![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16873 closed defect (can't reproduce)
Crash showing dock widget
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"incident" : "8269915B-72BC-417A-A2CC-4F267EBF5E75",
"pid" : 19767,
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"procLaunch" : "2025-02-15 22:04:28.4544 +0100",
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fault"},"pc":{"value":6811163936},"far":{"value":0}}},{"id":38550373,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":154}],"threadState":{"x":[{"value":13525102592},{"value":0},{"value":13524566016},{"value":0},{"value":278532},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13525102592},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6811163936},"far":{"value":0}}},{"id":38550374,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":154}],"threadState":{"x":[{"value":13535834112},{"value":168303},{"value":13535297536},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13535834112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6811163936},"far":{"value":0}}},{"id":38550628,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":600638291443712},{"value":0},{"value":600638291443712},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":139847},{"value":0},{"value":1},{"value":139847},{"value":0},{"value":2043},{"value":3089780731},{"value":18446744073709551569},{"value":8725816136},{"value":0},{"value":33000},{"value":32},{"value":600638291443712},{"value":0},{"value":600638291443712},{"value":13872147728},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6810995492},"cpsr":{"value":4096},"fp":{"value":13872147072},"sp":{"value":13872146992},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6810919412},"far":{"value":0}},"frames":[{"imageOffset":4596,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":153},{"imageOffset":80676,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":153},{"imageOffset":40500,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":153},{"imageOffset":5496,"symbol":"mach_msg","symbolLocation":24,"imageIndex":153},{"imageOffset":66741424,"imageIndex":91},{"imageOffset":66197236,"imageIndex":91},{"imageOffset":66429892,"imageIndex":91},{"imageOffset":66433464,"imageIndex":91},{"imageOffset":66432016,"imageIndex":91},{"imageOffset":66431744,"imageIndex":91},{"imageOffset":66589352,"imageIndex":91},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":154},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":154}]},{"id":38550629,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":708562229657600},{"value":0},{"value":708562229657600},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":164975},{"value":0},{"value":1},{"value":164975},{"value":2045},{"value":2722513099},{"value":203},{"value":18446744073709551569},{"value":409600},{"value":0},{"value":33000},{"value":32},{"value":708562229657600},{"value":0},{"value":708562229657600},{"value":13917859088},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6810995492},"cpsr":{"value":4096},"fp":{"value":13917858432},"sp":{"value":13917858352},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6810919412},"far":{"value":0}},"frames":[{"imageOffset":4596,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":153},{"imageOffset":80676,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":153},{"imageOffset":40500,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":153},{"imageOffset":5496,"symbol":"mach_msg","symbolLocation":24,"imageIndex":153},{"imageOffset":66741424,"imageIndex":91},{"imageOffset":66197236,"imageIndex":91},{"imageOffset":66429892,"imageIndex":91},{"imageOffset":66432404,"imageIndex":91},{"imageOffset":66432016,"imageIndex":91},{"imageOffset":66431744,"imageIndex":91},{"imageOffset":66589352,"imageIndex":91},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":154},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":154}]},{"id":38550630,"name":"ThreadPoolBackgroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":461756228960256},{"value":0},{"value":461756228960256},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":107511},{"value":0},{"value":1},{"value":107511},{"value":2045},{"value":2410301571},{"value":131},{"value":18446744073709551569},{"value":673792},{"value":0},{"value":33000},{"value":32},{"value":461756228960256},{"value":0},{"value":461756228960256},{"value":13442968848},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6810995492},"cpsr":{"value":4096},"fp":{"value":13442968192},"sp":{"value":13442968112},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6810919412},"far":{"value":0}},"frames":[{"imageOffset":4596,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":153},{"imageOffset":80676,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":153},{"imageOffset":40500,"symbol":"mach_msg_overwrite","symbolLocation":476,"imageIndex":153},{"imageOffset":5496,"symbol":"mach_msg","symbolLocation":24,"imageIndex":153},{"imageOffset":66741424,"imageIndex":91},{"imageOffset":66197236,"imageIndex":91},{"imageOffset":66429892,"imageIndex":91},{"imageOffset":66432404,"imageIndex":91},{"imageOffset":66431884,"imageIndex":91},{"imageOffset":66431792,"imageIndex":91},{"imageOffset":66589352,"imageIndex":91},{"imageOffset":28564,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":154},{"imageOffset":7476,"symbol":"thread_start","symbolLocation":8,"imageIndex":154}]}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6806700032,
"size" : 4220698624,
"uuid" : "3406ad1b-2469-30eb-9863-5dce861e6dea"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=84.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=84.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 112K 5 \nColorSync 608K 30 \nCoreAnimation 752K 47 \nCoreGraphics 32K 2 \nCoreUI image data 3824K 27 \nFoundation 144K 3 \nKernel Alloc Once 32K 1 \nMALLOC 83.6G 350 \nMALLOC guard page 192K 12 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 51 \nStack 184.2M 51 \nVM_ALLOCATE 249.0M 166 \nVM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated)\n__AUTH 2192K 402 \n__AUTH_CONST 31.7M 620 \n__CTF 824 1 \n__DATA 22.1M 770 \n__DATA_CONST 42.3M 779 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 562.9M 154 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2199K 1 \n__TEXT 940.3M 796 \ndyld private memory 320K 4 \nmapped file 211.6M 53 \nshared memory 3136K 25 \n=========== ======= ======= \nTOTAL 86.1G 4597 \nTOTAL, minus reserved VM space 85.9G 4597 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "a083754281ca4e2f521faa14b00f71d31e642b3d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63f9578e238e7b23a1f3030a",
"factorPackIds" : {
},
"deploymentId" : 240000005
},
{
"rolloutId" : "645c2d2f9e69a025b0a37e29",
"factorPackIds" : {
},
"deploymentId" : 240000003
}
],
"experiments" : [
]
}
}
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open ../fitting1.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at step 1,
values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at step 1,
values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #13, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #14, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #15, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #16, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #17, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #18, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #19, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #20, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #21, grid size 55,55,55,
pixel 13.3, shown at step 1, values float32
Opened ref_s114_8_symmetrized.em scaled as #22, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled as #23, grid size 128,128,128, pixel
13.3, shown at level 0.025, step 1, values float32
Opened ref_s140_8_symmetrized.em scaled as #24, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s162_8_symmetrized.em scaled as #25, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s200_8_symmetrized.em scaled as #26, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s114_8_symmetrized.em scaled gaussian10 as #27, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled gaussian10 as #28, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian15 as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian30 as #30, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s162_8_symmetrized.em scaled gaussian30 as #31, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s200_8_symmetrized.em scaled gaussian30 as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Log from Sat Feb 15 22:04:14 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open ../fitting.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0265, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0648, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0668, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0561, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0643, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #13, grid size 55,55,55,
pixel 13.3, shown at level 0.0113, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #14, grid size 55,55,55,
pixel 13.3, shown at level 0.0119, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #15, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #16, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #17, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #18, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #19, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #20, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #21, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_s114_8_symmetrized.em scaled as #22, grid size 128,128,128, pixel
13.3, shown at level 0.0515, step 1, values float32
Opened ref_s127_8_symmetrized.em scaled as #23, grid size 128,128,128, pixel
13.3, shown at level 0.0553, step 1, values float32
Opened ref_s140_8_symmetrized.em scaled as #24, grid size 128,128,128, pixel
13.3, shown at level 0.0645, step 1, values float32
Opened ref_s162_8_symmetrized.em scaled as #25, grid size 128,128,128, pixel
13.3, shown at level 0.0709, step 1, values float32
Opened ref_s200_8_symmetrized.em scaled as #26, grid size 128,128,128, pixel
13.3, shown at level 0.107, step 1, values float32
Opened ref_s114_8_symmetrized.em scaled gaussian10 as #27, grid size
128,128,128, pixel 13.3, shown at level 0.0423, step 1, values float32
Opened ref_s127_8_symmetrized.em scaled gaussian10 as #28, grid size
128,128,128, pixel 13.3, shown at level 0.0417, step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian15 as #29, grid size
128,128,128, pixel 13.3, shown at level 0.0319, step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian30 as #30, grid size
128,128,128, pixel 13.3, shown at level 0.0274, step 1, values float32
Opened ref_s162_8_symmetrized.em scaled gaussian30 as #31, grid size
128,128,128, pixel 13.3, shown at level 0.0122, step 1, values float32
Opened ref_s200_8_symmetrized.em scaled gaussian30 as #32, grid size
128,128,128, pixel 13.3, shown at level 0.0206, step 1, values float32
Log from Sat Dec 7 12:59:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open mock_maps.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0265, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0648, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0668, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0561, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0643, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #13, grid size 55,55,55,
pixel 13.3, shown at level 0.0113, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #14, grid size 55,55,55,
pixel 13.3, shown at level 0.0119, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #15, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #16, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #17, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #18, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #19, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #20, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #21, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Log from Sat Dec 7 09:38:15 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open cutting_rigid_bodies.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0265, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0866, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0668, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0561, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0643, step 1, values float32
Opened CR_map 20 as #25, grid size 77,120,72, pixel 6.67, shown at level
0.0439, step 1, values float32
Opened NRmap 20 as #34, grid size 68,120,66, pixel 6.67, shown at level
0.0471, step 1, values float32
Opened IRmap 20 as #44, grid size 60,81,62, pixel 6.67, shown at level 0.0418,
step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #47, grid size 55,55,55,
pixel 13.3, shown at level 0.0119, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #46, grid size 55,55,55,
pixel 13.3, shown at level 0.0113, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #48, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #49, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #50, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #51, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #52, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #53, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #54, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened volume sum as #82, grid size 55,55,55, pixel 13.3, shown at level
0.0782, step 1, values float32
Opened volume sum as #85, grid size 112,117,59, pixel 13.3, shown at level
0.0744, step 1, values float32
Log from Sat Nov 16 20:51:36 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open cutting_rigid_bodies.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0866, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0668, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0561, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0643, step 1, values float32
Opened CR_map 20 as #25, grid size 77,120,72, pixel 6.67, shown at level
0.0439, step 1, values float32
Opened NRmap 20 as #34, grid size 68,120,66, pixel 6.67, shown at level
0.0471, step 1, values float32
Opened IRmap 20 as #44, grid size 60,81,62, pixel 6.67, shown at level 0.0418,
step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #47, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #46, grid size 55,55,55,
pixel 13.3, shown at level 0.019, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #48, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #49, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #50, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #51, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #52, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #53, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #54, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened volume sum as #82, grid size 55,55,55, pixel 13.3, shown at level
0.0782, step 1, values float32
Opened volume sum as #85, grid size 112,117,59, pixel 13.3, shown at level
0.0964, step 1, values float32
Log from Sat Nov 16 19:30:18 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open 11-11-24_CR_NR_IRfit_(2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2_structureFitting).cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0866, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0668, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0561, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0643, step 1, values float32
