id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20512	Crash on Mac waking from sleep	i.lidbury@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-26.5.1-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

Thread 0x0000700025bd4000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700024bd1000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700023bce000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700022bcb000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700021bc8000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000700020bc5000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001fbc2000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001ebbf000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001dbbc000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001cbb9000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000070001bbb6000 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00007ff85a041900 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, 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 (total: 59)


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  ""uptime"" : 51000,
  ""procRole"" : ""Foreground"",
  ""version"" : 2,
  ""userID"" : 502,
  ""deployVersion"" : 210,
  ""modelCode"" : ""MacBookPro16,2"",
  ""coalitionID"" : 578,
  ""osVersion"" : {
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    ""build"" : ""25F80"",
    ""releaseType"" : ""User""
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  ""captureTime"" : ""2026-06-19 14:21:32.5599 +0100"",
  ""codeSigningMonitor"" : 0,
  ""incident"" : ""F1B84646-3AF5-48C0-A305-2C5350F359E6"",
  ""pid"" : 594,
  ""cpuType"" : ""X86-64"",
  ""procLaunch"" : ""2026-06-17 17:02:45.1996 +0100"",
  ""procStartAbsTime"" : 20510924764,
  ""procExitAbsTime"" : 51468490373098,
  ""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""},
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  ""parentProc"" : ""launchd"",
  ""parentPid"" : 1,
  ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"",
  ""crashReporterKey"" : ""F46F41C5-FF6C-941F-A528-C0FEEB51179E"",
  ""appleIntelligenceStatus"" : {""reasons"":[""deviceNotCapable""],""state"":""unavailable""},
  ""developerMode"" : 1,
  ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"",
  ""codeSigningTeamID"" : ""LWV8X224YF"",
  ""codeSigningFlags"" : 570491649,
  ""codeSigningValidationCategory"" : 6,
  ""codeSigningTrustLevel"" : 4294967295,
  ""codeSigningAuxiliaryInfo"" : 0,
  ""bootSessionUUID"" : ""12B739B9-50C9-436B-96F4-537EC7FD7D76"",
  ""wakeTime"" : 24518,
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  ""sleepWakeUUID"" : ""A1516D16-8DA1-4F03-87C4-F34361B08B06"",
  ""sip"" : ""enabled"",
  ""vmRegionInfo"" : ""0 is not in any region.  Bytes before following region: 4445683712\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      108fbc000-108fc0000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX"",
  ""exception"" : {""codes"":""0x000000000000000d, 0x0000000000000000"",""rawCodes"":[13,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""UNKNOWN_0xD at 0x0000000000000000""},
  ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":594},
  ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"",
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    ""name"" : ""_pdbio.cpython-311-darwin.so""
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    ""path"" : ""\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so"",
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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.  
How to cite UCSF ChimeraX  

> open /Users/bo1il/Documents/PusCD_PI_paper/PusCD1_simple.cxs format session

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian as #9,
grid size 384,384,384, pixel 0.729, shown at level 0.226, step 1, values
float32  
Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian copy
as #12, grid size 384,58,280, pixel 0.729, shown at level 0.171, step 1,
values float32  
Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc as #3, grid size
384,384,384, pixel 0.729, shown at level 0.109, step 2, values float32  
Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip as #4, grid
size 384,384,384, pixel 0.729, shown at level 0.155, step 1, values float32  
Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc gaussian as #6, grid
size 384,384,384, pixel 0.729, shown at level 0.898, step 1, values float32  
Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian as #7,
grid size 384,384,384, pixel 0.729, shown at level 0.175, step 1, values
float32  

> view name session-start

opened ChimeraX session  

> show #!3 models

> hide #!3 models

> close #3

> close #4

> open /Users/bo1il/Documents/PusCD_PI_paper/PusC1.fas

Unrecognized file suffix '.fas'  

> open
> ""/Users/bo1il/Library/CloudStorage/GoogleDrive-i.lidbury@sheffield.ac.uk/My
> Drive/PusC1.pdb""

