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" : {
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"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",
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"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 ",
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"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
[deleted to fit within ticket limits]
> 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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Alvin,
--Eric