![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 months ago
Closed 2 months ago
#18766 closed defect (duplicate)
Crash moving windows between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| 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-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85fa73a00 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.segment._segment (total: 60)
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{
"uptime" : 240000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 27370,
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"build" : "22H625",
"releaseType" : "User"
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"captureTime" : "2025-09-11 21:14:38.9517 +0100",
"incident" : "EF1DA1E7-9D29-49B2-AA68-628D29D49574",
"pid" : 2306,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-11 16:49:59.5725 +0100",
"procStartAbsTime" : 233658972533325,
"procExitAbsTime" : 245772275595504,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"67FBC5BD-9817-5885-9FE5-8E2771D6B9F4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "F46F41C5-FF6C-941F-A528-C0FEEB51179E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 8833,
"bridgeVersion" : {"build":"22P56054b","train":"9.6"},
"sleepWakeUUID" : "9B0EFE93-6438-4AAE-80C2-E921C7416C12",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487523816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff35000-7ffffff36000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2306},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487523816\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff35000-7ffffff36000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
Opened cryosparc_P13_J593_map_sharp.mrc as #6, grid size 320,320,320, pixel
0.931, shown at level 0.45, step 1, values float32
Opened cryosparc_P13_J593_map_sharp.mrc z flip as #10, grid size 320,320,320,
pixel 0.931, shown at level 0.438, step 1, values float32
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
Opened fold_puscd1_fj_model_0.cif map 6 as #2, grid size 73,87,62, pixel 2,
shown at level 0.105, step 1, values float32
Opened fold_puscd1_fj_model_0.cif map 7 as #1, grid size 65,78,56, pixel 2.33,
shown at step 1, values float32
Log from Tue Sep 9 22:50:05 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
> format session
Opened cryosparc_P13_J593_map_sharp.mrc as #6, grid size 320,320,320, pixel
0.931, shown at level 0.45, step 1, values float32
Opened cryosparc_P13_J593_map_sharp.mrc z flip as #10, grid size 320,320,320,
pixel 0.931, shown at level 0.438, step 1, values float32
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
Opened fold_puscd1_fj_model_0.cif map 6 as #2, grid size 73,87,62, pixel 2,
shown at level 0.105, step 1, values float32
Opened fold_puscd1_fj_model_0.cif map 7 as #1, grid size 65,78,56, pixel 2.33,
shown at step 1, values float32
Log from Tue Sep 9 17:01:25 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
Opened cryosparc_P13_J593_map_sharp.mrc as #6, grid size 320,320,320, pixel
0.931, shown at level 0.45, step 1, values float32
Opened cryosparc_P13_J593_map_sharp.mrc z flip as #10, grid size 320,320,320,
pixel 0.931, shown at level 0.438, step 1, values float32
Opened pred.rank_0.cif map 8 as #1, grid size 59,60,59, pixel 2.67, shown at
level 0.0985, step 1, values float32
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
Opened pred.rank_0.cif map 8 as #5, grid size 56,61,53, pixel 2.67, shown at
level 0.1, step 1, values float32
Opened fold_puscd1_fj_model_0.cif map 6 as #2, grid size 73,87,62, pixel 2,
shown at level 0.105, step 1, values float32
Log from Mon Sep 8 23:51:23 2025 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/bo1il/Downloads/cryosparc_P13_J590_map.mrc
Opened cryosparc_P13_J590_map.mrc as #1, grid size 320,320,320, pixel 0.931,
shown at level 0.312, step 2, values float32
> ui tool show Registration
> volume #1 style mesh
> volume #1 style surface
> volume #1 step 1
> volume #1 step 4
> volume #1 step 8
> volume #1 step 2
> volume #1 step 1
> volume #1 level 0.3522
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
i.lidbury@sheffield.ac.uk is subscribed to the ChimeraX announcements list
> volume #1 level 0.3217
> volume #1 style image
> volume #1 level -0.04093,0 level 0.312,0.8 level 0.6538,1
> volume #1 style surface
> volume #1 level 0.3329
> color bfactor
No atoms specified
> open /Users/bo1il/Downloads/cryosparc_P13_J588_002_volume_map_sharp.mrc
Opened cryosparc_P13_J588_002_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 0.931, shown at level 0.356, step 2, values float32
> volume #2 level 0.3563
> volume #1 level 0.2333
> volume #2 level 0.3605
> volume #1 level 0.4438
> volume #1 level 0.3153
> volume #1 level 0.2735
> hide #!1 models
> volume #2 level 0.423
> hide #!1 models
> hide #!2 models
> show #!2 models
> volume #2 style mesh
> volume #2 style surface
> volume #2 step 1
> volume #2 step 4
> volume #2 step 8
> volume #2 step 1
> volume #1 step 2
> volume #2 step 2
> volume #1 level 0.2735
> volume #1 level 0.3005
> hide #!2 models
> open /Users/bo1il/Downloads/cryosparc_P13_J590_map.mrc
Opened cryosparc_P13_J590_map.mrc as #3, grid size 320,320,320, pixel 0.931,
shown at level 0.312, step 2, values float32
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/bo1il/Downloads/cryosparc_P13_J588_002_volume_map_sharp.mrc
Opened cryosparc_P13_J588_002_volume_map_sharp.mrc as #4, grid size
320,320,320, pixel 0.931, shown at level 0.356, step 2, values float32
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #4 level 0.146
> volume #4 level 0.3992
> volume #4 level 0.3863
> open /Users/bo1il/Downloads/cryosparc_P13_J588_002_volume_map_sharp.mrc
Opened cryosparc_P13_J588_002_volume_map_sharp.mrc as #5, grid size
320,320,320, pixel 0.931, shown at level 0.356, step 2, values float32
> hide #!4 models
> volume #4 level 0.3563
> volume #3 level 0.1862
> volume #3 level 0.1797
> volume #3 level 0.1682
> volume #3 level 0.1715
> hide #!3 models
> open /Users/bo1il/Downloads/cryosparc_P13_J593_map_sharp.mrc
Opened cryosparc_P13_J593_map_sharp.mrc as #6, grid size 320,320,320, pixel
0.931, shown at level 0.36, step 2, values float32
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/pred.rank_0.cif
Summary of feedback from opening /Users/bo1il/Downloads/Chai_Discovery/PusCD-
GroPI/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': might have incorrect bonds
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #7
---
Chain | Description
B | Entity B
C | Entity C
Non-standard residues in pred.rank_0.cif #7
---
LIG1 — (LIG1)
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
[Repeated 4 time(s)]
> select #6
2 models selected
Drag select of 6 cryosparc_P13_J593_map_sharp.mrc
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-26.862,0,1,0,-115.39,0,0,1,-93.69
> view matrix models #6,1,0,0,-39.729,0,1,0,-122.78,0,0,1,3.5965
> view matrix models #6,1,0,0,-50.887,0,1,0,-163.04,0,0,1,-12.564
> view matrix models #6,1,0,0,-108.91,0,1,0,-150.22,0,0,1,-54.94
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.36718,-0.78686,-0.49602,282.49,0.60881,-0.60648,0.51141,-92.045,-0.70323,-0.1142,0.70173,111.87
> view matrix models
> #6,-0.50902,-0.82828,0.23421,197.98,0.41139,-0.47311,-0.77906,115.75,0.75608,-0.3002,0.58157,-61.514
> view matrix models
> #6,-0.26017,-0.86604,0.42696,136.69,-0.17659,-0.39205,-0.90284,211.05,0.94928,-0.31029,-0.050931,7.6798
> view matrix models
> #6,-0.70942,-0.69878,-0.091827,259.41,0.69555,-0.67314,-0.25117,20.934,0.1137,-0.24205,0.96358,-32.118
> view matrix models
> #6,-0.73516,-0.67748,-0.023822,249.85,0.63415,-0.67487,-0.37736,49.633,0.23958,-0.29253,0.92576,-38.009
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.83341,-0.4857,-0.26367,274.05,0.53041,-0.83696,-0.1348,51.007,-0.15521,-0.25219,0.95515,10.785
> view matrix models
> #6,-0.82073,-0.46462,-0.33246,279.68,0.52639,-0.84116,-0.12395,50.544,-0.22206,-0.27673,0.93494,27.333
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,268.3,0.43873,-0.86207,-0.25369,86.423,-0.15288,-0.34979,0.92427,28.964
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,220.9,0.43873,-0.86207,-0.25369,26.664,-0.15288,-0.34979,0.92427,19.798
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,213.04,0.43873,-0.86207,-0.25369,22.433,-0.15288,-0.34979,0.92427,42.777
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,217.17,0.43873,-0.86207,-0.25369,23.389,-0.15288,-0.34979,0.92427,25.236
> select /B
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> view matrix models #7,1,0,0,-57.355,0,1,0,8.4851,0,0,1,-17.271
> view matrix models #7,1,0,0,60.934,0,1,0,-64.84,0,0,1,3.5733
> view matrix models #7,1,0,0,87.523,0,1,0,-69.984,0,0,1,11.026
> view matrix models #7,1,0,0,27.825,0,1,0,-71.272,0,0,1,55.988
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.04218,0.22586,0.97325,21.068,0.85348,0.51457,-0.082425,-69.572,-0.51942,0.82717,-0.21447,61.738
> view matrix models
> #7,-0.28268,0.43103,0.85691,21.335,0.91891,0.37791,0.11304,-70.521,-0.27511,0.81939,-0.50291,63.641
> view matrix models
> #7,-0.26088,0.39846,0.8793,21.25,0.89843,0.43348,0.070121,-70.327,-0.35322,0.80829,-0.47107,63.366
> view matrix models
> #7,-0.25984,0.86692,-0.42537,28.27,0.41753,0.49805,0.76001,-74.752,0.87072,0.019872,-0.49138,65.291
> view matrix models
> #7,0.83386,0.16206,-0.52765,30.45,0.05788,0.92499,0.37557,-73.231,0.54894,-0.34371,0.76192,58.1
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.83386,0.16206,-0.52765,81.869,0.05788,0.92499,0.37557,-90.802,0.54894,-0.34371,0.76192,46.185
> view matrix models
> #7,0.83386,0.16206,-0.52765,5.1844,0.05788,0.92499,0.37557,-48.846,0.54894,-0.34371,0.76192,42.001
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.70453,-0.37246,0.60408,-1.0452,0.52563,0.84577,-0.091548,-45.653,-0.47682,0.38202,0.79165,40.303
> view matrix models
> #7,-0.23022,0.10096,0.96789,-4.3882,0.87465,0.45748,0.16033,-46.473,-0.4266,0.88347,-0.19363,45.635
> view matrix models
> #7,0.89803,-0.36715,-0.24238,3.8373,0.3686,0.92868,-0.041036,-46.157,0.24016,-0.052489,0.96931,40.388
> view matrix models
> #7,0.44768,0.30501,-0.84056,6.3479,0.21876,0.8741,0.4337,-48.938,0.86702,-0.37805,0.32459,44.822
> view matrix models
> #7,0.23318,0.58175,-0.77923,5.6615,0.05734,0.7917,0.60821,-50.086,0.97074,-0.18651,0.15125,45.861
> view matrix models
> #7,0.085716,0.72398,-0.68447,4.9136,0.17704,0.665,0.72556,-50.539,0.98046,-0.18337,-0.07117,47.089
> volume #6 level 0.4669
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.085716,0.72398,-0.68447,-5.5856,0.17704,0.665,0.72556,-79.501,0.98046,-0.18337,-0.07117,118.63
> view matrix models
> #7,0.085716,0.72398,-0.68447,-12.505,0.17704,0.665,0.72556,-73.757,0.98046,-0.18337,-0.07117,117
> view matrix models
> #7,0.085716,0.72398,-0.68447,-15.731,0.17704,0.665,0.72556,-78.955,0.98046,-0.18337,-0.07117,118.82
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.32341,0.59377,-0.73678,-15.098,-0.035716,0.78573,0.61754,-78.676,0.94559,-0.1734,0.27532,116.88
> view matrix models
> #7,0.55227,0.49308,-0.67221,-15.123,-0.076496,0.83291,0.5481,-78.362,0.83015,-0.25128,0.49771,115.53
> view matrix models
> #7,0.57603,0.15623,-0.80236,-14.299,0.017377,0.979,0.2031,-76.386,0.81724,-0.13093,0.56122,115.14
> fitmap #7 inMap #6
Fit molecule pred.rank_0.cif (#7) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12718 atoms
average map value = 0.2711, steps = 228
shifted from previous position = 5.35
rotated from previous position = 19.4 degrees
atoms outside contour = 10114, contour level = 0.46689
Position of pred.rank_0.cif (#7) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.81922655 0.21706516 0.53080184 144.72771357
-0.44485592 -0.82465806 -0.34934553 143.15830590
0.36189927 -0.52232347 0.77214449 177.22615796
Axis -0.24546648 0.23968327 -0.93930727
Axis point 66.97055549 84.15651319 0.00000000
Rotation angle (degrees) 159.36916615
Shift along axis -167.68296939
> view matrix models
> #7,0.80585,-0.050044,-0.59001,-13.789,0.10414,0.99287,0.058016,-79.74,0.5829,-0.10819,0.80531,116.49
> view matrix models
> #7,0.96008,-0.11104,-0.25674,-15.392,0.09599,0.99289,-0.070463,-79.049,0.26273,0.043007,0.96391,115.16
> fitmap #7 inMap #6
Fit molecule pred.rank_0.cif (#7) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12718 atoms
average map value = 0.2711, steps = 412
shifted from previous position = 2.7
rotated from previous position = 34.4 degrees
atoms outside contour = 10109, contour level = 0.46689
Position of pred.rank_0.cif (#7) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.81940588 0.21722995 0.53045750 144.71384776
-0.44486938 -0.82457659 -0.34952066 143.14662168
0.36147648 -0.52238358 0.77230186 177.21535710
Axis -0.24524826 0.23974084 -0.93934957
Axis point 66.98891942 84.14852751 0.00000000
Rotation angle (degrees) 159.36432906
Shift along axis -167.63989835
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> view matrix models
> #7,0.36946,0.74111,-0.56058,-14.698,-0.10099,0.63171,0.7686,-83.804,0.92374,-0.22735,0.30824,119.69
> fitmap #7 inMap #6
Fit molecule pred.rank_0.cif (#7) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12718 atoms
average map value = 0.2711, steps = 340
shifted from previous position = 3.15
rotated from previous position = 41 degrees
atoms outside contour = 10109, contour level = 0.46689
Position of pred.rank_0.cif (#7) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.81924418 0.21677611 0.53089273 144.71387139
-0.44468754 -0.82469403 -0.34947497 143.14970708
0.36206624 -0.52238671 0.77202342 177.22886428
Axis -0.24553427 0.23973321 -0.93927680
Axis point 66.94415189 84.16714449 0.00000000
Rotation angle (degrees) 159.38337324
Shift along axis -167.68143654
> volume #6 level 0.709
> view matrix models
> #7,0.72475,-0.2771,0.63083,-20.501,0.4164,0.9056,-0.080598,-78.545,-0.54895,0.32109,0.77172,115.08
> view matrix models
> #7,-0.010464,0.0073655,0.99992,-23.562,0.86487,0.50196,0.0053529,-78.323,-0.50188,0.86486,-0.011622,119.29
> view matrix models
> #7,-0.064555,0.010839,0.99786,-23.624,0.82575,0.56205,0.047316,-78.619,-0.56033,0.82703,-0.045234,119.4
> view matrix models
> #7,-0.00064568,0.0082131,0.99997,-23.55,0.87047,0.49221,-0.0034806,-78.265,-0.49222,0.87044,-0.0074671,119.28
> volume #6 level 0.393
> view matrix models
> #7,-0.23712,-0.16285,0.95773,-23.592,0.47148,0.84267,0.26002,-80.319,-0.8494,0.51321,-0.12304,119.52
> view matrix models
> #7,-0.68296,0.63085,-0.36823,-17.126,0.46202,0.76353,0.45118,-81.357,0.56578,0.13801,-0.81292,125.26
> view matrix models
> #7,-0.86504,0.24949,-0.43528,-16.91,0.45045,0.76824,-0.45485,-76.421,0.22092,-0.58954,-0.77694,124.78
> view matrix models
> #7,-0.8648,0.25852,-0.43044,-16.938,0.45536,0.76502,-0.4554,-76.411,0.21156,-0.58984,-0.77931,124.78
> view matrix models
> #7,0.60808,0.22043,-0.76266,-13.158,-0.21715,0.97022,0.10729,-80.429,0.7636,0.10037,0.63784,117.6
> volume show
> volume hide
> volume show
[Repeated 1 time(s)]
> volume hide
> volume show
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.60808,0.22043,-0.76266,-14.778,-0.21715,0.97022,0.10729,-106.17,0.7636,0.10037,0.63784,162.69
> view matrix models
> #7,0.60808,0.22043,-0.76266,-8.2706,-0.21715,0.97022,0.10729,-76.542,0.7636,0.10037,0.63784,77.705
> view matrix models
> #7,0.60808,0.22043,-0.76266,-0.75676,-0.21715,0.97022,0.10729,-64.133,0.7636,0.10037,0.63784,56.455
> color sel bychain
[Repeated 2 time(s)]
> show sel surfaces
> view matrix models
> #7,0.60808,0.22043,-0.76266,13.685,-0.21715,0.97022,0.10729,-46.533,0.7636,0.10037,0.63784,8.055
> volume #6 level 0.4505
> select /B
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> select /B
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> select /C
4460 atoms, 4565 bonds, 565 residues, 1 model selected
> show sel surfaces
> view matrix models
> #7,0.60808,0.22043,-0.76266,-47.65,-0.21715,0.97022,0.10729,-38.797,0.7636,0.10037,0.63784,50.525
> view matrix models
> #7,0.60808,0.22043,-0.76266,-66.097,-0.21715,0.97022,0.10729,-4.2803,0.7636,0.10037,0.63784,84.985
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GIPC/pred.rank_0.cif
Summary of feedback from opening /Users/bo1il/Downloads/Chai_Discovery/PusCD-
GIPC/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG3': might have incorrect bonds
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #8
---
Chain | Description
A | Entity A
B | Entity B
Non-standard residues in pred.rank_0.cif #8
---
LIG3 — (LIG3)
> view matrix models
> #7,0.60808,0.22043,-0.76266,-115.35,-0.21715,0.97022,0.10729,33.375,0.7636,0.10037,0.63784,54.447
> view matrix models
> #7,0.60808,0.22043,-0.76266,-114.59,-0.21715,0.97022,0.10729,42.14,0.7636,0.10037,0.63784,55.159
> ui mousemode right "translate selected models"
> select #8/A
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> view matrix models #8,1,0,0,-38.635,0,1,0,-23.851,0,0,1,26.696
> view matrix models #8,1,0,0,-7.5637,0,1,0,-85.342,0,0,1,120.03
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96817,-0.25006,0.011083,-5.5751,0.20477,0.81673,0.53946,-82.152,-0.14395,-0.52002,0.84194,123.58
> view matrix models
> #8,0.72352,-0.50325,-0.4725,-5.1751,0.10991,-0.59177,0.79858,-70.309,-0.6815,-0.62972,-0.37284,120.47
> view matrix models
> #8,0.66441,-0.31146,0.67938,-2.2911,-0.73664,-0.11947,0.66565,-73.508,-0.12616,-0.94272,-0.30881,122.51
> show sel surfaces
> view matrix models
> #8,0.53753,-0.23216,0.81065,-1.4485,-0.81435,0.10657,0.57051,-75.682,-0.21884,-0.96682,-0.13178,123.8
> view matrix models
> #8,0.50554,-0.23551,0.83004,-1.216,-0.82883,0.13475,0.54304,-76.018,-0.23974,-0.96248,-0.12708,123.85
> view matrix models
> #8,0.59008,-0.22405,0.77563,-1.8614,-0.7862,0.058962,0.61515,-75.146,-0.18356,-0.97279,-0.14136,123.69
> view matrix models
> #8,0.58449,-0.22508,0.77956,-1.8133,-0.78947,0.064112,0.61043,-75.206,-0.18738,-0.97223,-0.14022,123.7
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.58449,-0.22508,0.77956,-23.577,-0.78947,0.064112,0.61043,-74.42,-0.18738,-0.97223,-0.14022,111.82
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 6 maps.
[Repeated 1 time(s)]
> hide #!7 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 6 maps.
> close #7
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 6 maps.
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.2613, steps = 344
shifted from previous position = 9.88
rotated from previous position = 35 degrees
atoms outside contour = 9948, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.56950300 0.09879899 -0.81603008 154.02247720
0.82198717 0.06621528 -0.56564355 142.09367778
-0.00185136 -0.99290196 -0.11892130 163.92358900
Axis -0.36523978 -0.69599674 0.61821391
Axis point -6.02192633 0.00000000 176.24303141
Rotation angle (degrees) 144.20398623
Shift along axis -53.81202899
> view matrix models
> #8,0.2034,0.17146,0.96397,-13.146,-0.958,0.23815,0.15978,-77.17,-0.20217,-0.95597,0.2127,116.9
> view matrix models
> #8,0.2034,0.17146,0.96397,-90.241,-0.958,0.23815,0.15978,23.588,-0.20217,-0.95597,0.2127,48.307
> view matrix models
> #8,0.2034,0.17146,0.96397,-85.04,-0.958,0.23815,0.15978,9.4419,-0.20217,-0.95597,0.2127,53.042
> view matrix models
> #8,0.2034,0.17146,0.96397,-101.2,-0.958,0.23815,0.15978,5.5606,-0.20217,-0.95597,0.2127,30.249
> open
> /Users/bo1il/Documents/PusCD_PI_paper/fold_puscd1_fj/fold_puscd1_fj_model_0.cif
Chain information for fold_puscd1_fj_model_0.cif #7
---
Chain | Description
A | .
B | .