Opened CR_map 20 as #25, grid size 77,120,72, pixel 6.67, shown at level
0.0439, step 1, values float32
Opened NRmap 20 as #34, grid size 68,120,66, pixel 6.67, shown at level
0.0471, step 1, values float32
Opened IRmap 20 as #44, grid size 60,81,62, pixel 6.67, shown at level 0.0418,
step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian as #47, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian as #46, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian as #48, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #49, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc gaussian copy as #50, grid size 55,55,55,
pixel 13.3, shown at level 0.0431, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #51, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc gaussian copy as #52, grid size 55,55,55,
pixel 13.3, shown at level 0.0527, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #53, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc gaussian copy as #54, grid size 55,55,55,
pixel 13.3, shown at level 0.0508, step 1, values float32
Log from Mon Nov 11 13:29:20 2024UCSF ChimeraX version: 1.8rc202405230136
(2024-05-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> E:/ownCloud/Manuscripts/FluNPC/Modelling/mock/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2_structureFitting.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0866, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0866, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0861, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0866, step 1, values float32
Log from Mon Sep 23 14:46:37 2024UCSF ChimeraX version: 1.8rc202405230136
(2024-05-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> E:/ownCloud/Manuscripts/FluNPC/Modelling/mock/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2.cxs
Opened full.mrc as #5, grid size 128,128,128, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 6.67, shown at
level 0.0996, step 1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 6.67, shown at
level 0.0866, step 1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 6.67, shown at
level 0.0861, step 1, values float32
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at level 0.0851, step 1, values float32
Opened ref_mock_CR_cut_resampled.mrc as #3, grid size 55,55,55, pixel 13.3,
shown at level 0.0996, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc as #9, grid size 55,55,55, pixel 13.3,
shown at level 0.0866, step 1, values float32
Opened ref_mock_NR_cut_resampled.mrc as #10, grid size 55,55,55, pixel 13.3,
shown at level 0.0861, step 1, values float32
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at level 0.0866, step 1, values float32
Log from Fri Nov 17 14:58:14 2023
> lighting soft
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> //kosinski.embl.de/kosinski/ziemianowicz/cryoET/subtomo/novaSTA/mock/bin4/fullAlign/ref_3_symmetrized.em
Opened ref_3_symmetrized.em as #1, grid size 128,128,128, pixel 1, shown at
level 0.075, step 1, values float32
> open
> //kosinski.embl.de/kosinski/ziemianowicz/cryoET/subtomo/novaSTA/mock/bin2/refs_final/ref_CR_5.em
Opened ref_CR_5.em as #2, grid size 120,120,120, pixel 1, shown at level
0.0845, step 1, values float32
> open
> //kosinski.embl.de/kosinski/ziemianowicz/cryoET/subtomo/novaSTA/mock/bin2/refs_final/ref_IR_5.em
Opened ref_IR_5.em as #3, grid size 120,120,120, pixel 1, shown at level
0.0778, step 1, values float32
> open
> //kosinski.embl.de/kosinski/ziemianowicz/cryoET/subtomo/novaSTA/mock/bin2/refs_final/ref_NR_5.em
Opened ref_NR_5.em as #4, grid size 120,120,120, pixel 1, shown at level
0.0771, step 1, values float32
> volume scale #1-18 factor -1
Opened ref_3_symmetrized.em scaled as #5, grid size 128,128,128, pixel 1,
shown at step 1, values float32
Opened ref_CR_5.em scaled as #6, grid size 120,120,120, pixel 1, shown at step
1, values float32
Opened ref_IR_5.em scaled as #7, grid size 120,120,120, pixel 1, shown at step
1, values float32
Opened ref_NR_5.em scaled as #8, grid size 120,120,120, pixel 1, shown at step
1, values float32
> surface dust #5 size 10
> surface dust #6 size 10
> surface dust #7 size 10
> surface dust #8 size 10
> close #1-4
> volume #6-8 voxelSize 6.672
> volume #5 voxelSize 13.344
> surface dust #5 size 133
> surface dust #6 size 66.7
> surface dust #7 size 66.7
> surface dust #8 size 66.7
> volume #5 level 0.05942
> volume #5 level 0.08509
> volume #5 color #b2b2b264
> lighting simple
> lighting soft
> lighting full
> lighting soft
> ui mousemode right select
> select #6
2 models selected
> ui mousemode right translate
> ui mousemode right select
> select #6
2 models selected
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,65.465,0,1,0,233.44,0,0,1,752.29
> view matrix models #6,1,0,0,433.39,0,1,0,624.73,0,0,1,1049.2
> view matrix models #6,1,0,0,394.29,0,1,0,515.34,0,0,1,832.62
> view matrix models #6,1,0,0,887.19,0,1,0,683.01,0,0,1,767.54
> view matrix models #6,1,0,0,851.25,0,1,0,722.48,0,0,1,726.53
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99935,0.031179,-0.018259,846.19,-0.025046,0.962,0.27189,645.24,0.026042,-0.27126,0.96215,836.26
> view matrix models
> #6,0.98497,0.054119,-0.16406,897.27,-0.026896,0.98612,0.16382,676.95,0.17065,-0.15695,0.97275,732.43
> view matrix models
> #6,0.81681,-0.57627,0.027167,1135.5,0.5696,0.7981,-0.19645,656.29,0.091528,0.17594,0.98014,630.44
> view matrix models
> #6,0.83083,-0.55578,0.028688,1121.6,0.55079,0.81381,-0.18532,653.22,0.079651,0.16977,0.98226,636.59
> view matrix models
> #6,0.83101,-0.55238,0.065626,1106.4,0.55277,0.83322,0.013683,570.53,-0.062239,0.024906,0.99775,741.52
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.83101,-0.55238,0.065626,1077.2,0.55277,0.83322,0.013683,622.18,-0.062239,0.024906,0.99775,732.27
> ui tool show "Volume Viewer"
> ui tool show "Fit in Map"
> fitmap #6 inMap #5
Fit map ref_CR_5.em scaled in map ref_3_symmetrized.em scaled using 17265
points
correlation = 0.9298, correlation about mean = 0.2619, overlap = 260.9
steps = 88, shift = 19, angle = 11.6 degrees
Position of ref_CR_5.em scaled (#6) relative to ref_3_symmetrized.em scaled
(#5) coordinates:
Matrix rotation and translation
0.70727792 -0.70664600 0.02023306 1190.07123996
0.70627557 0.70756458 0.02296068 621.15883476
-0.03054127 -0.00194947 0.99953161 719.94110053
Axis -0.01761614 0.03590695 0.99919986
Axis point -117.87606667 1750.90808711 0.00000000
Rotation angle (degrees) 44.99349562
Shift along axis 720.70450680
> fitmap #6 inMap #5
Fit map ref_CR_5.em scaled in map ref_3_symmetrized.em scaled using 17265
points
correlation = 0.9298, correlation about mean = 0.2616, overlap = 260.9
steps = 44, shift = 0.211, angle = 0.0208 degrees
Position of ref_CR_5.em scaled (#6) relative to ref_3_symmetrized.em scaled
(#5) coordinates:
Matrix rotation and translation
0.70743731 -0.70648142 0.02040710 1189.83812540
0.70611750 0.70772961 0.02273492 621.23939272
-0.03050450 -0.00167372 0.99953323 720.02969492
Axis -0.01726545 0.03601234 0.99920219
Axis point -118.33151803 1750.80444584 0.00000000
Rotation angle (degrees) 44.98028289
Shift along axis 721.28443697
> select subtract #6
Nothing selected
> show #!7 models
> select add #7
2 models selected
> view matrix models #7,1,0,0,993.82,0,1,0,910.79,0,0,1,24.108
> view matrix models #7,1,0,0,949.46,0,1,0,804.57,0,0,1,497.41
> view matrix models #7,1,0,0,890.84,0,1,0,762.68,0,0,1,499.5
> view matrix models #7,1,0,0,874.5,0,1,0,794.18,0,0,1,501.78
> view matrix models #7,1,0,0,865.69,0,1,0,800.95,0,0,1,506.7
> fitmap #7 inMap #5
Fit map ref_IR_5.em scaled in map ref_3_symmetrized.em scaled using 17277
points
correlation = 0.874, correlation about mean = 0.1431, overlap = 161.8
steps = 180, shift = 67.7, angle = 43.7 degrees
Position of ref_IR_5.em scaled (#7) relative to ref_3_symmetrized.em scaled
(#5) coordinates:
Matrix rotation and translation
0.72328504 -0.69008663 0.02528236 1177.30591349
0.68992275 0.72370363 0.01611364 625.61885751
-0.02941674 0.00578812 0.99955048 463.62919779
Axis -0.00747613 0.03960455 0.99918746
Axis point -167.14577322 1778.24112269 0.00000000
Rotation angle (degrees) 43.67491364
Shift along axis 479.22815036
> fitmap #7 inMap #5
Fit map ref_IR_5.em scaled in map ref_3_symmetrized.em scaled using 17277
points
correlation = 0.874, correlation about mean = 0.1432, overlap = 161.8
steps = 44, shift = 0.0249, angle = 0.00626 degrees
Position of ref_IR_5.em scaled (#7) relative to ref_3_symmetrized.em scaled
(#5) coordinates:
Matrix rotation and translation
0.72327539 -0.69009276 0.02539085 1177.26818010
0.68992969 0.72369714 0.01610813 625.62053605
-0.02949139 0.00586728 0.99954781 463.65430075
Axis -0.00741472 0.03973659 0.99918268
Axis point -167.08172624 1778.10655962 0.00000000
Rotation angle (degrees) 43.67569370
Shift along axis 479.40625636
> show #!8 models
> select add #8
4 models selected
> select subtract #7
2 models selected
> view matrix models #8,1,0,0,918.09,0,1,0,306.75,0,0,1,24.317
> view matrix models #8,1,0,0,746.38,0,1,0,588.1,0,0,1,47.036
> view matrix models #8,1,0,0,754.92,0,1,0,600.15,0,0,1,47.942
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96728,-0.0021556,-0.2537,885.46,-0.006992,0.99936,-0.03515,619.43,0.25361,0.035774,0.96665,-60.777
> view matrix models
> #8,0.7683,-0.60469,-0.20991,1203.3,0.58701,0.79638,-0.14558,499.58,0.25519,-0.011369,0.96682,-41.799
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.7683,-0.60469,-0.20991,1110.2,0.58701,0.79638,-0.14558,604.05,0.25519,-0.011369,0.96682,158.6
> view matrix models
> #8,0.7683,-0.60469,-0.20991,1168.8,0.58701,0.79638,-0.14558,679.59,0.25519,-0.011369,0.96682,212.26
> view matrix models
> #8,0.7683,-0.60469,-0.20991,1161.9,0.58701,0.79638,-0.14558,686.87,0.25519,-0.011369,0.96682,159.99
> fitmap #8 inMap #5
Fit map ref_NR_5.em scaled in map ref_3_symmetrized.em scaled using 17265
points
correlation = 0.8614, correlation about mean = 0.1839, overlap = 162.4
steps = 92, shift = 61.1, angle = 16.5 degrees
Position of ref_NR_5.em scaled (#8) relative to ref_3_symmetrized.em scaled
(#5) coordinates:
Matrix rotation and translation
0.71339429 -0.70072086 0.00767191 1184.92544062
0.70076265 0.71335978 -0.00703776 632.46152513
-0.00054133 0.01039689 0.99994580 220.80756395
Axis 0.01243896 0.00585984 0.99990546
Axis point -180.39752481 1760.54784459 0.00000000
Rotation angle (degrees) 44.49186656
Shift along axis 239.23205658
> measure symmetry #5
Symmetry ref_3_symmetrized.em scaled: C8, center 64 64 65
> hide #!8 models
> hide #!7 models
> hide #!6 models
> select subtract #8
Nothing selected
> ui mousemode right select
> ui mousemode right "mark point"
> view orient
> ui tool show "Side View"
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> marker #1 position 1396,1338,851.9 color yellow radius 1
> marker #1 position 1406,1323,827.2 color yellow radius 1
> marker change #1:2 radius 10
> close #1
> color #5 #b2b2b2ff models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> marker #1 position 1396,1337,835.5 color yellow radius 10
> hide #!5 models
> show #!5 models
> color #5 #b2b2b264 models
> marker #1 position 1380,1350,807.3 color yellow radius 10
> close #1
> color #5 #b2b2b2ff models
> marker #1 position 1386,1344,823.1 color yellow radius 10
> color #5 #b2b2b264 models
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-180.45,0,1,0,-168.01,0,0,1,27.149
> view matrix models #1,1,0,0,-215.9,0,1,0,-185.04,0,0,1,-5.4459
> show #!7 models
> hide #!7 models
> view matrix models #1,1,0,0,-194.82,0,1,0,-206.59,0,0,1,25.838
> view matrix models #1,1,0,0,-189.62,0,1,0,-197.73,0,0,1,26.014
> volume boxes #5 centers #1 size 700
Opened box /M mark 1 M as #2, grid size 55,55,55, pixel 13.3, shown at level
0.0851, step 1, values float32
> hide #!5 models
> hide #1 models
> show #1 models
> show #!6 models
> show #!8 models
> show #!7 models
> fitmap #6 inMap #2
Fit map ref_CR_5.em scaled in map box /M mark 1 M using 17265 points
correlation = 0.9286, correlation about mean = 0.2666, overlap = 260
steps = 44, shift = 0.0809, angle = 0.0782 degrees
Position of ref_CR_5.em scaled (#6) relative to box /M mark 1 M (#2)
coordinates:
Matrix rotation and translation
0.70688736 -0.70705566 0.01955915 1190.58156412
0.70671431 0.70715572 0.02203786 621.41005917
-0.02941336 -0.00175555 0.99956579 719.59776936
Axis -0.01681729 0.03461400 0.99925925
Axis point -118.75387268 1750.22651276 0.00000000
Rotation angle (degrees) 45.02449329
Shift along axis 720.55185477
> fitmap #7 inMap #2
Fit map ref_IR_5.em scaled in map box /M mark 1 M using 17277 points
correlation = 0.8694, correlation about mean = 0.1533, overlap = 160
steps = 40, shift = 0.148, angle = 0.0655 degrees
Position of ref_IR_5.em scaled (#7) relative to box /M mark 1 M (#2)
coordinates:
Matrix rotation and translation
0.72255835 -0.69085036 0.02520332 1177.87359424
0.69069836 0.72297238 0.01570689 625.85412836
-0.02907242 0.00605875 0.99955895 463.31640834
Axis -0.00697802 0.03925492 0.99920486
Axis point -166.31523038 1776.59443436 0.00000000
Rotation angle (degrees) 43.73501117
Shift along axis 479.29663484
> fitmap #8 inMap #2
Fit map ref_NR_5.em scaled in map box /M mark 1 M using 17265 points
correlation = 0.8609, correlation about mean = 0.1947, overlap = 161.1
steps = 56, shift = 0.292, angle = 0.0349 degrees
Position of ref_NR_5.em scaled (#8) relative to box /M mark 1 M (#2)
coordinates:
Matrix rotation and translation
0.71340445 -0.70070368 0.00827327 1184.70607853
0.70075175 0.71337141 -0.00694387 632.48717256
-0.00103631 0.01075130 0.99994167 220.58271818
Axis 0.01262500 0.00664212 0.99989824
Axis point -180.34437777 1760.18133197 0.00000000
Rotation angle (degrees) 44.49114529
Shift along axis 239.71823609
> volume resample #6 onGrid #2
Opened ref_CR_5.em scaled resampled as #3, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> volume resample #7 onGrid #2
Opened ref_IR_5.em scaled resampled as #4, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> volume resample #8 onGrid #2
Opened ref_NR_5.em scaled resampled as #9, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> surface dust #2 size 133
> surface dust #3 size 133
> surface dust #4 size 133
> surface dust #9 size 133
> volume #4 level 0.06015
> volume #3 level 0.05808
> volume #9 level 0.06062
> show #!6 models
> hide #!2 models
> color #6 #ffffb264 models
> color #6 #00ffff64 models
> color #6 cyan models
> color #3 #cccc9964 models
> hide #!9 models
> hide #!4 models
> hide #1 models
> hide #!3 models
> show #!3 models
> color #6 cyan models
> color #6 #00ffff64 models
> hide #!3 models
> color #6 cyan models
> transparency #6.1 0
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!3 models
> color #3 #cccc9902 models
> color #3 #cccc99ff models
> show #!9 models
> show #!4 models
> save
> C:/Users/dziemianowicz/Desktop/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2.cxs includeMaps true
> hide #!2 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> color #3 #cccc9964 models
> show #!2 models
> close #3-4,9
> volume resample #2 onGrid #6
Opened box /M mark 1 M resampled as #3, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
> hide #!6 models
> show #!2 models
> volume #!2-3 showOutlineBox true
> volume resample #2 onGrid #7
Opened box /M mark 1 M resampled as #4, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> close #3
> volume resample #6 onGrid #4
Opened ref_CR_5.em scaled resampled as #3, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
