2008,0.45651,322.99,-0.01989,-0.90071,-0.43396,442.19,0.49833,-0.38522,0.77671,-20.166
> view matrix models
> #5,-0.91778,-0.012999,0.39688,311.19,-0.033872,-0.99326,-0.11086,384.91,0.39565,-0.11519,0.91115,-84.427
> view matrix models
> #5,-0.92008,-0.092652,0.38063,330.24,0.036985,-0.98783,-0.15106,381.14,0.38999,-0.12491,0.91231,-81.914
> view matrix models
> #5,-0.92081,-0.14037,0.36387,343.22,0.070303,-0.97744,-0.19917,384.86,0.38362,-0.15781,0.90991,-74.125
> view matrix models
> #5,-0.90137,-0.23742,0.36216,358.26,0.18937,-0.96821,-0.16341,353.92,0.38944,-0.078707,0.91768,-91.674
> view matrix models
> #5,-0.91318,-0.21739,0.34475,360.74,0.15071,-0.96603,-0.20993,371.32,0.37867,-0.13975,0.91492,-77.812
> view matrix models
> #5,-0.79261,-0.38378,0.47381,339.94,0.3287,-0.92343,-0.1981,329.62,0.51355,-0.0012739,0.85806,-113.45
> view matrix models
> #5,-0.82527,-0.3527,0.44105,347.65,0.32765,-0.93514,-0.13475,316.9,0.45997,0.033307,0.88731,-117.51
> view matrix models
> #5,-0.84093,-0.3241,0.43335,346.89,0.26592,-0.94495,-0.1907,342.78,0.4713,-0.045133,0.88082,-103.37
> view matrix models
> #5,-0.8011,-0.41235,0.43383,356.23,0.35913,-0.911,-0.20275,323.13,0.47883,-0.0066236,0.87788,-111.14
> view matrix models
> #5,-0.84269,-0.41546,0.34245,385.79,0.3308,-0.90136,-0.2795,344.54,0.4248,-0.12225,0.897,-84.819
> view matrix models
> #5,-0.79168,-0.41509,0.44827,351.66,0.24249,-0.88697,-0.39305,384.25,0.56075,-0.20247,0.80285,-71.174
> view matrix models
> #5,-0.80765,-0.39545,0.43739,353.39,0.27696,-0.90927,-0.31067,362.79,0.52056,-0.12977,0.8439,-87.449
> view matrix models
> #5,-0.80048,-0.3248,0.50372,323.24,0.18817,-0.93413,-0.3033,381.1,0.56905,-0.148,0.80887,-84.163
> view matrix models
> #5,-0.83802,-0.27227,0.47285,327.36,0.14615,-0.94695,-0.28624,386.73,0.5257,-0.17076,0.83336,-78.221
> view matrix models
> #5,-0.82968,-0.2976,0.47229,330.75,0.18414,-0.9446,-0.27172,376.23,0.52699,-0.13847,0.83852,-85.669
> volume #8 level 0.07251
> select subtract #5
Nothing selected
> ui tool show Rotamers
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/L:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/H
Alignment identifier is 5/H
> select #5/H:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/H:1-3
22 atoms, 21 bonds, 3 residues, 1 model selected
> ui tool show "Model Loops"
> modeller refine 5/H:1:all-missing numModels 5 fast false adjacentFlexible 1
> protocol standard
Webservices job id: VWCNQFID77H03PPS
Modeller job (ID VWCNQFID77H03PPS) finished
Modeller failure; standard error:
Traceback (most recent call last):
File "ModellerModelling.py", line 93, in <module>
a.make()
File "/usr/lib64/python3.6/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.6/site-packages/modeller/automodel/automodel.py",
line 701, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> ui tool show "Side View"
> show #9 models
> hide #9 models
> show #9 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/H:89
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:89-116
230 atoms, 242 bonds, 28 residues, 1 model selected
> select #5/H:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/H:28-36
71 atoms, 73 bonds, 9 residues, 1 model selected
> select #5/H:28
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/H:28-35
59 atoms, 60 bonds, 8 residues, 1 model selected
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-35
55 atoms, 56 bonds, 7 residues, 1 model selected
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.78057,-0.25347,0.57136,290.43,0.14361,-0.96236,-0.23074,376.82,0.60834,-0.098055,0.78759,-95.206
> view matrix models
> #5,-0.70706,-0.3336,0.62352,280.11,0.24945,-0.94271,-0.22152,352.57,0.6617,-0.0010907,0.74977,-113.49
> view matrix models
> #5,-0.69694,-0.29889,0.65187,265.15,0.22036,-0.95428,-0.20196,355.12,0.68243,0.0028993,0.73094,-113.36
> view matrix models
> #5,-0.71926,-0.31911,0.61712,281.06,0.26188,-0.94728,-0.18461,342.47,0.6435,0.028824,0.7649,-119.48
> view matrix models
> #5,-0.73098,-0.35003,0.58579,296.3,0.27751,-0.93672,-0.21342,344.64,0.62342,0.0065603,0.78186,-115.89
> view matrix models
> #5,-0.744,-0.38717,0.54457,315.27,0.29793,-0.92173,-0.24828,346.61,0.59808,-0.022477,0.80112,-110.67
> view matrix models
> #5,-0.64878,-0.44583,0.6167,292.42,0.35923,-0.89386,-0.26827,335.52,0.67084,0.047487,0.74008,-121.79
> view matrix models
> #5,-0.62439,-0.46334,0.62884,288.54,0.36562,-0.88479,-0.2889,337.64,0.69026,0.049536,0.72187,-121.21
> view matrix models
> #5,-0.63478,-0.46697,0.61562,294.17,0.35225,-0.88401,-0.30733,344.2,0.68773,0.021768,0.72564,-116.52
> view matrix models
> #5,-0.61524,-0.38128,0.69001,257.16,0.33568,-0.91865,-0.20832,329.96,0.71331,0.10345,0.69318,-128.41
> view matrix models
> #5,-0.76581,-0.22867,0.60103,276.2,0.13893,-0.9714,-0.19256,370.23,0.62788,-0.063967,0.77568,-102.1
> view matrix models
> #5,-0.78982,-0.28243,0.54445,303.82,0.18289,-0.95574,-0.23046,368.69,0.58544,-0.082452,0.80651,-98.621
> view matrix models
> #5,-0.79292,-0.27196,0.54527,302.22,0.18011,-0.95949,-0.21664,366.58,0.5821,-0.073569,0.80978,-100.47
> view matrix models
> #5,-0.79401,-0.27238,0.54346,302.92,0.18004,-0.95926,-0.21773,366.81,0.58063,-0.075037,0.8107,-100.16
> view matrix models
> #5,-0.80028,-0.30121,0.51848,315.31,0.14171,-0.93519,-0.32456,394.44,0.58264,-0.18627,0.7911,-75.192
> view matrix models
> #5,-0.78732,-0.26873,0.55489,298.36,0.10956,-0.94667,-0.303,397.03,0.60673,-0.17777,0.77478,-77.078
> view matrix models
> #5,-0.77396,-0.26304,0.57601,289.95,0.10485,-0.95032,-0.29309,396.17,0.62449,-0.16645,0.76309,-79.488
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.77396,-0.26304,0.57601,289.63,0.10485,-0.95032,-0.29309,395.77,0.62449,-0.16645,0.76309,-79.465
> select subtract #5
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1c-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/H:29
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:29-35
55 atoms, 56 bonds, 7 residues, 1 model selected
> ui tool show "Model Loops"
[Repeated 2 time(s)]
> ui tool show "Modeller Comparative"
> select #5/H:56
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:56-62
58 atoms, 59 bonds, 7 residues, 1 model selected
> select #5/H:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:55-62
69 atoms, 70 bonds, 8 residues, 1 model selected
> select #5/H:55
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/H:55-58
35 atoms, 35 bonds, 4 residues, 1 model selected
> select #5/H:54-55
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #5/H:54-59
49 atoms, 49 bonds, 6 residues, 1 model selected
> select #5/H:55-56
23 atoms, 23 bonds, 2 residues, 1 model selected
> select #5/H:55-59
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #5/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/H:59
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/H:55-59
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #5/H:100-144
341 atoms, 356 bonds, 45 residues, 1 model selected
> select #5/H:100-112
113 atoms, 120 bonds, 13 residues, 1 model selected
> select #5/H:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:174-185
87 atoms, 89 bonds, 12 residues, 1 model selected
> select #5/H:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/H:102-107
54 atoms, 56 bonds, 6 residues, 1 model selected
> select #3/B:290-291
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:290-310
150 atoms, 150 bonds, 21 residues, 1 model selected
> select #3/B:290-315
193 atoms, 195 bonds, 26 residues, 1 model selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> select #3/B:352
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B:341-352
91 atoms, 90 bonds, 12 residues, 1 model selected
> select
> #5/H:5-9,20-27,36-42,48-54,60-62,70-75,80-85,94-101,118-120,131-135,146-156,161-165,174-176,187-196,205-211,216-222
837 atoms, 847 bonds, 101 residues, 1 model selected
> select #5/H:127
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:127-130
27 atoms, 27 bonds, 4 residues, 1 model selected
> view matrix models
> #5,-0.77396,-0.26304,0.57601,280.18,0.10485,-0.95032,-0.29309,395.64,0.62449,-0.16645,0.76309,-74.626
> hide #!8 models
> show #!2 models
> hide #!2 models
> select #5/L:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:22-28
47 atoms, 46 bonds, 7 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-35
51 atoms, 51 bonds, 7 residues, 1 model selected
> select #5/L:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> select #5/L:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:29-34
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50-54
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-55
39 atoms, 39 bonds, 5 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-56
47 atoms, 47 bonds, 6 residues, 1 model selected
> select #5/L:51
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/L:51-62
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> show #!8 models