> view matrix models
> #8,0.2034,0.17146,0.96397,-103.34,-0.958,0.23815,0.15978,46.964,-0.20217,-0.95597,0.2127,51.644
> select #7/A#7/B
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> view matrix models #7,1,0,0,2.7231,0,1,0,-18.609,0,0,1,-6.4529
> view matrix models #7,1,0,0,2.3294,0,1,0,-19.363,0,0,1,-8.4484
> show sel surfaces
> color sel bychain
> view matrix models #7,1,0,0,2.3359,0,1,0,-15.559,0,0,1,-10.974
> view matrix models #7,1,0,0,-7.1514,0,1,0,-30.75,0,0,1,-8.4082
> view matrix models #7,1,0,0,-10.435,0,1,0,-46.252,0,0,1,4.7366
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.57616,-0.74762,0.33032,-0.67317,0.80503,0.44922,-0.38746,-39.395,0.14129,0.48915,0.86068,-1.5957
> view matrix models
> #7,0.91551,-0.18325,0.35813,-8.9624,0.30126,0.90227,-0.30845,-44.995,-0.26661,0.39028,0.88125,0.34996
> view matrix models
> #7,0.69718,-0.50677,0.50708,-4.9005,-0.66147,-0.18199,0.72756,-28.766,-0.27642,-0.84265,-0.46209,20.818
> view matrix models
> #7,0.73899,-0.4808,0.47194,-5.2672,-0.62513,-0.22814,0.74643,-28.235,-0.25122,-0.84663,-0.46916,20.84
> view matrix models
> #7,-0.46189,-0.32682,-0.82453,-1.1123,-0.16966,-0.87991,0.44381,-19.459,-0.87056,0.34488,0.35097,3.6322
> view matrix models
> #7,-0.89843,0.3581,0.25412,-11.409,-0.42147,-0.86564,-0.27023,-18.066,0.12321,-0.34989,0.92865,9.3924
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.89843,0.3581,0.25412,-77.217,-0.42147,-0.86564,-0.27023,-43.08,0.12321,-0.34989,0.92865,81.295
> view matrix models
> #7,-0.89843,0.3581,0.25412,-8.9585,-0.42147,-0.86564,-0.27023,-67.66,0.12321,-0.34989,0.92865,82.684
> view matrix models
> #7,-0.89843,0.3581,0.25412,-28.576,-0.42147,-0.86564,-0.27023,-73.492,0.12321,-0.34989,0.92865,112.9
> view matrix models
> #7,-0.89843,0.3581,0.25412,-29.001,-0.42147,-0.86564,-0.27023,-76.973,0.12321,-0.34989,0.92865,116
> view matrix models
> #7,-0.89843,0.3581,0.25412,-25.172,-0.42147,-0.86564,-0.27023,-77.024,0.12321,-0.34989,0.92865,111.48
> view matrix models
> #7,-0.89843,0.3581,0.25412,-27.165,-0.42147,-0.86564,-0.27023,-79.774,0.12321,-0.34989,0.92865,112.51
> view matrix models
> #7,-0.89843,0.3581,0.25412,-19.872,-0.42147,-0.86564,-0.27023,-81.696,0.12321,-0.34989,0.92865,114.01
> view matrix models
> #7,-0.89843,0.3581,0.25412,48.053,-0.42147,-0.86564,-0.27023,-99.699,0.12321,-0.34989,0.92865,97.98
> view matrix models
> #7,-0.89843,0.3581,0.25412,61.809,-0.42147,-0.86564,-0.27023,-99.499,0.12321,-0.34989,0.92865,96.221
> view matrix models
> #7,-0.89843,0.3581,0.25412,-11.612,-0.42147,-0.86564,-0.27023,-66.291,0.12321,-0.34989,0.92865,81.256
> view matrix models
> #7,-0.89843,0.3581,0.25412,-20.794,-0.42147,-0.86564,-0.27023,-80.896,0.12321,-0.34989,0.92865,108.74
> view matrix models
> #7,-0.89843,0.3581,0.25412,-15.504,-0.42147,-0.86564,-0.27023,-81.084,0.12321,-0.34989,0.92865,111.95
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.79602,0.0054454,-0.60524,-9.4554,-0.072712,-0.99358,0.086692,-80.306,-0.60088,0.11302,0.79131,106.89
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2386, steps = 136
shifted from previous position = 6.51
rotated from previous position = 9.54 degrees
atoms outside contour = 10093, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.73721975 -0.39509346 0.54809507 148.61314111
0.49665312 0.86687631 -0.04314092 143.82538912
-0.45808593 0.30401746 0.83530274 169.23238075
Axis 0.25001115 0.72461585 0.64220424
Axis point 64.27218026 0.00000000 -126.26857195
Rotation angle (degrees) 43.97033216
Shift along axis 250.05485212
> view matrix models
> #7,0.23928,-0.23804,0.94132,-18.716,-0.96484,-0.16686,0.20306,-88.17,0.10873,-0.95682,-0.26959,123.24
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2642, steps = 152
shifted from previous position = 13.2
rotated from previous position = 6.73 degrees
atoms outside contour = 9849, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.62875647 0.20154747 -0.75102858 149.89548181
0.67614392 0.61871695 -0.40002342 144.74541321
0.38405040 -0.75932072 -0.52529738 174.56099547
Axis -0.28032992 -0.88560811 0.37028829
Axis point 8.30788857 0.00000000 142.16439579
Rotation angle (degrees) 140.14497687
Shift along axis -105.57000605
> view matrix models
> #7,0.19518,-0.21094,0.95782,-18.132,-0.9528,-0.27233,0.13418,-79.633,0.23254,-0.9388,-0.25413,112.89
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2642, steps = 68
shifted from previous position = 0.451
rotated from previous position = 1.86 degrees
atoms outside contour = 9851, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.62862786 0.20133476 -0.75119327 149.89488802
0.67607967 0.61886600 -0.39990145 144.74531154
0.38437391 -0.75925569 -0.52515474 174.54292017
Axis -0.28026429 -0.88564124 0.37025873
Axis point 8.29693330 0.00000000 142.16438702
Rotation angle (degrees) 140.12619182
Shift along axis -105.57656063
> view matrix models
> #7,0.28446,-0.50066,0.81757,-13.881,-0.95645,-0.09,0.27767,-82.386,-0.065436,-0.86095,-0.50446,112.42
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2642, steps = 224
shifted from previous position = 5.51
rotated from previous position = 23.4 degrees
atoms outside contour = 9846, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.62871789 0.20140755 -0.75109840 149.89730825
0.67613864 0.61869347 -0.40006865 144.74473486
0.38412283 -0.75937697 -0.52516308 174.56860291
Axis -0.28029939 -0.88559546 0.37034164
Axis point 8.30120017 0.00000000 142.17978244
Rotation angle (degrees) 140.13829885
Shift along axis -105.55138043
> view matrix models
> #7,0.088613,-0.055644,0.99451,-20.105,-0.95327,-0.29427,0.068474,-79.145,0.28884,-0.9541,-0.079119,112.77
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2642, steps = 120
shifted from previous position = 1.96
rotated from previous position = 10.5 degrees
atoms outside contour = 9844, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.62850790 0.20091554 -0.75140586 149.90004535
0.67610473 0.61871945 -0.40008579 144.74356865
0.38452597 -0.75948614 -0.52471001 174.56155969
Axis -0.28019090 -0.88558002 0.37046065
Axis point 8.27545294 0.00000000 142.21238012
Rotation angle (degrees) 140.10751031
Shift along axis -105.51445050
> hide sel surfaces
> view matrix models
> #7,0.18359,-0.17425,0.96744,-18.624,-0.9567,-0.25782,0.13512,-79.803,0.22589,-0.95035,-0.21404,112.99
> view matrix models
> #7,0.27456,-0.94849,-0.15809,-5.8285,-0.55905,-0.29122,0.77631,-81.525,-0.78236,-0.12476,-0.61021,104.61
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-5.3718,-0.7954,-0.24943,0.55239,-81.249,-0.59013,0.11092,-0.79965,102.25
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,222.35,0.43873,-0.86207,-0.25369,21.025,-0.15288,-0.34979,0.92427,26.041
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-6.952,-0.7954,-0.24943,0.55239,-83.375,-0.59013,0.11092,-0.79965,101.58
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-23.553,-0.7954,-0.24943,0.55239,-93.113,-0.59013,0.11092,-0.79965,152.26
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-31.225,-0.7954,-0.24943,0.55239,-94.634,-0.59013,0.11092,-0.79965,183.25
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-25.238,-0.7954,-0.24943,0.55239,-85.809,-0.59013,0.11092,-0.79965,178.34
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-31.794,-0.7954,-0.24943,0.55239,-94.578,-0.59013,0.11092,-0.79965,185.97
> view matrix models
> #7,0.13819,-0.96202,-0.23542,-31.605,-0.7954,-0.24943,0.55239,-94.497,-0.59013,0.11092,-0.79965,185.32
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.45238,-0.88279,-0.1266,-33.028,-0.32541,-0.29556,0.89819,-95.19,-0.83034,-0.36513,-0.42097,190.03
> view matrix models
> #7,0.67803,-0.71458,-0.17218,-35.02,0.12231,-0.12131,0.98505,-97.752,-0.72479,-0.68895,0.0051501,192.61
> view matrix models
> #7,-0.38305,-0.48213,-0.78792,-35.518,-0.27981,-0.75234,0.5964,-88.746,-0.88033,0.44892,0.15328,178.42
> view matrix models
> #7,-0.7563,-0.016688,-0.65401,-41.418,-0.17994,-0.95581,0.23247,-85.206,-0.62899,0.2935,0.71988,178.47
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.7563,-0.016688,-0.65401,-25.708,-0.17994,-0.95581,0.23247,-82.412,-0.62899,0.2935,0.71988,118.42
> view matrix models
> #7,-0.7563,-0.016688,-0.65401,-16.013,-0.17994,-0.95581,0.23247,-84.709,-0.62899,0.2935,0.71988,117.59
> view matrix models
> #7,-0.7563,-0.016688,-0.65401,-29.012,-0.17994,-0.95581,0.23247,-97.936,-0.62899,0.2935,0.71988,148.42
> view matrix models
> #7,-0.7563,-0.016688,-0.65401,-14.334,-0.17994,-0.95581,0.23247,-85.255,-0.62899,0.2935,0.71988,116.56
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.81179,-0.14385,-0.56595,-13.039,-0.0638,-0.94153,0.33083,-85.777,-0.58046,0.30467,0.75515,116.3
> view matrix models
> #7,-0.24002,-0.38513,0.8911,-14.809,-0.42597,-0.78306,-0.45317,-85.15,0.87232,-0.48836,0.023899,127.56
> view matrix models
> #7,-0.0052243,-0.64083,0.76767,-11.427,-0.77655,-0.48107,-0.40687,-88.809,0.63004,-0.59825,-0.49512,130.58
> view matrix models
> #7,-0.012154,-0.64509,0.76401,-11.361,-0.77235,-0.47922,-0.41691,-88.802,0.63508,-0.59515,-0.49241,130.53
> view matrix models
> #7,0.10853,-0.49484,0.86218,-13.533,-0.79704,-0.56164,-0.22202,-88.39,0.59409,-0.6631,-0.45536,131.26
> view matrix models
> #7,-0.10562,0.024137,0.99411,-20.141,-0.61032,-0.79084,-0.04564,-86.227,0.78508,-0.61155,0.098257,128.86
> view matrix models
> #7,0.4606,-0.88729,-0.023866,-6.2068,-0.7799,-0.4174,0.4664,-92.253,-0.42379,-0.19621,-0.88425,127.33
> view matrix models
> #7,-0.76988,0.28999,-0.5685,-18.308,-0.45577,-0.87337,0.17172,-85.956,-0.44672,0.39131,0.80456,115.04
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.76988,0.28999,-0.5685,-9.2971,-0.45577,-0.87337,0.17172,-85.035,-0.44672,0.39131,0.80456,116.64
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.2637, steps = 236
shifted from previous position = 4.34
rotated from previous position = 20.8 degrees
atoms outside contour = 9786, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.72168833 -0.41492571 0.55407815 147.23969406
0.63167597 0.72212709 -0.28198924 145.66137149
-0.28311026 0.55350620 0.78324930 180.32826864
Axis 0.52901585 0.53008780 0.66268330
Axis point 1.49425007 3.74262573 0.00000000
Rotation angle (degrees) 52.15464355
Shift along axis 274.60597981
> select subtract #7
2 models selected
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 1 model selected
> view matrix models
> #8,0.2034,0.17146,0.96397,-124.77,-0.958,0.23815,0.15978,-1.0944,-0.20217,-0.95597,0.2127,82.483
> view matrix models
> #8,0.2034,0.17146,0.96397,-47.978,-0.958,0.23815,0.15978,-54.87,-0.20217,-0.95597,0.2127,118.59
> view matrix models
> #8,0.2034,0.17146,0.96397,3.4443,-0.958,0.23815,0.15978,-54.14,-0.20217,-0.95597,0.2127,62.01
> view matrix models
> #8,0.2034,0.17146,0.96397,4.0943,-0.958,0.23815,0.15978,-59.127,-0.20217,-0.95597,0.2127,72.93
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.3213,-0.035685,0.9463,5.5499,-0.92672,-0.21744,0.30645,-54.462,0.19483,-0.97542,-0.10294,70.589
> view matrix models
> #8,0.060837,0.20018,0.97787,4.5858,-0.82787,-0.53718,0.16147,-52.76,0.55762,-0.81937,0.13304,69.205
> view matrix models
> #8,0.051946,0.19618,0.97919,4.6537,-0.82926,-0.53787,0.15175,-52.806,0.55644,-0.81989,0.13474,69.223
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.051946,0.19618,0.97919,1.9521,-0.82926,-0.53787,0.15175,-68.931,0.55644,-0.81989,0.13474,65.792
> view matrix models
> #8,0.051946,0.19618,0.97919,1.7514,-0.82926,-0.53787,0.15175,-72.46,0.55644,-0.81989,0.13474,62.923
> view matrix models
> #8,0.051946,0.19618,0.97919,5.5485,-0.82926,-0.53787,0.15175,-68.884,0.55644,-0.81989,0.13474,58.327
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.83582,-0.41936,-0.35432,6.8457,0.079072,-0.73061,0.6782,-67.136,-0.54328,0.53884,0.64381,52.124
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.83582,-0.41936,-0.35432,0.042058,0.079072,-0.73061,0.6782,-69.299,-0.54328,0.53884,0.64381,60.254
> view matrix models
> #8,-0.83582,-0.41936,-0.35432,4.1655,0.079072,-0.73061,0.6782,-71.712,-0.54328,0.53884,0.64381,61.982
> view matrix models
> #8,-0.83582,-0.41936,-0.35432,1.4729,0.079072,-0.73061,0.6782,-69.938,-0.54328,0.53884,0.64381,67.592
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.3054, steps = 172
shifted from previous position = 3.53
rotated from previous position = 15.5 degrees
atoms outside contour = 8799, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
0.72600335 -0.13485960 0.67433822 148.38179579
0.64839456 0.46096464 -0.60588456 144.59900143
-0.22913672 0.87711145 0.42210410 127.83978296
Axis 0.77847493 0.47426465 0.41115669
Axis point 0.00000000 0.23689788 53.20432807
Rotation angle (degrees) 72.26974671
Shift along axis 236.65188523
> volume #6 step 1
> lighting soft
> view matrix models
> #8,-0.81531,-0.29983,-0.49536,3.1983,-0.18231,-0.67906,0.71108,-67.156,-0.54958,0.67006,0.49898,72.884
> view matrix models
> #8,-0.81531,-0.29983,-0.49536,1.2732,-0.18231,-0.67906,0.71108,-71.77,-0.54958,0.67006,0.49898,69.882
> hide sel surfaces
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.3054, steps = 56
shifted from previous position = 1.34
rotated from previous position = 0.023 degrees
atoms outside contour = 8679, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
0.72588993 -0.13453168 0.67452579 148.38475736
0.64843829 0.46089256 -0.60589259 144.59862739
-0.22937217 0.87719968 0.42179276 127.83948425
Axis 0.77846058 0.47444716 0.41097325
Axis point 0.00000000 0.18754344 53.17339984
Rotation angle (degrees) 72.28468909
Shift along axis 236.65470164
> material transparentCastShadows true
> select subtract #8
1 model selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
> select add #5
4 models selected
> select subtract #5
2 models selected
> material transparentCastShadows true
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,226.74,0.43873,-0.86207,-0.25369,23.759,-0.15288,-0.34979,0.92427,25.327
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,221.5,0.43873,-0.86207,-0.25369,21.769,-0.15288,-0.34979,0.92427,26.945
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> select subtract #6
Nothing selected
> select add #6
2 models selected
> hide #!7 models
> hide #!8 models
> material transparentCastShadows true
> show #!7 models
> show #!8 models
> ui tool show "Fit in Map"
> hide #!8 models
> select subtract #6
Nothing selected
> ui tool show "Fit in Map"
Average map value = 0 for 0 atoms, 12649 outside contour
Average map value = 0 for 0 atoms, 12748 outside contour
> show #!8 models
Average map value = 0 for 0 atoms, 12748 outside contour
> hide #!7 models
> show #!7 models
> volume #4 level 0.6309
> hide #!4 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> save /Users/bo1il/Downloads/PusCD1_modelbuild.cxs
> show #!1 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> show #!5 models
> show #!3 models
> show #!4 models
> hide #!1 models
> show #!2 models
> show #!1 models
> close #1
> hide #!3 models
> hide #!4 models
> hide #!5 models
> close #4
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> close #2
> close #3
> close #5
> save /Users/bo1il/Downloads/PusCD1_modelbuild.cxs
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!8 models
> show #!6 models
> select #7/A#7/B
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> select #8/A
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> hide #!8 models
> show #!8 models
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,1.6848,-0.18234,-0.67888,0.71125,-63.488,-0.5498,0.67012,0.49866,56.589
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,0.88923,-0.18234,-0.67888,0.71125,-70.655,-0.5498,0.67012,0.49866,65.929
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> ui mousemode right translate
> ui mousemode right select
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right "pick blobs"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,0.82406,-0.18234,-0.67888,0.71125,-69.827,-0.5498,0.67012,0.49866,66.231
> select #8/A
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 2 models selected
> select subtract #8
1 model selected
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> view matrix models
> #7,-0.78996,-0.055284,-0.61067,-13.616,-0.1561,-0.94498,0.28748,-86.393,-0.59296,0.32243,0.73786,122.23
> view matrix models
> #7,-0.78996,-0.055284,-0.61067,-2.8353,-0.1561,-0.94498,0.28748,-70.74,-0.59296,0.32243,0.73786,67.499
> view matrix models
> #7,-0.78996,-0.055284,-0.61067,-2.7951,-0.1561,-0.94498,0.28748,-69.639,-0.59296,0.32243,0.73786,71.231
> view matrix models
> #7,-0.78996,-0.055284,-0.61067,-2.1471,-0.1561,-0.94498,0.28748,-68.847,-0.59296,0.32243,0.73786,67.887
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.3018, steps = 216
shifted from previous position = 5.61
rotated from previous position = 16.6 degrees
atoms outside contour = 8692, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64734542 -0.29575770 0.70247511 149.44776290
0.70685086 0.57774380 -0.40813474 145.72812132
-0.28514165 0.76074929 0.58305639 129.61989089
Axis 0.63892519 0.53984246 0.54803715
Axis point 0.00000000 15.43966248 16.76702696
Rotation angle (degrees) 66.16696273
Shift along axis 245.19268367
> select #7/A#7/B
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> select subtract #7
2 models selected
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 1 model selected
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,-14.355,-0.18234,-0.67888,0.71125,-86.775,-0.5498,0.67012,0.49866,119.96
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,-15.768,-0.18234,-0.67888,0.71125,-86.581,-0.5498,0.67012,0.49866,124.73
> view matrix models
> #8,-0.81515,-0.30012,-0.49543,-15.638,-0.18234,-0.67888,0.71125,-86.415,-0.5498,0.67012,0.49866,124.23
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.2482, steps = 188
shifted from previous position = 6.16
rotated from previous position = 14.6 degrees
atoms outside contour = 9922, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
0.66618948 -0.01605435 0.74560970 148.31098349
0.58544370 0.63060244 -0.50950587 144.78460256
-0.46200351 0.77593996 0.42949964 179.20636619
Axis 0.68981497 0.64804729 0.32278479
Axis point 0.00000000 -100.37568302 33.90032069
Rotation angle (degrees) 68.70648457
Shift along axis 253.97949480
> view sel
> view
> view matrix models
> #8,-0.67283,-0.43838,-0.59593,-11.019,-0.095213,-0.74751,0.65739,-81.215,-0.73365,0.49905,0.46121,122.42
> view matrix models
> #8,-0.67283,-0.43838,-0.59593,-15.092,-0.095213,-0.74751,0.65739,-83.55,-0.73365,0.49905,0.46121,115.78
> view matrix models
> #8,-0.67283,-0.43838,-0.59593,-3.9509,-0.095213,-0.74751,0.65739,-76.354,-0.73365,0.49905,0.46121,75.188
> view matrix models
> #8,-0.67283,-0.43838,-0.59593,1.0316,-0.095213,-0.74751,0.65739,-70.987,-0.73365,0.49905,0.46121,61.52
> ui mousemode right translate
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.2728, steps = 120
shifted from previous position = 5.19
rotated from previous position = 15.4 degrees
atoms outside contour = 9546, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
0.78825845 -0.16363826 0.59318727 150.63175766
0.50858604 0.71591094 -0.47834274 143.78838362
-0.34639408 0.67874447 0.64754698 118.84957013
Axis 0.70765566 0.57463263 0.41112141
Axis point 0.00000000 -17.82175290 25.17309619
Rotation angle (degrees) 54.84024649
Shift along axis 238.08251514
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.78571,-0.31125,-0.53458,-24.877,-0.0047302,-0.86114,0.50834,-75.423,-0.61857,0.40194,0.67514,117.13
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.9917,0.086298,-0.095294,-26.062,-0.11195,-0.94412,0.31002,-75.411,-0.063214,0.31811,0.94594,118.18
> view matrix models
> #8,-0.19433,0.57922,0.79167,-27.389,-0.61023,-0.70326,0.36475,-76.515,0.76802,-0.41222,0.49013,121.18
> view matrix models
> #8,0.51335,-0.15351,0.84434,-22.348,-0.83943,-0.29436,0.45685,-79.054,0.17841,-0.94328,-0.27997,123.01
> view matrix models
> #8,0.58569,-0.48161,0.65193,-20.631,-0.79442,-0.18151,0.57961,-79.509,-0.16081,-0.85738,-0.48891,121.94
> view matrix models