> volume resample #7 onGrid #4
Opened ref_IR_5.em scaled resampled as #9, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
> volume resample #8 onGrid #4
Opened ref_NR_5.em scaled resampled as #10, grid size 120,120,120, pixel 6.67,
shown at step 1, values float32
> hide #!4 models
> surface dust #2 size 133
> surface dust #3 size 66.7
> surface dust #9 size 66.7
> surface dust #10 size 66.7
> hide #!2 models
> show #!4 models
> hide #!4 models
> volume #!3,9-10 showOutlineBox true
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!9 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> volume copy #9
Opened ref_IR_5.em scaled resampled copy as #11, grid size 120,120,120, pixel
6.67, shown at step 1, values float32
> surface dust #5 size 133
> surface dust #3 size 66.7
> surface dust #10 size 66.7
> surface dust #11 size 66.7
> hide #!10 models
> select add #11
1 atom, 1 residue, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,-5.0468,0,1,0,-463.11,0,0,1,27.319,#11,0.72256,-0.69085,0.025203,1362.4,0.6907,0.72297,0.015707,360.48,-0.029072,0.0060587,0.99956,464.62
> show #!9 models
> view matrix models
> #1,1,0,0,4.9566,0,1,0,-538.55,0,0,1,31.836,#11,0.72256,-0.69085,0.025203,1372.4,0.6907,0.72297,0.015707,285.04,-0.029072,0.0060587,0.99956,469.14
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.78798,0.61561,0.010553,-565.36,-0.61557,0.78805,-0.0070154,617.75,-0.012635,-0.00096835,0.99992,50.814,#11,0.99426,-0.099246,0.040078,1023.8,0.099726,0.99496,-0.010149,421.93,-0.038869,0.014087,0.99915,470
> hide #!3 models
> fitmap #11 inMap #5
Fit map ref_IR_5.em scaled resampled copy in map ref_3_symmetrized.em scaled
using 17277 points
correlation = 0.8742, correlation about mean = 0.1471, overlap = 161.9
steps = 72, shift = 59.7, angle = 7.15 degrees
Position of ref_IR_5.em scaled resampled copy (#11) relative to
ref_3_symmetrized.em scaled (#5) coordinates:
Matrix rotation and translation
0.99927504 0.02456670 0.02908378 920.62082425
-0.02438879 0.99968170 -0.00645611 463.83694210
-0.02923313 0.00574211 0.99955613 463.42997964
Axis 0.15818792 0.75626007 -0.63486005
Axis point 20700.19015266 0.00000000 -30038.33895686
Rotation angle (degrees) 2.20965102
Shift along axis 202.19926822
> fitmap #9 inMap #5
Fit map ref_IR_5.em scaled resampled in map ref_3_symmetrized.em scaled using
17277 points
correlation = 0.874, correlation about mean = 0.1432, overlap = 161.7
steps = 40, shift = 0.184, angle = 0.0738 degrees
Position of ref_IR_5.em scaled resampled (#9) relative to ref_3_symmetrized.em
scaled (#5) coordinates:
Matrix rotation and translation
0.72331078 -0.69006581 0.02511340 1177.35346030
0.68989359 0.72372581 0.01636423 625.52685270
-0.02946761 0.00548915 0.99955066 463.83291026
Axis -0.00787433 0.03952049 0.99918773
Axis point -167.01811187 1778.57910429 0.00000000
Rotation angle (degrees) 43.67291786
Shift along axis 478.90641520
> fitmap #11 inMap #5
Fit map ref_IR_5.em scaled resampled copy in map ref_3_symmetrized.em scaled
using 17277 points
correlation = 0.8742, correlation about mean = 0.1471, overlap = 161.9
steps = 44, shift = 0.0114, angle = 0.00507 degrees
Position of ref_IR_5.em scaled resampled copy (#11) relative to
ref_3_symmetrized.em scaled (#5) coordinates:
Matrix rotation and translation
0.99927746 0.02457290 0.02899555 920.65299941
-0.02439546 0.99968153 -0.00645743 463.83887527
-0.02914499 0.00574540 0.99955868 463.38260363
Axis 0.15850328 0.75519095 -0.63605293
Axis point 20752.49357784 0.00000000 -30133.02386553
Rotation angle (degrees) 2.20608489
Shift along axis 201.47757597
> measure rotation #9 toModel #11
Position of ref_IR_5.em scaled resampled #9 relative to ref_IR_5.em scaled
resampled copy #11 coordinates:
Matrix rotation and translation
0.70681672 -0.70738282 -0.00443586 252.55740604
0.70727842 0.70656994 0.02271895 167.94694563
-0.01293675 -0.01919552 0.99973205 6.84918994
Axis -0.02961510 0.00600640 0.99954333
Axis point -76.21786423 388.63585329 0.00000000
Rotation angle (degrees) 45.04433985
Shift along axis 0.37530600
> measure rotation #11 toModel #9
Position of ref_IR_5.em scaled resampled copy #11 relative to ref_IR_5.em
scaled resampled #9 coordinates:
Matrix rotation and translation
0.70681672 0.70727842 -0.01293675 -297.20844177
-0.70738282 0.70656994 -0.01919552 60.11997903
-0.00443586 0.02271895 0.99973205 -9.54262507
Axis 0.02961510 -0.00600640 -0.99954333
Axis point -76.21786432 388.63585377 0.00000000
Rotation angle (degrees) 45.04433982
Shift along axis 0.37530600
> hide #!11 models
> show #!10 models
> select add #11
1 atom, 1 residue, 3 models selected
> show #!8 models
> hide #!8 models
> show #!11 models
> hide #!11 models
> show #!3 models
> save
> C:/Users/dziemianowicz/Desktop/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2.cxs includeMaps true
> save C:/Users/dziemianowicz/Desktop/ref_mock_CR_cut_resampled.mrc models #3
> save C:/Users/dziemianowicz/Desktop/ref_mock_IR_cut_resampled.mrc models #9
> save C:/Users/dziemianowicz/Desktop/ref_mock_NR_cut_resampled.mrc models #10
> save C:/Users/dziemianowicz/Desktop/full.mrc models #5
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> volume #!3,5,9-10 showOutlineBox false
> volume #!3,5,9-10 showOutlineBox true
> close #12-13
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!6 models
> show #!11 models
> hide #!11 models
> show #!4 models
> hide #!4 models
> volume resample #4 onGrid #6
Opened box /M mark 1 M resampled resampled as #12, grid size 120,120,120,
pixel 6.67, shown at step 1, values float32
> close #12
> volume resample #4 onGrid #7
Opened box /M mark 1 M resampled resampled as #12, grid size 120,120,120,
pixel 6.67, shown at step 1, values float32
> hide #!12 models
> show #!11 models
> show #!2 models
> show #!12 models
> hide #!11 models
> hide #!12 models
> hide #!10 models
> hide #!9 models
> hide #!5 models
> hide #!3 models
> show #!5 models
> hide #!2 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!12 models
> close #12
> show #!11 models
> close #9-11
> show #!3 models
> close #3
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!6 models
> show #!7 models
> show #!8 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> volume resample #6 onGrid #2
Opened ref_CR_5.em scaled resampled as #3, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> volume resample #7 onGrid #2
Opened ref_IR_5.em scaled resampled as #9, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> volume resample #8 onGrid #2
Opened ref_NR_5.em scaled resampled as #10, grid size 55,55,55, pixel 13.3,
shown at step 1, values float32
> save C:/Users/dziemianowicz/Desktop/ref_mock_CR_cut_resampled.mrc models #3
> save C:/Users/dziemianowicz/Desktop/ref_mock_IR_cut_resampled.mrc models #9
> save C:/Users/dziemianowicz/Desktop/ref_mock_NR_cut_resampled.mrc models #10
> save C:/Users/dziemianowicz/Desktop/full.mrc models #5
> select add #9
1 atom, 1 residue, 3 models selected
> select subtract #1
2 models selected
> hide #1 models
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,9.1858,0,1,0,-14.378,0,0,1,7.8333
> undo
> volume copy #9
Opened ref_mock_IR_cut_resampled.mrc copy as #11, grid size 55,55,55, pixel
13.3, shown at step 1, values float32
> show #!9 models
> select subtract #9
Nothing selected
> select add #11
2 models selected
> view matrix models #11,1,0,0,186.34,0,1,0,-308.94,0,0,1,21.876
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.79283,0.60876,0.028774,-291.09,-0.60886,0.79326,-0.0062291,665.95,-0.026617,-0.012581,0.99957,68.716
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.79283,0.60876,0.028774,-280.51,-0.60886,0.79326,-0.0062291,621.21,-0.026617,-0.012581,0.99957,47.688
> fitmap #11 inMap #5
Fit map ref_mock_IR_cut_resampled.mrc copy in map full.mrc using 1367 points
correlation = 0.9062, correlation about mean = 0.08163, overlap = 14.53
steps = 80, shift = 89.4, angle = 8.14 degrees
Position of ref_mock_IR_cut_resampled.mrc copy (#11) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.70202181 0.71213715 -0.00510383 -348.92537502
-0.71214218 0.70203445 0.00107066 864.25061014
0.00434552 0.00288302 0.99998640 -8.15999927
Axis 0.00127245 -0.00663433 -0.99997718
Axis point 858.33187919 849.12305390 0.00000000
Rotation angle (degrees) 45.41059854
Shift along axis 1.98210265
> fitmap #11 inMap #5
Fit map ref_mock_IR_cut_resampled.mrc copy in map full.mrc using 1367 points
correlation = 0.9064, correlation about mean = 0.08152, overlap = 14.51
steps = 28, shift = 0.235, angle = 0.0212 degrees
Position of ref_mock_IR_cut_resampled.mrc copy (#11) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.70200112 0.71215803 -0.00503626 -349.00655738
-0.71216127 0.70201444 0.00143275 864.00716159
0.00455587 0.00258084 0.99998629 -7.83306658
Axis 0.00080604 -0.00673439 -0.99997700
Axis point 857.95928061 849.07960204 0.00000000
Rotation angle (degrees) 45.41224031
Shift along axis 1.73301452
> measure rotation #9 toModel #11
Position of ref_mock_IR_cut_resampled.mrc #9 relative to
ref_mock_IR_cut_resampled.mrc copy #11 coordinates:
Matrix rotation and translation
0.70200112 -0.71216127 0.00455587 860.35111745
0.71215803 0.70201444 0.00258084 -357.97746307
-0.00503626 0.00143275 0.99998629 4.83736516
Axis -0.00080604 0.00673439 0.99997700
Axis point 857.95928080 849.07960222 0.00000000
Rotation angle (degrees) 45.41224030
Shift along axis 1.73301452
> save
> C:/Users/dziemianowicz/Desktop/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2.cxs includeMaps true
——— End of log from Fri Nov 17 14:58:14 2023 ———
opened ChimeraX session
> save
> E:/ownCloud/Manuscripts/FluNPC/Modelling/mock/2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2_structureFitting.cxs includeMaps true
——— End of log from Mon Sep 23 14:46:37 2024 ———
opened ChimeraX session
> lighting simple
> hide #12 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> set bgColor white
> lighting simple
> surface dust #3 size 133
> surface dust #9 size 133
> surface dust #10 size 133
> surface dust #11 size 133
> volume #11 level 0.06428
> hide #!11 models
> volume #9 level 0.06676
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup155_CRconnector_CTD.pdb
Chain information for hNup155_CRconnector_CTD.pdb #13
---
Chain | Description
D | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup155_CRconnector_NTD.pdb
Chain information for hNup155_CRconnector_NTD.pdb #14
---
Chain | Description
D | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup358_1_CRinner.pdb
Chain information for hNup358_1_CRinner.pdb #15
---
Chain | Description
0 | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup358_1_CRouter.pdb
Chain information for hNup358_1_CRouter.pdb #16
---
Chain | Description
0 | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup358_2_CRinner.pdb
Chain information for hNup358_2_CRinner.pdb #17
---
Chain | Description
0 | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup358_2_CRouter.pdb
Chain information for hNup358_2_CRouter.pdb #18
---
Chain | Description
0 | No description available
> open E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/hNup358_CRmiddle.pdb
Chain information for hNup358_CRmiddle.pdb #19
---
Chain | Description
0 | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/Nup98_CRconnector.pdb
Chain information for Nup98_CRconnector.pdb #20
---
Chain | Description
U | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/Nup133_propeller_CRinner.pdb
Chain information for Nup133_propeller_CRinner.pdb #21
---
Chain | Description
K | No description available
R | No description available
S | No description available
> open
> E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/Nup133_propeller_CRouter.pdb
Chain information for Nup133_propeller_CRouter.pdb #22
---
Chain | Description
K | No description available
R | No description available
S | No description available
> open E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/Y_CRinner.pdb
Chain information for Y_CRinner.pdb #23
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> open E:/ownCloud/Manuscripts/FluNPC/Figures/npc_fitting/Y_CRouter.pdb
Chain information for Y_CRouter.pdb #24
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> volume #!3,9-10 showOutlineBox true
> ui tool show "Side View"
> volume #!3,9-10 showOutlineBox false
Drag select of 10914 residues, 148340 atoms, 4 pseudobonds
> ui mousemode right translate
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #13,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#14,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#15,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#16,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#17,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#18,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#19,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#20,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#21,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#22,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#23,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408,#24,1,0,0,812.53,0,1,0,94.109,0,0,1,3.3408
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#14,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#15,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#16,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#17,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#18,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#19,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#20,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#21,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#22,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#23,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822,#24,-0.76484,0.62396,0.16027,755.72,-0.63369,-0.77348,-0.012794,1876.2,0.11598,-0.11135,0.98699,73.822
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#14,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#15,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#16,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#17,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#18,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#19,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#20,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#21,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#22,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#23,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318,#24,-0.76484,0.62396,0.16027,785.69,-0.63369,-0.77348,-0.012794,2044.1,0.11598,-0.11135,0.98699,68.318
> view matrix models
> #13,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#14,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#15,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#16,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#17,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#18,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#19,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#20,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#21,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#22,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#23,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249,#24,-0.76484,0.62396,0.16027,737.61,-0.63369,-0.77348,-0.012794,2106.1,0.11598,-0.11135,0.98699,58.249