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #8
82 atoms, 83 bonds, 12 residues, 3 models selected
> select subtract #8
82 atoms, 83 bonds, 12 residues, 1 model selected
> hide #!8 models
> hide #8.1 models
> select add #9
3416 atoms, 3463 bonds, 426 residues, 2 models selected
> select subtract #9
82 atoms, 83 bonds, 12 residues, 1 model selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #5
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> view matrix models
> #5,-0.77396,-0.26304,0.57601,281.01,0.10485,-0.95032,-0.29309,395.7,0.62449,-0.16645,0.76309,-74.661
> view matrix models
> #5,-0.77396,-0.26304,0.57601,281.22,0.10485,-0.95032,-0.29309,395.6,0.62449,-0.16645,0.76309,-74.86
> view matrix models
> #5,-0.77396,-0.26304,0.57601,282.28,0.10485,-0.95032,-0.29309,396.27,0.62449,-0.16645,0.76309,-74.987
> view matrix models
> #5,-0.77396,-0.26304,0.57601,283.04,0.10485,-0.95032,-0.29309,396.66,0.62449,-0.16645,0.76309,-75.111
> view matrix models
> #5,-0.77396,-0.26304,0.57601,282.9,0.10485,-0.95032,-0.29309,397.32,0.62449,-0.16645,0.76309,-75.13
> view matrix models
> #5,-0.77396,-0.26304,0.57601,283.39,0.10485,-0.95032,-0.29309,397.2,0.62449,-0.16645,0.76309,-75.14
> view matrix models
> #5,-0.77396,-0.26304,0.57601,285.17,0.10485,-0.95032,-0.29309,397.62,0.62449,-0.16645,0.76309,-75.184
> view matrix models
> #5,-0.77396,-0.26304,0.57601,285.99,0.10485,-0.95032,-0.29309,397.56,0.62449,-0.16645,0.76309,-75.367
> view matrix models
> #5,-0.77396,-0.26304,0.57601,286.16,0.10485,-0.95032,-0.29309,397.36,0.62449,-0.16645,0.76309,-75.361
> select add #8.1
3401 atoms, 3493 bonds, 442 residues, 2 models selected
> show #8.1 models
> select subtract #5
1 model selected
> select add #8
2 models selected
> select subtract #8
Nothing selected
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #5/L:66-68
14 atoms, 13 bonds, 3 residues, 1 model selected
> select #5/L:115
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:115-121
57 atoms, 60 bonds, 7 residues, 1 model selected
> select #5/L:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:102-106
41 atoms, 40 bonds, 5 residues, 1 model selected
> select #5/L:96
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:94-96
26 atoms, 27 bonds, 3 residues, 1 model selected
> select #5/L:75
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:75-77
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #5/L:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/L:80-81
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:98
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/L:98-99
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #5/L:94
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:93-94
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #5/L:91
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:91
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:92
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/L:92-93
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #5/L:92-93
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #5/L:92-97
56 atoms, 59 bonds, 6 residues, 1 model selected
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-100
750 atoms, 769 bonds, 100 residues, 1 model selected
> select #5/L:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/L:1-111
834 atoms, 853 bonds, 111 residues, 1 model selected
> select #5/L:108
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/L:1-108
815 atoms, 834 bonds, 108 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-96
20 atoms, 21 bonds, 2 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-105
83 atoms, 85 bonds, 11 residues, 1 model selected
> select #5/L:95
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/L:95-102
57 atoms, 59 bonds, 8 residues, 1 model selected
> select #5/L:93
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/L:93-101
70 atoms, 74 bonds, 9 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B #9/C
Alignment identifier is 1
> ui mousemode right select
> select clear
> toolshed show
Downloading bundle ChimeraX_XMAS-1.1.2-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.0.1
[notice] To update, run:
/Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
Requirement already satisfied: ChimeraX-UI~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.24.3)
Requirement already satisfied: ChimeraX-Core~=1.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-XMAS==1.1.2) (1.5)
Collecting openpyxl
Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 8.0 MB/s eta 0:00:00
Collecting seaborn
Downloading seaborn-0.12.2-py3-none-any.whl (293 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 293.3/293.3 kB 18.8 MB/s eta 0:00:00
Collecting pandas
Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 8.1 MB/s eta 0:00:00
Collecting qtrangeslider
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2) (1.0)
Collecting et-xmlfile
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: python-dateutil>=2.8.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2.8.2)
Requirement already satisfied: numpy>=1.20.3 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (1.23.1)
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pandas->ChimeraX-XMAS==1.1.2) (2022.6)
Requirement already satisfied: matplotlib!=3.6.1,>=3.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from seaborn->ChimeraX-XMAS==1.1.2) (3.5.2)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.3->ChimeraX-XMAS==1.1.2)
(1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.3->ChimeraX-
XMAS==1.1.2) (1.0.1)
Requirement already satisfied: pyparsing>=2.2.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (3.0.9)
Requirement already satisfied: fonttools>=4.22.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(4.38.0)
Requirement already satisfied: packaging>=20.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (21.3)
Requirement already satisfied: kiwisolver>=1.0.1 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (1.4.4)
Requirement already satisfied: cycler>=0.10 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2)
(0.11.0)
Requirement already satisfied: pillow>=6.2.0 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from matplotlib!=3.6.1,>=3.1->seaborn->ChimeraX-XMAS==1.1.2) (9.2.0)
Requirement already satisfied: six>=1.5 in
/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from python-dateutil>=2.8.1->pandas->ChimeraX-XMAS==1.1.2) (1.16.0)
Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
seaborn, ChimeraX-XMAS
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
\---
Successfully installed ChimeraX-XMAS-1.1.2 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-1.5.3 qtrangeslider-0.1.5 seaborn-0.12.2
Installed ChimeraX-XMAS (1.1.2)
> toolshed install Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl
Missing or invalid "bundleNames" argument: Expected a bundle name or a wheel
file name
> toolshed install /Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-
> any.whl
bundle '/Users/alvinchew/Downloads/ChimeraX_XMAS-1.1.2-py3-none-any.whl'
already installed
> save "/Users/alvinchew/OneDrive - Nanyang Technological
> University/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms_10min_recolored.cxs"
> includeMaps true
——— End of log from Thu Mar 30 23:52:24 2023 ———
opened ChimeraX session
> select down
Nothing selected
> select down
Nothing selected
> ui tool show "Show Sequence Viewer"
> ui tool show "Change Chain IDs"
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-20
149 atoms, 151 bonds, 20 residues, 1 model selected
> select #3/B:1-20
149 atoms, 151 bonds, 20 residues, 1 model selected
> select #3/B:1-20,136-352
1872 atoms, 1920 bonds, 237 residues, 1 model selected
> select #3/B:1-20,136-352
1872 atoms, 1920 bonds, 237 residues, 1 model selected
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-180
1439 atoms, 1472 bonds, 180 residues, 1 model selected
> select #3/A
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/NS1chainA.pdb selectedOnly true relModel
> #8.1
> open /Users/alvinchew/Downloads/NS1chainA.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for NS1chainA.pdb #6
---
Chain | Description
A | No description available
> undo
> close #6
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> toolshed show
> xmas
Unknown command: xmas
> runscript xmas
Missing or invalid "scriptFile" argument: File 'xmas' does not exist
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-120
956 atoms, 977 bonds, 120 residues, 1 model selected
> select #3/A
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/NS1chainA.pdb models #3 selectedOnly true
> relModel #3
> open /Users/alvinchew/Downloads/NS1chainA.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/NS1chainA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for NS1chainA.pdb #6
---
Chain | Description
A | No description available
> close #6
> hide #3 models
> show #3 models