> #8,0.52652,-0.40743,0.74617,-20.785,-0.84679,-0.17327,0.50291,-79.801,-0.075615,-0.89665,-0.43624,122.34
> view matrix models
> #8,0.25982,-0.28161,0.92368,-20.8,-0.94319,-0.27912,0.18022,-80.089,0.20706,-0.91804,-0.33813,122.57
> view matrix models
> #8,0.21659,-0.24343,0.94543,-20.964,-0.93448,-0.33198,0.1286,-79.886,0.28256,-0.91134,-0.29938,122.58
> view matrix models
> #8,0.13515,-0.20076,0.97027,-21.111,-0.92127,-0.3859,0.048476,-79.786,0.3647,-0.90043,-0.23711,122.64
> view matrix models
> #8,0.50191,-0.15186,0.85148,-22.321,-0.85372,-0.24491,0.45955,-79.407,0.13875,-0.95758,-0.25257,123.26
> view matrix models
> #8,0.55481,-0.36368,0.74828,-21.142,-0.82585,-0.13181,0.54826,-79.972,-0.10076,-0.92215,-0.37347,122.8
> view matrix models
> #8,0.47118,-0.2282,0.85201,-21.702,-0.87867,-0.20583,0.43079,-79.786,0.077061,-0.95161,-0.2975,123.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.47118,-0.2282,0.85201,-20.265,-0.87867,-0.20583,0.43079,-77.363,0.077061,-0.95161,-0.2975,116.39
> view matrix models
> #8,0.47118,-0.2282,0.85201,-16.182,-0.87867,-0.20583,0.43079,-77.469,0.077061,-0.95161,-0.2975,115.73
> view matrix models
> #8,0.47118,-0.2282,0.85201,-16.83,-0.87867,-0.20583,0.43079,-77.928,0.077061,-0.95161,-0.2975,116.33
Average map value = 0.3018 for 12649 atoms, 8692 outside contour
> fitmap #7 inMap #6
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc (#6) using 12649 atoms
average map value = 0.3018, steps = 36
shifted from previous position = 0.00082
rotated from previous position = 0.00208 degrees
atoms outside contour = 8692, contour level = 0.45048
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64733905 -0.29578859 0.70246797 149.44782233
0.70685871 0.57775068 -0.40811140 145.72814650
-0.28513665 0.76073205 0.58308132 129.62070363
Axis 0.63890694 0.53983914 0.54806169
Axis point 0.00000000 15.44504638 16.76411302
Rotation angle (degrees) 66.16616556
Shift along axis 245.19315113
Window position QRect(2815,755 361x182) outside any known screen, using
primary screen
Average map value = 0.2396 for 12748 atoms, 10073 outside contour
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.2682, steps = 152
shifted from previous position = 4.72
rotated from previous position = 11.8 degrees
atoms outside contour = 9727, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.73245390 0.17218195 -0.65868403 149.64575982
0.64131169 0.49926503 -0.58262658 144.39789559
0.22854012 -0.84916889 -0.47611092 176.75611747
Axis -0.25668324 -0.85440684 0.45177722
Axis point 18.11149429 0.00000000 147.62454672
Rotation angle (degrees) 148.72107864
Shift along axis -81.93172076
> fitmap #8 inMap #6
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12748 atoms
average map value = 0.2682, steps = 36
shifted from previous position = 0.0171
rotated from previous position = 0.0553 degrees
atoms outside contour = 9717, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.73221869 0.17142977 -0.65914157 149.64793926
0.64141564 0.49898618 -0.58275103 144.40100580
0.22900166 -0.84948491 -0.47532475 176.77230905
Axis -0.25656598 -0.85428720 0.45207000
Axis point 18.06600191 0.00000000 147.70126667
Rotation angle (degrees) 148.68013221
Shift along axis -81.84104351
Opened pred.rank_0.cif map 8 as #1, grid size 59,60,59, pixel 2.67, shown at
level 0.0985, step 1, values float32
> fitmap #8 inMap #6 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc using
14055 points
correlation = 0.7355, correlation about mean = 0.2428, overlap = 1112
steps = 48, shift = 0.159, angle = 0.522 degrees
Position of pred.rank_0.cif map 8 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73319942 0.17544767 -0.65699066 149.65587737
0.63971804 0.50559938 -0.57890422 144.49385450
0.23060668 -0.84474101 -0.48294221 176.89604290
Axis -0.25650971 -0.85645531 0.44798110
Axis point 18.29059358 0.00000000 147.17310137
Rotation angle (degrees) 148.78970028
Shift along axis -82.89463191
Average map value = 0.2681 for 12748 atoms, 9744 outside contour
[Repeated 1 time(s)]Correlation = 0.7355, Correlation about mean = 0.2428,
Overlap = 1112
Average map value = 0.2681 for 12748 atoms, 9744 outside contour
Correlation = 0.7355, Correlation about mean = 0.2428, Overlap = 1112
> fitmap #8 inMap #6 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc using
14055 points
correlation = 0.7355, correlation about mean = 0.2426, overlap = 1112
steps = 28, shift = 0.0146, angle = 0.018 degrees
Position of pred.rank_0.cif map 8 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73316954 0.17525032 -0.65707667 149.65623813
0.63974782 0.50541285 -0.57903417 144.49805525
0.23061907 -0.84489358 -0.48266932 176.91016217
Axis -0.25648406 -0.85639174 0.44811730
Axis point 18.27931938 0.00000000 147.20371030
Rotation angle (degrees) 148.78327449
Shift along axis -82.85487554
Average map value = 0.2681 for 12748 atoms, 9744 outside contour
Opened pred.rank_0.cif map 6 as #1, grid size 73,74,72, pixel 2, shown at
level 0.109, step 1, values float32
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.15, overlap = 2668
steps = 44, shift = 0.0757, angle = 0.471 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73498069 0.18205166 -0.65319260 149.59553214
0.64015996 0.50393827 -0.57986330 144.45556345
0.22360367 -0.84433608 -0.48692708 176.93274571
Axis -0.25827361 -0.85624441 0.44737037
Axis point 18.57096442 0.00000000 146.80860622
Rotation angle (degrees) 149.20278165
Shift along axis -83.17137886
Average map value = 0.2681 for 12748 atoms, 9735 outside contour
Opened pred.rank_0.cif map 10 as #1, grid size 51,52,51, pixel 3.33, shown at
level 0.0849, step 1, values float32
> fitmap #8 inMap #6 resolution 10 metric correlation
Fit map pred.rank_0.cif map 10 in map cryosparc_P13_J593_map_sharp.mrc using
7812 points
correlation = 0.7396, correlation about mean = 0.3005, overlap = 559.7
steps = 48, shift = 0.0635, angle = 1.3 degrees
Position of pred.rank_0.cif map 10 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.72860672 0.16387481 -0.66503932 149.61293106
0.64203862 0.50161171 -0.57980350 144.41201124
0.23857632 -0.84942965 -0.47069162 176.96581830
Axis -0.25501650 -0.85465337 0.45225458
Axis point 17.48946596 0.00000000 148.24066539
Rotation angle (degrees) 148.08608359
Shift along axis -81.54237615
Average map value = 0.2682 for 12748 atoms, 9734 outside contour
Opened pred.rank_0.cif map 6 as #1, grid size 73,74,72, pixel 2, shown at
level 0.109, step 1, values float32
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 64, shift = 0.0635, angle = 1.3 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73497410 0.18203163 -0.65320560 149.59547764
0.64016356 0.50392902 -0.57986737 144.45530731
0.22361505 -0.84434592 -0.48690479 176.93263208
Axis -0.25827094 -0.85624068 0.44737905
Axis point 18.56976002 0.00000000 146.81037787
Rotation angle (degrees) 149.20168297
Shift along axis -83.16872175
Average map value = 0.2681 for 12748 atoms, 9735 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 28, shift = 0.0117, angle = 0.00772 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73498984 0.18201815 -0.65319164 149.59651377
0.64017481 0.50382176 -0.57994814 144.45968465
0.22353107 -0.84441283 -0.48682731 176.94350533
Axis -0.25827666 -0.85620890 0.44743658
Axis point 18.56858199 0.00000000 146.82289076
Rotation angle (degrees) 149.20423002
Shift along axis -83.15395970
Average map value = 0.2681 for 12748 atoms, 9729 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 44, shift = 0.00837, angle = 0.0322 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73513200 0.18247524 -0.65290407 149.59788621
0.64014063 0.50387964 -0.57993558 144.46614967
0.22316119 -0.84427963 -0.48722787 176.94891114
Axis -0.25836420 -0.85624740 0.44731234
Axis point 18.59291885 0.00000000 146.79233642
Rotation angle (degrees) 149.23136954
Shift along axis -83.19807243
Average map value = 0.2681 for 12748 atoms, 9734 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.15, overlap = 2668
steps = 28, shift = 0.0222, angle = 0.0242 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73519641 0.18277619 -0.65274735 149.59635573
0.64010047 0.50408241 -0.57980367 144.45710450
0.22306415 -0.84409347 -0.48759471 176.92872341
Axis -0.25840813 -0.85632065 0.44714671
Axis point 18.61169830 0.00000000 146.74913851
Rotation angle (degrees) 149.24416680
Shift along axis -83.24541888
Average map value = 0.2681 for 12748 atoms, 9731 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 28, shift = 0.0189, angle = 0.0362 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73506924 0.18227551 -0.65303051 149.59747343
0.64014676 0.50388984 -0.57991995 144.46399476
0.22335023 -0.84431669 -0.48707700 176.94610554
Axis -0.25832081 -0.85624122 0.44734922
Axis point 18.58258864 0.00000000 146.80382377
Rotation angle (degrees) 149.21883823
Shift along axis -83.18346479
Average map value = 0.2681 for 12748 atoms, 9731 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.15, overlap = 2668
steps = 28, shift = 0.0135, angle = 0.0291 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73516584 0.18268023 -0.65280864 149.59683531
0.64011426 0.50404777 -0.57981857 144.45949319
0.22312535 -0.84413493 -0.48749492 176.93351604
Axis -0.25839346 -0.85630576 0.44718369
Axis point 18.60506055 0.00000000 146.76077893
Rotation angle (degrees) 149.23880545
Shift along axis -83.23455785
Average map value = 0.2681 for 12748 atoms, 9733 outside contour
Opened fold_puscd1_fj_model_0.cif map 6 as #2, grid size 73,87,62, pixel 2,
shown at level 0.105, step 1, values float32
> fitmap #7 inMap #6 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc using 29813 points
correlation = 0.702, correlation about mean = 0.1265, overlap = 2965
steps = 48, shift = 0.285, angle = 0.979 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64113248 -0.31043058 0.70184186 149.62124312
0.71321769 0.57864897 -0.39558298 145.79489982
-0.28331902 0.75418713 0.59239523 129.83198854
Axis 0.62909146 0.53902627 0.56008447
Axis point 0.00000000 18.12737544 14.82345192
Rotation angle (degrees) 66.04065377
Shift along axis 245.42960801
Average map value = 0.3015 for 12649 atoms, 8685 outside contour
> fitmap #7 inMap #6 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc using 29813 points
correlation = 0.702, correlation about mean = 0.1266, overlap = 2965
steps = 40, shift = 0.0181, angle = 0.0265 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64092770 -0.31024457 0.70211110 149.62192738
0.71323815 0.57879662 -0.39533000 145.79393618
-0.28373055 0.75415037 0.59224505 129.84998814
Axis 0.62890123 0.53937157 0.55996567
Axis point 0.00000000 18.02138519 14.71339189
Rotation angle (degrees) 66.04715292
Shift along axis 245.44605406
Average map value = 0.3015 for 12649 atoms, 8693 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 40, shift = 0.014, angle = 0.0332 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73506887 0.18225772 -0.65303589 149.59712920
0.64016961 0.50378891 -0.57998242 144.46320858
0.22328597 -0.84438075 -0.48699540 176.94699967
Axis -0.25833041 -0.85621032 0.44740283
Axis point 18.58106542 0.00000000 146.81033254
Rotation angle (degrees) 149.21989939
Shift along axis -83.16978751
Average map value = 0.2681 for 12748 atoms, 9730 outside contour
> fitmap #7 inMap #6 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc using 29813 points
correlation = 0.702, correlation about mean = 0.1266, overlap = 2965
steps = 40, shift = 0.0174, angle = 0.0499 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64131230 -0.31071701 0.70155075 149.61882755
0.71317293 0.57865966 -0.39564803 145.79409261
-0.28302455 0.75406096 0.59269652 129.83282426
Axis 0.62913328 0.53877032 0.56028372
Axis point 0.00000000 18.21905078 14.88969453
Rotation angle (degrees) 66.02523523
Shift along axis 245.42293283
Average map value = 0.3015 for 12649 atoms, 8689 outside contour
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> show #1.1 models
> show #!2 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> view matrix models
> #8,0.35246,-0.10527,0.92989,-14.705,-0.93101,-0.14013,0.33702,-73.793,0.094827,-0.98452,-0.1474,88.503
> view matrix models
> #8,0.35246,-0.10527,0.92989,-15.67,-0.93101,-0.14013,0.33702,-73.292,0.094827,-0.98452,-0.1474,75.709
> hide #!1 models
> hide #!2 models
> show #!6 models
> show #!7 models
> show #!8 models
> view matrix models
> #8,0.35246,-0.10527,0.92989,-15.555,-0.93101,-0.14013,0.33702,-85.093,0.094827,-0.98452,-0.1474,114.39
> fitmap #7 inMap #6 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc using 29813 points
correlation = 0.702, correlation about mean = 0.1266, overlap = 2965
steps = 40, shift = 0.0168, angle = 0.0452 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.64096033 -0.31029738 0.70205796 149.62164932
0.71323419 0.57878804 -0.39534971 145.79386713
-0.28366678 0.75413522 0.59229488 129.84945340
Axis 0.62891502 0.53931729 0.56000246
Axis point 0.00000000 18.04015280 14.72795424
Rotation angle (degrees) 66.04483648
Shift along axis 245.44446965
Average map value = 0.3015 for 12649 atoms, 8694 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.15, overlap = 2668
steps = 88, shift = 4.24, angle = 0.0244 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73511290 0.18249716 -0.65291945 149.59605894
0.64011454 0.50406193 -0.57980596 144.45579322
0.22329889 -0.84416607 -0.48736151 176.92829984
Axis -0.25835118 -0.85630181 0.44721569
Axis point 18.59674372 0.00000000 146.76906144
Rotation angle (degrees) 149.22757657
Shift along axis -83.22096435
Average map value = 0.2681 for 12748 atoms, 9735 outside contour
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 28, shift = 0.0214, angle = 0.0282 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73502723 0.18213244 -0.65311771 149.59740396
0.64015987 0.50385426 -0.57993640 144.46421965
0.22345091 -0.84436879 -0.48694048 176.94789684
Axis -0.25829510 -0.85622405 0.44739693
Axis point 18.57434878 0.00000000 146.81656371
Rotation angle (degrees) 149.21083661
Shift along axis -83.16807089
Average map value = 0.2681 for 12748 atoms, 9727 outside contour
> view matrix models
> #8,0.35238,-0.10519,0.92993,-14.506,-0.93102,-0.14025,0.33693,-81.57,0.094976,-0.98451,-0.14736,116.32
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 52, shift = 0.895, angle = 0.024 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73513724 0.18247149 -0.65289921 149.59738039
0.64014630 0.50383722 -0.57996617 144.46413607
0.22312763 -0.84430575 -0.48719796 176.94607854
Axis -0.25836737 -0.85623482 0.44733459
Axis point 18.59362373 0.00000000 146.79254955
Rotation angle (degrees) 149.23236399
Shift along axis -83.19220429
Average map value = 0.2681 for 12748 atoms, 9732 outside contour
> select subtract #8
1 model selected
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> view matrix models
> #7,-0.74822,-0.1526,-0.64566,-1.2372,-0.26169,-0.8264,0.49857,-70.084,-0.60966,0.542,0.5784,73.485
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.21314,-0.94063,-0.26418,6.9295,-0.49456,-0.12932,0.85947,-79.545,-0.84261,0.31384,-0.43763,79.458
> view matrix models
> #7,-0.058198,-0.99813,-0.018456,6.8108,-0.63123,0.02247,0.77527,-81.071,-0.77341,0.056769,-0.63136,83.139
> view matrix models
> #7,-0.58308,-0.44461,-0.67995,2.3404,-0.077962,-0.80247,0.59158,-70.734,-0.80867,0.39795,0.43324,75.758
> view matrix models
> #7,-0.76243,-0.032723,0.64624,-6.64,-0.27454,-0.88801,-0.36886,-66.676,0.58594,-0.45865,0.66807,84.853
> view matrix models
> #7,-0.88829,0.028597,-0.45838,-3.9499,-0.1566,-0.95711,0.24376,-67.762,-0.43175,0.28832,0.85467,75.642
> view matrix models
> #7,-0.88571,-0.0016067,-0.46424,-3.5669,-0.13574,-0.9554,0.26228,-67.848,-0.44396,0.29532,0.84599,75.589
> view matrix models
> #7,-0.92739,0.26473,0.26431,-9.0093,-0.2679,-0.96313,0.024685,-66.973,0.2611,-0.047914,0.96412,79.1
> view matrix models
> #7,-0.86012,0.43294,0.26973,-11.093,-0.47942,-0.86673,-0.1376,-67.558,0.17422,-0.24767,0.95305,81.591
> view matrix models
> #7,-0.70393,0.45864,0.54234,-12.303,-0.64281,-0.73616,-0.21179,-68.847,0.30211,-0.49771,0.81303,84.999
> view matrix models
> #7,-0.72554,0.09422,0.6817,-8.3027,-0.42243,-0.84298,-0.33308,-67.271,0.54328,-0.52963,0.65142,85.782
> ui mousemode right "move picked models"
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,221.06,0.43873,-0.86207,-0.25369,20.965,-0.15288,-0.34979,0.92427,29.372
> fitmap #8 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29728 points
correlation = 0.7136, correlation about mean = 0.1499, overlap = 2668
steps = 52, shift = 2.59, angle = 0.0292 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.73526246 0.18289298 -0.65264022 149.59769303
0.64013019 0.50385140 -0.57997164 144.46480367
0.22276095 -0.84420609 -0.48753834 176.94570408
Axis -0.25845626 -0.85625819 0.44723850
Axis point 18.61626811 0.00000000 146.76251383
Rotation angle (degrees) 149.25765386
Shift along axis -83.22669972
Average map value = 0.2681 for 12748 atoms, 9732 outside contour
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.72554,0.09422,0.6817,-6.3607,-0.42243,-0.84298,-0.33308,-69.246,0.54328,-0.52963,0.65142,64.595
> view matrix models
> #7,-0.72554,0.09422,0.6817,8.8416,-0.42243,-0.84298,-0.33308,-71.228,0.54328,-0.52963,0.65142,68.441
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.49397,-0.20081,0.84597,11.821,-0.42237,-0.79503,-0.43535,-71.497,0.76,-0.57236,0.30791,69.922
> view matrix models
> #7,-0.4344,-0.25676,0.86335,12.421,-0.63519,-0.59227,-0.49574,-73.683,0.63862,-0.76374,0.094191,72.946
> view matrix models
> #7,-0.20664,-0.21983,0.9534,11.605,-0.95765,-0.15425,-0.24313,-79.634,0.20051,-0.96326,-0.17865,76.38
> view matrix models
> #7,0.35622,-0.025833,0.93405,9.081,-0.77848,-0.56106,0.28137,-76.381,0.51679,-0.82737,-0.21997,74.73
> view matrix models
> #7,0.37222,-0.724,0.58076,18.621,-0.91194,-0.16884,0.37399,-81.366,-0.17271,-0.66882,-0.72309,74.631
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.37222,-0.724,0.58076,4.6656,-0.91194,-0.16884,0.37399,-73.343,-0.17271,-0.66882,-0.72309,65.444
> view matrix models
> #7,0.37222,-0.724,0.58076,-1.0097,-0.91194,-0.16884,0.37399,-72.774,-0.17271,-0.66882,-0.72309,73.114
> view matrix models
> #7,0.37222,-0.724,0.58076,14.923,-0.91194,-0.16884,0.37399,-51.771,-0.17271,-0.66882,-0.72309,-7.3286
> view matrix models
> #7,0.37222,-0.724,0.58076,14.184,-0.91194,-0.16884,0.37399,-52.644,-0.17271,-0.66882,-0.72309,-3.3103
> view matrix models
> #7,0.37222,-0.724,0.58076,14.722,-0.91194,-0.16884,0.37399,-52.268,-0.17271,-0.66882,-0.72309,0.014185
> view matrix models
> #7,0.37222,-0.724,0.58076,15.207,-0.91194,-0.16884,0.37399,-50.815,-0.17271,-0.66882,-0.72309,-0.28845
> view matrix models
> #7,0.37222,-0.724,0.58076,14.571,-0.91194,-0.16884,0.37399,-52.862,-0.17271,-0.66882,-0.72309,0.52582
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/pred.rank_0.cif
Summary of feedback from opening /Users/bo1il/Downloads/Chai_Discovery/PusCD-
GroPI/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': might have incorrect bonds
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #3
---
Chain | Description
B | Entity B
C | Entity C
Non-standard residues in pred.rank_0.cif #3
---
LIG1 — (LIG1)
> hide #!7 models
> select subtract #7
2 models selected
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> select subtract #7
2 models selected
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> select subtract #7
2 models selected
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 1 model selected
> select subtract #8
1 model selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
Alignment identifier is 3/B
Alignment identifier is 3/C
> view matrix models #3,1,0,0,-22.954,0,1,0,-46.765,0,0,1,68.058
> view matrix models #3,1,0,0,-3.6679,0,1,0,-63.482,0,0,1,64.323
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.26944,0.20401,0.94116,-9.8312,0.87529,0.35565,-0.32768,-60.374,-0.40157,0.91208,-0.082744,69.489
> view matrix models