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#14,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#15,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#16,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#17,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#18,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#19,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#20,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#21,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#22,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#23,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44,#24,-0.78998,0.61093,0.052002,871.52,-0.613,-0.78515,-0.088211,2187.9,-0.013061,-0.10156,0.99474,87.44
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#14,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#15,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#16,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#17,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#18,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#19,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#20,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#21,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#22,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#23,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25,#24,-0.78998,0.61093,0.052002,897.81,-0.613,-0.78515,-0.088211,2196.7,-0.013061,-0.10156,0.99474,107.25
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#14,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#15,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#16,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#17,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#18,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#19,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#20,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#21,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#22,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#23,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78,#24,-0.72424,0.6889,0.029902,828.52,-0.68886,-0.7209,-0.076004,2154.6,-0.030803,-0.075644,0.99666,88.78
> save
> C:/Users/dziemianowicz/Desktop/11-11-24_CRfit_(2023-11_15_mock_densityPrepModelling_bin4-on-
> bin2_structureFitting).cxs includeMaps true
> ui tool show "Fit in Map"
> molmap sel 20
Opened map 20 as #25, grid size 77,120,72, pixel 6.67, shown at level 0.0439,
step 1, values float32
> color #25 #62b29aff models
> color #25 #b2a860ff models
> fitmap #25 inMap #3
Fit map map 20 in map ref_mock_CR_cut_resampled.mrc using 25762 points
correlation = 0.7559, correlation about mean = 0.401, overlap = 364.6
steps = 68, shift = 16.6, angle = 5.25 degrees
Position of map 20 (#25) relative to ref_mock_CR_cut_resampled.mrc (#3)
coordinates:
Matrix rotation and translation
-0.70319838 0.71082832 -0.01533465 863.66993448
-0.71088621 -0.70330354 -0.00221997 2061.83850275
-0.01236293 0.00934012 0.99987995 -5.00424343
Axis 0.00813080 -0.00209017 -0.99996476
Axis point 862.09061621 850.70351116 0.00000000
Rotation angle (degrees) 134.69325165
Shift along axis 7.71681113
> fitmap sel inMap #25
Fit molecules hNup155_CRconnector_CTD.pdb (#13), hNup155_CRconnector_NTD.pdb
(#14), hNup358_1_CRinner.pdb (#15), hNup358_1_CRouter.pdb (#16),
hNup358_2_CRinner.pdb (#17), hNup358_2_CRouter.pdb (#18), hNup358_CRmiddle.pdb
(#19), Nup98_CRconnector.pdb (#20), Nup133_propeller_CRinner.pdb (#21),
Nup133_propeller_CRouter.pdb (#22), Y_CRinner.pdb (#23), Y_CRouter.pdb (#24)
to map map 20 (#25) using 234892 atoms
average map value = 0.2728, steps = 68
shifted from previous position = 16.5
rotated from previous position = 5.26 degrees
atoms outside contour = 92, contour level = 0.043903
Position of hNup155_CRconnector_CTD.pdb (#13) relative to map 20 (#25)
coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup155_CRconnector_NTD.pdb (#14) relative to map 20 (#25)
coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup358_1_CRinner.pdb (#15) relative to map 20 (#25) coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup358_1_CRouter.pdb (#16) relative to map 20 (#25) coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup358_2_CRinner.pdb (#17) relative to map 20 (#25) coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup358_2_CRouter.pdb (#18) relative to map 20 (#25) coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
Position of hNup358_CRmiddle.pdb (#19) relative to map 20 (#25) coordinates:
Matrix rotation and translation
1.00000000 -0.00002411 -0.00000905 0.06603721
0.00002411 0.99999999 -0.00014999 0.15422880
0.00000906 0.00014999 0.99999999 -0.17855768
Axis 0.98557257 -0.05949059 0.15845370
Axis point 0.00000000 1219.74219065 1039.14042838
Rotation angle (degrees) 0.00871942
Shift along axis 0.02761617
[deleted to fit within ticket limits]
> close #22-31
> open MAPS/fullAlign/refs/ref_s114_8_symmetrized.em id 1000
Opened ref_s114_8_symmetrized.em as #22, grid size 128,128,128, pixel 1, shown
at level 0.0637, step 1, values float32
> open MAPS/fullAlign/refs/ref_s127_8_symmetrized.em id 1001
Opened ref_s127_8_symmetrized.em as #22, grid size 128,128,128, pixel 1, shown
at level 0.0711, step 1, values float32
> open MAPS/fullAlign/refs/ref_s140_8_symmetrized.em id 1002
Opened ref_s140_8_symmetrized.em as #22, grid size 128,128,128, pixel 1, shown
at level 0.0919, step 1, values float32
> open MAPS/fullAlign/refs/ref_s162_8_symmetrized.em id 1003
Opened ref_s162_8_symmetrized.em as #22, grid size 128,128,128, pixel 1, shown
at level 0.115, step 1, values float32
> open MAPS/fullAlign/refs/ref_s200_8_symmetrized.em id 1004
Opened ref_s200_8_symmetrized.em as #22, grid size 128,128,128, pixel 1, shown
at level 0.159, step 1, values float32
> volume #1000-1001 voxelSize 13.34
> volume scale #1000-1001 factor -1 inPlace true
Expected a keyword
> volume scale #1000-1001 factor -1
Opened ref_s114_8_symmetrized.em scaled as #22, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled as #23, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
> close #22-23
> volume #1000-1004 voxelSize 13.34
> volume scale #1000-1004 factor -1 inPlace true
Expected a keyword
> volume scale #1000-1004 factor -1
Opened ref_s114_8_symmetrized.em scaled as #22, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled as #23, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s140_8_symmetrized.em scaled as #24, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s162_8_symmetrized.em scaled as #25, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
Opened ref_s200_8_symmetrized.em scaled as #26, grid size 128,128,128, pixel
13.3, shown at step 1, values float32
> close #1000-1004
> hide #!23-26 target m
> open /Users/kosinski/Desktop/FluNPC_paper/mock_fits/mock_unit_fit.cif id 101
Summary of feedback from opening
/Users/kosinski/Desktop/FluNPC_paper/mock_fits/mock_unit_fit.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for mock_unit_fit.cif #27
---
Chain | Description
00 10 20 30 40 50 60 70 | No description available
01 02 03 04 05 | No description available
41 42 | No description available
A0 | No description available
A1 A2 | No description available
A3 A4 | No description available
A5 A6 A7 A8 | No description available
B0 B1 | No description available
C0 C1 C2 C3 C4 | No description available
D0 D2 | No description available
D1 D3 | No description available
D4 D5 D6 D7 | No description available
E0 E1 | No description available
F0 F1 F2 F3 | No description available
F4 F5 F6 F7 | No description available
H0 H1 H2 H3 | No description available
I0 I1 I2 I3 | No description available
J0 J1 J2 J3 J4 | No description available
K0 K1 K2 K3 | No description available
K4 K5 K6 K7 | No description available
L0 L1 L2 L3 | No description available
M0 M1 M2 M3 | No description available
N0 N1 N2 N3 | No description available
O0 O1 O2 O3 | No description available
P0 P1 P2 P3 | No description available
Q0 Q1 Q2 Q3 | No description available
R0 R1 R2 R3 | No description available
S0 S1 S2 S3 | No description available
T0 T1 | No description available
U0 | No description available
U1 U2 U3 U4 | No description available
V0 | No description available
W0 | No description available
> hide #!100-101 atoms
> show #!100-101 cartoons
> hide #!13 models
> hide #!101 models
> show #!101 models
> hide #!100 models
> volume #22 level 0.05621
> volume #22 level 0.05148
> show #!5 models
> hide #!5 models
> volume gaussian #22-26 sDev 30
Opened ref_s114_8_symmetrized.em scaled gaussian as #27, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled gaussian as #28, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s162_8_symmetrized.em scaled gaussian as #30, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s200_8_symmetrized.em scaled gaussian as #31, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> close #27-31
> volume gaussian #22-26 sDev 10
Opened ref_s114_8_symmetrized.em scaled gaussian as #27, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s127_8_symmetrized.em scaled gaussian as #28, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s140_8_symmetrized.em scaled gaussian as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s162_8_symmetrized.em scaled gaussian as #30, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
Opened ref_s200_8_symmetrized.em scaled gaussian as #31, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> hide #!28-31 target m
> volume #27 level 0.05372
> show #!5 models
> fitmap #22 inMap #5
Fit map ref_s114_8_symmetrized.em scaled in map full.mrc using 101620 points
correlation = 0.8388, correlation about mean = 0.3538, overlap = 548.6
steps = 152, shift = 4.55, angle = 18.6 degrees
Position of ref_s114_8_symmetrized.em scaled (#22) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.94749324 0.31977578 -0.00004036 -227.82384418
-0.31977579 0.94749324 -0.00008281 318.23385327
0.00001176 0.00009136 1.00000000 4.43690174
Axis 0.00027233 -0.00008148 -0.99999996
Axis point 855.13885862 852.85751479 0.00000000
Rotation angle (degrees) 18.64936658
Shift along axis -4.52487604
> close #27-31
> show #!22 models
> hide #!5 models
> fitmap #22-26 inMap #5
Multiple maps for #22-26
> fitmap #23 inMap #5
Fit map ref_s127_8_symmetrized.em scaled in map full.mrc using 20962 points
correlation = 0.8436, correlation about mean = 0.1454, overlap = 191.1
steps = 136, shift = 10.1, angle = 17.2 degrees
Position of ref_s127_8_symmetrized.em scaled (#23) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.95544690 -0.29516303 0.00003030 290.29635621
0.29516303 0.95544690 -0.00000235 -213.67839070
-0.00002825 0.00001119 1.00000000 10.07430928
Axis 0.00002294 0.00009919 0.99999999
Axis point 852.95808172 854.76220573 0.00000000
Rotation angle (degrees) 17.16731366
Shift along axis 10.05977370
> show #!23 models
> hide #!22 models
> volume #23 level 0.05528
> show #!22 models
> hide #!22 models
> hide #!23 models
> show #!24 models
> volume #24 level 0.06449
> fitmap #24 inMap #5
Fit map ref_s140_8_symmetrized.em scaled in map full.mrc using 113892 points
correlation = 0.3662, correlation about mean = 0.1585, overlap = 207.5
steps = 100, shift = 1.28, angle = 10.1 degrees
Position of ref_s140_8_symmetrized.em scaled (#24) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.98440820 -0.17589860 -0.00043258 164.82473649
0.17589844 0.98440824 -0.00038634 -135.69508372
0.00049379 0.00030422 0.99999983 -1.00262244
Axis 0.00196294 -0.00263323 0.99999461
Axis point 847.84365178 861.89405619 0.00000000
Rotation angle (degrees) 10.13100571
Shift along axis -0.32175916
> show #!5 models
> hide #!24 models
> show #!25 models
> hide #!5 models
> volume #25 level 0.07094
> fitmap #25 inMap #5
Fit map ref_s162_8_symmetrized.em scaled in map full.mrc using 136096 points
correlation = 0.1543, correlation about mean = 0.1074, overlap = 94.05
steps = 80, shift = 38.3, angle = 6.02 degrees
Position of ref_s162_8_symmetrized.em scaled (#25) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.99447770 0.10494784 0.00023836 -84.88622735
-0.10494792 0.99447765 0.00037210 94.34721978
-0.00019799 -0.00039506 0.99999990 -37.78618865
Axis -0.00365490 0.00207888 -0.99999116
Axis point 853.37844638 852.41286371 0.00000000
Rotation angle (degrees) 6.02421702
Shift along axis 38.29224197
> show #!5 models
> volume gaussian #25 sDev 30
Opened ref_s162_8_symmetrized.em scaled gaussian as #27, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #27 level 0.01191
> close #27
> show #!26 models
> hide #!26 models
> show #!22 models
> hide #!5 models
> volume gaussian #22 sDev 10
Opened ref_s114_8_symmetrized.em scaled gaussian as #27, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #27 color #b2b2ff69
> volume #27 level 0.03696
> save /Users/kosinski/Desktop/FluNPC_paper/all_maps.cxs includeMaps true
> volume gaussian #22 sDev 5
Opened ref_s114_8_symmetrized.em scaled gaussian as #28, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #26 level 0.1073
> volume #28 level 0.04505
> close #28
> rename #27 "ref_s114_8_symmetrized.em scaled gaussian10"
> show #!22 models
> show #!23 models
> hide #!22 models
> hide #!27 models
> show #!100 models
> volume gaussian #23 sDev 10
Opened ref_s127_8_symmetrized.em scaled gaussian as #28, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #28 level 0.03993
> rename #28 "ref_s127_8_symmetrized.em scaled gaussian10"
> volume #28 color #ffb2b263
> hide #!101 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!27 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #28 level 0.02258
> hide #!100 models
> show #!100 models
> volume #28 level 0.0128
> volume #28 level 0.03414
> hide #!27 models
> hide #!28 models
> save /Users/kosinski/Desktop/FluNPC_paper/all_maps.cxs includeMaps true
> show #!24 models
> volume gaussian #24 sDev 10
Opened ref_s140_8_symmetrized.em scaled gaussian as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #29 level 0.03431
> close #29
> volume gaussian #24 sDev 20
Opened ref_s140_8_symmetrized.em scaled gaussian as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #29 level 0.02465
> close #29
> volume gaussian #24 sDev 15
Opened ref_s140_8_symmetrized.em scaled gaussian as #29, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #29 level 0.03186
> fitmap #24 inMap #5
Fit map ref_s140_8_symmetrized.em scaled in map full.mrc using 113892 points
correlation = 0.3652, correlation about mean = 0.1579, overlap = 207.6
steps = 48, shift = 0.291, angle = 0.0129 degrees
Position of ref_s140_8_symmetrized.em scaled (#24) relative to full.mrc (#5)
coordinates:
Matrix rotation and translation
0.98443060 -0.17577340 -0.00031570 164.64275969
0.17577333 0.98443064 -0.00024273 -135.72520597
0.00035346 0.00018346 0.99999992 -0.49237413
Axis 0.00121234 -0.00190347 0.99999745
Axis point 848.47127079 861.52180882 0.00000000
Rotation angle (degrees) 10.12369218
Shift along axis -0.03442083
> show #!28 models
> rename #29 "ref_s140_8_symmetrized.em scaled gaussian15"
> volume #29 color #99bfe5a4
> volume #29 color #99bfe5a3
> volume gaussian #24 sDev 30
Opened ref_s140_8_symmetrized.em scaled gaussian as #30, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #30 level 0.02128
> volume #30 color #cccc996b
> volume #30 level 0.01873
> rename #30 "ref_s140_8_symmetrized.em scaled gaussian30"
> show #!25 models
> volume gaussian #25 sDev 30
Opened ref_s162_8_symmetrized.em scaled gaussian as #31, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #31 level 0.006317
> hide #!30 models
> rename #31 "ref_s162_8_symmetrized.em scaled gaussian30"
> volume #31 color #b2b2b273
> volume #31 level 0.01824
> show #!30 models
> fitmap #31 inMap #5
Fit map ref_s162_8_symmetrized.em scaled gaussian30 in map full.mrc using
150755 points
correlation = 0.4475, correlation about mean = 0.1854, overlap = 119.3
steps = 124, shift = 2.22, angle = 14 degrees