> save /Users/alvinchew/Downloads/D2NS1_A #3/A relModel #3/B
Cannot determine format for '/Users/alvinchew/Downloads/D2NS1_A'
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A relModel #3/B
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #6
---
Chain | Description
A B | No description available
> hide #3 models
> show #3 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> close #6
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #3/A selectedOnly true relModel
> #3/B
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_A.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 39
GLU B 51 1 13
Start residue of secondary structure not found: HELIX 2 2 ARG B 62 THR B 72 1
11
Start residue of secondary structure not found: HELIX 3 3 PRO B 73 GLU B 81 1
9
Start residue of secondary structure not found: HELIX 4 4 TRP B 115 ALA B 121
1 7
Start residue of secondary structure not found: HELIX 5 5 ASN B 145 ASN B 147
1 3
26 messages similar to the above omitted
Chain information for D2NS1_A.pdb #6
---
Chain | Description
A | No description available
> hide #3 models
> select #3/B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3/B:1-14
110 atoms, 111 bonds, 14 residues, 1 model selected
> show #3 models
> select add #8
110 atoms, 111 bonds, 14 residues, 5 models selected
> select subtract #8
110 atoms, 111 bonds, 14 residues, 1 model selected
> hide #!8 models
> hide #3 models
> show #3 models
> mmaker #6 to #3/A
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 eden2ns1.pdb, chain A (#3) with D2NS1_A.pdb, chain A (#6), sequence
alignment score = 1853.9
RMSD between 352 pruned atom pairs is 0.000 angstroms; (across all 352 pairs:
0.000)
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select add #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> save /Users/alvinchew/Downloads/D2NS1_A.pdb #6
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #7
---
Chain | Description
A | No description available
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true relModel
> #3/A
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #10
---
Chain | Description
B | No description available
> close #10
> save /Users/alvinchew/Downloads/D2NS1_B.pdb #3/B selectedOnly true
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #10
---
Chain | Description
B | No description available
> close #6
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> select #9/B-C:1
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #9/B-C:1-8
114 atoms, 112 bonds, 16 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #9/B
Alignment identifier is 9/B
> sequence chain #9/C
Alignment identifier is 9/C
> select #9/C:2-149,151-206
1648 atoms, 1670 bonds, 204 residues, 1 model selected
> select #9/C:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/C
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> save /Users/alvinchew/Downloads/ApoA1_Y.pdb #9/C selectedOnly true
> open /Users/alvinchew/Downloads/ApoA1_Y.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
ALA B 129 1 128
Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
1 20
Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
1 56
Chain information for ApoA1_Y.pdb #6
---
Chain | Description
C | No description available
> select #9/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/B
1667 atoms, 1690 bonds, 207 residues, 1 model selected
> save /Users/alvinchew/Downloads/ApoA1_X.pdb #9/B selectedOnly true
> open /Users/alvinchew/Downloads/ApoA1_X.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
ALA C 129 1 128
Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
1 20
Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
1 56
Chain information for ApoA1_X.pdb #11
---
Chain | Description
B | No description available
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #9 models
> hide #8.1 models
> hide #10 models
> hide #11 models
> select add #9
3334 atoms, 3380 bonds, 414 residues, 1 model selected
> select subtract #9
Nothing selected
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #3 models
> show #3 models
> hide #7 models
> hide #6 models
> show #!8 models
> hide #!8 models
> show #8.1 models
> hide #8.1 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
[Repeated 1 time(s)]
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min.defattr attrName
> Fab_rDeutdelta_10min models #5
No known/registered attribute Fab_rDeutdelta_10min
> setattr #5 residues Fab_rDeutdelta_10min_color models create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color create true type color
Expected a keyword
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Cannot determine format for '/Users/alvinchew/Downloads/'
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
No known/registered attribute Fab_rDeutdelta_10min_color
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
No known/registered attribute Fab_rDeutdelta_10min_color
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type color
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type float
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Expected a number
> setattr #5 residues Fab_rDeutdelta_10min_color value create true
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
Invalid color name or specifier
> setattr #5 residues Fab_rDeutdelta_10min_color value create true type string
Assigning Fab_rDeutdelta_10min_color attribute to 442 items
> save /Users/alvinchew/Downloads/ Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Cannot determine format for '/Users/alvinchew/Downloads/'
> save /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr attrName
> Fab_rDeutdelta_10min_color models #5
Saved attribute 'Fab_rDeutdelta_10min_color' of 442 residues using match mode:
1-to-1 to /Users/alvinchew/Downloads/Fab_rDeutdelta_10min_color.defattr
> ui tool show "Color Actions"
> close session
> open /Users/alvinchew/Downloads/ApoA1_X.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_X.pdb
---
warnings | Start residue of secondary structure not found: HELIX 4 4 ALA C 2
ALA C 129 1 128
Start residue of secondary structure not found: HELIX 5 5 PRO C 130 GLY C 149
1 20
Start residue of secondary structure not found: HELIX 6 6 GLY C 151 ALA C 206
1 56
Chain information for ApoA1_X.pdb #1
---
Chain | Description
B | No description available
> open /Users/alvinchew/Downloads/ApoA1_Y.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/ApoA1_Y.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 2
ALA B 129 1 128
Start residue of secondary structure not found: HELIX 2 2 PRO B 130 GLY B 149
1 20
Start residue of secondary structure not found: HELIX 3 3 GLY B 151 ALA B 206
1 56
Chain information for ApoA1_Y.pdb #2
---
Chain | Description
C | No description available
> open /Users/alvinchew/Downloads/D2NS1_B.pdb
Summary of feedback from opening /Users/alvinchew/Downloads/D2NS1_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 13 13 PRO A
39 GLU A 51 1 13
Start residue of secondary structure not found: HELIX 14 14 ARG A 62 THR A 72
1 11
Start residue of secondary structure not found: HELIX 15 15 PRO A 73 GLU A 81
1 9
Start residue of secondary structure not found: HELIX 16 16 TRP A 115 ALA A
121 1 7
Start residue of secondary structure not found: HELIX 17 17 ASN A 145 ASN A
147 1 3
26 messages similar to the above omitted
Chain information for D2NS1_B.pdb #3
---
Chain | Description
B | No description available
> open /Users/alvinchew/Downloads/D2NS1_A.pdb
Chain information for D2NS1_A.pdb #4
---
Chain | Description
A | No description available
> color #2 #e0e6ecff
> color #2 #b1b6bbff
> color #1 #d7d0cbff
> color #3 #93a3e1ff
> color #3 #8a9ae1ff
> color #3 #969ae1ff
> color #3 #8496e1ff
> color #4 #b7d7ecff
> save /Users/alvinchew/Downloads/NS1-apoAI_monomers-forwint.cxs includeMaps
> true
——— End of log from Sat Apr 1 16:55:32 2023 ———
opened ChimeraX session
> ui tool show XMAS
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy.txt
428 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 28 out of 33
Unique peptide pairs with pseudobonds: 28
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1wt_ApoA1_crosslinks_copy_1,2,3,4.tsv
Please select pseudobonds
Please select pseudobonds
Please select pseudobonds
> select subtract #5
Nothing selected
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
——— End of log from Mon Apr 3 15:19:20 2023 ———
opened ChimeraX session
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt
432 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 29 out of 29
Unique peptide pairs with pseudobonds: 26
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2.tsv
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Please select pseudobonds
/Users/wintwintphoo/Library/Application Support/ChimeraX/1.5/site-
packages/seaborn/categorical.py:166: FutureWarning: Setting a gradient palette
using color= is deprecated and will be removed in version 0.13. Set
`palette='dark:gray'` for same effect.