> #3,0.10045,-0.18918,0.97679,-10.156,0.88273,0.46988,0.00022224,-62.184,-0.45902,0.86222,0.21419,67.802
> view matrix models
> #3,0.59809,-0.10267,0.79483,-8.5214,0.7749,0.32714,-0.54084,-59.335,-0.20449,0.93938,0.27521,67.787
> view matrix models
> #3,-0.078708,0.37572,0.92339,-10.237,0.98452,0.17482,0.012784,-62.047,-0.15663,0.91009,-0.38366,71.459
> view matrix models
> #3,0.23733,-0.027328,0.97105,-9.9816,0.80839,0.55986,-0.18182,-61.309,-0.53868,0.82814,0.15496,68.028
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-37
289 atoms, 290 bonds, 37 residues, 1 model selected
> select #3/B:1-37
289 atoms, 290 bonds, 37 residues, 1 model selected
> select #3/B:63-64
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B:1-64
498 atoms, 504 bonds, 64 residues, 1 model selected
> select #3/B:90-91
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #3/B:1-91
707 atoms, 715 bonds, 91 residues, 1 model selected
> select #3/B:188-189
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/B:1-189
1439 atoms, 1457 bonds, 189 residues, 1 model selected
> hide sel cartoons
> view matrix models
> #3,0.03143,0.13149,0.99082,-10.623,0.90347,0.42026,-0.08443,-61.549,-0.42751,0.89783,-0.10558,69.631
> view matrix models
> #3,0.033598,0.14535,0.98881,-10.629,0.89601,0.43393,-0.094228,-61.521,-0.44277,0.88915,-0.11565,69.685
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.033598,0.14535,0.98881,-1.9974,0.89601,0.43393,-0.094228,-67.29,-0.44277,0.88915,-0.11565,72.556
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.21232,0.32305,0.92226,-2.2028,0.95848,0.25268,0.13215,-68.282,-0.19034,0.91203,-0.36328,74.343
> hide #!1 models
> hide #!8 models
> show #!8 models
> select add #6
1439 atoms, 1457 bonds, 189 residues, 3 models selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
> select subtract #3
2 models selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
> fitmap #3 inMap #6
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J593_map_sharp.mrc (#6)
using 12718 atoms
average map value = 0.3128, steps = 216
shifted from previous position = 2.15
rotated from previous position = 18.2 degrees
atoms outside contour = 8549, contour level = 0.45048
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J593_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
0.79796827 -0.21257802 -0.56396563 153.29138276
-0.44477546 -0.83916476 -0.31301327 143.32603497
-0.40672034 0.50061273 -0.76417633 127.18310011
Axis 0.94541929 -0.18271630 -0.26980940
Axis point 0.00000000 68.53989989 104.45256463
Rotation angle (degrees) 154.51346169
Shift along axis 84.42143191
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
> fitmap #3 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29213 points
correlation = 0.7175, correlation about mean = 0.146, overlap = 3100
steps = 120, shift = 0.267, angle = 0.356 degrees
Position of pred.rank_0.cif map 6 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80033612 -0.21298092 -0.56044735 153.32062628
-0.44514575 -0.83728122 -0.31749869 143.58622067
-0.40163088 0.50358642 -0.76491395 127.24976912
Axis 0.94602597 -0.18298286 -0.26749232
Axis point 0.00000000 68.53248303 104.49646081
Rotation angle (degrees) 154.28051977
Shift along axis 84.73313979
Average map value = 0.3128 for 12718 atoms, 8557 outside contour
[Repeated 1 time(s)]Correlation = 0.7175, Correlation about mean = 0.146,
Overlap = 3100
Opened pred.rank_0.cif map 8 as #4, grid size 56,61,53, pixel 2.67, shown at
level 0.1, step 1, values float32
> fitmap #3 inMap #6 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc using
13751 points
correlation = 0.7368, correlation about mean = 0.2274, overlap = 1292
steps = 64, shift = 0.201, angle = 0.233 degrees
Position of pred.rank_0.cif map 8 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.79912376 -0.21418416 -0.56171733 153.33427758
-0.44531221 -0.83860098 -0.31376016 143.70056901
-0.40385425 0.50087278 -0.76552479 127.08916880
Axis 0.94573498 -0.18326860 -0.26832438
Axis point 0.00000000 68.78044087 104.35050354
Rotation angle (degrees) 154.48878551
Shift along axis 84.57666454
Average map value = 0.3126 for 12718 atoms, 8574 outside contour
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.2026
> volume #4 level 0.1878
> fitmap #3 inMap #6 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc using
11321 points
correlation = 0.7539, correlation about mean = 0.1771, overlap = 1224
steps = 64, shift = 0.219, angle = 0.476 degrees
Position of pred.rank_0.cif map 8 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80258797 -0.21802194 -0.55526480 153.31073306
-0.44534105 -0.83828870 -0.31455270 143.70580779
-0.39689281 0.49973842 -0.76989454 127.31297337
Axis 0.94670570 -0.18412538 -0.26428423
Axis point 0.00000000 68.88162270 104.07895039
Rotation angle (degrees) 154.52827640
Shift along axis 85.03344856
Average map value = 0.3126 for 12718 atoms, 8562 outside contour
Opened pred.rank_0.cif map 4 as #4, grid size 94,103,87, pixel 1.33, shown at
level 0.107, step 1, values float32
> fitmap #3 inMap #6 resolution 4 metric correlation
Fit map pred.rank_0.cif map 4 in map cryosparc_P13_J593_map_sharp.mrc using
77705 points
correlation = 0.6537, correlation about mean = 0.0562, overlap = 1.05e+04
steps = 104, shift = 0.244, angle = 0.144 degrees
Position of pred.rank_0.cif map 4 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80158091 -0.21839348 -0.55657195 153.27498103
-0.44702048 -0.83710066 -0.31533344 143.47026579
-0.39703998 0.50156433 -0.76863026 127.36282405
Axis 0.94640521 -0.18482348 -0.26487253
Axis point 0.00000000 68.74135581 104.20748884
Rotation angle (degrees) 154.43217259
Shift along axis 84.80865337
Average map value = 0.3128 for 12718 atoms, 8566 outside contour
Opened pred.rank_0.cif map 10 as #4, grid size 49,52,46, pixel 3.33, shown at
level 0.0869, step 1, values float32
> fitmap #3 inMap #6 resolution 10 metric correlation
Fit map pred.rank_0.cif map 10 in map cryosparc_P13_J593_map_sharp.mrc using
7621 points
correlation = 0.7404, correlation about mean = 0.2773, overlap = 650.8
steps = 68, shift = 0.528, angle = 0.506 degrees
Position of pred.rank_0.cif map 10 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80156217 -0.21959719 -0.55612513 153.27078374
-0.44424060 -0.84125977 -0.30811085 143.66161637
-0.40018542 0.49402336 -0.77187599 126.87720643
Axis 0.94650735 -0.18400671 -0.26507615
Axis point 0.00000000 69.18050656 103.61154968
Rotation angle (degrees) 154.92946010
Shift along axis 85.00510070
Average map value = 0.3124 for 12718 atoms, 8573 outside contour
> fitmap #3 inMap #6 resolution 10 metric correlation
Fit map pred.rank_0.cif map 10 in map cryosparc_P13_J593_map_sharp.mrc using
7621 points
correlation = 0.7404, correlation about mean = 0.2774, overlap = 650.8
steps = 48, shift = 0.00698, angle = 0.0129 degrees
Position of pred.rank_0.cif map 10 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80161922 -0.21969430 -0.55600453 153.27342552
-0.44431699 -0.84118021 -0.30821789 143.66037921
-0.39998630 0.49411565 -0.77192014 126.88351251
Axis 0.94652183 -0.18405646 -0.26498990
Axis point 0.00000000 69.17959521 103.61279639
Rotation angle (degrees) 154.92320965
Shift along axis 85.01217363
Average map value = 0.3125 for 12718 atoms, 8570 outside contour
> show #!4 models
Average map value = 0.3125 for 12718 atoms, 8570 outside contour
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
Correlation = 0.7172, Correlation about mean = 0.1426, Overlap = 3100
> fitmap #3 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29213 points
correlation = 0.7175, correlation about mean = 0.146, overlap = 3100
steps = 64, shift = 0.393, angle = 0.715 degrees
Position of pred.rank_0.cif map 6 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80032927 -0.21297698 -0.56045862 153.32194159
-0.44516080 -0.83726499 -0.31752040 143.58498922
-0.40162785 0.50361508 -0.76489668 127.25071708
Axis 0.94602367 -0.18298768 -0.26749713
Axis point 0.00000000 68.53094704 104.49885941
Rotation angle (degrees) 154.27876004
Shift along axis 84.73270059
Average map value = 0.3128 for 12718 atoms, 8557 outside contour
> show #!4 models
> color #4 #23c2f7ff models
> color #4 #2385f7ff models
> hide sel cartoons
[Repeated 1 time(s)]Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/B:114
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:1-114
887 atoms, 895 bonds, 114 residues, 1 model selected
> hide sel cartoons
> hide sel surfaces
> select #3/B:135-136
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #3/B:1-136
1042 atoms, 1053 bonds, 136 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> fitmap #3 inMap #6 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc using
29213 points
correlation = 0.7175, correlation about mean = 0.146, overlap = 3100
steps = 104, shift = 0.00528, angle = 0.0104 degrees
Position of pred.rank_0.cif map 6 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.80026999 -0.21307543 -0.56050585 153.31902435
-0.44520634 -0.83730575 -0.31734903 143.58796840
-0.40169549 0.50350566 -0.76493319 127.24787703
Axis 0.94600919 -0.18302394 -0.26752356
Axis point 0.00000000 68.54210485 104.49327007
Rotation angle (degrees) 154.28777535
Shift along axis 84.71936382
Average map value = 0.3128 for 12718 atoms, 8560 outside contour
> hide #!8 models
> hide #!6 models
> show #!1 models
> view matrix models
> #3,-0.60919,0.73498,0.29782,-1.7726,0.76335,0.44168,0.4714,-68.434,0.21492,0.51451,-0.83011,73.249
> view matrix models
> #3,-0.6944,0.63457,0.33931,0.15425,0.63086,0.31001,0.71128,-67.315,0.34616,0.70796,-0.6156,67.302
> view matrix models
> #3,-0.61725,0.77158,0.15381,-0.86871,0.56007,0.29362,0.77467,-66.837,0.55256,0.56431,-0.61338,66.716
> view matrix models
> #3,-0.25625,0.96223,-0.091973,-5.377,0.4187,0.19625,0.88667,-64.919,0.87122,0.18869,-0.45317,66.403
> view matrix models
> #3,0.58871,0.80815,0.017584,-14.273,0.0022187,-0.023368,0.99972,-58.204,0.80834,-0.58851,-0.01555,73.282
> view matrix models
> #3,0.54,0.67796,-0.49878,-7.424,0.39388,0.32016,0.8616,-66.004,0.74382,-0.66172,-0.094143,75.683
> view matrix models
> #3,0.97577,0.21717,-0.026807,-10.786,-0.13637,0.69935,0.70164,-63.258,0.17112,-0.68098,0.71202,75.473
> view matrix models
> #3,0.99114,0.076954,0.10821,-10.358,-0.12654,0.79446,0.59399,-63.643,-0.040261,-0.60242,0.79716,76.18
> view matrix models
> #3,0.92747,0.056688,0.36958,-11.676,-0.20464,0.90422,0.37485,-62.194,-0.31293,-0.42329,0.85023,76.593
> view matrix models
> #3,0.78706,0.047102,0.61508,-12.09,-0.17216,0.97424,0.14569,-61.439,-0.59237,-0.22055,0.77489,77.923
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.78706,0.047102,0.61508,0.71442,-0.17216,0.97424,0.14569,-73.836,-0.59237,-0.22055,0.77489,15.345
> view matrix models
> #3,0.78706,0.047102,0.61508,4.541,-0.17216,0.97424,0.14569,-75.535,-0.59237,-0.22055,0.77489,33.245
> view matrix models
> #3,0.78706,0.047102,0.61508,13.659,-0.17216,0.97424,0.14569,-77.058,-0.59237,-0.22055,0.77489,69.823
> view matrix models
> #3,0.78706,0.047102,0.61508,7.3253,-0.17216,0.97424,0.14569,-68.709,-0.59237,-0.22055,0.77489,62.864
> view matrix models
> #3,0.78706,0.047102,0.61508,2.1977,-0.17216,0.97424,0.14569,-57.109,-0.59237,-0.22055,0.77489,71.731
> view matrix models
> #3,0.78706,0.047102,0.61508,3.3167,-0.17216,0.97424,0.14569,-63.414,-0.59237,-0.22055,0.77489,77.495
> ui mousemode right "translate selected models"
> ui mousemode right select
> view
> hide #!3 models
> hide #!4 models
> volume flip #1
Opened pred.rank_0.cif map 6 z flip as #5, grid size 73,74,72, pixel 2, shown
at step 1, values float32
> hide #!2 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!4 models
> volume flip #4
Opened pred.rank_0.cif map 6 z flip as #9, grid size 69,75,64, pixel 2, shown
at step 1, values float32
> select add #9
1042 atoms, 1053 bonds, 136 residues, 4 models selected
Drag select of 14 pred.rank_0.cif map 6 z flip
[Repeated 1 time(s)]
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.4308,0.35211,0.83092,-47.64,0.8368,0.5006,0.22172,-83.98,-0.33789,0.79083,-0.51031,75.789
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.9126,-0.37289,0.16765,-11.91,-0.40866,-0.81941,0.40196,-64.544,-0.012516,-0.43534,-0.90018,99.872,#9,-0.98755,0.15011,0.046963,-46.744,0.15206,0.98752,0.041044,-106.62,-0.040215,0.047675,-0.99805,101.68
> view matrix models
> #5,0.015791,-0.21248,0.97704,-9.3926,-0.9829,-0.18258,-0.02382,-88.614,0.18345,-0.95996,-0.21173,120.78,#9,-0.13737,0.55451,0.82076,-43.366,0.90036,0.4153,-0.12989,-82.187,-0.41289,0.72114,-0.55631,78.449
> view matrix models
> #5,0.54921,-0.81934,0.16447,-4.9215,-0.81455,-0.56883,-0.11374,-78.612,0.18675,-0.071504,-0.9798,87.075,#9,-0.75403,0.6415,-0.14114,-55.205,0.64352,0.67842,-0.35444,-90.484,-0.13163,-0.35808,-0.92437,104.9
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.75403,0.6415,-0.14114,-116.73,0.64352,0.67842,-0.35444,-73.716,-0.13163,-0.35808,-0.92437,106.32
> view matrix models
> #9,-0.75403,0.6415,-0.14114,-86.843,0.64352,0.67842,-0.35444,-104.94,-0.13163,-0.35808,-0.92437,190.93
> view matrix models
> #9,-0.75403,0.6415,-0.14114,43.646,0.64352,0.67842,-0.35444,-70.139,-0.13163,-0.35808,-0.92437,56.396
> view matrix models
> #5,0.54921,-0.81934,0.16447,11.735,-0.81455,-0.56883,-0.11374,-78.738,0.18675,-0.071504,-0.9798,70.877
> view matrix models
> #5,0.54921,-0.81934,0.16447,-17.802,-0.81455,-0.56883,-0.11374,-78.013,0.18675,-0.071504,-0.9798,102.86
> view matrix models
> #5,0.54921,-0.81934,0.16447,-5.0181,-0.81455,-0.56883,-0.11374,-79.247,0.18675,-0.071504,-0.9798,88.612
> ui mousemode right pivot
> ui mousemode right "move picked models"
> view matrix models
> #5,0.54921,-0.81934,0.16447,-6.8305,-0.81455,-0.56883,-0.11374,-78.299,0.18675,-0.071504,-0.9798,90.396
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.54921,-0.81934,0.16447,-161.86,-0.81455,-0.56883,-0.11374,-142.93,0.18675,-0.071504,-0.9798,187.19,#9,-0.75403,0.6415,-0.14114,-111.39,0.64352,0.67842,-0.35444,-134.77,-0.13163,-0.35808,-0.92437,153.19
> view matrix models
> #5,0.54921,-0.81934,0.16447,-147.08,-0.81455,-0.56883,-0.11374,-126.26,0.18675,-0.071504,-0.9798,181.98,#9,-0.75403,0.6415,-0.14114,-96.601,0.64352,0.67842,-0.35444,-118.1,-0.13163,-0.35808,-0.92437,147.98
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.57178,-0.80905,0.136,-145.73,-0.81995,-0.56909,0.061828,-133.1,0.027376,-0.14687,-0.98878,181.78,#9,-0.77113,0.61557,-0.16259,-96.527,0.63667,0.74666,-0.19274,-117.87,0.0027576,-0.25214,-0.96769,148.36
> ui mousemode right "move picked models"
> view matrix models
> #5,0.57178,-0.80905,0.136,-155.51,-0.81995,-0.56909,0.061828,-126.26,0.027376,-0.14687,-0.98878,175.44
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> select subtract #5
2 models selected
> view matrix models
> #9,-0.63379,0.76348,0.12414,-97.16,0.7407,0.64528,-0.187,-117.64,-0.22288,-0.026566,-0.97448,147.85
> view matrix models
> #9,-0.53316,0.83558,0.13245,-96.91,0.846,0.52738,0.07839,-118.35,-0.0043515,0.15385,-0.98808,148.51
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.53316,0.83558,0.13245,-106.9,0.846,0.52738,0.07839,-120.89,-0.0043515,0.15385,-0.98808,154.85
> view matrix models
> #9,-0.53316,0.83558,0.13245,-106.47,0.846,0.52738,0.07839,-122.38,-0.0043515,0.15385,-0.98808,156.59
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #5
4 models selected
> select subtract #9
2 models selected
> view matrix models
> #5,0.44181,-0.89669,0.027418,-155.45,-0.89254,-0.44243,-0.087294,-128.01,0.090406,0.014095,-0.99581,174.21
> view matrix models
> #5,0.51592,-0.84308,-0.1518,-157.04,-0.84398,-0.5306,0.078478,-126.4,-0.14671,0.087626,-0.98529,174.03
> view matrix models
> #5,0.44191,-0.88033,-0.17244,-156.83,-0.86674,-0.46856,0.17093,-126.21,-0.23128,0.073925,-0.97008,174.32
> view matrix models
> #5,0.36885,-0.88945,-0.26987,-157.3,-0.90055,-0.41386,0.13318,-126.8,-0.23014,0.1939,-0.95364,173.59
> view matrix models
> #5,0.46154,-0.8824,-0.091394,-156.32,-0.87146,-0.47025,0.13938,-126.4,-0.16596,0.015317,-0.98601,174.55
> ui mousemode right "move picked models"
> view matrix models
> #5,0.46154,-0.8824,-0.091394,-155.48,-0.87146,-0.47025,0.13938,-126.5,-0.16596,0.015317,-0.98601,173.71
> show #!6 models
> view matrix models
> #6,-0.88552,-0.36672,-0.28526,183.24,0.43873,-0.86207,-0.25369,-38.386,-0.15288,-0.34979,0.92427,17.334
> volume flip #6
Opened cryosparc_P13_J593_map_sharp.mrc z flip as #10, grid size 320,320,320,
pixel 0.931, shown at step 1, values float32
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,152.09,0.43873,-0.86207,-0.25369,-92.623,-0.15288,-0.34979,0.92427,21.848
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,95.23,0.43873,-0.86207,-0.25369,-42.189,-0.15288,-0.34979,0.92427,-48.163
> hide #!5 models
> hide #!9 models
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,82.693,0.43873,-0.86207,-0.25369,-22.473,-0.15288,-0.34979,0.92427,17.371
> show #!8 models
> view matrix models
> #8,0.3528,-0.10591,0.92969,-36.111,-0.93093,-0.13995,0.33733,-159.72,0.094385,-0.98448,-0.14797,74.152
> view matrix models
> #8,0.3528,-0.10591,0.92969,-49.7,-0.93093,-0.13995,0.33733,-166.94,0.094385,-0.98448,-0.14797,65.737
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,93.204,0.43873,-0.86207,-0.25369,-15.386,-0.15288,-0.34979,0.92427,18.057
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,166.69,0.43873,-0.86207,-0.25369,-72.216,-0.15288,-0.34979,0.92427,23.058
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,163.81,0.43873,-0.86207,-0.25369,-79.076,-0.15288,-0.34979,0.92427,33.295
> view matrix models
> #10,-0.88552,-0.36672,-0.28526,166.33,0.43873,-0.86207,-0.25369,-76.319,-0.15288,-0.34979,0.92427,31.405
> view matrix models
> #8,0.3528,-0.10591,0.92969,-46.323,-0.93093,-0.13995,0.33733,-159.95,0.094385,-0.98448,-0.14797,60.168
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.46154,-0.8824,-0.091394,-155.48,-0.87146,-0.47025,0.13938,-126.5,-0.16596,0.015317,-0.98601,173.71
[Repeated 5 time(s)]
> ui mousemode right "rotate selected models"
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 3 models selected
> view matrix models
> #8,0.24336,0.052451,0.96852,-47.272,-0.9578,-0.14446,0.24849,-160.22,0.15294,-0.98812,0.015084,60.74,#5,0.4003,-0.91167,0.092878,-170.74,-0.91247,-0.38717,0.13231,-115.21,-0.084667,-0.13771,-0.98685,153.77
> view matrix models
> #8,0.44506,-0.26451,0.85554,-45.484,-0.88852,-0.24946,0.3851,-158.98,0.11156,-0.93156,-0.34604,59.007,#5,0.50063,-0.82071,-0.27532,-135.51,-0.84908,-0.52749,0.028495,-121.66,-0.16862,0.21951,-0.96093,187.18
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.44506,-0.26451,0.85554,-54.454,-0.88852,-0.24946,0.3851,-156.34,0.11156,-0.93156,-0.34604,60.173,#5,0.50063,-0.82071,-0.27532,-144.47,-0.84908,-0.52749,0.028495,-119.01,-0.16862,0.21951,-0.96093,188.34
> view matrix models
> #8,0.44506,-0.26451,0.85554,-52.932,-0.88852,-0.24946,0.3851,-160.68,0.11156,-0.93156,-0.34604,65.702,#5,0.50063,-0.82071,-0.27532,-142.95,-0.84908,-0.52749,0.028495,-123.36,-0.16862,0.21951,-0.96093,193.87
> fitmap #8 inMap #10
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12748 atoms
average map value = 0.3248, steps = 120
shifted from previous position = 4.58
rotated from previous position = 19.4 degrees
atoms outside contour = 8666, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
-0.66806955 0.03810702 -0.74312241 149.69266416
0.58822505 0.63867887 -0.49606510 144.47193930
0.45571302 -0.76852921 -0.44909741 117.64677328
Axis -0.20229350 -0.89008647 0.40844022
Axis point 22.99452857 0.00000000 119.65387905
Rotation angle (degrees) 137.66705988
Shift along axis -110.82269701
> view matrix models
> #8,0.24588,-0.04873,0.96807,-52.889,-0.9158,-0.3389,0.21554,-164.8,0.31758,-0.93956,-0.12796,67.921,#5,0.50063,-0.82071,-0.27532,-143.07,-0.84908,-0.52749,0.028495,-123.12,-0.16862,0.21951,-0.96093,195.07
> fitmap #8 inMap #10
Fit molecule pred.rank_0.cif (#8) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12748 atoms
average map value = 0.3248, steps = 64
shifted from previous position = 1.24