Chain information for PusC1.pdb #3  
---  
Chain | Description  
A | No description available  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> select #1/A

Nothing selected  

> select #1/C

Nothing selected  

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #!3 to #10/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 PusCD1-CC_real_space_refined_008.pdb, chain C (#10) with PusC1.pdb,
chain A (#3), sequence alignment score = 4108.5  
RMSD between 532 pruned atom pairs is 0.739 angstroms; (across all 830 pairs:
6.554)  
  

> select #10/C:453, 886, 455

16 atoms, 13 bonds, 3 residues, 1 model selected  

> select #3/A:453, 886, 455

22 atoms, 19 bonds, 3 residues, 1 model selected  

> show sel atoms

> select #3/A:482, 886, 483

20 atoms, 18 bonds, 3 residues, 1 model selected  

> show sel atoms

> select #10/C:453, 886, 455

16 atoms, 13 bonds, 3 residues, 1 model selected  

> select #10/C:453, 886, 455, 454

22 atoms, 20 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #10/C:453, 858, 455, 454

24 atoms, 22 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #10/C:855-860, 453-456

59 atoms, 58 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #10/C:854-860, 453-456

63 atoms, 62 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #10/C:853-860, 453-456

69 atoms, 68 bonds, 12 residues, 1 model selected  

> show sel cartoons

> hide #3/A ribbons

> show #3/A:482, 886, 483

> show #3/A:482, 886, 483 ribbons

> show #3/A:480-484, 880-888 ribbons

> select #10/C:853-860, 452-456

73 atoms, 72 bonds, 13 residues, 1 model selected  

> show sel cartoons

> close #12

> close #6

> volume #7 style mesh

> volume #7 color #808bc3a0

> volume #7 color #808bc3

> volume #7 color #808bc36a

> ui mousemode right select

Drag select of 29 atoms, 27 residues, 22 bonds, 7
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian , 6
pseudobonds  

> ui tool show ""Volume Viewer""

> volume zone #3 #10 nearAtoms sel range 3 newMap true

> volume zone #3 nearAtoms sel range 3 newMap true

Drag select of 38 atoms, 27 residues, 27 bonds, 7
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian , 7
pseudobonds  

> volume zone #3/A nearAtoms sel range 3 newMap true

> volume zone #7 nearAtoms sel range 3 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #4, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  
Drag select of 114 atoms, 27 residues, 105 bonds, 12 pseudobonds, 4
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone  

> volume zone #7 nearAtoms sel range 2 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #6, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #11, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> close #4

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!11 models

> ui mousemode right translate

> ui mousemode right select

Drag select of 33 atoms, 32 bonds, 11 cryosparc_P13_J1050_006_volume_map_sharp
(1).mrc z flip gaussian zone  

> select clear

> hide #!11 models

Drag select of 42 atoms, 41 bonds  

> hide sel atoms

Drag select of 4 atoms, 5 bonds  
Drag select of 6 atoms, 6 bonds  

> hide sel atoms

> undo

Drag select of 5 atoms, 4 bonds  

> hide sel atoms

> select #10/D:64,62,289,61,

Expected an objects specifier or a keyword  

> select #10/D:64,62,289,61

41 atoms, 40 bonds, 4 residues, 1 model selected  

> hide sel atoms

Drag select of 43 atoms, 27 residues, 37 bonds, 5 pseudobonds  

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #4, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> select #10/C:854-860, 453-456