warnings.warn(msg, FutureWarning)
> color #1 #684bdfff
> undo
> select subtract #6
Nothing selected
> select add #5
102 pseudobonds, 1 model selected
> select subtract #5
Nothing selected
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS.txt
432 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 29 out of 29
Unique peptide pairs with pseudobonds: 26
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_ApoA1_xlinks_forXMAS_1,2,3,4.tsv
Peptide pair mapping of XlinkX evidence file:
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS.txt
436 Peptide pairs are disregarded due to lacking/decoy sequence
Unique peptide pairs: 25 out of 25
Unique peptide pairs with pseudobonds: 20
Pseudobonds are stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.pb
Mapping information is stored in
/Users/wintwintphoo/Downloads/media-2/20220215_denv2_ns1_apoA1_InterX_links_forXMAS_1,2,3,4.tsv
> select subtract #7
Nothing selected
> close #7
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
[Repeated 1 time(s)]Pseudobonds are stored in
/Users/wintwintphoo/Downloads/20220215_denv_ns1_apoA1_xmas_xlinks_list.pb
> select subtract #8
195 pseudobonds, 2 models selected
> select add #8
275 pseudobonds, 3 models selected
> hide #8 models
> show #8 models
> hide #7 models
> save /Users/wintwintphoo/Downloads/NS1-apoAI_models-forwint_forAlvin.cxs
——— End of log from Mon Apr 3 16:43:31 2023 ———
opened ChimeraX session
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> select subtract #7
275 pseudobonds, 3 models selected
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> open "/Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Writing/202211_LATEST_NS1manuscript/EM
> Maps_docked structures/EDEN2 sNS1wt-Fab562/sNS1wt-Fab562.mrc"
Opened sNS1wt-Fab562.mrc as #9, grid size 416,416,416, pixel 0.85, shown at
level 0.0324, step 2, values float32
> volume #9 step 1
> volume #9 color #b2b2b25f
> volume #9 color #b2b2b24d
> volume #9 color #aebfbb4d
> volume #9 color #96bdbf4d
> volume #9 color #b4e3e64d
> select subtract #5
173 pseudobonds, 2 models selected
> select subtract #6
80 pseudobonds, 1 model selected
> select subtract #8
Nothing selected
> select add #9
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.87886,-0.26868,-0.39424,454.61,-2.4853e-05,0.82637,-0.56313,136.08,0.47709,-0.4949,-0.72627,325.9
> view matrix models
> #9,-0.58078,0.6843,0.44094,79.244,0.37206,0.7049,-0.6039,98.706,-0.72406,-0.18668,-0.66399,474.16
> volume #9 level 0.08346
> view matrix models
> #9,-0.62302,0.6249,0.47048,91.383,0.37769,0.76704,-0.51866,70.685,-0.68498,-0.14544,-0.71389,469.61
> view matrix models
> #9,-0.59735,0.62471,0.5029,80.705,0.44544,0.7799,-0.43971,41.448,-0.6669,-0.038648,-0.74414,453.65
> view matrix models
> #9,-0.73179,-0.006901,0.6815,180.03,-0.57374,0.54594,-0.61055,294.56,-0.36785,-0.83779,-0.40347,474.63
> view matrix models
> #9,-0.79319,-0.093028,0.60182,221,-0.596,0.32149,-0.73582,361.32,-0.12503,-0.94233,-0.31045,432.17
> view matrix models
> #9,-0.58382,-0.31126,0.74985,193.7,-0.73407,0.59693,-0.32375,259.38,-0.34683,-0.73946,-0.57698,486.91
> view matrix models
> #9,-0.34202,-0.16644,0.92484,92.532,-0.84723,0.48035,-0.22687,281.13,-0.40649,-0.86114,-0.3053,466.79
> view matrix models
> #9,-0.55882,0.49146,0.66797,65.577,-0.45981,0.4867,-0.74277,309.92,-0.69014,-0.72222,-0.045999,443.36
> view matrix models
> #9,-0.54201,-0.3239,0.77544,183.64,-0.79241,0.50424,-0.34326,289.48,-0.27982,-0.80052,-0.52997,476.72
> view matrix models
> #9,-0.58956,-0.063726,0.80521,141.21,-0.57182,0.737,-0.36035,213.39,-0.57047,-0.67289,-0.47094,494.64
> view matrix models
> #9,-0.39155,-0.00207,0.92016,73.642,-0.67059,0.68539,-0.28381,225.21,-0.63008,-0.72818,-0.26975,476.42
> view matrix models
> #9,-0.28776,-0.19817,0.93698,86.145,-0.87695,0.44774,-0.17463,282.08,-0.38491,-0.87193,-0.30263,464.35
> view matrix models
> #9,-0.25456,-0.094965,0.96238,57.53,-0.75216,0.64493,-0.13531,218.34,-0.60782,-0.75832,-0.2356,471.22
> view matrix models
> #9,0.08179,0.053136,0.99523,-33.823,-0.83033,0.55594,0.038556,214.45,-0.55124,-0.82952,0.089591,411.62
> view matrix models
> #9,-0.066864,0.18014,0.98137,-26.974,-0.92402,0.35991,-0.12902,296.95,-0.37644,-0.91543,0.14239,385.61
> view matrix models
> #9,-0.1796,0.42981,0.88488,-32.014,-0.68511,0.59085,-0.42605,271.28,-0.70595,-0.68276,0.18835,394.65
> view matrix models
> #9,-0.38938,-0.35219,0.85108,147.19,-0.71886,0.6939,-0.041736,186.13,-0.57587,-0.62806,-0.52337,497.8
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.38938,-0.35219,0.85108,163.76,-0.71886,0.6939,-0.041736,188.56,-0.57587,-0.62806,-0.52337,496.31
> view matrix models
> #9,-0.38938,-0.35219,0.85108,168.86,-0.71886,0.6939,-0.041736,197.29,-0.57587,-0.62806,-0.52337,495.68
> view matrix models
> #9,-0.38938,-0.35219,0.85108,169.85,-0.71886,0.6939,-0.041736,197.13,-0.57587,-0.62806,-0.52337,494.81
> volume #9 level 0.09622
> volume #9 level 0.1218
> volume #9 level 0.1102
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.37051,-0.036777,0.9281,96.88,-0.68448,0.68625,-0.24606,231.42,-0.62786,-0.72644,-0.27943,474.52
> view matrix models
> #9,-0.31168,-0.049862,0.94888,84.726,-0.69125,0.69707,-0.19043,220.1,-0.65194,-0.71527,-0.25173,471.56
> view matrix models
> #9,-0.1857,-0.07265,0.97992,60.36,-0.66701,0.74162,-0.07142,185.28,-0.72154,-0.66687,-0.18618,462.98
> view matrix models
> #9,-0.23942,-0.0021906,0.97091,59.372,-0.51422,0.84851,-0.12489,149.75,-0.82356,-0.52917,-0.20428,460.62
> view matrix models
> #9,-0.22507,0.022971,0.97407,51.838,-0.51742,0.84429,-0.13947,153.84,-0.8256,-0.5354,-0.17814,457.06
> view matrix models
> #9,-0.22651,0.020133,0.9738,52.639,-0.51714,0.84474,-0.13775,153.38,-0.82538,-0.5348,-0.18093,457.45
> view matrix models
> #9,-0.21551,0.029869,0.97604,48.561,-0.50806,0.85017,-0.1382,150.91,-0.83393,-0.52567,-0.16805,454.92
> view matrix models
> #9,-0.26159,0.28099,0.92337,23.126,-0.7227,0.57709,-0.38035,282.89,-0.63974,-0.76682,0.052114,420.27
> view matrix models
> #9,-0.41669,0.2104,0.88436,70.441,-0.68255,0.57014,-0.45725,291.66,-0.60041,-0.79415,-0.093959,445.96
> view matrix models
> #9,-0.43816,0.2546,0.86209,70.827,-0.46829,0.75397,-0.46068,222.24,-0.76728,-0.60556,-0.21113,465.21
> view matrix models
> #9,-0.40829,0.25984,0.87509,62.119,-0.47771,0.75607,-0.44739,221.01,-0.77788,-0.6007,-0.18457,461.17
> view matrix models
> #9,-0.44661,0.14869,0.88229,86.897,-0.5092,0.76859,-0.38728,212.93,-0.7357,-0.62223,-0.26755,473.29
> view matrix models
> #9,-0.44407,0.15675,0.88217,85.065,-0.50686,0.76795,-0.3916,213.45,-0.73884,-0.62104,-0.26158,472.5
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.44407,0.15675,0.88217,83.534,-0.50686,0.76795,-0.3916,214.96,-0.73884,-0.62104,-0.26158,474.33
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.47173,0.10261,0.87575,99.098,-0.49372,0.79217,-0.35876,202.13,-0.73056,-0.60161,-0.32303,481.23
> view matrix models
> #9,-0.46188,0.17351,0.86981,86.145,-0.45527,0.79525,-0.40039,202.72,-0.76118,-0.58093,-0.28831,476.44
> view matrix models
> #9,-0.17678,0.17743,0.96813,15.981,-0.55919,0.79135,-0.24714,192.57,-0.80997,-0.58505,-0.040674,438.48
> view matrix models
> #9,-0.20822,0.22068,0.95286,16.964,-0.47946,0.8261,-0.2961,181.71,-0.8525,-0.51851,-0.066201,439.34
> view matrix models
> #9,-0.23313,0.22067,0.94708,22.5,-0.51218,0.80002,-0.31248,195.19,-0.82664,-0.55792,-0.073484,442.99
> view matrix models
> #9,-0.272,0.31817,0.90818,19.883,-0.43497,0.80119,-0.41096,200.1,-0.85838,-0.50681,-0.07953,440.9
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.272,0.31817,0.90818,20.776,-0.43497,0.80119,-0.41096,197.63,-0.85838,-0.50681,-0.07953,443.72
> view matrix models
> #9,-0.272,0.31817,0.90818,21.653,-0.43497,0.80119,-0.41096,197.64,-0.85838,-0.50681,-0.07953,444.39
> view matrix models
> #9,-0.272,0.31817,0.90818,21.578,-0.43497,0.80119,-0.41096,197.39,-0.85838,-0.50681,-0.07953,444.75
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.34138,0.16793,0.9248,56.875,-0.43348,0.8449,-0.31343,170.87,-0.834,-0.50788,-0.21564,466.63
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> combine #1-4
Remapping chain ID 'B' in D2NS1_B.pdb #3 to 'D'
> hide #10 models
> show #10 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #10 models
> show #10 models
> hide #5 models
> show #5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #2 models
> show #3 models
> show #4 models
> view matrix models
> #9,0.52951,-0.025333,0.84793,-49.614,-0.39781,0.87542,0.27457,46.784,-0.74925,-0.4827,0.45346,319.24
> undo
> select subtract #9
Nothing selected
> ui mousemode right zoom
> molmap #1-4 onGrid #9 sigmaFactor 6