Position of ref_s162_8_symmetrized.em scaled gaussian30 (#31) relative to
full.mrc (#5) coordinates:
Matrix rotation and translation
0.93974023 0.34188911 0.00036374 -240.17076996
-0.34188919 0.93974026 0.00016990 343.84769519
-0.00028373 -0.00028402 0.99999992 -35.71451857
Axis -0.00066385 0.00094690 -0.99999933
Axis point 855.25533194 853.15447994 0.00000000
Rotation angle (degrees) 19.99202705
Shift along axis 36.19951967
> hide #!30 models
> show #!25 models
> view position #25 sameAsModels #31
> volume gaussian #25 sDev 20
Opened ref_s162_8_symmetrized.em scaled gaussian as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #32 level 0.02573
> volume #32 level 0.02263
> volume #32 level 0.01726
> close #32
> volume #31 level 0.01638
> show #!30 models
> hide #!31 models
> show #!31 models
> fitmap #31 inMap #30
Fit map ref_s162_8_symmetrized.em scaled gaussian30 in map
ref_s140_8_symmetrized.em scaled gaussian30 using 172137 points
correlation = 0.8743, correlation about mean = 0.3353, overlap = 121.4
steps = 64, shift = 45.7, angle = 3.38 degrees
Position of ref_s162_8_symmetrized.em scaled gaussian30 (#31) relative to
ref_s140_8_symmetrized.em scaled gaussian30 (#30) coordinates:
Matrix rotation and translation
0.83388722 0.55193481 -0.00026108 -327.83351276
-0.55193487 0.83388717 -0.00029238 614.42309728
0.00005633 0.00038791 0.99999992 9.07539927
Axis 0.00061628 -0.00028754 -0.99999977
Axis point 856.83845289 851.83882932 0.00000000
Rotation angle (degrees) 33.49986145
Shift along axis -9.45410625
> hide #!30 models
> show #!5 models
> hide #!5 models
> volume #31 level 0.01042
> volume #31 level 0.02141
> show #!5 models
> hide #!5 models
> volume #31 level 0.01638
> volume gaussian #26 sDev 30
Opened ref_s200_8_symmetrized.em scaled gaussian as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #32 level 0.01286
> fitmap #31 inMap #31
Fit map ref_s162_8_symmetrized.em scaled gaussian30 in map
ref_s162_8_symmetrized.em scaled gaussian30 using 172137 points
correlation = 0.9992, correlation about mean = 0.9896, overlap = 132.3
steps = 48, shift = 0.646, angle = 0.0211 degrees
Position of ref_s162_8_symmetrized.em scaled gaussian30 (#31) relative to
ref_s162_8_symmetrized.em scaled gaussian30 (#31) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
-0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 -0.00094019 -0.99999956
Axis point -0.00000000 1971.73139810 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
> fitmap #31 inMap #30
Fit map ref_s162_8_symmetrized.em scaled gaussian30 in map
ref_s140_8_symmetrized.em scaled gaussian30 using 172137 points
correlation = 0.8744, correlation about mean = 0.3356, overlap = 121.4
steps = 48, shift = 0.639, angle = 0.0312 degrees
Position of ref_s162_8_symmetrized.em scaled gaussian30 (#31) relative to
ref_s140_8_symmetrized.em scaled gaussian30 (#30) coordinates:
Matrix rotation and translation
0.83388133 0.55194378 -0.00004131 -328.01457050
-0.55194377 0.83388130 -0.00022021 614.37415694
-0.00008710 0.00020643 0.99999997 9.28777029
Axis 0.00038650 0.00004148 -0.99999992
Axis point 856.65100098 852.10974361 0.00000000
Rotation angle (degrees) 33.50046934
Shift along axis -9.38906453
> fitmap #32 inMap #30
Fit map ref_s200_8_symmetrized.em scaled gaussian in map
ref_s140_8_symmetrized.em scaled gaussian30 using 171984 points
correlation = 0.6798, correlation about mean = 0.3373, overlap = 52.97
steps = 160, shift = 30.1, angle = 21.8 degrees
Position of ref_s200_8_symmetrized.em scaled gaussian (#32) relative to
ref_s140_8_symmetrized.em scaled gaussian30 (#30) coordinates:
Matrix rotation and translation
0.84859250 0.52904671 -0.00059740 -319.73642561
-0.52904695 0.84859248 -0.00036035 583.06370821
0.00031630 0.00062184 0.99999976 29.05657264
Axis 0.00092827 -0.00086353 -0.99999920
Axis point 858.76914414 850.08146997 0.00000000
Rotation angle (degrees) 31.94110424
Shift along axis -29.85684560
> volume #32 level 0.008438
> volume #32 level 0.01938
> close #32
> volume gaussian #26 sDev 60
Opened ref_s200_8_symmetrized.em scaled gaussian as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #32 level 0.003754
> volume #32 level 0.01333
> close #32
> volume gaussian #26 sDev 40
Opened ref_s200_8_symmetrized.em scaled gaussian as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #32 level 0.00825
> close #32
> volume gaussian #26 sDev 30
Opened ref_s200_8_symmetrized.em scaled gaussian as #32, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #32 level 0.01307
> fitmap #32 inMap #30
Fit map ref_s200_8_symmetrized.em scaled gaussian in map
ref_s140_8_symmetrized.em scaled gaussian30 using 166983 points
correlation = 0.6846, correlation about mean = 0.3336, overlap = 52.6
steps = 156, shift = 29.8, angle = 21.7 degrees
Position of ref_s200_8_symmetrized.em scaled gaussian (#32) relative to
ref_s140_8_symmetrized.em scaled gaussian30 (#30) coordinates:
Matrix rotation and translation
0.84934508 0.52783762 -0.00061550 -319.28338424
-0.52783787 0.84934508 -0.00035053 581.37389437
0.00033775 0.00062260 0.99999975 28.71266283
Axis 0.00092180 -0.00090297 -0.99999917
Axis point 858.78257308 849.95074861 0.00000000
Rotation angle (degrees) 31.85950563
Shift along axis -29.53192011
> volume #32 level 0.02065
> view position #26 sameAsModels #32
> rename #32 "ref_s200_8_symmetrized.em scaled gaussian30"
> show #!27 models
> show #!28 models
> show #!29 models
> show #!30 models
> show #!31 models
> hide #!100 models
> hide #!30 models
> close #100-101
> save /Users/kosinski/Desktop/FluNPC_paper/all_maps.cxs includeMaps true
> hide #!27-32 target m
> show #!22 models
> hide #!22 models
> show #!27 models
> cd mock_fits
Current working directory is: /Users/kosinski/Desktop/FluNPC_paper/mock_fits
> open Y_CRinner.pdb
Summary of feedback from opening Y_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 136 136 VAL K 90 THR K 97 1 8
Start residue of secondary structure not found: HELIX 137 137 THR K 134 LEU K
136 1 3
Start residue of secondary structure not found: HELIX 138 138 ALA K 153 LEU K
155 1 3
Start residue of secondary structure not found: HELIX 139 139 GLY K 250 SER K
260 1 11
Start residue of secondary structure not found: HELIX 140 140 SER K 270 LEU K
272 1 3
32 messages similar to the above omitted
Chain information for Y_CRinner.pdb #33
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> open Y_CRouter.pdb
Summary of feedback from opening Y_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 ASN A 180 VAL A 197 1 18
Start residue of secondary structure not found: HELIX 3 3 LEU A 205 VAL A 212
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS A 218 THR A 231
1 14
Start residue of secondary structure not found: HELIX 5 5 ALA A 241 SER A 246
1 6
Start residue of secondary structure not found: HELIX 6 6 VAL A 248 ALA A 281
1 34
64 messages similar to the above omitted
Chain information for Y_CRouter.pdb #34
---
Chain | Description
A | No description available
C | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
U | No description available
V | No description available
W | No description available
> open Y_NRinner.pdb
Summary of feedback from opening Y_NRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL K 90 THR K 97 1 8
Start residue of secondary structure not found: HELIX 2 2 THR K 134 LEU K 136
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA K 153 LEU K 155
1 3
Start residue of secondary structure not found: HELIX 4 4 GLY K 250 SER K 260
1 11
Start residue of secondary structure not found: HELIX 5 5 SER K 270 LEU K 272
1 3
32 messages similar to the above omitted
Chain information for Y_NRinner.pdb #35
---
Chain | Description
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open Y_NRouter.pdb
Summary of feedback from opening Y_NRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 ASN A 180 VAL A 197 1 18
Start residue of secondary structure not found: HELIX 3 3 LEU A 205 VAL A 212
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS A 218 THR A 231
1 14
Start residue of secondary structure not found: HELIX 5 5 ALA A 241 SER A 246
1 6
Start residue of secondary structure not found: HELIX 6 6 VAL A 248 ALA A 281
1 34
64 messages similar to the above omitted
Chain information for Y_NRouter.pdb #36
---
Chain | Description
A | No description available
C | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
> open Nup133_propeller_CRinner.pdb
Summary of feedback from opening Nup133_propeller_CRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE R 67 ASN R 71 1 5
Start residue of secondary structure not found: HELIX 2 2 VAL R 89 GLY R 92 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 4 4 ILE R 186 LYS R 192
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL R 262 THR R 268
1 7
120 messages similar to the above omitted
Chain information for Nup133_propeller_CRinner.pdb #37
---
Chain | Description
K | No description available
> open Nup133_propeller_CRouter.pdb
Summary of feedback from opening Nup133_propeller_CRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE R 67 ASN R 71 1 5
Start residue of secondary structure not found: HELIX 2 2 VAL R 89 GLY R 92 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 4 4 ILE R 186 LYS R 192
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL R 262 THR R 268
1 7
120 messages similar to the above omitted
Chain information for Nup133_propeller_CRouter.pdb #38
---
Chain | Description
K | No description available
> open Nup133_propeller_NRinner.pdb
Summary of feedback from opening Nup133_propeller_NRinner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE R 67 ASN R 71 1 5
Start residue of secondary structure not found: HELIX 2 2 VAL R 89 GLY R 92 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 4 4 ILE R 186 LYS R 192
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL R 262 THR R 268
1 7
197 messages similar to the above omitted
Chain information for Nup133_propeller_NRinner.pdb #39
---
Chain | Description
K | No description available
> open Nup133_propeller_NRouter.pdb
Summary of feedback from opening Nup133_propeller_NRouter.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE R 67 ASN R 71 1 5
Start residue of secondary structure not found: HELIX 2 2 VAL R 89 GLY R 92 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO R 169 MET R 172
1 4
Start residue of secondary structure not found: HELIX 4 4 ILE R 186 LYS R 192
1 7
Start residue of secondary structure not found: HELIX 5 5 VAL R 262 THR R 268
1 7
197 messages similar to the above omitted
Chain information for Nup133_propeller_NRouter.pdb #40
---
Chain | Description
K | No description available
> open hNup155_CRconnector_CTD.pdb
Summary of feedback from opening hNup155_CRconnector_CTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA D 12 MET D 39 1 28
Start residue of secondary structure not found: HELIX 2 2 LEU D 43 LEU D 46 1
4
Start residue of secondary structure not found: HELIX 3 3 ASP D 62 ASP D 64 1
3
Start residue of secondary structure not found: HELIX 4 4 PRO D 91 GLY D 98 1
8
Start residue of secondary structure not found: HELIX 5 5 PRO D 110 ILE D 112
1 3
52 messages similar to the above omitted
Chain information for hNup155_CRconnector_CTD.pdb #41
---
Chain | Description
D | No description available
> open hNup155_CRconnector_NTD.pdb
Summary of feedback from opening hNup155_CRconnector_NTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 24 24 THR D 869 GLN D 886 1 18
Start residue of secondary structure not found: HELIX 25 25 LYS D 890 GLN D
910 1 21
Start residue of secondary structure not found: HELIX 26 26 LEU D 913 VAL D
923 1 11
Start residue of secondary structure not found: HELIX 27 27 TYR D 926 GLU D
938 1 13
Start residue of secondary structure not found: HELIX 28 28 LEU D 945 HIS D
952 1 8
23 messages similar to the above omitted
Chain information for hNup155_CRconnector_NTD.pdb #42
---
Chain | Description
D | No description available
> open hNup155_NRconnector_CTD.pdb
Summary of feedback from opening hNup155_NRconnector_CTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA D 12 MET D 39 1 28
Start residue of secondary structure not found: HELIX 2 2 LEU D 43 LEU D 46 1
4
Start residue of secondary structure not found: HELIX 3 3 ASP D 62 ASP D 64 1
3
Start residue of secondary structure not found: HELIX 4 4 PRO D 91 GLY D 98 1
8
Start residue of secondary structure not found: HELIX 5 5 PRO D 110 ILE D 112
1 3
52 messages similar to the above omitted
Chain information for hNup155_NRconnector_CTD.pdb #43
---
Chain | Description
D | No description available
> open hNup155_NRconnector_NTD.pdb
Summary of feedback from opening hNup155_NRconnector_NTD.pdb
---
warnings | Start residue of secondary structure not found: HELIX 24 24 THR D 869 GLN D 886 1 18
Start residue of secondary structure not found: HELIX 25 25 LYS D 890 GLN D
910 1 21
Start residue of secondary structure not found: HELIX 26 26 LEU D 913 VAL D
923 1 11
Start residue of secondary structure not found: HELIX 27 27 TYR D 926 GLU D
938 1 13
Start residue of secondary structure not found: HELIX 28 28 LEU D 945 HIS D
952 1 8
23 messages similar to the above omitted
Chain information for hNup155_NRconnector_NTD.pdb #44
---
Chain | Description
D | No description available
> open hNup358_1_CRinner.pdb
Chain information for hNup358_1_CRinner.pdb #45
---
Chain | Description
0 | No description available
> open hNup358_1_CRouter.pdb
Chain information for hNup358_1_CRouter.pdb #46
---
Chain | Description
0 | No description available
> open hNup358_2_CRinner.pdb
Chain information for hNup358_2_CRinner.pdb #47
---
Chain | Description
0 | No description available
> open hNup358_2_CRouter.pdb
Chain information for hNup358_2_CRouter.pdb #48
---
Chain | Description
0 | No description available
> open hNup358_CRmiddle.pdb
Chain information for hNup358_CRmiddle.pdb #49
---
Chain | Description
0 | No description available
> open hNup93_CR_outer.pdb
Summary of feedback from opening hNup93_CR_outer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS02 5 GLY02 17 1 13
Start residue of secondary structure not found: HELIX 2 2 PRO02 22 LYS02 25 1
4
Start residue of secondary structure not found: HELIX 3 3 SER02 26 LYS02 28 1
3
Start residue of secondary structure not found: HELIX 4 4 GLY02 29 TYR02 36 1
8
Start residue of secondary structure not found: HELIX 5 5 TYR02 37 ALA02 39 1
3
46 messages similar to the above omitted
Chain information for hNup93_CR_outer.pdb #50
---
Chain | Description
A | No description available
> open hNup93_NR_outer.pdb
Summary of feedback from opening hNup93_NR_outer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY L 147 ALA L 150 1 4
Start residue of secondary structure not found: HELIX 2 2 SER L 151 SER L 153
1 3
Start residue of secondary structure not found: HELIX 3 3 MET L 154 SER L 161
1 8
Start residue of secondary structure not found: HELIX 4 4 PHE L 162 LYS L 164
1 3
Start residue of secondary structure not found: HELIX 5 5 VAL L 170 ILE L 191
1 22
52 messages similar to the above omitted
Chain information for hNup93_NR_outer.pdb #51
---
Chain | Description
A | No description available
> open hNups_IRcyt_inner.pdb
Summary of feedback from opening hNups_IRcyt_inner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 209 209 GLN F 183 ALA F 194 1 12
Start residue of secondary structure not found: HELIX 210 210 GLN F 220 LEU F
225 1 6
Start residue of secondary structure not found: HELIX 211 211 SER F 247 GLU F
250 1 4
Start residue of secondary structure not found: SHEET 79 79 1 TRP F 175 PHE F
179 0
Start residue of secondary structure not found: SHEET 80 80 1 ILE F 199 MET F