63 atoms, 62 bonds, 11 residues, 1 model selected  

> select #10/C:854-859, 452-456

60 atoms, 59 bonds, 11 residues, 1 model selected  

> select #10/C:855-859, 452-456

56 atoms, 55 bonds, 10 residues, 1 model selected  

> select #10/C:855-869, 452-456

135 atoms, 136 bonds, 20 residues, 1 model selected  

> select #10/C:857-869, 452-456

124 atoms, 124 bonds, 18 residues, 1 model selected  

> select #10/C:853-869, 452-456

145 atoms, 146 bonds, 22 residues, 1 model selected  

> select #10/C:852-869, 452-456

153 atoms, 154 bonds, 23 residues, 1 model selected  

> show sel cartoons

> select #10/C:852-859, 452-456

74 atoms, 73 bonds, 13 residues, 1 model selected  

> select #10/C:852-860, 452-456

81 atoms, 80 bonds, 14 residues, 1 model selected  

> select #10/C:852-860, 452-456

81 atoms, 80 bonds, 14 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #12, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #14, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!4 models

> show #!4 models

> close #4

> show #!12 models

> hide #!12 models

> hide #!10 models

> show #!10 models

> show #!7 models

> hide #!7 models

> hide #!14 models

> show #!14 models

> color #14 black models

> select #10/C:852-859, 452-456 /D:LIP

90 atoms, 89 bonds, 5 pseudobonds, 14 residues, 2 models selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #4, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> close #14

> hide #8 models

> ui mousemode right label

> label delete residues

> ui mousemode right label

> label #3/A:483

> label #10/C:455

> label delete residues

> label #10/C:455

> ui mousemode right ""move label""

> select #10/C:852-860-869

Nothing selected  

> select #10/C:860-869

79 atoms, 80 bonds, 10 residues, 1 model selected  

> select #10/C:861-869

72 atoms, 73 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> select #10/C:852-860, 452-456 /D:LIP

97 atoms, 96 bonds, 5 pseudobonds, 15 residues, 2 models selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #14, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> close #4

> color #14 black models

> color #14 #000000cc models

> select #10/C:857

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #10/C:885

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/C:885

Nothing selected  

> select #3/A:885

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui mousemode right select

Drag select of 34 atoms, 28 residues, 28 bonds, 14
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone  

> select clear

Drag select of 15 atoms, 19 residues, 12 bonds, 14
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone  

> show sel atoms

> select clear

> ui mousemode right distance

> distance #3/A:886@OG #10/C:858@OG

Distance between PusC1.pdb #3/A SER 886 OG and
PusCD1-CC_real_space_refined_008.pdb #10/C SER 858 OG: 2.445Å  

> distance #10/C:858@OG #3/A:886@OG

Distance already exists; modify distance properties with 'distance style'  

> show #!13 models

> color #13 #3836faff models

> color #13 #3640faff models

> color #13 #50fa0dff models

> color #13 #ddfa49ff models

> color #13 #fa132fff models

> color #13 #fa28ebff models

> color #13 #fa00f0ff models

> color #13 black models

> color #13 #060006ff models

> color #13 black models

> ui mousemode right ""move label""

> ui mousemode right distance

> distance #10/C:454@OG #3/A:482@OG

Distance between PusCD1-CC_real_space_refined_008.pdb #10/C SER 454 OG and
PusC1.pdb #3/A SER 482 OG: 4.328Å  

> color #13 black models

> ui mousemode right translate

> color #13.1 #9a292fff models

> color #13.1 #121f9aff models

> color #13.1 black models

> color #13 #1e33ffff models

> color #13 #2642ffff models

> color #13 #faff4cff models

> color #13 #faff54ff models

> color #13 #b1b43cff models

> color #13.1 black models

> show #3/A ribbons

> show #10/C:480-520 ribbons

> show #10/C:530-550 ribbons

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #10/C:483-437 ribbons

> select #10/C:483-437 ribbon

Expected a keyword  

> select #10/C:483-437

Nothing selected  

> select #10/C:483-487

43 atoms, 44 bonds, 5 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #4, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> hide sel atoms

> show sel atoms

> select #10/C:511-515

43 atoms, 43 bonds, 5 residues, 1 model selected  

> select #3/A:511-515

43 atoms, 44 bonds, 5 residues, 1 model selected  

> show sel atoms

> select #10/C:270-280

74 atoms, 75 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #10/C:270-285

117 atoms, 119 bonds, 16 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #10/C:275-279

35 atoms, 34 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> select #10/C:267-279

86 atoms, 86 bonds, 13 residues, 1 model selected  

> show sel cartoons

> select #10/C:265-279

99 atoms, 100 bonds, 15 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select #10/C:550-570

178 atoms, 181 bonds, 21 residues, 1 model selected  

> show sel cartoons

> view

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #15, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

Cell requested for row 9 is out of bounds for table with 16 rows! Resizing
table model.  