Missing or invalid "resolution" argument: Expected a number
> molmap #1-4 resolution 8 onGrid #9
Missing or invalid "resolution" argument: Expected a number
> molmap #1-4 8 onGrid #9
Opened map 8 as #11, grid size 416,416,416, pixel 0.85, shown at level 0.0635,
step 1, values float32
> volume #11 level 0.03753
> mmaker #9 to #11
No 'to' model specified
> fitmap #9 to #11
Expected a keyword
> Fit #9 in map #11
Unknown command: Fit #9 in map #11
> fitmap #9 inMap map #11
Invalid "inMap" argument: invalid density map specifier
> fitmap #9 inMap #11
Fit map sNS1wt-Fab562.mrc in map map 8 using 131473 points
correlation = 0.6323, correlation about mean = 0.08876, overlap = 2834
steps = 292, shift = 12.1, angle = 16.9 degrees
Position of sNS1wt-Fab562.mrc (#9) relative to map 8 (#11) coordinates:
Matrix rotation and translation
0.96199493 -0.17308261 0.21120645 -4.02299000
0.19395657 0.97754937 -0.08232910 -24.62700524
-0.19221500 0.12016506 0.97396805 10.65384009
Axis 0.34805838 0.69342351 0.63088763
Axis point 91.81802475 0.00000000 16.19663836
Rotation angle (degrees) 16.91131195
Shift along axis -11.75580388
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs" includeMaps true
——— End of log from Wed Apr 19 14:11:57 2023 ———
opened ChimeraX session
> open /Users/alvinchew/Library/CloudStorage/OneDrive-
> NanyangTechnologicalUniversity(1)/202112_FlaviNS1/Data_EM_Alvin/F562a.pdb
Chain information for F562a.pdb #12
---
Chain | Description
C | No description available
D | No description available
> color #12 #8b92d7ff
> color #12 #718dd7ff
> color #12 #7693d7ff
> color #12 #849ed7ff
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.59826,0.23414,-0.76633,188.86,-0.29309,-0.82615,-0.48122,476.1,-0.74578,0.5125,-0.42563,337.4
> view matrix models
> #12,0.8198,-0.22926,-0.52475,175.64,-0.56234,-0.49535,-0.66212,513.22,-0.10814,0.8379,-0.53501,149.05
> view matrix models
> #12,0.70505,-0.47588,-0.52578,246.35,-0.42704,-0.87682,0.22096,392.51,-0.56617,0.068741,-0.82142,443.24
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.70505,-0.47588,-0.52578,242.09,-0.42704,-0.87682,0.22096,378.11,-0.56617,0.068741,-0.82142,460.51
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.89785,-0.43928,-0.030063,102.58,-0.37117,-0.71836,-0.58838,480.03,0.23687,0.53943,-0.80803,185.85
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.89785,-0.43928,-0.030063,97.925,-0.37117,-0.71836,-0.58838,480.91,0.23687,0.53943,-0.80803,179.17
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.96357,-0.26121,-0.057389,55.865,-0.25517,-0.8337,-0.48973,456.47,0.080078,0.48653,-0.86998,236.41
> view matrix models
> #12,0.90596,-0.39388,-0.15525,110.13,-0.42323,-0.85213,-0.30783,467.19,-0.011043,0.34459,-0.93869,295.05
> view matrix models
> #12,0.89108,-0.41763,-0.17768,121.79,-0.45249,-0.84775,-0.2767,467.81,-0.035067,0.32696,-0.94439,304.83
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.89108,-0.41763,-0.17768,121.19,-0.45249,-0.84775,-0.2767,465.74,-0.035067,0.32696,-0.94439,307.63
> view matrix models
> #12,0.89108,-0.41763,-0.17768,120.89,-0.45249,-0.84775,-0.2767,466.02,-0.035067,0.32696,-0.94439,307.05
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.90549,-0.36137,-0.22248,115.49,-0.40743,-0.88694,-0.21757,451.86,-0.11871,0.28765,-0.95035,334.75
Must specify one map, got 0
> fitmap #12 inMap #9
Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms
average map value = 0.09851, steps = 92
shifted from previous position = 4.5
rotated from previous position = 18.4 degrees
atoms outside contour = 1988, contour level = 0.11015
Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates:
Matrix rotation and translation
-0.10510217 -0.15771336 0.98187577 53.64785327
-0.09250566 -0.98151278 -0.16755707 397.45943422
0.99014960 -0.10843968 0.08856975 -3.70781985
Axis 0.66871425 -0.09359056 0.73760562
Axis point 22.55285651 199.33929044 0.00000000
Rotation angle (degrees) 177.46657060
Shift along axis -4.05827537
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> select #12/C:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/C:1-18
131 atoms, 132 bonds, 18 residues, 1 model selected
> color #12 #d0d2dfff
> select #12/C:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/C:5-14
71 atoms, 71 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #cbd8ffff
> color sel #9fbcffff
> color sel #93abffff
> color sel #88a4ffff
> color sel #8484f7ff
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/C:15-35
163 atoms, 168 bonds, 21 residues, 1 model selected
> color sel #fdf2f2ff
> select #12/C:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/C:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #fae0e0ff
> select #12/C:22
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:22-35
112 atoms, 116 bonds, 14 residues, 1 model selected
> color sel #fbe8e7ff
> select #12/C:36-37
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #12/C:36-42
77 atoms, 81 bonds, 7 residues, 1 model selected
> select #12/C:30
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/C:30-35
43 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #3535f5ff
> select #12/C:36-37
26 atoms, 28 bonds, 2 residues, 1 model selected
> select #12/C:36-47
115 atoms, 120 bonds, 12 residues, 1 model selected
> color sel #fbe8e7ff
> select #12/C:48-49
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #12/C:48-57
94 atoms, 97 bonds, 10 residues, 1 model selected
> select #12/C:58-59
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #12/C:58-61
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #f1f1feff
> select #12/C:62-63
20 atoms, 20 bonds, 2 residues, 1 model selected
> select #12/C:62-73
99 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #fadfdfff
> select #12/C:79
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:79-94
126 atoms, 128 bonds, 16 residues, 1 model selected
> color sel #efeffeff
> select #12/C:95
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:95-103
82 atoms, 85 bonds, 9 residues, 1 model selected
> color sel #ddddfcff
> select #12/C:102
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:102-103
24 atoms, 25 bonds, 2 residues, 1 model selected
> color sel #c9d0ffff
> hide #!9 models
> select #12/C:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:104-105
18 atoms, 18 bonds, 2 residues, 1 model selected
> set bgColor white
> select #12/C:104
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:104-112
73 atoms, 78 bonds, 9 residues, 1 model selected
> color sel #d3d3fbff
> color sel #bec7feff
> select #12/C:113
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/C:113-120
65 atoms, 67 bonds, 8 residues, 1 model selected
> color sel #d3d9feff
> select #12/C:123
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:123-145
153 atoms, 157 bonds, 23 residues, 1 model selected
> color sel #f6f6feff
> color sel #e7e8ffff
> color sel #edf0ffff
> select #12/C:146
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:146-156
79 atoms, 79 bonds, 11 residues, 1 model selected
> color sel #fdf1f1ff
> select #12/C:157
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:157-168
93 atoms, 97 bonds, 12 residues, 1 model selected
> color sel #fbeae9ff
> select #12/C:169
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C:169-176
54 atoms, 54 bonds, 8 residues, 1 model selected
> color sel #f0f0feff
> select #12/C:177-178
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #12/C:177-179
23 atoms, 24 bonds, 3 residues, 1 model selected
> select #12/C:177
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:177-178
18 atoms, 19 bonds, 2 residues, 1 model selected
> color sel #ffe7efff
> color sel #fdf6ffff
> color sel #fff0ffff
> color sel #ffeffdff
> color sel #ffedfaff
> color sel #ffecf9ff
> color sel #ffecfaff
> color sel #ffebf9ff
> color sel #ffecfaff
[Repeated 1 time(s)]
> color sel #ffecfbff
> color sel #ffecfcff
[Repeated 1 time(s)]
> color sel #ffedfdff
> color sel #ffecfdff
> color sel #ffedfdff
> color sel #ffeaffff
> color sel #ffeafeff
[Repeated 1 time(s)]
> color sel #ffe9feff
[Repeated 1 time(s)]
> color sel #ffe8feff
> color sel #ffe8fdff
[Repeated 1 time(s)]
> color sel #ffe8fcff
[Repeated 1 time(s)]
> color sel #ffe8fbff
[Repeated 2 time(s)]
> color sel #ffe8faff
> color sel #ffe8f8ff
[Repeated 1 time(s)]
> color sel #ffe8f7ff
[Repeated 1 time(s)]
> color sel #ffe9f7ff
> color sel #ffe8f6ff
> color sel #ffe9f6ff
[Repeated 1 time(s)]
> color sel #ffe9f5ff
> color sel #ffeaf5ff
[Repeated 1 time(s)]
> color sel #ffeaf4ff
[Repeated 1 time(s)]
> color sel #ffebf4ff
> color sel #ffebf3ff
[Repeated 2 time(s)]
> color sel #ffecf2ff
[Repeated 1 time(s)]
> color sel #ffecf1ff