rotated from previous position = 0.00256 degrees
atoms outside contour = 8664, contour level = 0.45048
Position of pred.rank_0.cif (#8) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
-0.66805082 0.03812225 -0.74313847 149.69840132
0.58822875 0.63870388 -0.49602851 144.47287546
0.45573570 -0.76850768 -0.44911126 117.62807226
Axis -0.20229975 -0.89009354 0.40842172
Axis point 22.99931910 0.00000000 119.64416175
Rotation angle (degrees) 137.66578818
Shift along axis -110.83646319
> fitmap #8 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29728 points
correlation = 0.8005, correlation about mean = 0.3531, overlap = 3147
steps = 48, shift = 0.113, angle = 0.11 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66886251 0.03937357 -0.74234268 149.66929476
0.58777036 0.63939843 -0.49567695 144.38698223
0.45513618 -0.76786676 -0.45081226 117.56194914
Axis -0.20238520 -0.89037867 0.40775735
Axis point 23.09876895 0.00000000 119.45081265
Rotation angle (degrees) 137.74318669
Shift along axis -110.91319029
Average map value = 0.3247 for 12748 atoms, 8663 outside contour
> fitmap #8 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29728 points
correlation = 0.8005, correlation about mean = 0.3531, overlap = 3147
steps = 40, shift = 0.00909, angle = 0.00387 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66884220 0.03940953 -0.74235908 149.66869046
0.58782232 0.63935766 -0.49566793 144.38890524
0.45509892 -0.76789886 -0.45079519 117.55312419
Axis -0.20241634 -0.89036563 0.40777037
Axis point 23.09612982 0.00000000 119.44751829
Rotation angle (degrees) 137.74333102
Shift along axis -110.91962563
Average map value = 0.3247 for 12748 atoms, 8663 outside contour
> volume #10 level 0.3556
> volume #10 style mesh
> volume #10 style surface
> fitmap #8 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29728 points
correlation = 0.8005, correlation about mean = 0.353, overlap = 3146
steps = 40, shift = 0.0102, angle = 0.00341 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66887362 0.03940551 -0.74233098 149.66960139
0.58777987 0.63939119 -0.49567501 144.39009329
0.45510756 -0.76787115 -0.45083368 117.54304013
Axis -0.20239649 -0.89037766 0.40775394
Axis point 23.10222817 0.00000000 119.43989467
Rotation angle (degrees) 137.74488099
Shift along axis -110.92567879
Average map value = 0.3247 for 12748 atoms, 6633 outside contour
> fitmap #8 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29728 points
correlation = 0.8005, correlation about mean = 0.3531, overlap = 3147
steps = 40, shift = 0.00912, angle = 0.01 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66891286 0.03936926 -0.74229754 149.66869419
0.58781227 0.63926810 -0.49579535 144.38916238
0.45500804 -0.76797549 -0.45075639 117.55216860
Axis -0.20239869 -0.89034078 0.40783337
Axis point 23.10067681 0.00000000 119.45119113
Rotation angle (degrees) 137.74850458
Shift along axis -110.90660953
Average map value = 0.3247 for 12748 atoms, 6629 outside contour
> fitmap #8 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29728 points
correlation = 0.8005, correlation about mean = 0.353, overlap = 3146
steps = 28, shift = 0.00981, angle = 0.00903 degrees
Position of pred.rank_0.cif map 6 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66886886 0.03938664 -0.74233627 149.66966638
0.58778372 0.63937747 -0.49568815 144.39013030
0.45510960 -0.76788354 -0.45081050 117.54235302
Axis -0.20239358 -0.89037276 0.40776609
Axis point 23.10170774 0.00000000 119.44149575
Rotation angle (degrees) 137.74427549
Shift along axis -110.92343296
Average map value = 0.3247 for 12748 atoms, 6633 outside contour
Opened pred.rank_0.cif map 4 as #1, grid size 100,102,99, pixel 1.33, shown at
level 0.105, step 1, values float32
> fitmap #8 inMap #10 resolution 4 metric correlation
Fit map pred.rank_0.cif map 4 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 78470 points
correlation = 0.7235, correlation about mean = 0.1566, overlap = 1.085e+04
steps = 60, shift = 0.0572, angle = 0.217 degrees
Position of pred.rank_0.cif map 4 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66692567 0.03955341 -0.74407370 149.71828620
0.59044504 0.63718012 -0.49535457 144.38694441
0.45451601 -0.76969930 -0.44830589 117.51449390
Axis -0.20361735 -0.88958755 0.40886913
Axis point 22.87659236 0.00000000 119.62148842
Rotation angle (degrees) 137.64848792
Shift along axis -110.88201968
Average map value = 0.3246 for 12748 atoms, 6624 outside contour
Opened pred.rank_0.cif map 8 as #1, grid size 59,60,59, pixel 2.67, shown at
level 0.0985, step 1, values float32
> fitmap #8 inMap #10 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 14055 points
correlation = 0.8169, correlation about mean = 0.4654, overlap = 1282
steps = 60, shift = 0.0175, angle = 0.306 degrees
Position of pred.rank_0.cif map 8 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66860113 0.03556769 -0.74277013 149.70899770
0.58636180 0.63951897 -0.49718740 144.40108081
0.45733178 -0.76795209 -0.44843865 117.50778497
Axis -0.20087351 -0.89032539 0.40862028
Axis point 23.14594564 0.00000000 119.64257084
Rotation angle (degrees) 137.62592761
Shift along axis -110.62045545
Average map value = 0.3246 for 12748 atoms, 6636 outside contour
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
25466 atoms, 25984 bonds, 3276 residues, 5 models selected
> show sel cartoons
> view matrix models
> #8,0.24657,-0.046954,0.96799,-52.263,-0.91484,-0.34089,0.2165,-164.15,0.31981,-0.93893,-0.12701,66.616,#3,0.78706,0.047102,0.61508,3.7701,-0.17216,0.97424,0.14569,-62.629,-0.59237,-0.22055,0.77489,77.495,#5,0.50063,-0.82071,-0.27532,-142.62,-0.84908,-0.52749,0.028495,-122.34,-0.16862,0.21951,-0.96093,195.07
> fitmap #8 inMap #10 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 14055 points
correlation = 0.8169, correlation about mean = 0.4653, overlap = 1282
steps = 44, shift = 0.903, angle = 0.0117 degrees
Position of pred.rank_0.cif map 8 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.66857921 0.03559245 -0.74278867 149.71008364
0.58629502 0.63967229 -0.49706891 144.40290543
0.45744943 -0.76782324 -0.44853927 117.49310913
Axis -0.20085363 -0.89037241 0.40852759
Axis point 23.15113825 0.00000000 119.62692737
Rotation angle (degrees) 137.62275634
Shift along axis -110.64300103
Average map value = 0.3246 for 12748 atoms, 6638 outside contour
> select subtract #3
12748 atoms, 13008 bonds, 1638 residues, 5 models selected
> select add #3
25466 atoms, 25984 bonds, 3276 residues, 5 models selected
> select subtract #5
25466 atoms, 25984 bonds, 3276 residues, 4 models selected
> select subtract #8
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
> view matrix models
> #3,0.78706,0.047102,0.61508,-66.503,-0.17216,0.97424,0.14569,-153.7,-0.59237,-0.22055,0.77489,99.695
> view matrix models
> #3,0.78706,0.047102,0.61508,-110.64,-0.17216,0.97424,0.14569,-169.74,-0.59237,-0.22055,0.77489,142.71
> view matrix models
> #3,0.78706,0.047102,0.61508,-87.866,-0.17216,0.97424,0.14569,-161.36,-0.59237,-0.22055,0.77489,110.84
> view matrix models
> #3,0.78706,0.047102,0.61508,-84.262,-0.17216,0.97424,0.14569,-172.51,-0.59237,-0.22055,0.77489,123.31
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.41481,0.40236,0.81611,-87.041,0.85204,0.48651,0.19322,-171.29,-0.31931,0.77551,-0.54464,130.65
> view matrix models
> #3,-0.50623,0.62422,0.59505,-86.008,0.85785,0.43522,0.27326,-171.71,-0.088405,0.64879,-0.75581,132.14
> view matrix models
> #3,-0.65162,0.7584,0.014866,-83.061,0.43433,0.35697,0.827,-175.28,0.62189,0.54534,-0.56201,132.05
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.65162,0.7584,0.014866,-67.763,0.43433,0.35697,0.827,-182.41,0.62189,0.54534,-0.56201,128.43
> hide #!10 models
> view matrix models
> #3,-0.65162,0.7584,0.014866,-59.632,0.43433,0.35697,0.827,-185.88,0.62189,0.54534,-0.56201,124.86
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.53983,0.84058,0.044839,-59.667,0.53678,0.30272,0.78755,-185.51,0.64842,0.44921,-0.61462,125.21
> view matrix models
> #3,-0.67555,0.0052812,0.73729,-63.432,0.69592,0.33489,0.63525,-184.48,-0.24356,0.94224,-0.22991,121.8
> view matrix models
> #3,-0.53931,0.25515,0.80252,-63.667,0.8213,0.3699,0.43432,-183.22,-0.18603,0.89335,-0.40904,122.87
> show #!10 models
> view matrix models
> #3,-0.58948,0.37045,0.71783,-63.299,0.80338,0.36148,0.47319,-183.45,-0.084181,0.85563,-0.5107,123.57
> volume #10 level 0.4422
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.58948,0.37045,0.71783,-67.493,0.80338,0.36148,0.47319,-176.67,-0.084181,0.85563,-0.5107,117.2
> view matrix models
> #3,-0.58948,0.37045,0.71783,-66.857,0.80338,0.36148,0.47319,-175.23,-0.084181,0.85563,-0.5107,115.26
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.42921,0.20151,0.88044,-67.492,0.87381,0.33931,0.34832,-174.45,-0.22856,0.91884,-0.32171,114.02
> fitmap #3 inMap #10
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12718 atoms
average map value = 0.3873, steps = 72
shifted from previous position = 4.3
rotated from previous position = 7.18 degrees
atoms outside contour = 6979, contour level = 0.44223
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
0.73869368 -0.10552508 -0.66572976 153.86327524
-0.53440184 -0.69361319 -0.48302735 143.60598788
-0.41078744 0.71257646 -0.56876048 170.67430897
Axis 0.92286811 -0.19678604 -0.33104335
Axis point 0.00000000 50.43540843 143.78278248
Rotation angle (degrees) 139.62667723
Shift along axis 57.23526184
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-118
916 atoms, 926 bonds, 118 residues, 1 model selected
> hide sel cartoons
> volume #10 level 0.5495
Opened pred.rank_0.cif map 8 as #4, grid size 56,61,53, pixel 2.67, shown at
level 0.1, step 1, values float32
> fitmap #3 inMap #10 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 13751 points
correlation = 0.8288, correlation about mean = 0.491, overlap = 1515
steps = 48, shift = 0.157, angle = 0.276 degrees
Position of pred.rank_0.cif map 8 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.74022282 -0.10925087 -0.66342628 153.80182582
-0.53542286 -0.69260274 -0.48334649 143.59352304
-0.40668483 0.71299769 -0.57117576 170.82051385
Axis 0.92333541 -0.19815240 -0.32891846
Axis point 0.00000000 50.52784635 143.66133971
Rotation angle (degrees) 139.62117968
Shift along axis 57.37124977
Average map value = 0.3872 for 12718 atoms, 8948 outside contour
> volume #10 level 0.5289
> volume #10 level 0.4381
> view matrix models
> #3,-0.35282,0.087905,0.93155,-71.273,0.86343,0.41422,0.28794,-176.1,-0.36056,0.90592,-0.22205,115.28
> view matrix models
> #3,-0.37538,0.16218,0.91257,-71.217,0.87703,0.38066,0.29311,-176.11,-0.29985,0.91038,-0.28513,115.7
> fitmap #3 inMap #10
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12718 atoms
average map value = 0.3873, steps = 60
shifted from previous position = 0.31
rotated from previous position = 2.43 degrees
atoms outside contour = 6921, contour level = 0.4381
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
0.73868763 -0.10552066 -0.66573718 153.86153328
-0.53440825 -0.69360649 -0.48302988 143.60546341
-0.41078999 0.71258363 -0.56874964 170.67680955
Axis 0.92286599 -0.19678774 -0.33104826
Axis point 0.00000000 50.43422926 143.78445414
Rotation angle (degrees) 139.62616936
Shift along axis 57.23152092
Opened pred.rank_0.cif map 6 as #4, grid size 69,75,64, pixel 2, shown at
level 0.112, step 1, values float32
> fitmap #3 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29213 points
correlation = 0.8152, correlation about mean = 0.3877, overlap = 3727
steps = 36, shift = 0.072, angle = 0.22 degrees
Position of pred.rank_0.cif map 6 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
0.73993116 -0.10861944 -0.66385518 153.88774678
-0.53484612 -0.69352350 -0.48266426 143.60314936
-0.40797245 0.71219869 -0.57125434 170.74661505
Axis 0.92327504 -0.19772154 -0.32934693
Axis point 0.00000000 50.56719476 143.63192102
Rotation angle (degrees) 139.67830222
Shift along axis 57.45240519
Average map value = 0.3873 for 12718 atoms, 6932 outside contour
> show #!1 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> select add #9
916 atoms, 926 bonds, 118 residues, 4 models selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 4 models selected
> select subtract #3
3 models selected
> select add #5
4 models selected
> close #3
> close #9
> show #!1 models
> show #!4 models
> view matrix models
> #5,0.50063,-0.82071,-0.27532,-142.62,-0.84908,-0.52749,0.028495,-122.34,-0.16862,0.21951,-0.96093,195.07
> close #5
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 1 model selected
> hide #!10 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select subtract #8
1 model selected
> show #!10 models
> show #!7 models
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> view matrix models
> #7,0.57165,-0.26251,0.77737,8.2917,-0.74565,0.22915,0.6257,-58.526,-0.34238,-0.93733,-0.064743,1.8352
> view matrix models
> #7,0.61257,-0.18089,0.76944,7.3096,-0.70992,0.30211,0.6362,-59.457,-0.34753,-0.93595,0.056647,1.449
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.61257,-0.18089,0.76944,-94.163,-0.70992,0.30211,0.6362,-137.46,-0.34753,-0.93595,0.056647,87.563
> view matrix models
> #7,0.61257,-0.18089,0.76944,-101.49,-0.70992,0.30211,0.6362,-141.76,-0.34753,-0.93595,0.056647,103.01
> view matrix models
> #7,0.61257,-0.18089,0.76944,-77.086,-0.70992,0.30211,0.6362,-169.7,-0.34753,-0.93595,0.056647,119.88
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.1113,-0.085927,0.99006,-78.707,-0.97768,-0.18813,0.093583,-161.98,0.17822,-0.97838,-0.10495,120.67
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.1113,-0.085927,0.99006,-74.649,-0.97768,-0.18813,0.093583,-175.06,0.17822,-0.97838,-0.10495,122.28
> view matrix models
> #7,0.1113,-0.085927,0.99006,-72.389,-0.97768,-0.18813,0.093583,-170.88,0.17822,-0.97838,-0.10495,124.22
> view matrix models
> #7,0.1113,-0.085927,0.99006,-68.18,-0.97768,-0.18813,0.093583,-173.38,0.17822,-0.97838,-0.10495,122.31
> view matrix models
> #7,0.1113,-0.085927,0.99006,-70.153,-0.97768,-0.18813,0.093583,-176.13,0.17822,-0.97838,-0.10495,112.62
> view matrix models
> #7,0.1113,-0.085927,0.99006,-67.046,-0.97768,-0.18813,0.093583,-174.86,0.17822,-0.97838,-0.10495,112.21
> view matrix models
> #7,0.1113,-0.085927,0.99006,-67.472,-0.97768,-0.18813,0.093583,-175.66,0.17822,-0.97838,-0.10495,107.24
> view matrix models
> #7,0.1113,-0.085927,0.99006,-67.94,-0.97768,-0.18813,0.093583,-176.26,0.17822,-0.97838,-0.10495,107.42
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.17392,-0.18173,0.96785,-66.736,-0.97655,-0.15847,0.14572,-176.78,0.1269,-0.97049,-0.20503,107.65
> view matrix models
> #7,0.11516,-0.1418,0.98317,-67.243,-0.97399,-0.21055,0.083716,-175.96,0.19514,-0.96725,-0.16235,107.46
> view matrix models
> #7,0.193,-0.21396,0.95759,-66.321,-0.96679,-0.20811,0.14835,-176.19,0.16754,-0.95442,-0.24702,107.57
> view matrix models
> #7,0.27278,-0.27204,0.92281,-65.543,-0.95424,-0.19869,0.2235,-176.54,0.12255,-0.94155,-0.31379,107.64
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.27278,-0.27204,0.92281,-66.594,-0.95424,-0.19869,0.2235,-177.48,0.12255,-0.94155,-0.31379,112.34
> fitmap #7 inMap #10
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc z flip (#10) using 12649 atoms
average map value = 0.4096, steps = 80
shifted from previous position = 1.3
rotated from previous position = 3.5 degrees
atoms outside contour = 6473, contour level = 0.4381
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64092906 0.28191777 -0.71395539 150.24286720
0.70679434 0.57955901 -0.40565146 145.31927441
0.29941892 -0.76461344 -0.57071410 167.18605306
Axis -0.31052477 -0.87663276 0.36754506
Axis point 11.52176376 0.00000000 134.98350275
Rotation angle (degrees) 144.69053086
Shift along axis -112.59736156
> hide #!7 models
> show #!7 models
> fitmap #7 inMap #10 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc z flip using 29813 points
correlation = 0.847, correlation about mean = 0.4561, overlap = 3898
steps = 44, shift = 0.0494, angle = 0.0812 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64005647 0.28151612 -0.71489607 150.28218550
0.70715071 0.57968453 -0.40485024 145.29166242
0.30044232 -0.76466628 -0.57010516 167.17760015
Axis -0.31065474 -0.87661375 0.36748057
Axis point 11.44477597 0.00000000 135.02299159
Rotation angle (degrees) 144.61095593
Shift along axis -112.61602138
Average map value = 0.4096 for 12649 atoms, 6473 outside contour
> view matrix models
> #7,0.22175,-0.24374,0.94415,-67.508,-0.96664,-0.18223,0.17999,-177.7,0.12818,-0.95257,-0.27602,112.09
> fitmap #7 inMap #10 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc z flip using 29813 points
correlation = 0.847, correlation about mean = 0.456, overlap = 3898
steps = 60, shift = 0.414, angle = 0.0125 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64016476 0.28142594 -0.71483461 150.28492735
0.70709888 0.57960922 -0.40504853 145.29222029
0.30033357 -0.76475655 -0.57004137 167.18053027
Axis -0.31060671 -0.87659444 0.36756721
Axis point 11.45471759 0.00000000 135.03199146
Rotation angle (degrees) 144.61688276
Shift along axis -112.59177879
Average map value = 0.4096 for 12649 atoms, 6474 outside contour
> view matrix models
> #7,0.2219,-0.24361,0.94415,-68.385,-0.96662,-0.18219,0.18017,-178.28,0.12812,-0.95261,-0.2759,111.85
> view matrix models
> #7,0.2219,-0.24361,0.94415,-67.61,-0.96662,-0.18219,0.18017,-178.13,0.12812,-0.95261,-0.2759,111
> hide #!8 models
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/pred.rank_0.cif
Summary of feedback from opening /Users/bo1il/Downloads/Chai_Discovery/PusCD-
GroPI/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': might have incorrect bonds
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #3
---
Chain | Description
B | Entity B
C | Entity C
Non-standard residues in pred.rank_0.cif #3
---
LIG1 — (LIG1)
> select subtract #7
2 models selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> view matrix models #3,1,0,0,-29.532,0,1,0,-138.51,0,0,1,11.181
> view matrix models #3,1,0,0,-52.968,0,1,0,-154.31,0,0,1,57.522
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.88382,0.053437,-0.46476,-50.594,0.11063,0.9414,0.31862,-155.89,0.45455,-0.33302,0.82612,59.156
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.88382,0.053437,-0.46476,-51.831,0.11063,0.9414,0.31862,-158.2,0.45455,-0.33302,0.82612,64.321
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.83797,0.13047,-0.52988,-51.554,0.091252,0.92383,0.37178,-158.51,0.53803,-0.35989,0.76224,64.787
> view matrix models
> #3,0.82428,0.14469,-0.54739,-51.48,0.091492,0.92005,0.38098,-158.56,0.55875,-0.36411,0.74514,64.909
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.82428,0.14469,-0.54739,-48.186,0.091492,0.92005,0.38098,-160.55,0.55875,-0.36411,0.74514,66.668
> view matrix models
> #3,0.82428,0.14469,-0.54739,-48.387,0.091492,0.92005,0.38098,-162.46,0.55875,-0.36411,0.74514,70.713
> view matrix models
> #3,0.82428,0.14469,-0.54739,-50.298,0.091492,0.92005,0.38098,-161.43,0.55875,-0.36411,0.74514,70.517
Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/B:2
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/B:2-174
1321 atoms, 1338 bonds, 173 residues, 1 model selected
> hide sel cartoons
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> view matrix models
> #3,0.82428,0.14469,-0.54739,-49.381,0.091492,0.92005,0.38098,-161.35,0.55875,-0.36411,0.74514,67.355
> view matrix models
> #3,0.82428,0.14469,-0.54739,-48.519,0.091492,0.92005,0.38098,-163.41,0.55875,-0.36411,0.74514,68.573
> fitmap #3 inMap #10
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12718 atoms
average map value = 0.3353, steps = 116
shifted from previous position = 2.97
rotated from previous position = 14.9 degrees
atoms outside contour = 8191, contour level = 0.4381
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
-0.74973996 0.10098207 0.65398213 144.40821399
-0.50510195 -0.72580599 -0.46698788 142.87247267
0.42750674 -0.68044712 0.59517200 118.99838083
Axis -0.31330354 0.33240790 -0.88957624