> ui mousemode right select

Drag select of 125 atoms, 116 bonds  

> hide sel atoms

Drag select of 15 atoms, 13 bonds, 15 cryosparc_P13_J1050_006_volume_map_sharp
(1).mrc z flip gaussian zone  
Drag select of 4 atoms, 3 bonds  

> hide #!15 models

> show #!15 models

> hide #!4 models

> show #!4 models

Drag select of 12 atoms, 11 bonds  

> hide sel atoms

Drag select of 15 atoms, 13 bonds  

> hide sel atoms

> ui mousemode right translate

> select #10/C: 170-450

1946 atoms, 1970 bonds, 264 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #16, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> hide #!15 models

> hide sel cartoons

> show sel cartoons

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> show sel cartoons

> open ""/Users/bo1il/Downloads/PusCD1-CC_real_space_refined_008 (1).pdb""

Chain information for PusCD1-CC_real_space_refined_008 (1).pdb #17  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #17/C to #3/A 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 PusC1.pdb, chain A (#3) with PusCD1-CC_real_space_refined_008
(1).pdb, chain C (#17), sequence alignment score = 4116.9  
RMSD between 788 pruned atom pairs is 0.719 angstroms; (across all 830 pairs:
1.283)  
  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #17#!3 atoms

> hide #17#!3 cartoons

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> show #17#!3 cartoons

> open
> ""/Users/bo1il/Library/CloudStorage/GoogleDrive-i.lidbury@sheffield.ac.uk/My
> Drive/PusC1.pdb""

Chain information for PusC1.pdb #18  
---  
Chain | Description  
A | No description available  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #18/A to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusC1.pdb, chain A (#18), sequence alignment score = 4074.4  
RMSD between 785 pruned atom pairs is 0.713 angstroms; (across all 829 pairs:
1.272)  
  

> select #10/B /D

9008 atoms, 9216 bonds, 8 pseudobonds, 1132 residues, 2 models selected  

> select #17/B /D

9008 atoms, 9216 bonds, 1132 residues, 1 model selected  

> hide sel cartoons

> color #18 #dea0deff

> close #16

> show #!15 models

> hide #!15 models

> close #15

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> select #17:LIP

32 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel atoms

> volume zone #7 nearAtoms sel range 1.5 newMap true

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian zone
as #15, grid size 384,384,384, pixel 0.729, shown at step 1, values float32  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #17#!13-15,18 target m

> show #!4 target m

> hide #!3 target m

> show #!3 target m

> hide #!4 target m

> show #!2 models

> hide #!3 models

> close #2

> show #!4 models

> close #4

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!14 models

> hide #!14 models

> show #!15 models

> close #15

> show #17 models

> show #!18 models

> show #!3 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> close #12

> show #!11 models

> hide #!11 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> open /Users/bo1il/Downloads/PusCD1-OC-chainB-Gly.pdb format pdb

Chain information for PusCD1-OC-chainB-Gly.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #!2 to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusCD1-OC-chainB-Gly.pdb, chain C (#2), sequence alignment score = 4429.4  
RMSD between 877 pruned atom pairs is 0.323 angstroms; (across all 879 pairs:
0.369)  
  

> select #2/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> select #2/B /D

6738 atoms, 6842 bonds, 1131 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide #17 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!2 models

> show #!2 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> select #17:LIP

32 atoms, 32 bonds, 2 residues, 1 model selected  

> show #!2-3,18 atoms

> hide #!2-3,18 atoms

> show #17 models

> hide #17 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> show #17 models