[Repeated 2 time(s)]
> color sel #ffecf0ff
[Repeated 1 time(s)]
> color sel #ffebefff
> color sel #ffebeeff
> color sel #ffeaedff
[Repeated 1 time(s)]
> color sel #ffe9ecff
[Repeated 1 time(s)]
> color sel #ffe8ebff
> color sel #ffe7ebff
[Repeated 1 time(s)]
> color sel #ffe6eaff
> color sel #ffe6e9ff
[Repeated 1 time(s)]
> select #12/C:181
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:181-187
53 atoms, 53 bonds, 7 residues, 1 model selected
> color sel #fff7fdff
> color sel #f9f3ffff
> select #12/C:188-189
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/C:188-198
73 atoms, 73 bonds, 11 residues, 1 model selected
> color sel #f4efffff
> select #12/C:200
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/C:200-208
69 atoms, 70 bonds, 9 residues, 1 model selected
> color sel #cdd3ffff
> color sel #8e8ef8ff
> color sel #9da0ffff
> color sel #9c9fffff
> color sel #9c9effff
> color sel #9b9effff
> color sel #9b9dffff
> color sel #9a9cffff
> color sel #9696f8ff
> select #12/C:209
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:209-213
41 atoms, 42 bonds, 5 residues, 1 model selected
> color sel #f1f1feff
> select #12/C:214-215
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/C:214-223
79 atoms, 78 bonds, 10 residues, 1 model selected
> color sel #b8b8faff
> select #12/C:224-225
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #12/C:224-228
36 atoms, 36 bonds, 5 residues, 1 model selected
> color sel #f8f6ffff
> color sel #dad8e0ff
> color sel #c5c3caff
> color sel #c4c3caff
> color sel #b5b4baff
> color sel #b4b3baff
> color sel dim gray
> select #12/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C:1-4
29 atoms, 28 bonds, 4 residues, 1 model selected
> color sel dim gray
> select #12/C:122
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/C:121-122
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel dim gray
> select #12/C:178-179
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/C:178-180
19 atoms, 19 bonds, 3 residues, 1 model selected
> color sel dim gray
> select #12/C:73-74
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #12/C:73-78
54 atoms, 54 bonds, 6 residues, 1 model selected
> color sel dim gray
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/D
Alignment identifier is 12/D
> select #12/D:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D
1632 atoms, 1668 bonds, 214 residues, 1 model selected
> color sel dim gray
> view matrix models
> #12,0.71436,-0.39661,-0.57653,226.88,-0.66803,-0.63185,-0.39307,496.97,-0.20839,0.66593,-0.71632,245.16
> undo
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> ui mousemode right zoom
> select #12/D:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #12/D:7-14
58 atoms, 58 bonds, 8 residues, 1 model selected
> color sel #e0e0fcff
> select #12/D:15
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:15-21
47 atoms, 46 bonds, 7 residues, 1 model selected
> color sel #fdf4f4ff
> color sel #ffefedff
> select #12/D:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:22-26
36 atoms, 35 bonds, 5 residues, 1 model selected
> color sel #fff1f0ff
> color sel #fff2f0ff
> select #12/D:27
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> color sel #e0e0fcff
> select #12/D:29
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:29-36
61 atoms, 62 bonds, 8 residues, 1 model selected
> color sel #f9f9ffff
> select #12/D:37
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #12/D:37-38
26 atoms, 28 bonds, 2 residues, 1 model selected
> color sel #ededfdff
> select #12/D:39
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:39-48
74 atoms, 74 bonds, 10 residues, 1 model selected
> color sel #dcdcfcff
> select
> #12/D:7-10,13-17,22-28,35-40,47-50,64-69,72-77,86-92,102-107,114-118,129-137,144-150,153-155,159-163,175-182,191-198,205-210
797 atoms, 797 bonds, 102 residues, 1 model selected
> select #12/D:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel #e4e4fdff
> select #12/D:50
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:50-56
55 atoms, 55 bonds, 7 residues, 1 model selected
> color sel #5c5cf6ff
> select #12/D:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:57-58
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:57-58
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel #fdf6f6ff
> select #12/D:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:58-67
68 atoms, 69 bonds, 10 residues, 1 model selected
> color sel #efeffeff
> select #12/D:58-67
68 atoms, 69 bonds, 10 residues, 1 model selected
> select #12/D:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:58-69
78 atoms, 79 bonds, 12 residues, 1 model selected
> color sel #e8e8fdff
> select #12/D:70
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/D:70-73
34 atoms, 35 bonds, 4 residues, 1 model selected
> color sel #d8d8fcff
> select #12/D:74-75
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/D:74-79
41 atoms, 40 bonds, 6 residues, 1 model selected
> color sel #f4f4feff
> select #12/D:80
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/D:80-81
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel #fff6f4ff
> select #12/D:82
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:82-84
22 atoms, 21 bonds, 3 residues, 1 model selected
> color sel #efeffeff
> select #12/D:85
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/D:85-87
18 atoms, 17 bonds, 3 residues, 1 model selected
> select #12/D:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/D:84-87
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel #ffdedeff
> color sel #ffe8e9ff
> select #12/D:88
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/D:88-97
96 atoms, 102 bonds, 10 residues, 1 model selected
> select #12/D:98
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/D:98-105
56 atoms, 56 bonds, 8 residues, 1 model selected
> color sel #d0d0fbff
> select #12/D:114
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #12/D:114-125
97 atoms, 100 bonds, 12 residues, 1 model selected
> color sel #d6d6fcff
> select #12/D:128-129
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #12/D:128-131
22 atoms, 21 bonds, 4 residues, 1 model selected
> color sel #dfdffcff
> select #12/D:132-133
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #12/D:132-137
44 atoms, 43 bonds, 6 residues, 1 model selected
> color sel #fbeae9ff
> color sel #ffeeeaff
> select #12/D:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/D:138-146
79 atoms, 81 bonds, 9 residues, 1 model selected
> color sel #c9c9fbff
> select #12/D:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:147-158
95 atoms, 96 bonds, 12 residues, 1 model selected
> color sel #f7cbcaff
> select #12/D:161
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:161-179
144 atoms, 144 bonds, 19 residues, 1 model selected
> color sel #c9c9fbff
> select #12/D:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #12/D:183-204
176 atoms, 180 bonds, 22 residues, 1 model selected
> color sel #bbbbfaff
> select #12/D:205
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #12/D:205-213
72 atoms, 72 bonds, 9 residues, 1 model selected
> color sel #fbebffff
> color sel #f1eaffff
> color sel #f6eeffff
[Repeated 2 time(s)]
> color sel #f7eeffff
[Repeated 1 time(s)]
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/B #4/A #10/D #10/A
Alignment identifier is 1
> show #!9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> select #3/B:1-81 #4/A:1-81 #10/D,A:1-81
2576 atoms, 2632 bonds, 14 pseudobonds, 324 residues, 5 models selected
> select #3/B:1-275 #4/A:1-275 #10/D,A:1-275
8808 atoms, 9044 bonds, 154 pseudobonds, 1100 residues, 5 models selected
> select #3/B:276 #4/A:276 #10/D,A:276
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:276-352 #4/A:276-352 #10/D,A:276-352
2396 atoms, 2440 bonds, 1 pseudobond, 308 residues, 4 models selected
> select #3/B:101-352 #4/A:101-352 #10/D,A:101-352
8076 atoms, 8300 bonds, 31 pseudobonds, 1008 residues, 5 models selected
> select #3/B #4/A #10/D,A
11204 atoms, 11488 bonds, 155 pseudobonds, 1408 residues, 5 models selected
> select subtract #5
11204 atoms, 11488 bonds, 53 pseudobonds, 1408 residues, 4 models selected
> select subtract #4
8403 atoms, 8616 bonds, 21 pseudobonds, 1056 residues, 3 models selected
> select subtract #3
5602 atoms, 5744 bonds, 704 residues, 1 model selected
> select add #10
8936 atoms, 9124 bonds, 1118 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select add #4
5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected
> select add #5
5602 atoms, 5744 bonds, 144 pseudobonds, 704 residues, 4 models selected
> select subtract #5
5602 atoms, 5744 bonds, 42 pseudobonds, 704 residues, 3 models selected