Axis point 68.74746673 82.62151647 0.00000000
Rotation angle (degrees) 160.08298070
Shift along axis -103.60979745
> hide #3 models
> show #3 models
> fitmap #3 inMap #10 resolution 6 metric correlation
Fit map pred.rank_0.cif map 6 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 29213 points
correlation = 0.8144, correlation about mean = 0.3754, overlap = 3234
steps = 40, shift = 0.0791, angle = 0.16 degrees
Position of pred.rank_0.cif map 6 (#4) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.75106311 0.10133149 0.65240795 144.46373917
-0.50344821 -0.72718205 -0.46663279 142.88976220
0.42713475 -0.67892429 0.59717477 118.93972520
Axis -0.31247254 0.33158033 -0.89017717
Axis point 68.78508008 82.57651371 0.00000000
Rotation angle (degrees) 160.14163062
Shift along axis -103.63894422
Average map value = 0.3352 for 12718 atoms, 8212 outside contour
Opened pred.rank_0.cif map 8 as #5, grid size 56,61,53, pixel 2.67, shown at
level 0.1, step 1, values float32
> fitmap #3 inMap #10 resolution 8 metric correlation
Fit map pred.rank_0.cif map 8 in map cryosparc_P13_J593_map_sharp.mrc z flip
using 13751 points
correlation = 0.8288, correlation about mean = 0.4835, overlap = 1316
steps = 40, shift = 0.095, angle = 0.0956 degrees
Position of pred.rank_0.cif map 8 (#5) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.75011847 0.10118482 0.65351658 144.53592183
-0.50445520 -0.72654959 -0.46653043 142.89195054
0.42760641 -0.67962293 0.59604147 118.88065172
Axis -0.31308584 0.33191819 -0.88983570
Axis point 68.82540584 82.57045370 0.00000000
Rotation angle (degrees) 160.10423620
Shift along axis -103.60796085
Average map value = 0.3351 for 12718 atoms, 8216 outside contour
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select add #7
25367 atoms, 25882 bonds, 3268 residues, 2 models selected
> select subtract #7
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
Opened fold_puscd1_fj_model_0.cif map 8 as #2, grid size 59,70,51, pixel 2.67,
shown at level 0.0906, step 1, values float32
> fitmap #7 inMap #10 resolution 8 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 8 in map
cryosparc_P13_J593_map_sharp.mrc z flip using 14195 points
correlation = 0.8602, correlation about mean = 0.571, overlap = 1576
steps = 64, shift = 1.18, angle = 0.142 degrees
Position of fold_puscd1_fj_model_0.cif map 8 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.63978744 0.27950391 -0.71592569 150.23631207
0.70716090 0.57890632 -0.40594448 145.25946719
0.30099084 -0.76599284 -0.56803123 167.21628664
Axis -0.31026611 -0.87631212 0.36852681
Axis point 11.34322390 0.00000000 135.20743979
Rotation angle (degrees) 144.53362503
Shift along axis -112.28218231
Average map value = 0.4096 for 12649 atoms, 6474 outside contour
> show #!2 models
> hide #!2 models
Opened fold_puscd1_fj_model_0.cif map 6 as #2, grid size 73,87,62, pixel 2,
shown at level 0.105, step 1, values float32
> fitmap #7 inMap #10 resolution 6 metric correlation
Fit map fold_puscd1_fj_model_0.cif map 6 in map
cryosparc_P13_J593_map_sharp.mrc z flip using 29813 points
correlation = 0.847, correlation about mean = 0.456, overlap = 3898
steps = 48, shift = 0.0664, angle = 0.145 degrees
Position of fold_puscd1_fj_model_0.cif map 6 (#2) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64001954 0.28154996 -0.71491580 150.28294930
0.70722830 0.57955942 -0.40489383 145.29286004
0.30033835 -0.76474865 -0.57004945 167.18065812
Axis -0.31070049 -0.87657562 0.36753285
Axis point 11.43907743 0.00000000 135.02993672
Rotation angle (degrees) 144.61256231
Shift along axis -112.60877983
Average map value = 0.4096 for 12649 atoms, 6473 outside contour
> show #!2 models
> hide #!10 models
> hide #!7 models
> view matrix models
> #3,0.72726,0.37071,-0.57764,-43.874,-0.0027002,0.84314,0.53769,-162.07,0.68636,-0.38948,0.61418,76.408
> view matrix models
> #3,0.72726,0.37071,-0.57764,-45.025,-0.0027002,0.84314,0.53769,-163.18,0.68636,-0.38948,0.61418,73.441
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> ui tool show "Side View"
> view
> view orient
> ui tool show ViewDockX
No suitable models found for ViewDockX
> view orient
Drag select of 4 pred.rank_0.cif map 6 , 2 fold_puscd1_fj_model_0.cif map 6
> view sel
[Repeated 1 time(s)]
> select subtract #2
2 models selected
> select subtract #4
Nothing selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/bo1il/Desktop/movie1.mp4
Movie saved to /Users/bo1il/Desktop/movie1.mp4
> open /Users/bo1il/Downloads/placed_model.pdb
Summary of feedback from opening /Users/bo1il/Downloads/placed_model.pdb
---
warning | Ignored bad PDB record found on line 22712
Chain information for placed_model.pdb #9
---
Chain | Description
A C | No description available
B D | No description available
> hide #9 models
> show #9 models
> hide #!4 models
> hide #!2 models
> show #!10 models
> hide #9 models
> show #9 models
> hide #!10 models
Drag select of 82 residues
> view
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #2
636 atoms, 82 residues, 3 models selected
> select subtract #2
636 atoms, 82 residues, 1 model selected
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 1 model selected
Drag select of 49 residues
Drag select of 52 residues
Drag select of 541 residues
> ui mousemode right "translate selected models"
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 1 model selected
> view matrix models #9,1,0,0,-81.475,0,1,0,-284.82,0,0,1,-133.41
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.87325,-0.48726,0.0042683,265.49,0.48254,-0.86593,-0.13161,-75.637,0.067824,-0.11287,0.99129,-126.41
> view matrix models
> #9,-0.95614,-0.29264,0.012414,249.34,0.28666,-0.94363,-0.16551,-30.616,0.060148,-0.15469,0.98613,-118.64
> show #!4 models
> hide #!4 models
> view matrix models
> #9,-0.7981,-0.51367,-0.31493,304.33,0.51804,-0.85191,0.076685,-113.13,-0.30769,-0.10195,0.94601,-65.407
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.7981,-0.51367,-0.31493,243.53,0.51804,-0.85191,0.076685,-169.39,-0.30769,-0.10195,0.94601,19.766
> show #!4 models
> view matrix models
> #9,-0.7981,-0.51367,-0.31493,179.42,0.51804,-0.85191,0.076685,-154.05,-0.30769,-0.10195,0.94601,11.196
> view matrix models
> #9,-0.7981,-0.51367,-0.31493,178.58,0.51804,-0.85191,0.076685,-150.83,-0.30769,-0.10195,0.94601,17.968
> view matrix models
> #9,-0.7981,-0.51367,-0.31493,179.51,0.51804,-0.85191,0.076685,-150.95,-0.30769,-0.10195,0.94601,12.856
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.81417,-0.50686,-0.28324,176.35,0.51018,-0.85739,0.067831,-147.73,-0.27723,-0.089276,0.95665,4.9938
> select subtract #9
Nothing selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
[Repeated 2 time(s)]
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.95684,-0.12274,-0.26341,140.8,0.18198,-0.95977,-0.21383,-43.562,-0.22657,-0.25254,0.94069,22.685
> view matrix models
> #9,-0.92193,-0.26197,-0.28532,158.33,0.33146,-0.91471,-0.23118,-69.65,-0.20043,-0.3077,0.93013,28.066
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.92193,-0.26197,-0.28532,154.7,0.33146,-0.91471,-0.23118,-66.537,-0.20043,-0.3077,0.93013,26.953
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.88562,-0.25842,-0.38587,163.38,0.34338,-0.92379,-0.16942,-76.001,-0.31268,-0.28255,0.90686,43.527
> hide #!2 models
> select subtract #9
Nothing selected
> save /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
> show #3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #9 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#3) with placed_model.pdb, chain A (#9),
sequence alignment score = 4500.1
RMSD between 817 pruned atom pairs is 0.692 angstroms; (across all 896 pairs:
1.426)
> show #!8 models
> hide #!8 models
> ui mousemode right translate
> show #!7 models
> ui tool show Matchmaker
> matchmaker #!7 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker placed_model.pdb, chain A (#9) with fold_puscd1_fj_model_0.cif,
chain A (#7), sequence alignment score = 4633.3
RMSD between 896 pruned atom pairs is 0.001 angstroms; (across all 896 pairs:
0.001)
> hide #3 models
> show #3 models
> show #!4 models
> hide #!4 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> view
> ui tool show Matchmaker
> select #9/C
6896 atoms, 7031 bonds, 896 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!7 to #9/C pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker placed_model.pdb, chain C (#9) with fold_puscd1_fj_model_0.cif,
chain A (#7), sequence alignment score = 4633.3
RMSD between 896 pruned atom pairs is 0.001 angstroms; (across all 896 pairs:
0.001)
> save /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
——— End of log from Mon Sep 8 23:51:23 2025 ———
opened ChimeraX session
> show #!10 models
> hide #9 models
> hide #3 models
> hide #!7 models
> volume erase #10 center -112.17,-208.73,144.53 radius 30.239
> volume erase #10 center -129.67,-190.52,114.68 radius 30.239
> volume erase #10 center -132.43,-184.89,109.16 radius 30.239
> volume erase #10 center -129.72,-177.57,87.745 radius 30.239
> volume erase #10 center -122.26,-173.95,71.006 radius 30.239
> volume erase #10 center -118.54,-168.83,63.457 radius 30.239
> volume erase #10 center -120.29,-163.97,80.312 radius 30.239
> volume erase #10 center -129.45,-173.17,108.83 radius 30.239
> volume erase #10 center -123.17,-197.62,132.25 radius 30.239
> volume erase #10 center -74.157,-228.12,147.95 radius 30.239
> volume erase #10 center -38.239,-230.35,139.75 radius 30.239
> volume erase #10 center -40.33,-226.58,139.34 radius 30.239
> volume erase #10 center -24.622,-225.47,105.39 radius 30.239
> volume erase #10 center -43.412,-259.16,102.75 radius 30.239
> volume erase #10 center -47.921,-258.77,116.33 radius 30.239
> volume erase #10 center -13.378,-226.72,62.416 radius 30.239
> volume erase #10 center -16.68,-227.44,57.894 radius 30.239
> volume erase #10 center -7.3198,-198.45,41.169 radius 30.239
> volume erase #10 center -43.484,-173.97,12.974 radius 30.239
> volume erase #10 center -71.257,-156.71,12.442 radius 30.239
> volume erase #10 center -91.293,-155.64,25.226 radius 30.239
> volume erase #10 center -112.35,-153.88,52.608 radius 30.239
> volume erase #10 center -125.39,-185.52,48.177 radius 30.239
> volume erase #10 center -127.16,-193.89,51.756 radius 30.239
> volume erase #10 center -132.13,-197.99,67.29 radius 30.239
> volume erase #10 center -135.65,-204.35,82.675 radius 30.239
[Repeated 1 time(s)]
> volume erase #10 center -130.23,-215.87,72.52 radius 30.239
> volume erase #10 center -125.54,-211.41,54.036 radius 30.239
> volume erase #10 center -115.53,-194.6,145.42 radius 30.239
> volume erase #10 center -97.216,-209.94,152.93 radius 30.239
> volume erase #10 center -16.928,-215.46,89.65 radius 30.239
> volume erase #10 center -25.637,-203.94,88.941 radius 19.812
> volume erase #10 center -16.689,-191.29,62.747 radius 12.662
> volume erase #10 center -38.605,-222.78,44.925 radius 12.662
> volume erase #10 center -33.934,-228.71,76.707 radius 12.662
> ui mousemode right "map eraser"
> volume erase #10 center -20.452,-232.48,76.222 radius 27.856
> ui mousemode right translate
[Repeated 1 time(s)]
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 1 model selected
> select subtract #9
Nothing selected
> close #11
> ui mousemode right translate
> show #3 models
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.72726,0.37071,-0.57764,-45.508,-0.0027002,0.84314,0.53769,-165.95,0.68636,-0.38948,0.61418,71.004
> view matrix models
> #3,0.72726,0.37071,-0.57764,-48.502,-0.0027002,0.84314,0.53769,-165.41,0.68636,-0.38948,0.61418,69.677
> view matrix models
> #3,0.72726,0.37071,-0.57764,-46.529,-0.0027002,0.84314,0.53769,-166.34,0.68636,-0.38948,0.61418,70.46
> view matrix models
> #3,0.72726,0.37071,-0.57764,-47.21,-0.0027002,0.84314,0.53769,-165.84,0.68636,-0.38948,0.61418,69.933
> fitmap #3 inMap #10
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J593_map_sharp.mrc z
flip (#10) using 12718 atoms
average map value = 0.3349, steps = 40
shifted from previous position = 0.944
rotated from previous position = 0.202 degrees
atoms outside contour = 8192, contour level = 0.4381
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J593_map_sharp.mrc
z flip (#10) coordinates:
Matrix rotation and translation
-0.74829454 0.10138273 0.65557367 144.38155424
-0.50691216 -0.72485002 -0.46651100 142.80236378
0.42789643 -0.68140589 0.59379345 119.02165136
Axis -0.31411226 0.33279623 -0.88914574
Axis point 68.74978652 82.58597956 0.00000000
Rotation angle (degrees) 159.99714118
Shift along axis -103.65552197
> show #!4 models
> select add #4
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
> select subtract #4
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> volume #6 style image region 0,0,159,319,319,159 step 1 showOutlineBox true
> volume #6 region 0,0,0,319,319,319 step 1
> volume #6 style mesh region 0,0,0,319,319,319 step 1
> volume #6 style surface
> hide #!6 models
> hide #!10 models
> ui mousemode right "map eraser"
> volume erase #4 center -13.158,-205.48,84.347 radius 28.54
> volume erase #4 center -24.176,-205.87,107.22 radius 28.54
> volume erase #4 center -28.302,-210.44,102.23 radius 28.54
> volume erase #4 center -38.026,-214.23,103.77 radius 28.54
> volume erase #4 center -43.734,-233.71,96.718 radius 28.54
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #3 models
> show #3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show sel surfaces
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #4.1 target m
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> ui mousemode right translate
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> save /Users/bo1il/Desktop/image35.png supersample 3
> hide #!4 models
> save /Users/bo1il/Desktop/image36.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/bo1il/Desktop/image37.png supersample 3
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> select subtract #3
2 models selected
> select add #1
2 models selected
> select subtract #1
Nothing selected
> show #!1 target m
> show #1.1 models
> select add #1
4 models selected
> close #1
> show #!2 models
> show #!3 models
> view
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
> volume erase #2 center -50.05,-206.86,44.29 radius 31.059
> volume erase #2 center -90.176,-218.18,38.495 radius 31.059
> volume erase #2 center -98.193,-238.39,44.518 radius 31.059
> show #!8 models
> select add #8
12748 atoms, 13008 bonds, 1638 residues, 1 model selected
> close #11
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!2 models
> hide #!10 models
> show #!10 models
> close #8
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.24769,-0.24813,0.93653,-67.532,-0.96256,-0.17294,0.20875,-175.44,0.11016,-0.95316,-0.28168,115.78
> view matrix models
> #7,0.24769,-0.24813,0.93653,-67.083,-0.96256,-0.17294,0.20875,-179.04,0.11016,-0.95316,-0.28168,114.26
> view matrix models
> #7,0.24769,-0.24813,0.93653,-66.304,-0.96256,-0.17294,0.20875,-179.16,0.11016,-0.95316,-0.28168,110.94
> view matrix models
> #7,0.24769,-0.24813,0.93653,-67.438,-0.96256,-0.17294,0.20875,-178.31,0.11016,-0.95316,-0.28168,110.26
> fitmap #7 inMap #10
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc z flip (#10) using 12649 atoms
average map value = 0.4086, steps = 52
shifted from previous position = 1.87
rotated from previous position = 1.75 degrees
atoms outside contour = 6487, contour level = 0.4381
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64094900 0.28120005 -0.71422049 150.23338458
0.70679316 0.57912504 -0.40627283 145.30434024
0.29937903 -0.76520632 -0.56993989 167.14981044
Axis -0.31037875 -0.87648479 0.36802098
Axis point 11.50813731 0.00000000 135.02875915
Rotation angle (degrees) 144.67465829
Shift along axis -112.47165626
> fitmap #7 inMap #10
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc z flip (#10) using 12649 atoms
average map value = 0.4086, steps = 48
shifted from previous position = 0.00244
rotated from previous position = 0.00182 degrees
atoms outside contour = 6488, contour level = 0.4381
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64094908 0.28119335 -0.71422306 150.23307636
0.70680060 0.57910211 -0.40629257 145.30452097
0.29936131 -0.76522613 -0.56992260 167.14738762
Axis -0.31038097 -0.87647780 0.36803577
Axis point 11.50786829 0.00000000 135.02906528
Rotation angle (degrees) 144.67494127
Shift along axis -112.46945720
> view matrix models
> #7,0.22298,-0.24308,0.94403,-67.916,-0.96646,-0.18173,0.18148,-178.71,0.12744,-0.95283,-0.27545,112.37
> fitmap #7 inMap #10
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J593_map_sharp.mrc z flip (#10) using 12649 atoms
average map value = 0.4086, steps = 48
shifted from previous position = 0.719
rotated from previous position = 0.00947 degrees
atoms outside contour = 6482, contour level = 0.4381
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64100716 0.28116161 -0.71418342 150.23471035
0.70670839 0.57923527 -0.40626316 145.30251611
0.29945463 -0.76513701 -0.56999323 167.16929565
Axis -0.31032765 -0.87651947 0.36798148
Axis point 11.51350759 0.00000000 135.03430167
Rotation angle (degrees) 144.67472109
Shift along axis -112.46726382
> show #!4 models
> hide #!4 models
> close #5
> ui tool show "Fit in Map"
Average map value = 0.4086 for 12649 atoms, 6482 outside contour
Opened fold_puscd1_fj_model_0.cif map 7 as #1, grid size 65,78,56, pixel 2.33,
shown at level 0.0982, step 1, values float32
> fitmap #7 inMap #10 resolution 7
Fit map fold_puscd1_fj_model_0.cif map 7 in map
cryosparc_P13_J593_map_sharp.mrc z flip using 20067 points
correlation = 0.858, correlation about mean = 0.5372, overlap = 2399
steps = 60, shift = 0.0684, angle = 0.169 degrees
Position of fold_puscd1_fj_model_0.cif map 7 (#1) relative to
cryosparc_P13_J593_map_sharp.mrc z flip (#10) coordinates:
Matrix rotation and translation
-0.64052017 0.28086519 -0.71473677 150.25141405
0.70781376 0.57694270 -0.40759882 145.24009847
0.29788185 -0.76697579 -0.56834368 167.19532327
Axis -0.31082190 -0.87580470 0.36926396
Axis point 11.43827028 0.00000000 135.18769476
Rotation angle (degrees) 144.68245239
Shift along axis -112.16418256
Average map value = 0.4085 for 12649 atoms, 6493 outside contour
> show #!1 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> show #!3 models
> hide #!3 models
> show #!3 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!10 models
> view sel
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!10 models
> hide #!10 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #1.1 models
> show #!10 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 5 models selected
> hide sel surfaces
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> select add #9
35420 atoms, 36158 bonds, 4558 residues, 8 models selected
> select subtract #9
12718 atoms, 12976 bonds, 1638 residues, 7 models selected
> select add #9
35420 atoms, 36158 bonds, 4558 residues, 8 models selected
> select subtract #9
12718 atoms, 12976 bonds, 1638 residues, 7 models selected
> select subtract #3
2 models selected
> select #9/D
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> select #9/B
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> hide sel surfaces
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel cartoons
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> save /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
——— End of log from Tue Sep 9 17:01:25 2025 ———
> view name session-start
opened ChimeraX session
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select add #7
17104 atoms, 17466 bonds, 2194 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!7 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#3) with fold_puscd1_fj_model_0.cif,
chain A (#7), sequence alignment score = 5296.1
RMSD between 811 pruned atom pairs is 0.690 angstroms; (across all 1066 pairs:
23.082)
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #9 models
> show #!7 models
> show #9 models
> view sel
> select subtract #7
4455 atoms, 4560 bonds, 564 residues, 3 models selected