> hide #!2 models

> show #!2 models

> select #10/C: 170-450

1946 atoms, 1970 bonds, 264 residues, 1 model selected  

> select #18/C: 170-450

Nothing selected  

> select #17/C: 170-450

1946 atoms, 1970 bonds, 264 residues, 1 model selected  

> select #17/C: 450-457

51 atoms, 50 bonds, 8 residues, 1 model selected  

> open /Users/bo1il/Downloads/cryosparc_P13_J1225_003_volume_map_sharp.mrc

Opened cryosparc_P13_J1225_003_volume_map_sharp.mrc as #4, grid size
384,384,384, pixel 0.729, shown at level 0.0403, step 2, values float32  

> volume flip #4

Opened cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip as #12, grid size
384,384,384, pixel 0.729, shown at step 1, values float32  

> ui mousemode right ""translate selected atoms""

> ui mousemode right ""move picked models""

> view matrix models #12,1,0,0,-6.3617,0,1,0,-46.565,0,0,1,-1.1753

> ui mousemode right ""rotate selected models""

> view matrix models
> #17,0.97038,-0.11034,0.2149,-38.961,-0.23752,-0.59798,0.76551,102.87,0.044039,-0.79388,-0.60648,323.92

> undo

> ui mousemode right select

Drag select of 12 cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip  

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.40435,0.90644,0.12196,-65.885,-0.059409,-0.10703,0.99248,-14.75,0.91267,-0.40855,0.010574,59.122

> ui mousemode right ""translate selected models""

> view matrix models
> #12,0.40435,0.90644,0.12196,-72.955,-0.059409,-0.10703,0.99248,-27.667,0.91267,-0.40855,0.010574,62.023

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,-0.19159,0.93024,-0.31297,63.574,0.15887,-0.28528,-0.94518,221.56,-0.96853,-0.23081,-0.093128,311.89

> view matrix models
> #12,-0.73219,0.63116,-0.25599,172.69,0.26592,-0.081121,-0.96058,180.33,-0.62704,-0.7714,-0.10844,341.75

> view matrix models
> #12,-0.72372,0.69007,-0.0059364,130.45,-0.045518,-0.056318,-0.99737,224.91,-0.68859,-0.72155,0.072169,319.61

> ui mousemode right ""translate selected models""

> view matrix models
> #12,-0.72372,0.69007,-0.0059364,124.6,-0.045518,-0.056318,-0.99737,232.33,-0.68859,-0.72155,0.072169,315.6

> view matrix models
> #12,-0.72372,0.69007,-0.0059364,122.45,-0.045518,-0.056318,-0.99737,243.45,-0.68859,-0.72155,0.072169,312.46

> hide #!12 models

> show #!12 models

> view matrix models
> #12,-0.72372,0.69007,-0.0059364,112.21,-0.045518,-0.056318,-0.99737,246.06,-0.68859,-0.72155,0.072169,315.11

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,-0.59747,0.80131,-0.030514,82.445,-0.021626,-0.054141,-0.9983,242.57,-0.8016,-0.59579,0.049677,316.25

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #17 models

> hide #!12 models

> show #!12 models

> fitmap #2 inMap #12

Fit molecule PusCD1-OC-chainB-Gly.pdb (#2) to map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) using 20198 atoms  
average map value = 0.0593, steps = 116  
shifted from previous position = 7.41  
rotated from previous position = 9.39 degrees  
atoms outside contour = 5112, contour level = 0.040254  
  
Position of PusCD1-OC-chainB-Gly.pdb (#2) relative to
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99993475 -0.00672186 0.00923401 -0.22418772  
0.00674610 0.99997385 -0.00259640 -0.25370862  
-0.00921632 0.00265852 0.99995398 0.76965024  
Axis 0.22419010 0.78714347 0.57458155  
Axis point 71.37620754 0.00000000 29.45052285  
Rotation angle (degrees) 0.67151038  
Shift along axis 0.19226108  
  