> select add #7
5602 atoms, 5744 bonds, 97 pseudobonds, 704 residues, 3 models selected
> select subtract #7
5602 atoms, 5744 bonds, 704 residues, 2 models selected
> color sel dim gray
> select subtract #3
2801 atoms, 2872 bonds, 352 residues, 1 model selected
> select subtract #4
Nothing selected
> select #3/B:175 #4/A:175 #10/D,A:175
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:175-178 #4/A:175-178 #10/D,A:175-178
120 atoms, 116 bonds, 16 residues, 3 models selected
> ui tool show "Color Actions"
> color sel #d8d8fcff
> select #3/B:180 #4/A:180 #10/D,A:180
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:180-185 #4/A:180-185 #10/D,A:180-185
180 atoms, 176 bonds, 24 residues, 3 models selected
> select #3/B:179 #4/A:179 #10/D,A:179
24 atoms, 20 bonds, 4 residues, 3 models selected
> select #3/B:179-186 #4/A:179-186 #10/D,A:179-186
224 atoms, 220 bonds, 32 residues, 3 models selected
> color sel #e5e3ffff
> select #3/B:187-188 #4/A:187-188 #10/D,A:187-188
52 atoms, 48 bonds, 8 residues, 3 models selected
> select #3/B:187-198 #4/A:187-198 #10/D,A:187-198
368 atoms, 368 bonds, 48 residues, 3 models selected
> color sel #dbdcffff
> select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
64 atoms, 64 bonds, 8 residues, 3 models selected
> select #3/B:199-200 #4/A:199-200 #10/D,A:199-200
64 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #d2d5ffff
> select #3/B:201 #4/A:201 #10/D,A:201
56 atoms, 60 bonds, 4 residues, 3 models selected
> select #3/B:201-211 #4/A:201-211 #10/D,A:201-211
384 atoms, 396 bonds, 44 residues, 3 models selected
> color sel #d9dbffff
> select #3/B:212 #4/A:212 #10/D,A:212
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:212-217 #4/A:212-217 #10/D,A:212-217
192 atoms, 192 bonds, 24 residues, 3 models selected
> color sel #f7f5ffff
> select #3/B:218 #4/A:218 #10/D,A:218
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:218-220 #4/A:218-220 #10/D,A:218-220
96 atoms, 92 bonds, 12 residues, 3 models selected
> select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
68 atoms, 64 bonds, 8 residues, 3 models selected
> select #3/B:218-219 #4/A:218-219 #10/D,A:218-219
68 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #c9d5ffff
> color sel #cad4ffff
[Repeated 1 time(s)]
> color sel #cbd4ffff
> color sel #ccd4ffff
[Repeated 1 time(s)]
> color sel #cdd3ffff
> color sel #ced3ffff
[Repeated 2 time(s)]
> color sel #cfd3ffff
> color sel #cfd2ffff
[Repeated 1 time(s)]
> color sel #d0d2ffff
[Repeated 2 time(s)]
> color sel #d1d2ffff
> color sel #d1d1ffff
[Repeated 2 time(s)]
> select #3/B:220 #4/A:220 #10/D,A:220
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:220-231 #4/A:220-231 #10/D,A:220-231
396 atoms, 412 bonds, 48 residues, 3 models selected
> color sel #c8c9ffff
> select #3/B:232-233 #4/A:232-233 #10/D,A:232-233
80 atoms, 84 bonds, 8 residues, 3 models selected
> select #3/B:232-240 #4/A:232-240 #10/D,A:232-240
284 atoms, 288 bonds, 36 residues, 3 models selected
> color sel #d4d6ffff
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:242 #4/A:242 #10/D,A:242
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241-242 #4/A:241-242 #10/D,A:241-242
64 atoms, 60 bonds, 8 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:241 #4/A:241 #10/D,A:241
32 atoms, 28 bonds, 4 residues, 3 models selected
> color sel #dddfffff
> select #3/B:242 #4/A:242 #10/D,A:242
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:242-247 #4/A:242-247 #10/D,A:242-247
204 atoms, 208 bonds, 24 residues, 3 models selected
> color sel #d3d6ffff
> select #3/B:248 #4/A:248 #10/D,A:248
20 atoms, 16 bonds, 4 residues, 3 models selected
> select #3/B:248-254 #4/A:248-254 #10/D,A:248-254
192 atoms, 196 bonds, 28 residues, 3 models selected
> select #3/B:254 #4/A:254 #10/D,A:254
40 atoms, 40 bonds, 4 residues, 3 models selected
> select #3/B:254 #4/A:254 #10/D,A:254
40 atoms, 40 bonds, 4 residues, 3 models selected
> select #3/B:253 #4/A:253 #10/D,A:253
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:248-253 #4/A:248-253 #10/D,A:248-253
152 atoms, 152 bonds, 24 residues, 3 models selected
> color sel #dedfffff
> color sel #e1e1ffff
> select #3/B:254-255 #4/A:254-255 #10/D,A:254-255
72 atoms, 72 bonds, 8 residues, 3 models selected
> select #3/B:254-262 #4/A:254-262 #10/D,A:254-262
324 atoms, 340 bonds, 36 residues, 3 models selected
> color sel #d6d6ffff
> select #3/B:263 #4/A:263 #10/D,A:263
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:263-265 #4/A:263-265 #10/D,A:263-265
84 atoms, 80 bonds, 12 residues, 3 models selected
> color sel #dad9ffff
> select #3/B:266 #4/A:266 #10/D,A:266
16 atoms, 12 bonds, 4 residues, 3 models selected
> select #3/B:266-267 #4/A:266-267 #10/D,A:266-267
44 atoms, 44 bonds, 8 residues, 3 models selected
> color sel #cfcfffff
> color sel #d0cfffff
> color sel #d0d0ffff
> color sel #cecbffff
> select #3/B:268-269 #4/A:268-269 #10/D,A:268-269
96 atoms, 104 bonds, 8 residues, 3 models selected
> select #3/B:268-273 #4/A:268-273 #10/D,A:268-273
220 atoms, 228 bonds, 24 residues, 3 models selected
> color sel #d3d1ffff
> select #3/B:274 #4/A:274 #10/D,A:274
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:274-275 #4/A:274-275 #10/D,A:274-275
68 atoms, 64 bonds, 8 residues, 3 models selected
> color sel #c3c6ffff
> select #3/B:276 #4/A:276 #10/D,A:276
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:276-277 #4/A:276-277 #10/D,A:276-277
76 atoms, 76 bonds, 8 residues, 3 models selected
> color sel #d1d4ffff
> select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
76 atoms, 76 bonds, 8 residues, 3 models selected
> select #3/B:278-279 #4/A:278-279 #10/D,A:278-279
76 atoms, 76 bonds, 8 residues, 3 models selected
> color sel #dddcffff
> select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
340 atoms, 340 bonds, 48 residues, 3 models selected
> select #3/B:287-298 #4/A:287-298 #10/D,A:287-298
340 atoms, 340 bonds, 48 residues, 3 models selected
> select #3/B:287-300 #4/A:287-300 #10/D,A:287-300
412 atoms, 412 bonds, 56 residues, 3 models selected
> select #3/B:287-288 #4/A:287-288 #10/D,A:287-288
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:287-299 #4/A:287-299 #10/D,A:287-299
384 atoms, 384 bonds, 52 residues, 3 models selected
> color sel #d3d2ffff
> color sel #cbccffff
> select #3/B:300 #4/A:300 #10/D,A:300
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:300-309 #4/A:300-309 #10/D,A:300-309
272 atoms, 268 bonds, 40 residues, 3 models selected
> color sel #bfc3ffff
> select #3/B:310 #4/A:310 #10/D,A:310
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:310 #4/A:310 #10/D,A:310
36 atoms, 32 bonds, 4 residues, 3 models selected
> color sel #c8ceffff
> select #3/B:311-312 #4/A:311-312 #10/D,A:311-312
80 atoms, 84 bonds, 8 residues, 3 models selected
> select #3/B:311-333 #4/A:311-333 #10/D,A:311-333
756 atoms, 784 bonds, 1 pseudobond, 92 residues, 4 models selected
> color (#3-4,10 & sel) #d2d3ffff
> select #3/B:334 #4/A:334 #10/D,A:334
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:334 #4/A:334 #10/D,A:334
36 atoms, 32 bonds, 4 residues, 3 models selected
> color sel #cbd5ffff
> color sel #cbceffff
> select #3/B:335 #4/A:335 #10/D,A:335
32 atoms, 28 bonds, 4 residues, 3 models selected
> select #3/B:335-340 #4/A:335-340 #10/D,A:335-340
208 atoms, 208 bonds, 24 residues, 3 models selected
> color sel #ceceffff
> color sel #cfd1ffff
> select #3/B:341 #4/A:341 #10/D,A:341
36 atoms, 32 bonds, 4 residues, 3 models selected
> select #3/B:341-349 #4/A:341-349 #10/D,A:341-349
288 atoms, 284 bonds, 36 residues, 3 models selected
> color sel #caceffff
> color sel #c8ccffff
> color sel #c3caffff
> color sel #bdcbffff
> select #3/B:350 #4/A:350 #10/D,A:350
28 atoms, 24 bonds, 4 residues, 3 models selected
> select #3/B:350-352 #4/A:350-352 #10/D,A:350-352
76 atoms, 72 bonds, 12 residues, 3 models selected
> color sel #ffebf3ff
> color sel #ffe8efff
> select #3/B:301-302 #4/A:301-302 #10/D,A:301-302
56 atoms, 52 bonds, 8 residues, 3 models selected
> select #3/B:301-310 #4/A:301-310 #10/D,A:301-310
280 atoms, 276 bonds, 40 residues, 3 models selected
> color sel #8c8cf7ff
> color sel #8587ffff
> color sel #8282ffff
> color sel #7c83ffff
> select add #3
3011 atoms, 3079 bonds, 45 pseudobonds, 382 residues, 5 models selected
> select add #4
5742 atoms, 5882 bonds, 90 pseudobonds, 724 residues, 5 models selected
> select subtract #3
2941 atoms, 3010 bonds, 45 pseudobonds, 372 residues, 4 models selected
> select subtract #4
140 atoms, 138 bonds, 20 residues, 1 model selected
> select add #12
3541 atoms, 3631 bonds, 462 residues, 2 models selected