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 1 model selected
> select subtract #9
Nothing selected
> select #9/D
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> select #9/B
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> show sel cartoons
> select #9/A
6896 atoms, 7031 bonds, 896 residues, 1 model selected
> select #9/C
6896 atoms, 7031 bonds, 896 residues, 1 model selected
> hide sel cartoons
> select #9/D
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> hide sel cartoons
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> select add #9
22723 atoms, 23203 bonds, 2921 residues, 2 models selected
> select #9/B
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> show sel surfaces
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 4 models selected
> select #9/A
6896 atoms, 7031 bonds, 896 residues, 1 model selected
> show sel surfaces
> select add #3
19614 atoms, 20007 bonds, 2534 residues, 7 models selected
> show sel surfaces
> select subtract #3
6896 atoms, 7031 bonds, 896 residues, 4 models selected
> ui mousemode right rotate
> view sel
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> show sel surfaces
> hide #!7 models
> show #!7 models
> show sel surfaces
> select add #7
12670 atoms, 12927 bonds, 1631 residues, 3 models selected
> show sel surfaces
> hide sel cartoons
> select subtract #7
21 atoms, 21 bonds, 1 residue, 4 models selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide #!9 models
> hide #!3 models
> show #!3 models
> select subtract #3.3
1 model selected
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!6 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> save /Users/bo1il/Downloads/Chai_Discovery/PusCD-GroPI/CryoMap_PusCD1.cxs
——— End of log from Tue Sep 9 22:50:05 2025 ———
> view name session-start
opened ChimeraX session
> open /Users/bo1il/Downloads/cryosparc_P13_J679_map_sharp.mrc
Opened cryosparc_P13_J679_map_sharp.mrc as #5, grid size 320,320,320, pixel
0.931, shown at level 0.343, step 2, values float32
> hide #!5 models
> show #!5 models
> volume flip #5
Opened cryosparc_P13_J679_map_sharp.mrc z flip as #8, grid size 320,320,320,
pixel 0.931, shown at step 1, values float32
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
21 atoms, 21 bonds, 1 residue, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.72646,0.37042,-0.57883,-94.977,0.00014451,0.84221,0.53915,-287.63,0.68721,-0.39175,0.61178,57.778,#8,1,0,0,-47.132,0,1,0,-121.36,0,0,1,-11.611
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 4 models selected
> select subtract #3
6 models selected
> view matrix models #8,1,0,0,-118.56,0,1,0,-444.11,0,0,1,-105.06
> view sel
> hide #!3 models
> show #!1 models
> select add #1
5 models selected
> select subtract #1
3 models selected
> select add #1
5 models selected
> select subtract #1
3 models selected
> show #1.1 models
> hide #1.1 models
> hide #!1 models
> show #!3 models
> view matrix models #8,1,0,0,-117.92,0,1,0,-441.94,0,0,1,-76.823
> view
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 3 models selected
> show sel cartoons
> hide sel surfaces
> select subtract #8
12718 atoms, 12976 bonds, 1638 residues, 4 models selected
> view matrix models
> #3,0.72646,0.37042,-0.57883,-48.955,0.00014451,0.84221,0.53915,-291.19,0.68721,-0.39175,0.61178,54.861
> view matrix models
> #3,0.72646,0.37042,-0.57883,37.353,0.00014451,0.84221,0.53915,-297.76,0.68721,-0.39175,0.61178,45.54
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.71485,0.044193,-0.69788,38.066,-0.50028,-0.66498,-0.55455,-292.09,-0.48859,0.74555,-0.45325,49.528
> view matrix models
> #3,0.70355,0.018544,-0.71041,38.126,-0.36363,-0.84949,-0.38229,-292.8,-0.61057,0.52728,-0.59091,50.171
> view matrix models
> #3,0.65514,-0.057564,-0.75331,38.315,-0.43546,-0.84358,-0.31425,-293.27,-0.61739,0.53392,-0.57772,50.089
> view matrix models
> #3,0.058156,-0.21298,0.97532,28.11,-0.55633,-0.81813,-0.14548,-294.36,0.82892,-0.53414,-0.16606,50.015
> view matrix models
> #3,-0.14889,-0.11002,0.98271,27.771,-0.57372,-0.79982,-0.17647,-294.22,0.80541,-0.59007,0.055965,48.783
> view matrix models
> #3,-0.45845,0.14274,0.87718,27.876,-0.54824,-0.82226,-0.15273,-294.31,0.69947,-0.55092,0.45522,46.451
> view matrix models
> #3,-0.37174,0.077261,0.92511,27.745,-0.54542,-0.82457,-0.15031,-294.32,0.75121,-0.56045,0.34867,47.104
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.37174,0.077261,0.92511,27.543,-0.54542,-0.82457,-0.15031,-299.85,0.75121,-0.56045,0.34867,37.908
> view matrix models
> #3,-0.37174,0.077261,0.92511,26.192,-0.54542,-0.82457,-0.15031,-299.6,0.75121,-0.56045,0.34867,37.596
> view matrix models
> #3,-0.37174,0.077261,0.92511,28.23,-0.54542,-0.82457,-0.15031,-302.62,0.75121,-0.56045,0.34867,34.327
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.47881,0.193,0.85644,28.435,-0.54519,-0.83,-0.11775,-302.8,0.68813,-0.5233,0.50263,33.393
> fitmap #3 inMap #8
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12718 atoms
average map value = 0.2149, steps = 108
shifted from previous position = 2.6
rotated from previous position = 6.07 degrees
atoms outside contour = 8937, contour level = 0.3426
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.55758950 0.22863368 0.79801039 144.85840474
-0.54588772 -0.82521665 -0.14499678 140.09630212
0.62538032 -0.51647276 0.58494046 111.99649990
Axis -0.42397565 0.19702741 -0.88398238
Axis point 67.26718358 70.97484799 0.00000000
Rotation angle (degrees) 154.01814726
Shift along axis -132.81655770
> view matrix models
> #3,-0.58091,0.13807,0.80217,26.905,-0.42045,-0.89475,-0.15048,-301.63,0.69697,-0.42469,0.57782,35.285
> view matrix models
> #3,-0.59716,0.17041,0.78381,26.976,-0.47537,-0.86226,-0.1747,-301.58,0.64608,-0.47693,0.59592,35.131
> view matrix models
> #3,-0.78637,0.031984,0.61693,27.67,-0.30139,-0.8916,-0.33794,-300.45,0.53925,-0.45169,0.71077,34.356
> fitmap #3 inMap #8
Fit molecule pred.rank_0.cif (#3) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12718 atoms
average map value = 0.3843, steps = 136
shifted from previous position = 7.75
rotated from previous position = 17.2 degrees
atoms outside contour = 5904, contour level = 0.3426
Position of pred.rank_0.cif (#3) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.74030915 0.09029180 0.66617547 144.33972183
-0.50928815 -0.72216655 -0.46808232 142.75148768
0.43882564 -0.68580090 0.58061105 119.09955418
Axis -0.32150324 0.33572563 -0.88539481
Axis point 68.04681192 83.02807867 0.00000000
Rotation angle (degrees) 160.20872247
Shift along axis -103.93048213
> ui mousemode right translate
Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/C:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C:1-112
854 atoms, 872 bonds, 112 residues, 1 model selected
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-141
1081 atoms, 1093 bonds, 141 residues, 1 model selected
> hide sel cartoons
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 2 models selected
> show #!7 models
> select add #7
25367 atoms, 25882 bonds, 3268 residues, 5 models selected
> select subtract #3
12649 atoms, 12906 bonds, 1630 residues, 6 models selected
> hide sel cartoons
> hide sel surfaces
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.73057,-0.17641,-0.65966,-45.975,-0.22127,-0.85277,0.4731,-181.61,-0.646,0.49159,0.58397,93.552
> view matrix models
> #7,-0.73057,-0.17641,-0.65966,38.38,-0.22127,-0.85277,0.4731,-252.63,-0.646,0.49159,0.58397,94.549
> view matrix models
> #7,-0.73057,-0.17641,-0.65966,31.705,-0.22127,-0.85277,0.4731,-289.35,-0.646,0.49159,0.58397,96.509
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.9415,-0.22855,-0.24767,30.391,0.22712,0.97325,-0.034726,-310.12,0.24898,-0.023557,0.96822,101.21
> view matrix models
> #7,0.61656,-0.29052,-0.73175,32.757,0.53644,0.83531,0.12036,-309.05,0.57627,-0.46675,0.67086,107.36
> view matrix models
> #7,-0.39625,0.51617,-0.75931,23.477,0.75536,0.6534,0.049982,-306.72,0.52193,-0.55375,-0.64881,112.48
> view matrix models
> #7,-0.7664,0.64073,0.045754,19.654,0.56732,0.70855,-0.41965,-305.87,-0.3013,-0.29566,-0.90653,110.48
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.7664,0.64073,0.045754,27.83,0.56732,0.70855,-0.41965,-293.87,-0.3013,-0.29566,-0.90653,112.36
> view matrix models
> #7,-0.7664,0.64073,0.045754,39.053,0.56732,0.70855,-0.41965,-296.48,-0.3013,-0.29566,-0.90653,87.228
> view matrix models
> #7,-0.7664,0.64073,0.045754,38.414,0.56732,0.70855,-0.41965,-297.07,-0.3013,-0.29566,-0.90653,98.626
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.61219,0.75384,-0.23864,37.85,0.7779,0.6283,-0.010862,-297.43,0.14175,-0.19229,-0.97105,97.389
> view matrix models
> #7,-0.45995,0.56696,-0.68338,41.415,0.78265,0.62237,-0.010415,-297.36,0.41941,-0.53964,-0.72999,100.75
> view matrix models
> #7,-0.39579,0.49042,-0.77643,42.602,0.80954,0.58549,-0.042855,-296.83,0.43358,-0.64551,-0.62875,101.72
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.39579,0.49042,-0.77643,31.347,0.80954,0.58549,-0.042855,-300.56,0.43358,-0.64551,-0.62875,99.092
> view matrix models
> #7,-0.39579,0.49042,-0.77643,32.702,0.80954,0.58549,-0.042855,-299.8,0.43358,-0.64551,-0.62875,91.254
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.64021,0.4158,-0.64595,33.307,0.71491,0.63022,-0.30287,-299.51,0.28115,-0.65569,-0.70073,91.66
> fitmap #7 inMap #8
Fit molecule fold_puscd1_fj_model_0.cif (#7) to map
cryosparc_P13_J679_map_sharp.mrc z flip (#8) using 12649 atoms
average map value = 0.4755, steps = 120
shifted from previous position = 3.61
rotated from previous position = 10.4 degrees
atoms outside contour = 4623, contour level = 0.3426
Position of fold_puscd1_fj_model_0.cif (#7) relative to
cryosparc_P13_J679_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.64038664 0.27902451 -0.71557685 150.14070839
0.70550281 0.58197216 -0.40444302 145.54924724
0.30359629 -0.76384140 -0.56953978 167.05067550
Axis -0.30934782 -0.87724099 0.36708605
Axis point 11.35850464 0.00000000 135.01307847
Rotation angle (degrees) 144.48634926
Shift along axis -112.80549387
Alignment identifier is 7/A
Alignment identifier is 7/B
> select #7/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A:1-147
1124 atoms, 1136 bonds, 147 residues, 1 model selected
> select #7/A:1-147
1124 atoms, 1136 bonds, 147 residues, 1 model selected
> select #7/A:137
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #7/A:1-137
1050 atoms, 1061 bonds, 137 residues, 1 model selected
> hide sel cartoons
> select add #8
1050 atoms, 1061 bonds, 137 residues, 4 models selected
> hide #!7 models
> hide #!3 models
No map chosen to save
> select add #7
12649 atoms, 12906 bonds, 1630 residues, 4 models selected
> select subtract #7
4 models selected
No map chosen to save
> show #!9 models
> select add #9
22702 atoms, 23182 bonds, 2920 residues, 3 models selected
> select subtract #8
22702 atoms, 23182 bonds, 2920 residues, 3 models selected
> view matrix models
> #9,0.070442,0.58817,-0.80566,-2.4681,-0.056634,0.80873,0.58545,-368.69,0.99591,0.0043875,0.090279,-94.547
> view matrix models
> #9,0.14486,0.71555,-0.68338,-53.081,-0.91127,0.36557,0.1896,-107.31,0.38549,0.59527,0.70502,-192.49
> view matrix models
> #9,0.24461,0.88242,-0.40187,-141.1,-0.80539,0.41569,0.42254,-171.09,0.53992,0.2203,0.81238,-180.92
> view matrix models
> #9,0.5946,-0.060479,-0.80174,9.5482,0.13614,0.99034,0.026259,-328.32,0.79241,-0.12476,0.59709,-132.82
> view matrix models
> #9,0.42305,-0.33858,-0.84047,81.42,0.60088,0.7991,-0.019462,-363.46,0.67822,-0.49679,0.5415,-53.338
> view matrix models
> #9,0.66526,-0.48057,-0.57139,19.004,0.62405,0.77804,0.072203,-379.75,0.40987,-0.40461,0.8175,-73.678
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.66526,-0.48057,-0.57139,26.74,0.62405,0.77804,0.072203,-457.66,0.40987,-0.40461,0.8175,-64.857
> view matrix models
> #9,0.66526,-0.48057,-0.57139,60.553,0.62405,0.77804,0.072203,-521.72,0.40987,-0.40461,0.8175,-70.673
> view matrix models
> #9,0.66526,-0.48057,-0.57139,61.351,0.62405,0.77804,0.072203,-526.29,0.40987,-0.40461,0.8175,-70.224
> view matrix models
> #9,0.66526,-0.48057,-0.57139,59.443,0.62405,0.77804,0.072203,-526.19,0.40987,-0.40461,0.8175,-50.598
> view matrix models
> #9,0.66526,-0.48057,-0.57139,80.967,0.62405,0.77804,0.072203,-522.3,0.40987,-0.40461,0.8175,-43.676
> hide #!9 models
> show #!7 models
> view matrix models
> #9,0.66526,-0.48057,-0.57139,87.927,0.62405,0.77804,0.072203,-534.26,0.40987,-0.40461,0.8175,-36.055
> show #!3 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!8 models
> show #!8 models
> ui tool show "Side View"
> hide #!8 models
> show #!8 models
> view
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 2 models selected
> select subtract #3
3 models selected
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 1 model selected
> show sel surfaces
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #3
12718 atoms, 12976 bonds, 1638 residues, 2 models selected
Alignment identifier is 3/B
Alignment identifier is 3/C
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-110
853 atoms, 861 bonds, 110 residues, 1 model selected
> select #3/B:1-110
853 atoms, 861 bonds, 110 residues, 1 model selected
> select #3/B:1-110
853 atoms, 861 bonds, 110 residues, 1 model selected
> select #3/B:1-110
853 atoms, 861 bonds, 110 residues, 1 model selected
> hide sel surfaces
> open /Users/bo1il/Downloads/Chai_Discovery/PusCD_chai/pred.rank_0.cif
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #11
---
Chain | Description
A | Entity A
B | Entity B
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> ui tool show "Render/Select by Attribute"
> ui tool show Matchmaker
> matchmaker #11 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#3) with pred.rank_0.cif, chain A (#11),
sequence alignment score = 5415.4
RMSD between 827 pruned atom pairs is 0.542 angstroms; (across all 1072 pairs:
18.177)
> hide #!3 models
> select add #11
13550 atoms, 13816 bonds, 1747 residues, 3 models selected
Alignment identifier is 1
Alignment identifier is 11/B
> select #3/B:1 #11/A:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:1-125 #11/A:1-125
1926 atoms, 1946 bonds, 250 residues, 2 models selected
Entity B [ID: 1] region chains A,B [1-125] RMSD: 51.833
> hide sel & #11 cartoons
> select add #11
13660 atoms, 13928 bonds, 1762 residues, 3 models selected
> select #3/B:1 #11/A:1
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/B:1-127 #11/A:1-127
1948 atoms, 1968 bonds, 254 residues, 2 models selected
Entity B [ID: 1] region chains A,B [1-127] RMSD: 51.574
> select #3/B:128 #11/A:128
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #3/B:128-1025 #11/A:128-1025
13812 atoms, 14078 bonds, 1796 residues, 2 models selected
Entity B [ID: 1] region chains A,B [128-1025] RMSD: 4.271
> select #3/B:128-1072 #11/A:128-1072
14526 atoms, 14810 bonds, 1890 residues, 2 models selected
Entity B [ID: 1] region chains A,B [128-1025] + 1 other block RMSD: 4.167
> show sel & #11 surfaces
> select #11/B:1
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #11/B
4460 atoms, 4565 bonds, 565 residues, 1 model selected
> show sel surfaces
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #11
12697 atoms, 12955 bonds, 1637 residues, 2 models selected
> view matrix models
> #11,0.22719,0.54228,0.8089,34.277,-0.84315,0.52518,-0.11526,-302,-0.48732,-0.65584,0.57654,57.374
> view matrix models
> #11,0.22719,0.54228,0.8089,40.162,-0.84315,0.52518,-0.11526,-296.39,-0.48732,-0.65584,0.57654,114.12
> fitmap #11 inMap #8
Fit molecule pred.rank_0.cif (#11) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12697 atoms
average map value = 0.2097, steps = 176
shifted from previous position = 10.2
rotated from previous position = 10.5 degrees
atoms outside contour = 8870, contour level = 0.3426
Position of pred.rank_0.cif (#11) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
0.09695424 0.46319523 0.88093703 155.42325447
-0.81395822 0.54626807 -0.19764416 143.41643551
-0.57277561 -0.69788349 0.42998457 181.24775336
Axis -0.25028739 0.72734374 -0.63900494
Axis point 208.66246176 0.00000000 51.79075423
Rotation angle (degrees) 87.90230858
Shift along axis -50.40564442
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.54134,-0.56584,0.62192,39.031,-0.77948,0.61504,-0.11891,-298.63,-0.31522,-0.54914,-0.774,103.01
> view matrix models
> #11,0.041837,-0.37054,-0.92788,36.911,-0.99725,-0.072298,-0.016094,-296.76,-0.06112,0.926,-0.37254,99.841
> view matrix models
> #11,-0.31525,-0.71152,-0.62798,37.575,-0.93802,0.33401,0.092454,-297.68,0.14397,0.6182,-0.77272,100.6
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.31525,-0.71152,-0.62798,37.63,-0.93802,0.33401,0.092454,-297.34,0.14397,0.6182,-0.77272,98.71
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.17456,-0.42799,-0.88677,36.818,-0.92072,0.39017,-0.0070641,-297.64,0.34901,0.81523,-0.46216,99.028
> view matrix models
> #11,-0.14585,-0.61462,-0.77522,37.564,-0.94657,0.31452,-0.071277,-297.6,0.28763,0.72341,-0.62765,98.887
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.14585,-0.61462,-0.77522,32.241,-0.94657,0.31452,-0.071277,-299.66,0.28763,0.72341,-0.62765,97.575
> fitmap #11 inMap #8
Fit molecule pred.rank_0.cif (#11) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12697 atoms
average map value = 0.3883, steps = 164
shifted from previous position = 5.76
rotated from previous position = 15.2 degrees
atoms outside contour = 5958, contour level = 0.3426
Position of pred.rank_0.cif (#11) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.20063210 -0.54891956 -0.81143951 148.15137971
-0.83149561 0.53339969 -0.15524116 140.94952145
0.51803649 0.64356203 -0.56344130 169.11418420
Axis 0.50668490 -0.84329333 -0.17923942
Axis point 71.33247027 0.00000000 123.30747204
Rotation angle (degrees) 127.97640075
Shift along axis -74.10765335
> hide sel surfaces
> view matrix models
> #11,-0.20063,-0.54892,-0.81144,32.805,-0.8315,0.5334,-0.15524,-299.42,0.51804,0.64356,-0.56344,89.748
> fitmap #11 inMap #8
Fit molecule pred.rank_0.cif (#11) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12697 atoms
average map value = 0.3883, steps = 84
shifted from previous position = 3.95
rotated from previous position = 0.0123 degrees
atoms outside contour = 5958, contour level = 0.3426
Position of pred.rank_0.cif (#11) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.20081319 -0.54880751 -0.81147051 148.14401239
-0.83145476 0.53351488 -0.15506403 140.95470831
0.51803190 0.64356211 -0.56344544 169.11314950
Axis 0.50659016 -0.84333933 -0.17929080
Axis point 71.32844509 0.00000000 123.29824717
Rotation angle (degrees) 127.97894632
Shift along axis -74.14478137
> view matrix models
> #11,-0.20081,-0.54881,-0.81147,29.043,-0.83145,0.53351,-0.15506,-302.42,0.51803,0.64356,-0.56345,86.18
> view matrix models
> #11,-0.20081,-0.54881,-0.81147,29.543,-0.83145,0.53351,-0.15506,-302.43,0.51803,0.64356,-0.56345,89.066
> view matrix models
> #11,-0.20081,-0.54881,-0.81147,32.723,-0.83145,0.53351,-0.15506,-301.93,0.51803,0.64356,-0.56345,88.646
> fitmap #11 inMap #8
Fit molecule pred.rank_0.cif (#11) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12697 atoms
average map value = 0.3883, steps = 68
shifted from previous position = 4.52
rotated from previous position = 0.00372 degrees
atoms outside contour = 5960, contour level = 0.3426
Position of pred.rank_0.cif (#11) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.20084854 -0.54880693 -0.81146215 148.14693413
-0.83147690 0.53349588 -0.15501070 140.95061348
0.51798266 0.64357836 -0.56347215 169.11247016
Axis 0.50658697 -0.84333665 -0.17931241
Axis point 71.33193402 0.00000000 123.29374073
Rotation angle (degrees) 127.98189257
Shift along axis -74.14347478
> select #11/B:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #11/B:265-425
1271 atoms, 1305 bonds, 161 residues, 1 model selected
> open "/Users/bo1il/Downloads/AF-A5FCA0-F1-model_v4 (2).pdb"
AF-A5FCA0-F1-model_v4 (2).pdb title:
Alphafold monomer V2.0 prediction for ragb/susd domain protein (A5FCA0) [more
info...]