> surface dust #12 size 7.29

> ui mousemode right select

> ui mousemode right translate

> open /Users/bo1il/Downloads/cryosparc_P13_J1223_002_volume_map_sharp.mrc

Opened cryosparc_P13_J1223_002_volume_map_sharp.mrc as #15, grid size
384,384,384, pixel 0.729, shown at level 0.0367, step 2, values float32  

> select ~sel & ##selected

Nothing selected  

> volume flip #15

Opened cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip as #16, grid size
384,384,384, pixel 0.729, shown at step 1, values float32  

> ui mousemode right select

> select #16

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #16,-0.34687,0.75719,-0.55349,164.43,-0.74535,-0.58075,-0.32738,372.06,-0.56933,0.29899,0.76582,72.469

> view matrix models
> #16,-0.73917,0.66151,-0.12659,174.66,-0.65447,-0.74985,-0.09691,350.56,-0.15903,0.011216,0.98721,22.993

> view matrix models
> #16,-0.79843,0.60189,0.01568,171.69,-0.60182,-0.79701,-0.050881,343.19,-0.018127,-0.050061,0.99858,9.7558

> view matrix models
> #16,-0.38339,0.75711,-0.52895,166.27,-0.7445,-0.59227,-0.30812,370.86,-0.54656,0.27568,0.79074,68.99

> view matrix models
> #16,-0.53631,0.57,-0.62248,227.18,-0.47934,-0.81273,-0.33122,366.76,-0.6947,0.12074,0.7091,123.09

> view matrix models
> #16,-0.42936,0.87803,0.21145,53.246,-0.12026,0.17646,-0.97693,267.39,-0.89509,-0.44489,0.029825,324.76

> view matrix models
> #16,-0.7031,0.70179,0.11461,130.41,-0.11959,0.042172,-0.99193,288.05,-0.70096,-0.71113,0.054277,330.59

> ui mousemode right ""translate selected models""

> view matrix models
> #16,-0.7031,0.70179,0.11461,127.79,-0.11959,0.042172,-0.99193,257.88,-0.70096,-0.71113,0.054277,338.35

> view matrix models
> #16,-0.7031,0.70179,0.11461,90.305,-0.11959,0.042172,-0.99193,271.44,-0.70096,-0.71113,0.054277,314.86

> view matrix models
> #16,-0.7031,0.70179,0.11461,82.739,-0.11959,0.042172,-0.99193,248.21,-0.70096,-0.71113,0.054277,311.16

> surface dust #16 size 7.29

> ui mousemode right ""rotate selected models""

> view matrix models
> #16,-0.69944,0.71311,0.047384,90.196,-0.027323,0.039571,-0.99884,236.67,-0.71416,-0.69993,-0.0081929,320.32

> ui mousemode right ""translate selected models""

> view matrix models
> #16,-0.69944,0.71311,0.047384,99.845,-0.027323,0.039571,-0.99884,230.3,-0.71416,-0.69993,-0.0081929,325.82

> ui mousemode right ""rotate selected models""

> view matrix models
> #16,-0.6984,0.71446,-0.042198,112.13,0.023067,-0.036459,-0.99907,233.31,-0.71534,-0.69872,0.0089825,323.41

> view matrix models
> #16,-0.69213,0.71588,-0.09208,118.08,0.019239,-0.10923,-0.99383,242.69,-0.72152,-0.68963,0.061829,315.64

> ui mousemode right ""translate selected models""

> view matrix models
> #16,-0.69213,0.71588,-0.09208,114.31,0.019239,-0.10923,-0.99383,243.83,-0.72152,-0.68963,0.061829,319.24

> ui mousemode right ""rotate selected models""

> view matrix models
> #16,-0.66133,0.74956,-0.028414,96.631,0.017512,-0.022442,-0.99959,233.47,-0.74989,-0.66156,0.0017156,327.95

> ui mousemode right ""translate selected models""