204 0
3 messages similar to the above omitted
Chain information for hNups_IRcyt_inner.pdb #52
---
Chain | Description
4 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open hNups_IRcyt_outer.pdb
Summary of feedback from opening hNups_IRcyt_outer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 158 158 GLN F 183 TYR F 196 1 14
Start residue of secondary structure not found: HELIX 159 159 LYS F 218 LYS F
227 1 10
Start residue of secondary structure not found: HELIX 160 160 LYS F 246 GLU F
250 1 5
Start residue of secondary structure not found: SHEET 51 51 1 TRP F 175 PHE F
179 0
Start residue of secondary structure not found: SHEET 52 52 1 ILE F 199 MET F
204 0
2 messages similar to the above omitted
Chain information for hNups_IRcyt_outer.pdb #53
---
Chain | Description
A | No description available
B | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open hNups_IRnuc_inner.pdb
Summary of feedback from opening hNups_IRnuc_inner.pdb
---
warnings | Start residue of secondary structure not found: HELIX 204 204 GLN F 183 ALA F 194 1 12
Start residue of secondary structure not found: HELIX 205 205 GLN F 220 LEU F
225 1 6
Start residue of secondary structure not found: HELIX 206 206 LYS F 246 GLU F
250 1 5
Start residue of secondary structure not found: SHEET 77 77 1 TRP F 175 PHE F
179 0
Start residue of secondary structure not found: SHEET 78 78 1 ILE F 199 MET F
204 0
3 messages similar to the above omitted
Chain information for hNups_IRnuc_inner.pdb #54
---
Chain | Description
4 | No description available
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open hNups_IRnuc_outer.pdb
Summary of feedback from opening hNups_IRnuc_outer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 159 159 GLN F 183 TYR F 196 1 14
Start residue of secondary structure not found: HELIX 160 160 LYS F 218 LYS F
227 1 10
Start residue of secondary structure not found: HELIX 161 161 LYS F 246 GLU F
250 1 5
Start residue of secondary structure not found: SHEET 51 51 1 TRP F 175 PHE F
179 0
Start residue of secondary structure not found: SHEET 52 52 1 ILE F 199 MET F
204 0
2 messages similar to the above omitted
Chain information for hNups_IRnuc_outer.pdb #55
---
Chain | Description
A | No description available
B | No description available
D | No description available
F | No description available
H | No description available
I | No description available
J | No description available
U | No description available
> open hNup53_dimer_IRcyt_innerF7.pdb
Chain information for hNup53_dimer_IRcyt_innerF7.pdb #56
---
Chain | Description
F | No description available
> open hNup53_dimer_IRcyt_outerG7.pdb
Chain information for hNup53_dimer_IRcyt_outerG7.pdb #57
---
Chain | Description
F | No description available
> open hNup53_dimer_IRnuc_innerF0.pdb
Chain information for hNup53_dimer_IRnuc_innerF0.pdb #58
---
Chain | Description
F | No description available
> open hNup53_dimer_IRnuc_outerG0.pdb
Chain information for hNup53_dimer_IRnuc_outerG0.pdb #59
---
Chain | Description
F | No description available
> open hGp210.pdb
Summary of feedback from opening hGp210.pdb
---
warnings | Start residue of secondary structure not found: HELIX 195 195 LEU40 4 LEU40 6 1 3
Start residue of secondary structure not found: HELIX 196 196 SER40 136 ALA40
141 1 6
Start residue of secondary structure not found: HELIX 197 197 GLN40 422 GLY40
424 1 3
Start residue of secondary structure not found: HELIX 198 198 LEU41 4 LEU41 6
1 3
Start residue of secondary structure not found: HELIX 199 199 SER41 136 ALA41
141 1 6
1692 messages similar to the above omitted
Chain information for hGp210.pdb #60
---
Chain | Description
10 11 12 13 14 15 16 17 | No description available
> hide #37-41,43,45-51,56-60#!33-36,42,44,52-55 atoms
> show #37-41,43,45-51,56-60#!33-36,42,44,52-55 cartoons
> select #33,34,37,38,41,45-50
182469 atoms, 186348 bonds, 4 pseudobonds, 22818 residues, 13 models selected
> color (#37-38,41,45-50#!33-34 & sel) forest green
> volume #27 level 0.01976
> ui tool show "Fit in Map"
> fitmap sel inMap #27
Fit molecules Y_CRinner.pdb (#33), Y_CRouter.pdb (#34),
Nup133_propeller_CRinner.pdb (#37), Nup133_propeller_CRouter.pdb (#38),
hNup155_CRconnector_CTD.pdb (#41), hNup358_1_CRinner.pdb (#45),
hNup358_1_CRouter.pdb (#46), hNup358_2_CRinner.pdb (#47),
hNup358_2_CRouter.pdb (#48), hNup358_CRmiddle.pdb (#49), hNup93_CR_outer.pdb
(#50) to map ref_s114_8_symmetrized.em scaled gaussian10 (#27) using 182469
atoms
average map value = 0.04359, steps = 68
shifted from previous position = 10.8
rotated from previous position = 7.52 degrees
atoms outside contour = 33869, contour level = 0.019759
Position of Y_CRinner.pdb (#33) relative to ref_s114_8_symmetrized.em scaled
gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of Y_CRouter.pdb (#34) relative to ref_s114_8_symmetrized.em scaled
gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of Nup133_propeller_CRinner.pdb (#37) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of Nup133_propeller_CRouter.pdb (#38) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup155_CRconnector_CTD.pdb (#41) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup358_1_CRinner.pdb (#45) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup358_1_CRouter.pdb (#46) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup358_2_CRinner.pdb (#47) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup358_2_CRouter.pdb (#48) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup358_CRmiddle.pdb (#49) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
Position of hNup93_CR_outer.pdb (#50) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.92633696 -0.36703643 0.08475907 306.52046777
0.36000984 0.92882839 0.08758280 -360.97205062
-0.11087271 -0.05061708 0.99254479 204.74843815
Axis -0.18053899 0.25556580 0.94978513
Axis point 1159.59731211 625.45276431 0.00000000
Rotation angle (degrees) 22.50366311
Shift along axis 46.87601686
> select #35,36,39,40,43,51
135371 atoms, 138333 bonds, 4 pseudobonds, 16966 residues, 8 models selected
> color (#39-40,43,51#!35-36 & sel) forest green
> fitmap sel inMap #27
Fit molecules Y_NRinner.pdb (#35), Y_NRouter.pdb (#36),
Nup133_propeller_NRinner.pdb (#39), Nup133_propeller_NRouter.pdb (#40),
hNup155_NRconnector_CTD.pdb (#43), hNup93_NR_outer.pdb (#51) to map
ref_s114_8_symmetrized.em scaled gaussian10 (#27) using 135371 atoms
average map value = 0.04386, steps = 72
shifted from previous position = 35
rotated from previous position = 16.8 degrees
atoms outside contour = 13049, contour level = 0.019759
Position of Y_NRinner.pdb (#35) relative to ref_s114_8_symmetrized.em scaled
gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
Position of Y_NRouter.pdb (#36) relative to ref_s114_8_symmetrized.em scaled
gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
Position of Nup133_propeller_NRinner.pdb (#39) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
Position of Nup133_propeller_NRouter.pdb (#40) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
Position of hNup155_NRconnector_CTD.pdb (#43) relative to
ref_s114_8_symmetrized.em scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
Position of hNup93_NR_outer.pdb (#51) relative to ref_s114_8_symmetrized.em
scaled gaussian10 (#27) coordinates:
Matrix rotation and translation
0.99401905 -0.10915621 -0.00332412 25.40496005
0.10637983 0.97471964 -0.19648143 112.03007427
0.02468725 0.19495266 0.98050191 -239.83738167
Axis 0.87426608 -0.06256326 0.48139866
Axis point -0.00000000 1023.33648273 406.59029089
Rotation angle (degrees) 12.93610944
Shift along axis -100.25566559
> fitmap sel inMap #22
Fit molecules Y_NRinner.pdb (#35), Y_NRouter.pdb (#36),
Nup133_propeller_NRinner.pdb (#39), Nup133_propeller_NRouter.pdb (#40),
hNup155_NRconnector_CTD.pdb (#43), hNup93_NR_outer.pdb (#51) to map
ref_s114_8_symmetrized.em scaled (#22) using 135371 atoms
average map value = 0.04593, steps = 84
shifted from previous position = 34.5
rotated from previous position = 16.1 degrees
atoms outside contour = 78828, contour level = 0.051481
Position of Y_NRinner.pdb (#35) relative to ref_s114_8_symmetrized.em scaled
(#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Y_NRouter.pdb (#36) relative to ref_s114_8_symmetrized.em scaled
(#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Nup133_propeller_NRinner.pdb (#39) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Nup133_propeller_NRouter.pdb (#40) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of hNup155_NRconnector_CTD.pdb (#43) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of hNup93_NR_outer.pdb (#51) relative to ref_s114_8_symmetrized.em
scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
> volume #27 level 0.03784
> fitmap sel inMap #22
Fit molecules Y_NRinner.pdb (#35), Y_NRouter.pdb (#36),
Nup133_propeller_NRinner.pdb (#39), Nup133_propeller_NRouter.pdb (#40),
hNup155_NRconnector_CTD.pdb (#43), hNup93_NR_outer.pdb (#51) to map
ref_s114_8_symmetrized.em scaled (#22) using 135371 atoms
average map value = 0.04593, steps = 84
shifted from previous position = 34.5
rotated from previous position = 16.1 degrees
atoms outside contour = 78828, contour level = 0.051481
Position of Y_NRinner.pdb (#35) relative to ref_s114_8_symmetrized.em scaled
(#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Y_NRouter.pdb (#36) relative to ref_s114_8_symmetrized.em scaled
(#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Nup133_propeller_NRinner.pdb (#39) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of Nup133_propeller_NRouter.pdb (#40) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of hNup155_NRconnector_CTD.pdb (#43) relative to
ref_s114_8_symmetrized.em scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Position of hNup93_NR_outer.pdb (#51) relative to ref_s114_8_symmetrized.em
scaled (#22) coordinates:
Matrix rotation and translation
0.99432359 -0.10622502 0.00607049 13.78029717
0.10561610 0.97849987 -0.17715316 98.01028917
0.01287812 0.17678871 0.98416457 -204.79668577
Axis 0.85793602 -0.01650132 0.51349147
Axis point 0.00000000 921.36960175 432.58513698
Rotation angle (degrees) 11.90415885
Shift along axis -94.95603801
Opened map 5 as #61, grid size 279,311,161, pixel 1.67, shown at level 0.099,
step 1, values float32
> fitmap sel inMap #22 resolution 5
Fit map map 5 in map ref_s114_8_symmetrized.em scaled using 517233 points
correlation = 0.7731, correlation about mean = 0.00546, overlap = 8436
steps = 88, shift = 34.5, angle = 16.1 degrees
Position of map 5 (#61) relative to ref_s114_8_symmetrized.em scaled (#22)
coordinates:
Matrix rotation and translation
0.99433066 -0.10612973 0.00655912 13.24617429
0.10561848 0.97864038 -0.17637387 97.76850483
0.01229949 0.17606671 0.98430139 -203.36458032
Axis 0.85710467 -0.01396009 0.51495310
Axis point 0.00000000 916.82309117 435.79587291
Rotation angle (degrees) 11.86459561
Shift along axis -94.73472126
Average map value = 0.04593 for 135371 atoms, 78850 outside contour
> volume #27 level 0.02329
> fitmap sel inMap #22 resolution 5
Fit map map 5 in map ref_s114_8_symmetrized.em scaled using 517233 points
correlation = 0.7731, correlation about mean = 0.00546, overlap = 8436
steps = 88, shift = 34.5, angle = 16.1 degrees
Position of map 5 (#61) relative to ref_s114_8_symmetrized.em scaled (#22)
coordinates:
Matrix rotation and translation
0.99433066 -0.10612973 0.00655912 13.24617429
0.10561848 0.97864038 -0.17637387 97.76850483
0.01229949 0.17606671 0.98430139 -203.36458032
Axis 0.85710467 -0.01396009 0.51495310
Axis point 0.00000000 916.82309117 435.79587291
Rotation angle (degrees) 11.86459561
Shift along axis -94.73472126
Average map value = 0.04593 for 135371 atoms, 78850 outside contour
Average map value = 0.04143 for 135371 atoms, 87409 outside contour
Correlation = 0.7636, Correlation about mean = 0.002241, Overlap = 7603
> fitmap sel inMap #22 resolution 5 metric cam
Fit map map 5 in map ref_s114_8_symmetrized.em scaled using 517233 points
correlation = 0.7515, correlation about mean = 0.009778, overlap = 7556
steps = 88, shift = 11.6, angle = 15.2 degrees
Position of map 5 (#61) relative to ref_s114_8_symmetrized.em scaled (#22)
coordinates:
Matrix rotation and translation
0.90021108 -0.39271725 0.18813075 354.51999680
0.36399997 0.91577240 0.16989685 -354.45717546
-0.23900637 -0.08446344 0.96733752 398.08312585
Axis -0.28093399 0.47176129 0.83577352
Axis point 1207.95311902 642.93278989 0.00000000
Rotation angle (degrees) 26.91734829
Shift along axis 65.89144332
Average map value = 0.04112 for 135371 atoms, 86650 outside contour
> select #33,34,37,38,41,45-50
182469 atoms, 186348 bonds, 4 pseudobonds, 22818 residues, 13 models selected
Opened map 5 as #62, grid size 300,291,181, pixel 1.67, shown at level 0.0978,
step 1, values float32
> fitmap sel inMap #22 resolution 5 metric cam
Fit map map 5 in map ref_s114_8_symmetrized.em scaled using 699485 points
correlation = 0.7102, correlation about mean = 0.01257, overlap = 1.126e+04
steps = 88, shift = 6.64, angle = 10.8 degrees
Position of map 5 (#62) relative to ref_s114_8_symmetrized.em scaled (#22)
coordinates:
Matrix rotation and translation
0.96842465 -0.24758374 0.02925719 171.88499938
0.24875664 0.96740146 -0.04748216 -125.75486552
-0.01654764 0.05326081 0.99844352 -43.94156834
Axis 0.19810691 0.09007332 0.97603302
Axis point 581.60515752 636.20993654 0.00000000
Rotation angle (degrees) 14.72998625
Shift along axis -20.16397247
Average map value = 0.04543 for 182469 atoms, 98736 outside contour
> volume #27 level 0.03564
> select #42,44,52-59,60
295428 atoms, 301444 bonds, 14 pseudobonds, 37714 residues, 17 models selected
> color (#56-60#!42,44,52-55 & sel) orange red
> color (#56-60#!42,44,52-55 & sel) hot pink
> volume #27 level 0.01888
> volume #27 level 0.04226
Opened map 5 as #63, grid size 406,391,198, pixel 1.67, shown at level 0.0945,
step 1, values float32
> fitmap sel inMap #22 resolution 5 metric cam
Fit map map 5 in map ref_s114_8_symmetrized.em scaled using 1147433 points
correlation = 0.6019, correlation about mean = 0.01254, overlap = 1.381e+04
steps = 72, shift = 7.07, angle = 3.85 degrees
Position of map 5 (#63) relative to ref_s114_8_symmetrized.em scaled (#22)
coordinates:
Matrix rotation and translation
0.94608647 -0.31689192 0.06708123 254.88742675
0.31749742 0.94825758 0.00171668 -222.53407273
-0.06415429 0.01967399 0.99774604 54.49434570
Axis 0.02770890 0.20250199 0.97888976
Axis point 818.84623269 663.68179793 0.00000000
Rotation angle (degrees) 18.90712889
Shift along axis 15.34301389
Average map value = 0.03446 for 295412 atoms, 192237 outside contour
> select clear
> cd ../s114_fits
Current working directory is: /Users/kosinski/Desktop/FluNPC_paper/s114_fits
> save /Users/kosinski/Desktop/FluNPC_paper/s114_fits/[NAME] models #33-60
> selectedOnly false relModel #5
Cannot determine format for
'/Users/kosinski/Desktop/FluNPC_paper/s114_fits/[NAME]'
> save [NAME] models #33-60 selectedOnly false relModel #5 format pdb
> open s114_unit_fit.cif
Summary of feedback from opening s114_unit_fit.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for s114_unit_fit.cif #64
---
Chain | Description
00 10 20 30 40 50 60 70 | No description available
01 02 03 04 05 | No description available
41 42 | No description available
A0 | No description available
A1 A2 | No description available
A3 A4 | No description available
A5 A6 A7 A8 | No description available
B0 B1 | No description available
C0 C1 C2 C3 C4 | No description available
D0 D2 | No description available
D1 D3 | No description available
D4 D5 D6 D7 | No description available