> select add #10
12337 atoms, 12617 bonds, 1560 residues, 2 models selected
> select subtract #10
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.82562,-0.34186,-0.44887,168.94,-0.52138,-0.76634,-0.37535,482.82,-0.21567,0.54392,-0.81094,284.87
> view matrix models
> #12,0.82562,-0.34186,-0.44887,169.91,-0.52138,-0.76634,-0.37535,479.02,-0.21567,0.54392,-0.81094,283.58
> view matrix models
> #12,0.82562,-0.34186,-0.44887,170.32,-0.52138,-0.76634,-0.37535,480.41,-0.21567,0.54392,-0.81094,282.28
> view matrix models
> #12,0.82562,-0.34186,-0.44887,171.18,-0.52138,-0.76634,-0.37535,479.61,-0.21567,0.54392,-0.81094,282.22
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.94747,-0.06803,0.31253,-40.388,-0.27852,-0.65592,0.70156,212.57,0.15727,-0.75175,-0.64041,392.6
> view matrix models
> #12,0.65713,0.16685,-0.73508,171.79,0.09209,-0.98566,-0.1414,332.31,-0.74813,0.025227,-0.66307,473.05
> view matrix models
> #12,0.95731,-0.18789,-0.21965,72.476,-0.15301,-0.97411,0.16641,333.66,-0.24523,-0.1257,-0.96128,433.82
> view matrix models
> #12,0.96798,-0.24602,-0.049963,50.221,-0.17279,-0.7973,0.57833,234.35,-0.18211,-0.55117,-0.81427,467.97
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> show #!9 models
> fitmap #12 inMap #9
Fit molecule F562a.pdb (#12) to map sNS1wt-Fab562.mrc (#9) using 3401 atoms
average map value = 0.09851, steps = 252
shifted from previous position = 4.87
rotated from previous position = 66.7 degrees
atoms outside contour = 1988, contour level = 0.11015
Position of F562a.pdb (#12) relative to sNS1wt-Fab562.mrc (#9) coordinates:
Matrix rotation and translation
-0.10506635 -0.15760122 0.98189762 53.59780496
-0.09254653 -0.98152811 -0.16744470 397.44466486
0.99014960 -0.10846402 0.08854013 -3.70228919
Axis 0.66872859 -0.09356170 0.73759629
Axis point 22.53945284 199.32977295 0.00000000
Rotation angle (degrees) 177.47248714
Shift along axis -4.07401058
> volume #9 level 0.08287
> volume #9 level 0.06241
> hide #10 models
> show #10 models
> hide #10 models
> color #5 #7b137cff models
> color #5 #7c0e7cff models
> color #5 #fe1effff models
> color #5 #ee1cefff models
> hide #5 models
> show #5 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> show #7 models
> hide #7 models
> hide #4 models
> show #4 models
> hide #8 models
> show #8 models
> select add #2
5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected
> select subtract #2
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select add #2
5068 atoms, 5183 bonds, 29 pseudobonds, 649 residues, 4 models selected
> select subtract #2
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
1667 atoms, 1690 bonds, 29 pseudobonds, 207 residues, 3 models selected
> select add #1
3334 atoms, 3380 bonds, 58 pseudobonds, 414 residues, 4 models selected
> select add #3
6135 atoms, 6252 bonds, 103 pseudobonds, 766 residues, 6 models selected
> select add #4
8936 atoms, 9124 bonds, 148 pseudobonds, 1118 residues, 7 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#2,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#3,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#4,1,0,0,-1.2223,0,1,0,1.8538,0,0,1,0.27533,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#2,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#3,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#4,1,0,0,-0.55596,0,1,0,1.8607,0,0,1,0.33178,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#2,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#3,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#4,1,0,0,-0.68222,0,1,0,1.9897,0,0,1,0.3731,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#2,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#3,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#4,0.99968,0.01848,-0.017519,-0.75045,-0.018381,0.99981,0.0057709,4.0941,0.017623,-0.005447,0.99983,-1.6124,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#2,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#3,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#4,0.99895,0.041357,0.019524,-12.294,-0.041363,0.99914,-0.00012487,9.3748,-0.019512,-0.00068282,0.99981,3.9302,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#2,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#3,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#4,0.99756,0.056365,0.04122,-19.199,-0.056012,0.99838,-0.0096742,13.936,-0.041698,0.0073418,0.9991,6.3748,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#2,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#3,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#4,0.99732,0.064513,0.034504,-19.405,-0.064796,0.99787,0.0071201,12.257,-0.033971,-0.0093368,0.99938,8.1881,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#2,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#3,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#4,0.99543,0.089424,0.033513,-23.673,-0.09018,0.99569,0.021758,14.2,-0.031423,-0.02468,0.9992,10.732,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#2,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#3,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#4,0.99543,0.089424,0.033513,-24.695,-0.09018,0.99569,0.021758,12.433,-0.031423,-0.02468,0.9992,10.949,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#2,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#3,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#4,0.99325,0.11577,-0.0074717,-21.346,-0.11546,0.99274,0.033636,15.045,0.011311,-0.032546,0.99941,5.0242,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#2,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#3,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#4,0.98411,0.17655,-0.018861,-29.201,-0.17622,0.98419,0.018033,30.268,0.021747,-0.014422,0.99966,-0.31268,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#2,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#3,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#4,0.98312,0.18157,-0.022504,-29.276,-0.18111,0.98324,0.020831,30.746,0.025909,-0.016403,0.99953,-0.62775,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#2,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#3,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#4,0.97783,0.20908,-0.011102,-35.867,-0.20922,0.97778,-0.013144,43.339,0.008107,0.015175,0.99985,-3.6449,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> view matrix models
> #1,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#2,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#3,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#4,0.9833,0.18192,0.0055417,-34.889,-0.18172,0.983,-0.026391,40.159,-0.010249,0.024943,0.99964,-2.2795,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#2,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#3,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#4,0.9833,0.18192,0.0055417,-35.853,-0.18172,0.983,-0.026391,40.8,-0.010249,0.024943,0.99964,-2.2243,#5,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0
> ui mousemode right zoom
> select subtract #1
7269 atoms, 7434 bonds, 119 pseudobonds, 911 residues, 6 models selected
> select subtract #2
5602 atoms, 5744 bonds, 90 pseudobonds, 704 residues, 4 models selected
> select subtract #3
2801 atoms, 2872 bonds, 45 pseudobonds, 352 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #12
3401 atoms, 3493 bonds, 442 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #12/C
Alignment identifier is 12/C
> select subtract #12
Nothing selected
> select #12/C:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #12/C
1769 atoms, 1825 bonds, 228 residues, 1 model selected
> hide #!9 models
> save "/Users/alvinchew/OneDrive - Nanyang Technological University
> (1)/202112_FlaviNS1/Data_HDXMS_Nikhil/chimerax_NS1-fab562_hdxms10minLXL-
> MS_recolored.cxs" includeMaps true
——— End of log from Wed Apr 19 17:03:52 2023 ———
opened ChimeraX session
> show #!9 models
> color #9 #b4e3e61f models
> color #9 #b4e3e61c models
> color #9 #b4e3e61b models
> color #9 #e4ebc51b models
> color #9 #e3ebbc1b models
> color #9 #ebe98a1b models
> color #9 #e9eb971b models
> color #9 #e1eba01b models
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63ZP/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 13 days, 18 hours, 3 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
CB242Y:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-XMAS: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
et-xmlfile: 1.1.0
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 1.5.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
seaborn: 0.12.2
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
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