Chain information for AF-A5FCA0-F1-model_v4 (2).pdb #12
---
Chain | Description | UniProt
A | ragb/susd domain protein | A5FCA0_FLAJ1 1-588
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #12 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain C (#3) with AF-A5FCA0-F1-model_v4 (2).pdb,
chain A (#12), sequence alignment score = 2730.6
RMSD between 362 pruned atom pairs is 0.736 angstroms; (across all 565 pairs:
6.444)
> hide #12 models
> show #12 models
> hide #!11 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
13989 atoms, 14281 bonds, 1799 residues, 3 models selected
> select subtract #3
1271 atoms, 1305 bonds, 161 residues, 5 models selected
> select add #3
13989 atoms, 14281 bonds, 1799 residues, 3 models selected
Alignment identifier is 3/B
Alignment identifier is 1
> select #3/C:1-2 #11/B:1-2
26 atoms, 24 bonds, 4 residues, 2 models selected
> select #3/C:1-424 #11/B:1-424
6656 atoms, 6816 bonds, 848 residues, 2 models selected
Entity C [ID: 1] region chains B,C [1-424] RMSD: 74.142
> select #3/C:1-424 #11/B:1-424
6656 atoms, 6816 bonds, 848 residues, 2 models selected
Entity C [ID: 1] region chains B,C [1-424] RMSD: 74.142
> select #3/C:564-565 #11/B:564-565
40 atoms, 40 bonds, 4 residues, 2 models selected
> select #3/C:46-565 #11/B:46-565
8264 atoms, 8460 bonds, 1040 residues, 2 models selected
Entity C [ID: 1] region chains B,C [46-565] RMSD: 77.302
> hide sel & #!3 surfaces
> hide #!8 models
> select add #3
16850 atoms, 17206 bonds, 2158 residues, 4 models selected
> select subtract #3
4132 atoms, 4230 bonds, 520 residues, 5 models selected
> hide #!3 models
> show #!3 models
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/B:1-101
781 atoms, 789 bonds, 101 residues, 1 model selected
> select #3/B:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/B:1-110
853 atoms, 861 bonds, 110 residues, 1 model selected
> select #3/B:155
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/B:1-155
1179 atoms, 1192 bonds, 155 residues, 1 model selected
> select #3/B
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> hide sel surfaces
> show #!10 models
> hide #!10 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> view matrix models
> #3,-0.74031,0.090292,0.66618,34.189,-0.50929,-0.72217,-0.46808,-303.41,0.43883,-0.6858,0.58061,62.365
> view matrix models
> #3,-0.74031,0.090292,0.66618,27.03,-0.50929,-0.72217,-0.46808,-298.75,0.43883,-0.6858,0.58061,42.819
> view matrix models
> #3,-0.74031,0.090292,0.66618,26.707,-0.50929,-0.72217,-0.46808,-299.51,0.43883,-0.6858,0.58061,42.013
> ui tool show Matchmaker
> matchmaker #!3 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A5FCA0-F1-model_v4 (2).pdb, chain A (#12) with pred.rank_0.cif,
chain C (#3), sequence alignment score = 2730.6
RMSD between 362 pruned atom pairs is 0.736 angstroms; (across all 565 pairs:
6.444)
> hide sel cartoons
> select #12
4650 atoms, 4759 bonds, 588 residues, 1 model selected
> show sel surfaces
> select #3/C:1 #11/B:1
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #3/C:1-495 #11/B:1-495
7758 atoms, 7938 bonds, 990 residues, 2 models selected
Entity C [ID: 1] region chains B,C [1-495] RMSD: 73.031
> select #3/C #11/B
8920 atoms, 9130 bonds, 1130 residues, 2 models selected
Entity C [ID: 1] region chains B,C [1-495] + 1 other block RMSD: 75.633
> show sel & #!3 surfaces
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> view matrix models
> #3,-0.74031,0.090292,0.66618,26.637,-0.50929,-0.72217,-0.46808,-298.21,0.43883,-0.6858,0.58061,43.62,#11,-0.20085,-0.54881,-0.81146,30.444,-0.83148,0.5335,-0.15501,-300.01,0.51798,0.64358,-0.56347,93.633
> view matrix models
> #3,-0.74031,0.090292,0.66618,26.462,-0.50929,-0.72217,-0.46808,-299.57,0.43883,-0.6858,0.58061,43.042,#11,-0.20085,-0.54881,-0.81146,30.269,-0.83148,0.5335,-0.15501,-301.38,0.51798,0.64358,-0.56347,93.055
> ui tool show Matchmaker
> matchmaker #!3 to #12
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A5FCA0-F1-model_v4 (2).pdb, chain A (#12) with pred.rank_0.cif,
chain C (#3), sequence alignment score = 2730.6
RMSD between 362 pruned atom pairs is 0.736 angstroms; (across all 565 pairs:
6.444)
> select add #12
13570 atoms, 13889 bonds, 1718 residues, 5 models selected
> select add #11
21807 atoms, 22279 bonds, 2790 residues, 6 models selected
> select subtract #11
9110 atoms, 9324 bonds, 1153 residues, 6 models selected
> select subtract #12
4460 atoms, 4565 bonds, 565 residues, 3 models selected
> select add #12
9110 atoms, 9324 bonds, 1153 residues, 3 models selected
Alignment identifier is 3/C
Alignment identifier is 12/A
> hide #!3 models
> show #!11 models
> hide #!11 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open /Users/bo1il/Downloads/AF-A5FCA1-F1-model_v4.pdb
AF-A5FCA1-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for susc-like tonb-dependent receptor
(A5FCA1) [more info...]
Chain information for AF-A5FCA1-F1-model_v4.pdb #13
---
Chain | Description | UniProt
A | susc-like tonb-dependent receptor | A5FCA1_FLAJ1 1-1094
Computing secondary structure
> hide #13 models
> show #13 models
> ui tool show Matchmaker
> matchmaker #13 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#3) with AF-A5FCA1-F1-model_v4.pdb, chain
A (#13), sequence alignment score = 5372.2
RMSD between 819 pruned atom pairs is 0.670 angstroms; (across all 1072 pairs:
26.326)
> select add #13
17533 atoms, 17906 bonds, 2247 residues, 5 models selected
> select subtract #12
12883 atoms, 13147 bonds, 1659 residues, 4 models selected
Alignment identifier is 3/C
Alignment identifier is 13/A
> select #13/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #13/A:1-158
1227 atoms, 1244 bonds, 158 residues, 1 model selected
> select #13/A:1-158
1227 atoms, 1244 bonds, 158 residues, 1 model selected
> select #13/A:1-158,168-169
1240 atoms, 1256 bonds, 160 residues, 1 model selected
> select #13/A:1-169
1304 atoms, 1322 bonds, 169 residues, 1 model selected
> select #13/A:1-176
1360 atoms, 1379 bonds, 176 residues, 1 model selected
> hide sel cartoons
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!9 models
> select #13/A:177
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #13/A:177-1028
6557 atoms, 6684 bonds, 852 residues, 1 model selected
> select #13/A:177-1094
7063 atoms, 7202 bonds, 918 residues, 1 model selected
> show sel surfaces
> hide #!8 models
> select add #12
11713 atoms, 11961 bonds, 1506 residues, 3 models selected
> select add #13
13073 atoms, 13341 bonds, 1682 residues, 4 models selected
> select subtract #13
4650 atoms, 4759 bonds, 588 residues, 3 models selected
Alignment identifier is 12/A
> select #12/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:1-23
189 atoms, 192 bonds, 23 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #12
4650 atoms, 4759 bonds, 588 residues, 2 models selected
> fitmap #12 inMap #8
Fit molecule AF-A5FCA0-F1-model_v4 (2).pdb (#12) to map
cryosparc_P13_J679_map_sharp.mrc z flip (#8) using 4650 atoms
average map value = 0.4614, steps = 84
shifted from previous position = 0.578
rotated from previous position = 5.3 degrees
atoms outside contour = 1675, contour level = 0.3426
Position of AF-A5FCA0-F1-model_v4 (2).pdb (#12) relative to
cryosparc_P13_J679_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.68257622 -0.08965048 -0.72529476 150.85944567
0.16411772 0.98590231 0.03258845 108.42797905
0.71214821 -0.14127783 0.68766671 115.12831993
Axis -0.11827720 -0.97785913 0.17263263
Axis point -86.48707647 0.00000000 228.88927167
Rotation angle (degrees) 47.30678623
Shift along axis -103.99561784
> view matrix models
> #12,0.68258,-0.08965,-0.72529,32.816,0.16412,0.9859,0.032588,-332.52,0.71215,-0.14128,0.68767,36.786
> fitmap #12 inMap #8
Fit molecule AF-A5FCA0-F1-model_v4 (2).pdb (#12) to map
cryosparc_P13_J679_map_sharp.mrc z flip (#8) using 4650 atoms
average map value = 0.4614, steps = 52
shifted from previous position = 1.81
rotated from previous position = 0.0114 degrees
atoms outside contour = 1673, contour level = 0.3426
Position of AF-A5FCA0-F1-model_v4 (2).pdb (#12) relative to
cryosparc_P13_J679_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.68269711 -0.08974563 -0.72516920 150.86345222
0.16415010 0.98589908 0.03252298 108.43343455
0.71202486 -0.14123994 0.68780221 115.12716776
Axis -0.11822567 -0.97784519 0.17274683
Axis point -86.53047717 0.00000000 228.94906715
Rotation angle (degrees) 47.29691788
Shift along axis -103.97919228
> hide #!13 models
> select add #13
13073 atoms, 13341 bonds, 1682 residues, 3 models selected
> select subtract #12
8423 atoms, 8582 bonds, 1094 residues, 3 models selected
> select subtract #13
1 model selected
> select add #13
8423 atoms, 8582 bonds, 1094 residues, 1 model selected
> show #!13 models
> fitmap #13 inMap #8
Fit molecule AF-A5FCA1-F1-model_v4.pdb (#13) to map
cryosparc_P13_J679_map_sharp.mrc z flip (#8) using 8423 atoms
average map value = 0.3889, steps = 56
shifted from previous position = 0.151
rotated from previous position = 1.78 degrees
atoms outside contour = 3864, contour level = 0.3426
Position of AF-A5FCA1-F1-model_v4.pdb (#13) relative to
cryosparc_P13_J679_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.09582207 0.77900764 0.61964928 146.18390601
-0.80551823 -0.30502555 0.50803522 158.28229245
0.58477218 -0.54781978 0.59827668 119.81550351
Axis -0.55442699 0.01831388 -0.83203083
Axis point 103.97879882 59.60221200 0.00000000
Rotation angle (degrees) 107.78604556
Shift along axis -177.83973407
> show #!11 models
> ui mousemode right translate
> hide #!12 models
> hide #!13 models
> select subtract #13
1 model selected
> select add #11
12697 atoms, 12955 bonds, 1637 residues, 1 model selected
> fitmap #11 inMap #8
Fit molecule pred.rank_0.cif (#11) to map cryosparc_P13_J679_map_sharp.mrc z
flip (#8) using 12697 atoms
average map value = 0.3883, steps = 68
shifted from previous position = 0.862
rotated from previous position = 0.0173 degrees
atoms outside contour = 5958, contour level = 0.3426
Position of pred.rank_0.cif (#11) relative to cryosparc_P13_J679_map_sharp.mrc
z flip (#8) coordinates:
Matrix rotation and translation
-0.20058858 -0.54886634 -0.81148627 148.15094532
-0.83145338 0.53345199 -0.15528764 140.96476946
0.51812112 0.64356407 -0.56336115 169.11549024
Axis 0.50667153 -0.84330320 -0.17923077
Axis point 71.32959064 0.00000000 123.31620114
Rotation angle (degrees) 127.97000578
Shift along axis -74.12287544
> open "/Users/bo1il/Downloads/AF-A5FCA0-F1-model_v4 (2).pdb"
AF-A5FCA0-F1-model_v4 (2).pdb title:
Alphafold monomer V2.0 prediction for ragb/susd domain protein (A5FCA0) [more
info...]
Chain information for AF-A5FCA0-F1-model_v4 (2).pdb #14
---
Chain | Description | UniProt
A | ragb/susd domain protein | A5FCA0_FLAJ1 1-588
Computing secondary structure
> hide #14 models
> show #14 models
> hide #!11 models
> hide #14 models
> show #14 models
> ui tool show Matchmaker
> matchmaker #14 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#11) with AF-A5FCA0-F1-model_v4 (2).pdb,
chain A (#14), sequence alignment score = 2637
RMSD between 373 pruned atom pairs is 0.693 angstroms; (across all 565 pairs:
6.104)
> hide #14 models
> show #14 models
> select subtract #11
2 models selected
> fitmap #14 inMap #8
Fit molecule AF-A5FCA0-F1-model_v4 (2).pdb (#14) to map
cryosparc_P13_J679_map_sharp.mrc z flip (#8) using 4650 atoms
average map value = 0.5181, steps = 128
shifted from previous position = 4.03
rotated from previous position = 10.9 degrees
atoms outside contour = 1466, contour level = 0.3426
Position of AF-A5FCA0-F1-model_v4 (2).pdb (#14) relative to
cryosparc_P13_J679_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
-0.67838994 0.10891469 0.72658425 146.76188761
0.14782930 0.98896007 -0.01022093 109.47467900
-0.71967603 0.10047667 -0.68700135 175.86167328
Axis 0.07628990 0.99672493 0.02681894
Axis point 106.38065690 0.00000000 56.87542511
Rotation angle (degrees) 133.48902427
Shift along axis 125.02901616
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #!11 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-A5FCA0-F1-model_v4 (2).pdb, chain A (#14) with pred.rank_0.cif,
chain B (#11), sequence alignment score = 2637
RMSD between 373 pruned atom pairs is 0.693 angstroms; (across all 565 pairs:
6.104)
> select add #14
4650 atoms, 4759 bonds, 588 residues, 1 model selected
> show sel surfaces
> hide #!14 models
> hide #!8 models
> show #!8 models
> ui tool show "Segment Map"
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 181 regions.
Showing 60 of 181 region surfaces
2460 watershed regions, grouped to 181 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 181 regions, 60 surfaces
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!8 models
> show #!8 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 2 of 181 regions.
Showing 2 of 181 region surfaces
2460 watershed regions, grouped to 181 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 181 regions, 2 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 4 of 181 regions.
Showing 4 of 181 region surfaces
2460 watershed regions, grouped to 181 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 181 regions, 4 surfaces
> close #15
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 4 of 181 regions.
Showing 4 of 181 region surfaces
2460 watershed regions, grouped to 181 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 181 regions, 4 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 749 regions.
Showing 60 of 749 region surfaces
2460 watershed regions, grouped to 749 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 749 regions, 60 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 749 regions.
Showing 60 of 749 region surfaces
2460 watershed regions, grouped to 749 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 749 regions, 60 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 749 regions.
Showing 60 of 749 region surfaces
2460 watershed regions, grouped to 749 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 749 regions, 60 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 558 regions.
Showing 60 of 558 region surfaces
2460 watershed regions, grouped to 558 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 558 regions, 60 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 523 regions.
Showing 60 of 523 region surfaces
2460 watershed regions, grouped to 523 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 523 regions, 60 surfaces
Segmenting cryosparc_P13_J679_map_sharp.mrc z flip, density threshold 0.342595
Only showing 60 of 527 regions.
Showing 60 of 527 region surfaces
2460 watershed regions, grouped to 527 regions
Showing cryosparc_P13_J679_map_sharp z flip.seg - 527 regions, 60 surfaces
Overlapping 4650 atoms with 527 regions
Selected 2 regions
Overlapping 4650 atoms with 527 regions
Selected 2 regions
Overlapping 4650 atoms with 527 regions
Selected 2 regions
Overlapping 4650 atoms with 527 regions
Selected 2 regions
> select #15.3
1 model selected
> ui mousemode right "move picked models"
> view matrix models #15.3,1,0,0,0.23324,0,1,0,-39.82,0,0,1,5.7524
> view matrix models #15.3,1,0,0,5.5658,0,1,0,-53.804,0,0,1,-2.6862
> view matrix models #15.3,1,0,0,-45.286,0,1,0,-125.85,0,0,1,-2.5758
> view matrix models #15.3,1,0,0,-127.75,0,1,0,-335.23,0,0,1,-46.162
> view matrix models #15.3,1,0,0,-152.2,0,1,0,-447.44,0,0,1,-81.892
> ui mousemode right translate
> ui mousemode right "move picked models"
> view matrix models #15.3,1,0,0,-116.91,0,1,0,-438.17,0,0,1,-92.627
> view matrix models #15.3,1,0,0,-115.27,0,1,0,-444.19,0,0,1,-77.638
> view matrix models #15.3,1,0,0,-126.16,0,1,0,-451.05,0,0,1,-103.35
> view matrix models #15.3,1,0,0,-127.23,0,1,0,-446.18,0,0,1,-73.721
> view matrix models #15.3,1,0,0,-118.38,0,1,0,-441.86,0,0,1,-78.341
> view matrix models #15.3,1,0,0,-118.35,0,1,0,-442.6,0,0,1,-76.141
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> close #5
> close #1
> close #4
> ui mousemode right translate
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> show #!11 models
> hide #!11 models
> show #!11 models
> select #11/A
8237 atoms, 8390 bonds, 1072 residues, 1 model selected
> hide sel cartoons
> select #11/B
4460 atoms, 4565 bonds, 565 residues, 1 model selected
> show sel surfaces
> hide #!14 models
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!12 models
> hide #!12 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> close #6
> hide #!15 models
> hide #!11 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #7.2 models
> show #7.2 models
> hide #7.1 models
> show #7.1 models
> hide #!7 models
> show #!7 models
> hide #7.1 models
> hide #!7 models
> hide #7.2 models
> show #7.2 models
> hide #7.2 models
> show #7.1 models
> show #7.2 models
> select #7/B
4455 atoms, 4560 bonds, 564 residues, 1 model selected
> show sel surfaces
> select #7/A
8194 atoms, 8346 bonds, 1066 residues, 1 model selected
> hide sel cartoons
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!14 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> select ::name="LIG1"
21 atoms, 21 bonds, 1 residue, 1 model selected
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> ui tool show "Volume Viewer"
> select add #15
21 atoms, 21 bonds, 1 residue, 65 models selected
> select subtract #15
21 atoms, 21 bonds, 1 residue, 2 models selected
> select add #15
21 atoms, 21 bonds, 1 residue, 65 models selected
> show #!14 models
> hide #!15 models
> show #!15 models
> show #!3 models
> hide #!3 models
> hide #!11 models
> show #!11 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!11 models
> show #!11 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> ui tool show Matchmaker
> matchmaker #!3 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain A (#11) with pred.rank_0.cif, chain B (#3),
sequence alignment score = 5415.4
RMSD between 827 pruned atom pairs is 0.542 angstroms; (across all 1072 pairs:
18.177)
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #11/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#11) with pred.rank_0.cif, chain C (#3),
sequence alignment score = 2691.9
RMSD between 395 pruned atom pairs is 0.673 angstroms; (across all 565 pairs:
4.755)
> show #!3 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!11 models
> show #!11 models
> open /Users/bo1il/Downloads/Chai_Discovery/PusD1-GroPi/pred.rank_0.cif
Summary of feedback from opening
/Users/bo1il/Downloads/Chai_Discovery/PusD1-GroPi/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #1
---
Chain | Description
B | Entity B
Non-standard residues in pred.rank_0.cif #1
---
LIG1 — (LIG1)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> ui tool show Matchmaker
> hide #1 models
> show #1 models
> close #13
> close #10
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> open /Users/bo1il/Downloads/Chai_Discovery/PusD1-GroPi/pred.rank_0.cif
Summary of feedback from opening
/Users/bo1il/Downloads/Chai_Discovery/PusD1-GroPi/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #4
---
Chain | Description
B | Entity B
Non-standard residues in pred.rank_0.cif #4
---
LIG1 — (LIG1)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #4 models
> show #4 models
> select ::name="LIG1"
63 atoms, 63 bonds, 3 residues, 3 models selected
> hide #4 models
> show #4 models
> ui mousemode right "move picked models"
> view matrix models #1,1,0,0,64.725,0,1,0,-248.39,0,0,1,95.025
> hide #1 models
> show #1 models
> close #4
> view matrix models #1,1,0,0,68.986,0,1,0,-316.34,0,0,1,102.43
> ui tool show Matchmaker
> matchmaker #1/B to #3/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#3) with pred.rank_0.cif, chain B (#1),
sequence alignment score = 24.4
RMSD between 8 pruned atom pairs is 1.368 angstroms; (across all 71 pairs:
22.703)
> ui tool show Matchmaker
> matchmaker #1/B to #11/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#11) with pred.rank_0.cif, chain B (#1),
sequence alignment score = 2716.5
RMSD between 372 pruned atom pairs is 0.677 angstroms; (across all 565 pairs:
6.286)
> view matrix models
> #3,0.74805,-0.18656,-0.63688,38.546,-0.56122,-0.69003,-0.45705,-294.35,-0.35419,0.69932,-0.62088,102.1
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #1/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#1) with pred.rank_0.cif, chain C (#3),
sequence alignment score = 2671.5
RMSD between 363 pruned atom pairs is 0.594 angstroms; (across all 565 pairs:
8.325)
> ui mousemode right translate
> ui tool show Matchmaker
> matchmaker #!3 to #1/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker pred.rank_0.cif, chain B (#1) with pred.rank_0.cif, chain C (#3),
sequence alignment score = 2671.5
RMSD between 363 pruned atom pairs is 0.594 angstroms; (across all 565 pairs:
8.325)
> hide #1 models
> show #1 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!3 models
> hide #!11 models
> select add #1
4502 atoms, 4607 bonds, 567 residues, 3 models selected
Alignment identifier is 1/B
> show sel & #1 surfaces
> hide sel & #!1 cartoons
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!1 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!15 models
> show #!3 models
> hide #!14 models
> hide #!1 models
> show #!8 models
> hide #!8 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!15 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> hide #!7 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!14 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!3 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.7.3
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.16054.5.2,0)
OS Loader Version: 577.140.2~30
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 6 days, 11 hours, 52 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2412M:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 0FFXD43B6W0L
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C VGA Adapter
Adapter Firmware Version: 1.91
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving windows between screens |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
What we know about this ChimeraX crash was shown in the bug report panel:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The ChimeraX daily build uses a newer Qt version (6.9.2 vs 6.8.2 in the release you are using) and we have not seen these Mac multi-display crashes the newer Qt.
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Reported by Ian Lidbury