E0 E1 | No description available
F0 F1 F2 F3 | No description available
F4 F5 F6 F7 | No description available
H0 H1 H2 H3 | No description available
I0 I1 I2 I3 | No description available
J0 J1 J2 J3 J4 | No description available
K0 K1 K2 K3 | No description available
K4 K5 K6 K7 | No description available
L0 L1 L2 L3 | No description available
M0 M1 M2 M3 | No description available
N0 N1 N2 N3 | No description available
O0 O1 O2 O3 | No description available
P0 P1 P2 P3 | No description available
Q0 Q1 Q2 Q3 | No description available
R0 R1 R2 R3 | No description available
S0 S1 S2 S3 | No description available
T0 T1 | No description available
U0 | No description available
U1 U2 U3 U4 | No description available
V0 | No description available
W0 | No description available
> close #64
> close #61-63
> show #!28 models
> hide #!27 models
> select #33,34,37,38,41,45-50
182469 atoms, 186348 bonds, 4 pseudobonds, 22818 residues, 13 models selected
Opened map 5 as #61, grid size 300,291,181, pixel 1.67, shown at level 0.0978,
step 1, values float32
> fitmap sel inMap #28 resolution 5 metric cam
Fit map map 5 in map ref_s127_8_symmetrized.em scaled gaussian10 using 699485
points
correlation = 0.7643, correlation about mean = 0.014, overlap = 1.283e+04
steps = 72, shift = 21.9, angle = 3.9 degrees
Position of map 5 (#61) relative to ref_s127_8_symmetrized.em scaled
gaussian10 (#28) coordinates:
Matrix rotation and translation
0.94757032 0.31743914 0.03664523 -271.47506028
-0.31624790 0.94803656 -0.03484183 367.69147701
-0.04580118 0.02142610 0.99872077 9.48515239
Axis 0.08771301 0.12852122 -0.98782019
Axis point 988.95044591 1022.43201598 0.00000000
Rotation angle (degrees) 18.70829966
Shift along axis 14.07463752
Average map value = 0.05178 for 182469 atoms, 52300 outside contour
> volume #28 level 0.02258
> volume #28 level 0.0297
> select #35,36,39,40,43,51
135371 atoms, 138333 bonds, 4 pseudobonds, 16966 residues, 8 models selected
Opened map 5 as #62, grid size 279,311,161, pixel 1.67, shown at level 0.099,
step 1, values float32
> fitmap sel inMap #28 resolution 5 metric cam
Fit map map 5 in map ref_s127_8_symmetrized.em scaled gaussian10 using 517233
points
correlation = 0.8117, correlation about mean = 0.01121, overlap = 9933
steps = 80, shift = 48.4, angle = 5.96 degrees
Position of map 5 (#62) relative to ref_s127_8_symmetrized.em scaled
gaussian10 (#28) coordinates:
Matrix rotation and translation
0.95315639 0.25655904 0.16021971 -266.02426514
-0.26717242 0.96243875 0.04827584 226.94920270
-0.14181605 -0.08882071 0.98590014 316.16898661
Axis -0.22114773 0.48720788 -0.84482079
Axis point 848.23046240 1275.98494096 0.00000000
Rotation angle (degrees) 18.05718192
Shift along axis -97.70403190
Average map value = 0.05407 for 135371 atoms, 22393 outside contour
> volume #28 level 0.05193
> fitmap sel inMap #28 resolution 5 metric cam
Fit map map 5 in map ref_s127_8_symmetrized.em scaled gaussian10 using 517233
points
correlation = 0.8117, correlation about mean = 0.01121, overlap = 9933
steps = 80, shift = 48.4, angle = 5.96 degrees
Position of map 5 (#62) relative to ref_s127_8_symmetrized.em scaled
gaussian10 (#28) coordinates:
Matrix rotation and translation
0.95315639 0.25655904 0.16021971 -266.02426514
-0.26717242 0.96243875 0.04827584 226.94920270
-0.14181605 -0.08882071 0.98590014 316.16898661
Axis -0.22114773 0.48720788 -0.84482079
Axis point 848.23046240 1275.98494096 0.00000000
Rotation angle (degrees) 18.05718192
Shift along axis -97.70403190
Average map value = 0.05407 for 135371 atoms, 61352 outside contour
> select #42,44,52-59,60
295428 atoms, 301444 bonds, 14 pseudobonds, 37714 residues, 17 models selected
Opened map 5 as #63, grid size 406,391,198, pixel 1.67, shown at level 0.0945,
step 1, values float32
> fitmap sel inMap #28 resolution 5 metric cam
Fit map map 5 in map ref_s127_8_symmetrized.em scaled gaussian10 using 1147433
points
correlation = 0.6655, correlation about mean = 0.01359, overlap = 1.44e+04
steps = 60, shift = 34.3, angle = 1.56 degrees
Position of map 5 (#63) relative to ref_s127_8_symmetrized.em scaled
gaussian10 (#28) coordinates:
Matrix rotation and translation
0.95164235 0.29602862 0.08212118 -253.75691069
-0.29420955 0.95514624 -0.03371053 344.60483176
-0.08841701 0.00791954 0.99605206 104.19916636
Axis 0.06760432 0.27694208 -0.95850547
Axis point 1035.88666133 1021.48921398 0.00000000
Rotation angle (degrees) 17.93242176
Shift along axis -21.59495385
Average map value = 0.03694 for 287357 atoms, 196532 outside contour
> select #42,44,52-59
183060 atoms, 186644 bonds, 14 pseudobonds, 23066 residues, 16 models selected
Opened map 5 as #64, grid size 235,211,198, pixel 1.67, shown at level 0.0961,
step 1, values float32
> fitmap sel inMap #28 resolution 5 metric cam
Fit map map 5 in map ref_s127_8_symmetrized.em scaled gaussian10 using 705734
points
correlation = 0.7947, correlation about mean = 0.006114, overlap = 1.29e+04
steps = 56, shift = 29, angle = 5.78 degrees
Position of map 5 (#64) relative to ref_s127_8_symmetrized.em scaled
gaussian10 (#28) coordinates:
Matrix rotation and translation
0.96050351 0.24998890 0.12222339 -248.27092262
-0.25465330 0.96673688 0.02390625 228.98033169
-0.11218156 -0.05408663 0.99221466 207.33896756
Axis -0.13881071 0.41719084 -0.89815555
Axis point 840.16624667 1157.09167349 0.00000000
Rotation angle (degrees) 16.31586813
Shift along axis -56.23148345
Average map value = 0.05199 for 183060 atoms, 89680 outside contour
> volume #28 level 0.01991
> volume #28 level 0.0417
> cd s127_fits
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd ../s127_fits
Current working directory is: /Users/kosinski/Desktop/FluNPC_paper/s127_fits
> cd ..
Current working directory is: /Users/kosinski/Desktop/FluNPC_paper
> save s127_fits/[NAME] models #33-60 selectedOnly false relModel #5 format
> pdb
> open s127_fits/s127_unit_fit.cif
Summary of feedback from opening s127_fits/s127_unit_fit.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for s127_unit_fit.cif #65
---
Chain | Description
00 10 20 30 40 50 60 70 | No description available
01 02 03 04 05 | No description available
41 42 | No description available
A0 | No description available
A1 A2 | No description available
A3 A4 | No description available
A5 A6 A7 A8 | No description available
B0 B1 | No description available
C0 C1 C2 C3 C4 | No description available
D0 D2 | No description available
D1 D3 | No description available
D4 D5 D6 D7 | No description available
E0 E1 | No description available
F0 F1 F2 F3 | No description available
F4 F5 F6 F7 | No description available
H0 H1 H2 H3 | No description available
I0 I1 I2 I3 | No description available
J0 J1 J2 J3 J4 | No description available
K0 K1 K2 K3 | No description available
K4 K5 K6 K7 | No description available
L0 L1 L2 L3 | No description available
M0 M1 M2 M3 | No description available
N0 N1 N2 N3 | No description available
O0 O1 O2 O3 | No description available
P0 P1 P2 P3 | No description available
Q0 Q1 Q2 Q3 | No description available
R0 R1 R2 R3 | No description available
S0 S1 S2 S3 | No description available
T0 T1 | No description available
U0 | No description available
U1 U2 U3 U4 | No description available
V0 | No description available
W0 | No description available
> close #65
> hide #!28 models
> show #!29 models
> select #33,34,37,38,41,45-50
182469 atoms, 186348 bonds, 4 pseudobonds, 22818 residues, 13 models selected
> fitmap sel inMap #29 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian15 using 699485
points
correlation = 0.6454, correlation about mean = 0.01026, overlap = 6685
steps = 80, shift = 46.7, angle = 17.2 degrees
Position of map 5 (#61) relative to ref_s140_8_symmetrized.em scaled
gaussian15 (#29) coordinates:
Matrix rotation and translation
0.96537112 0.26039664 -0.01588059 -197.40121007
-0.25217799 0.91584624 -0.31246109 716.40935231
-0.06681963 0.30564564 0.94979781 -267.09226544
Axis 0.76821481 0.06330966 -0.63705408
Axis point -0.00000000 1067.97880210 1992.22209732
Rotation angle (degrees) 23.72208628
Shift along axis 63.86131610
Average map value = 0.02701 for 182469 atoms, 102303 outside contour
> volume #29 level 0.01509
> volume #29 level 0.01072
> fitmap sel inMap #29 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian15 using 699485
points
correlation = 0.6454, correlation about mean = 0.01026, overlap = 6685
steps = 80, shift = 46.7, angle = 17.2 degrees
Position of map 5 (#61) relative to ref_s140_8_symmetrized.em scaled
gaussian15 (#29) coordinates:
Matrix rotation and translation
0.96537112 0.26039664 -0.01588059 -197.40121007
-0.25217799 0.91584624 -0.31246109 716.40935231
-0.06681963 0.30564564 0.94979781 -267.09226544
Axis 0.76821481 0.06330966 -0.63705408
Axis point 0.00000000 1067.97880210 1992.22209732
Rotation angle (degrees) 23.72208628
Shift along axis 63.86131610
Average map value = 0.02701 for 182469 atoms, 54508 outside contour
> fitmap sel inMap #24 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled using 699485 points
correlation = 0.5764, correlation about mean = 0.007842, overlap = 9547
steps = 84, shift = 17, angle = 7.48 degrees
Position of map 5 (#61) relative to ref_s140_8_symmetrized.em scaled (#24)
coordinates:
Matrix rotation and translation
0.94826186 0.30065651 0.10200548 -351.66313708
-0.30289503 0.95299933 0.00684622 336.77051013
-0.09515279 -0.03738897 0.99476028 155.43945501
Axis -0.06950010 0.30976511 -0.94826964
Axis point 924.06017913 1332.97513734 0.00000000
Rotation angle (degrees) 18.55642133
Shift along axis -18.63814008
Average map value = 0.03856 for 182469 atoms, 127872 outside contour
> volume #29 level 0.02821
> volume #29 level 0.01692
> select #35,36,39,40,43,51
135371 atoms, 138333 bonds, 4 pseudobonds, 16966 residues, 8 models selected
> fitmap sel inMap #24 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled using 517233 points
correlation = 0.7022, correlation about mean = 0.008504, overlap = 8796
steps = 112, shift = 25.7, angle = 6.72 degrees
Position of map 5 (#62) relative to ref_s140_8_symmetrized.em scaled (#24)
coordinates:
Matrix rotation and translation
0.95093702 0.18942199 0.24461827 -265.14887053
-0.21837667 0.97103186 0.09699874 201.75367205
-0.21915844 -0.14565862 0.96475548 504.26581864
Axis -0.36570705 0.69895435 -0.61459025
Axis point 1847.97862242 0.00000000 1562.11871497
Rotation angle (degrees) 19.37591866
Shift along axis -71.93343665
Average map value = 0.04787 for 135371 atoms, 91671 outside contour
> volume #29 level 0.04024
> fitmap sel inMap #29 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian15 using 517233
points
correlation = 0.8132, correlation about mean = 0.009664, overlap = 7871
steps = 72, shift = 31.6, angle = 12.3 degrees
Position of map 5 (#62) relative to ref_s140_8_symmetrized.em scaled
gaussian15 (#29) coordinates:
Matrix rotation and translation
0.93446871 0.11487327 0.33700499 -214.87882254
-0.17750942 0.97081142 0.16129350 119.48809730
-0.30863998 -0.21054529 0.92758398 719.34252275
Axis -0.46457745 0.80667241 -0.36530456
Axis point 1989.97702753 0.00000000 1116.32913075
Rotation angle (degrees) 23.59007627
Shift along axis -66.56349771
Average map value = 0.04286 for 135371 atoms, 59626 outside contour
> fitmap sel inMap #24 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled using 517233 points
correlation = 0.7022, correlation about mean = 0.008504, overlap = 8796
steps = 112, shift = 25.7, angle = 6.72 degrees
Position of map 5 (#62) relative to ref_s140_8_symmetrized.em scaled (#24)
coordinates:
Matrix rotation and translation
0.95093702 0.18942199 0.24461827 -265.14887053
-0.21837667 0.97103186 0.09699874 201.75367205
-0.21915844 -0.14565862 0.96475548 504.26581864
Axis -0.36570705 0.69895435 -0.61459025
Axis point 1847.97862242 0.00000000 1562.11871497
Rotation angle (degrees) 19.37591866
Shift along axis -71.93343665
Average map value = 0.04787 for 135371 atoms, 91671 outside contour
> volume #29 level 0.05664
> volume #29 level 0.03842
> select #42,44,52-59
183060 atoms, 186644 bonds, 14 pseudobonds, 23066 residues, 16 models selected
> volume #29 level 0.02821
> volume #29 level 0.0191
> volume #29 level 0.04607
> volume #29 level 0.03186
> show #!30 models
> hide #!29 models
> volume #30 level 0.02765
> fitmap sel inMap #30 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian30 using 705734
points
correlation = 0.7739, correlation about mean = 0.003967, overlap = 6266
steps = 180, shift = 76, angle = 71.1 degrees
Position of map 5 (#64) relative to ref_s140_8_symmetrized.em scaled
gaussian30 (#30) coordinates:
Matrix rotation and translation
0.28354390 0.84824112 -0.44731404 376.54979096
-0.93641570 0.34545827 0.06151596 1727.35374663
0.20670870 0.40142942 0.89225889 -614.54698570
Axis 0.17604095 -0.33871793 -0.92427255
Axis point 1361.67788369 716.41876548 0.00000000
Rotation angle (degrees) 74.89252106
Shift along axis 49.21139834
Average map value = 0.02527 for 183060 atoms, 105203 outside contour
> volume #30 level 0.0234
> fitmap sel inMap #30 resolution 5 metric cam
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian30 using 705734
points
correlation = 0.7739, correlation about mean = 0.003967, overlap = 6266
steps = 180, shift = 76, angle = 71.1 degrees
Position of map 5 (#64) relative to ref_s140_8_symmetrized.em scaled
gaussian30 (#30) coordinates:
Matrix rotation and translation
0.28354390 0.84824112 -0.44731404 376.54979096
-0.93641570 0.34545827 0.06151596 1727.35374663
0.20670870 0.40142942 0.89225889 -614.54698570
Axis 0.17604095 -0.33871793 -0.92427255
Axis point 1361.67788369 716.41876548 0.00000000
Rotation angle (degrees) 74.89252106
Shift along axis 49.21139834
Average map value = 0.02527 for 183060 atoms, 83629 outside contour
> fitmap sel inMap #30 resolution 5
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian30 using 705734
points
correlation = 0.8526, correlation about mean = 0.0007888, overlap = 9523
steps = 88, shift = 106, angle = 36 degrees
Position of map 5 (#64) relative to ref_s140_8_symmetrized.em scaled
gaussian30 (#30) coordinates:
Matrix rotation and translation
0.82662429 0.50727871 -0.24364030 -36.97723621
-0.41377261 0.84131241 0.34782993 422.68841509
0.38142433 -0.18671299 0.90534730 -158.02044533
Axis -0.43289180 -0.50619947 -0.74589998
Axis point 768.64884573 403.94482171 0.00000000
Rotation angle (degrees) 38.12720074
Shift along axis -80.09006414
Average map value = 0.03839 for 183060 atoms, 14970 outside contour
> show #!29 models
> hide #!30 models
> fitmap sel inMap #29 resolution 5
Fit map map 5 in map ref_s140_8_symmetrized.em scaled gaussian15 using 705734
points
correlation = 0.8061, correlation about mean = 0.0001589, overlap = 1.038e+04
steps = 96, shift = 98.3, angle = 33.1 degrees
Position of map 5 (#64) relative to ref_s140_8_symmetrized.em scaled
gaussian15 (#29) coordinates:
Matrix rotation and translation
0.84211124 0.50515028 -0.18886995 -95.04569615
-0.43602447 0.84382563 0.31279541 461.40672991
0.31738200 -0.18105661 0.93085293 -104.78444961
Axis -0.41948523 -0.43001790 -0.79944778
Axis point 804.74480270 501.77564385 0.00000000
Rotation angle (degrees) 36.06059638
Shift along axis -74.77319354
Average map value = 0.04184 for 183060 atoms, 53556 outside contour
> show #!30 models
> hide #!29 models
> volume #30 level 0.02744
> hide #!30 models
> show #!29 models
> show #!30 models
> hide #!29 models
> save s140_fits/[NAME] models #33-60 selectedOnly false relModel #5 format
> pdb
Cannot save 's140_fits/[NAME]': Unable to open file 's140_fits/Y_CRinner.pdb'
for writing
> cd ..