> view matrix models
> #16,-0.66133,0.74956,-0.028414,99.211,0.017512,-0.022442,-0.99959,233.81,-0.74989,-0.66156,0.0017156,324.78

> ui tool show ""Fit in Map""

> fitmap #16 inMap #12

Fit map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 566324 points  
correlation = 0.9391, correlation about mean = 0.5893, overlap = 1864  
steps = 128, shift = 1.28, angle = 5.53 degrees  
  
Position of cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99999146 -0.00040151 0.00410775 -0.37639661  
0.00041474 0.99999471 -0.00322035 0.52536490  
-0.00410644 0.00322202 0.99998636 -0.11896691  
Axis 0.61525415 0.78446521 0.07795299  
Axis point -32.61103982 0.00000000 117.21683234  
Rotation angle (degrees) 0.29997547  
Shift along axis 0.17127708  
  

> fitmap #16 inMap #12

Fit map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 566324 points  
correlation = 0.9391, correlation about mean = 0.5893, overlap = 1864  
steps = 28, shift = 0.0122, angle = 0.00674 degrees  
  
Position of cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99999154 -0.00039872 0.00408961 -0.38028230  
0.00041236 0.99999433 -0.00333662 0.53917095  
-0.00408826 0.00333828 0.99998605 -0.14761720  
Axis 0.63046615 0.77242697 0.07660949  
Axis point -39.61053619 0.00000000 118.40506528  
Rotation angle (degrees) 0.30330361  
Shift along axis 0.16540619  
  

> fitmap #16 inMap #12

Fit map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 566324 points  
correlation = 0.9391, correlation about mean = 0.5893, overlap = 1864  
steps = 28, shift = 0.0159, angle = 0.00521 degrees  
  
Position of cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99999154 -0.00040480 0.00408834 -0.37044775  
0.00041807 0.99999462 -0.00324585 0.53057846  
-0.00408701 0.00324753 0.99998636 -0.12312869  
Axis 0.62002935 0.78063437 0.07857211  
Axis point -33.87808502 0.00000000 117.05439728  
Rotation angle (degrees) 0.30002205  
Shift along axis 0.17482483  
  

> view matrix models
> #16,-0.59701,0.80145,-0.035557,83.073,-0.017569,-0.057374,-0.9982,242.58,-0.80204,-0.59531,0.048333,316.22

> ui tool show ""Fit in Map""

> fitmap #5 inMap #9

Fit molecule pred.rank_1.cif (#5) to map
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9) using
12718 atoms  
average map value = 0.005391, steps = 268  
shifted from previous position = 1.69  
rotated from previous position = 3.31 degrees  
atoms outside contour = 12609, contour level = 0.22551  
  
Position of pred.rank_1.cif (#5) relative to
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9)
coordinates:  
Matrix rotation and translation  
-0.99652584 0.07203427 0.04180118 113.20952751  
-0.00999639 -0.60173430 0.79863379 117.67519723  
0.08268221 0.79544134 0.60036385 96.57683547  
Axis -0.03481079 -0.44577061 -0.89447011  
Axis point 55.41826489 33.38451895 0.00000000  
Rotation angle (degrees) 177.37181864  
Shift along axis -142.78214968  
  

> fitmap #5 inMap #9

Fit molecule pred.rank_1.cif (#5) to map
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9) using
12718 atoms  
average map value = 0.005433, steps = 116  
shifted from previous position = 0.0547  
rotated from previous position = 0.34 degrees  
atoms outside contour = 12608, contour level = 0.22551  
  
Position of pred.rank_1.cif (#5) relative to
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9)
coordinates:  
Matrix rotation and translation  
-0.99659404 0.07048628 0.04280216 113.19392925  
-0.00873405 -0.60634110 0.79515673 117.71445655  
0.08200035 0.79207461 0.60489155 96.59913257  
Axis -0.03484929 -0.44321150 -0.89573941  
Axis point 55.39071424 33.62228933 -0.00000000  
Rotation angle (degrees) 177.46551777  
Shift along axis -142.64477910  
  