Current working directory is: /Users/kosinski/Desktop
> save s140_fits/[NAME] models #33-60 selectedOnly false relModel #5 format
> pdb
Cannot save 's140_fits/[NAME]': Unable to open file 's140_fits/Y_CRinner.pdb'
for writing
> cd /Users/kosinski/Desktop/FluNPC_paper
Current working directory is: /Users/kosinski/Desktop/FluNPC_paper
> save s140_fits/[NAME] models #33-60 selectedOnly false relModel #5 format
> pdb
> open s140_fits/s140_unit_fit.cif
Summary of feedback from opening s140_fits/s140_unit_fit.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for s140_unit_fit.cif #65
---
Chain | Description
00 10 20 30 40 50 60 70 | No description available
01 02 03 04 05 | No description available
41 42 | No description available
A0 | No description available
A1 A2 | No description available
A3 A4 | No description available
A5 A6 A7 A8 | No description available
B0 B1 | No description available
C0 C1 C2 C3 C4 | No description available
D0 D2 | No description available
D1 D3 | No description available
D4 D5 D6 D7 | No description available
E0 E1 | No description available
F0 F1 F2 F3 | No description available
F4 F5 F6 F7 | No description available
H0 H1 H2 H3 | No description available
I0 I1 I2 I3 | No description available
J0 J1 J2 J3 J4 | No description available
K0 K1 K2 K3 | No description available
K4 K5 K6 K7 | No description available
L0 L1 L2 L3 | No description available
M0 M1 M2 M3 | No description available
N0 N1 N2 N3 | No description available
O0 O1 O2 O3 | No description available
P0 P1 P2 P3 | No description available
Q0 Q1 Q2 Q3 | No description available
R0 R1 R2 R3 | No description available
S0 S1 S2 S3 | No description available
T0 T1 | No description available
U0 | No description available
U1 U2 U3 U4 | No description available
V0 | No description available
W0 | No description available
> close #65
> hide #!30 models
> show #!31 models
> select clear
> ui tool show "Side View"
> view
> volume zone #31 nearAtoms 33-60 nearAtoms 20
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #31 nearAtoms 33-60 range 20
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #31 nearAtoms #33-60 range 20
> volume #31 level 0.01321
> volume zone #31 nearAtoms #33-60 range 40
> volume zone #31 nearAtoms #33-60 range 40 newMap true
Opened ref_s162_8_symmetrized.em scaled gaussian30 zone as #65, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #65 color #b2b2ff62
> volume #65 color #b2b2ff61
> close #65
> volume zone #31 nearAtoms #33-60 range 60 newMap true
Opened ref_s162_8_symmetrized.em scaled gaussian30 zone as #65, grid size
128,128,128, pixel 13.3, shown at step 1, values float32
> volume #65 color #ffb2ff62
> volume #65 color #ffb2ff61
> select #33,34,37,38,41,45-50
182469 atoms, 186348 bonds, 4 pseudobonds, 22818 residues, 13 models selected
> fitmap sel inMap #31 resolution 5
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 using 699485
points
correlation = 0.6672, correlation about mean = 0.003878, overlap = 4637
steps = 440, shift = 15.5, angle = 34.2 degrees
Position of map 5 (#61) relative to ref_s162_8_symmetrized.em scaled
gaussian30 (#31) coordinates:
Matrix rotation and translation
0.71627592 -0.67424908 0.17982488 790.61443806
0.54608762 0.70203488 0.45709445 -706.08014788
-0.43443885 -0.22920560 0.87104975 908.31094446
Axis -0.44888350 0.40176720 0.79817713
Axis point 1649.11455071 536.17154007 0.00000000
Rotation angle (degrees) 49.85829224
Shift along axis 86.41940099
Average map value = 0.01876 for 182469 atoms, 64754 outside contour
> show #!31 models
> volume unzone #31
> volume #65 level 0.001727
> volume #31 level 0.001472
> fitmap sel inMap #65 resolution 5
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 zone using
699485 points
correlation = 0.6642, correlation about mean = 0.004073, overlap = 4582
steps = 144, shift = 26.2, angle = 20.4 degrees
Position of map 5 (#61) relative to ref_s162_8_symmetrized.em scaled
gaussian30 zone (#65) coordinates:
Matrix rotation and translation
0.85060397 -0.46504078 0.24537717 331.12306823
0.38492638 0.86864503 0.31190943 -557.24031715
-0.35819627 -0.17085925 0.91787938 698.34484741
Axis -0.42022634 0.52538093 0.73985451
Axis point 1651.42267052 258.09982776 0.00000000
Rotation angle (degrees) 35.05867901
Shift along axis 84.76351521
Average map value = 0.01854 for 182469 atoms, 32229 outside contour
> volume #65 level 0.01584
> volume #65 level 0.001727
> show #!31 models
> volume #31 level 0.01224
> select #42,44,52-59
183060 atoms, 186644 bonds, 14 pseudobonds, 23066 residues, 16 models selected
> select #35,36,39,40,43,51
135371 atoms, 138333 bonds, 4 pseudobonds, 16966 residues, 8 models selected
> volume #65 level 0.01397
> fitmap sel inMap #65 resolution 5
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 zone using
517233 points
correlation = 0.8408, correlation about mean = 0.007212, overlap = 6166
steps = 88, shift = 78.7, angle = 20.9 degrees
Position of map 5 (#62) relative to ref_s162_8_symmetrized.em scaled
gaussian30 zone (#65) coordinates:
Matrix rotation and translation
0.97656043 -0.21216629 0.03626551 127.97144758
0.21468675 0.97221958 -0.09326676 -61.50392883
-0.01546998 0.09886636 0.99498046 -22.41543771
Axis 0.40796805 0.10985315 0.90636326
Axis point 365.90814853 514.40928313 0.00000000
Rotation angle (degrees) 13.61966493
Shift along axis 25.13533229
Average map value = 0.0336 for 135371 atoms, 4454 outside contour
> volume #65 level 0.02723
> fitmap sel inMap #65 resolution 5
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 zone using
517233 points
correlation = 0.8408, correlation about mean = 0.007212, overlap = 6166
steps = 88, shift = 78.7, angle = 20.9 degrees
Position of map 5 (#62) relative to ref_s162_8_symmetrized.em scaled
gaussian30 zone (#65) coordinates:
Matrix rotation and translation
0.97656043 -0.21216629 0.03626551 127.97144758
0.21468675 0.97221958 -0.09326676 -61.50392883
-0.01546998 0.09886636 0.99498046 -22.41543771
Axis 0.40796805 0.10985315 0.90636326
Axis point 365.90814853 514.40928313 0.00000000
Rotation angle (degrees) 13.61966493
Shift along axis 25.13533229
Average map value = 0.0336 for 135371 atoms, 42029 outside contour
> fitmap sel inMap #65 resolution 5
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 zone using
517233 points
correlation = 0.8408, correlation about mean = 0.007212, overlap = 6166
steps = 88, shift = 78.7, angle = 20.9 degrees
Position of map 5 (#62) relative to ref_s162_8_symmetrized.em scaled
gaussian30 zone (#65) coordinates:
Matrix rotation and translation
0.97656043 -0.21216629 0.03626551 127.97144758
0.21468675 0.97221958 -0.09326676 -61.50392883
-0.01546998 0.09886636 0.99498046 -22.41543771
Axis 0.40796805 0.10985315 0.90636326
Axis point 365.90814853 514.40928313 0.00000000
Rotation angle (degrees) 13.61966493
Shift along axis 25.13533229
Average map value = 0.0336 for 135371 atoms, 42029 outside contour
> fitmap sel inMap #65 resolution 5 metric cam
Fit map map 5 in map ref_s162_8_symmetrized.em scaled gaussian30 zone using
517233 points
correlation = 0.8053, correlation about mean = 0.00637, overlap = 5243
steps = 84, shift = 37.4, angle = 31.9 degrees
Position of map 5 (#62) relative to ref_s162_8_symmetrized.em scaled
gaussian30 zone (#65) coordinates:
Matrix rotation and translation
0.79902921 -0.45534728 0.39269730 363.23846334
0.13675962 0.77359578 0.61874581 -148.32875041
-0.58553320 -0.44069084 0.68039875 1510.51664433
Axis -0.67963851 0.62754400 0.37984211
Axis point 0.00000000 2276.22663450 1309.74376032
Rotation angle (degrees) 51.20675903
Shift along axis 233.80415930
Average map value = 0.02857 for 135371 atoms, 59181 outside contour
> volume #65 level 0.01618
> volume #65 level 0.01176
> close #61-65
> select clear
> save /Users/kosinski/Desktop/FluNPC_paper/all_maps.cxs includeMaps true
——— End of log from Sat Dec 7 12:59:06 2024 ———
opened ChimeraX session
> close #33-100
> hide target m
> open ../s127_fits/s127_CR.cif
Chain information for s127_CR.cif
---
Chain | Description
33.6/0 33.7/0 33.8/0 33.9/0 33.10/0 | No description available
33.1/A 33.2/A | No description available
33.11/A | No description available
33.1/C 33.2/C | No description available
33.5/D | No description available
33.2/J | No description available
33.1/K 33.2/K | No description available
33.3/K 33.4/K | No description available
33.1/L 33.2/L | No description available
33.1/M 33.2/M | No description available
33.1/N 33.2/N | No description available
33.1/O 33.2/O | No description available
33.1/P 33.2/P | No description available
33.1/Q 33.2/Q | No description available
33.1/R 33.2/R | No description available
33.1/S 33.2/S | No description available
33.2/U | No description available
33.2/V | No description available
33.2/W | No description available
> open ../s127_fits/s127_Gp210.cif
Chain information for s127_Gp210.cif #34
---
Chain | Description
10 11 12 13 14 15 16 17 | No description available
> open ../s127_fits/s127_IR.cif
Summary of feedback from opening ../s127_fits/s127_IR.cif
---
warnings | Unknown polymer entity '1' on line 106
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 6406
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for s127_IR.cif
---
Chain | Description
35.3/4 35.5/4 | No description available
35.3/A 35.4/A 35.5/A 35.6/A | No description available
35.4/B 35.6/B | No description available
35.3/C 35.5/C | No description available
35.1/D 35.2/D | No description available
35.3/D 35.4/D 35.5/D 35.6/D | No description available
35.3/E 35.5/E | No description available
35.3/F 35.4/F 35.5/F 35.6/F | No description available
35.7/F 35.8/F 35.9/F 35.10/F | No description available
35.3/H 35.4/H 35.5/H 35.6/H | No description available
35.3/I 35.4/I 35.5/I 35.6/I | No description available
35.3/J 35.4/J 35.5/J 35.6/J | No description available
35.3/U 35.4/U 35.5/U 35.6/U | No description available
> open ../s127_fits/s127_NR.cif
Chain information for s127_NR.cif
---
Chain | Description
36.2/A | No description available
36.6/A | No description available
36.2/C | No description available
36.5/D | No description available
36.1/K 36.2/K | No description available
36.3/K 36.4/K | No description available
36.1/L 36.2/L | No description available
36.1/M 36.2/M | No description available
36.1/N 36.2/N | No description available
36.1/O 36.2/O | No description available
36.1/P 36.2/P | No description available
36.1/Q 36.2/Q | No description available
36.1/R 36.2/R | No description available
36.1/S 36.2/S | No description available
36.1/T 36.2/T | No description available
> color #33,36,37,40,41,44 royal blue
> color #35,39,43 deep pink
> color #34,38,42 light slate gray
> hide atoms
> show cartoons
> show #23 models
> surface dust #23 size 400
> color #23 #929292
> transparency #23 30
> volume #23 level 0.025
> volume erase #23 center 839.61,848.11,851.74 radius 312.09
> set bgColor white
> lighting soft
> lighting ambientIntensity 1.4
> material ambientReflectivity 1
> lighting shadows false
> lighting depthCue false
> graphics silhouettes true color black
> graphics silhouettes true width 3
> ribbon style width 3 thick 1
> measure symmetry #28
Symmetry ref_s127_8_symmetrized.em scaled gaussian10: C8, center 64 64 64
> sym #33-36 symmetry #28
Made 8 copies for s127_CR.cif, s127_CR.cif, s127_CR.cif, s127_CR.cif,
s127_CR.cif, s127_CR.cif, s127_CR.cif, s127_CR.cif, s127_CR.cif, s127_CR.cif,
s127_CR.cif, s127_Gp210.cif, s127_IR.cif, s127_IR.cif, s127_IR.cif,
s127_IR.cif, s127_IR.cif, s127_IR.cif, s127_IR.cif, s127_IR.cif, s127_IR.cif,
s127_IR.cif, s127_NR.cif, s127_NR.cif, s127_NR.cif, s127_NR.cif, s127_NR.cif,
s127_NR.cif symmetry #28
> hide #!37 models
> volume #23 level 0.025
> volume #23 level 0.05109
> surface dust #23 size 400
> hide #!36 models
> show #!36 models
> show #!37 models
> hide #!37.2-8 target m
> volume #23 level 0.04385
> volume #23 level 0.0337
> volume #23 level 0.025
> ui tool show "Side View"
> show #!37.2-8 target m
> hide #!37.2-8 target m
> show #!37.2-8 target m
> view name CR_zoom
> close #34,36#35.7-10#33,35,37#35.1-6
> save ../fitting1.cxs includeMaps true
——— End of log from Sat Feb 15 22:04:14 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: Z17G002M6D/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 67 days, 12 hours, 40 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2718Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash showing dock widget |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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