> fitmap #5 inMap #9

Fit molecule pred.rank_1.cif (#5) to map
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9) using
12718 atoms  
average map value = 0.005435, steps = 136  
shifted from previous position = 0.00733  
rotated from previous position = 0.00792 degrees  
atoms outside contour = 12608, contour level = 0.22551  
  
Position of pred.rank_1.cif (#5) relative to
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9)
coordinates:  
Matrix rotation and translation  
-0.99660354 0.07042695 0.04267855 113.19564787  
-0.00879732 -0.60634877 0.79515018 117.71180684  
0.08187809 0.79207401 0.60490889 96.59259333  
Axis -0.03478045 -0.44320713 -0.89574425  
Axis point 55.39550495 33.62274602 0.00000000  
Rotation angle (degrees) 177.46540536  
Shift along axis -142.62996749  
  

> fitmap #5 inMap #9

Fit molecule pred.rank_1.cif (#5) to map
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9) using
12718 atoms  
average map value = 0.005435, steps = 88  
shifted from previous position = 0.00689  
rotated from previous position = 0.00799 degrees  
atoms outside contour = 12608, contour level = 0.22551  
  
Position of pred.rank_1.cif (#5) relative to
cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian (#9)
coordinates:  
Matrix rotation and translation  
-0.99660291 0.07037414 0.04278023 113.20009955  
-0.00869136 -0.60641975 0.79509721 117.71676840  
0.08189706 0.79202437 0.60497132 96.59407993  
Axis -0.03481338 -0.44316886 -0.89576190  
Axis point 55.39468998 33.63013186 0.00000000  
Rotation angle (degrees) 177.47053815  
Shift along axis -142.63458164  
  

> fitmap #16 inMap #12

Fit map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 566324 points  
correlation = 0.9391, correlation about mean = 0.5893, overlap = 1864  
steps = 48, shift = 0.0879, angle = 0.00199 degrees  
  
Position of cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99999142 -0.00039601 0.00411842 -0.37971809  
0.00040932 0.99999467 -0.00323105 0.52779921  
-0.00411712 0.00323271 0.99998628 -0.11291893  
Axis 0.61558803 0.78432704 0.07669722  
Axis point -31.01450049 -0.00000000 117.77828880  
Rotation angle (degrees) 0.30080832  
Shift along axis 0.17155671  
  

> ui mousemode right translate

> fitmap #16 inMap #12

Fit map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 566324 points  
correlation = 0.9391, correlation about mean = 0.5893, overlap = 1864  
steps = 36, shift = 0.00837, angle = 0.0026 degrees  
  
Position of cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99999153 -0.00040244 0.00409116 -0.37891437  
0.00041580 0.99999456 -0.00326667 0.53077031  
-0.00408982 0.00326834 0.99998628 -0.12885190  
Axis 0.62222817 0.77894954 0.07790841  
Axis point -35.09433773 0.00000000 118.04087160  
Rotation angle (degrees) 0.30087825  
Shift along axis 0.16763344  
  

> ui mousemode right select

> select clear

Drag select of 1 residues, 12 cryosparc_P13_J1225_003_volume_map_sharp.mrc z
flip , 16 cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip  

> select clear

> ui mousemode right translate

> hide #!12 models

> show #!12 models

> hide #!2 models

> show #!2 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> fitmap #2 inMap #12

Fit molecule PusCD1-OC-chainB-Gly.pdb (#2) to map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) using 20198 atoms  
average map value = 0.0593, steps = 44  
shifted from previous position = 0.00885  
rotated from previous position = 0.00705 degrees  
atoms outside contour = 5106, contour level = 0.040254  
  
Position of PusCD1-OC-chainB-Gly.pdb (#2) relative to
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
0.99993553 -0.00664775 0.00920375 -0.23718169  
0.00667277 0.99997410 -0.00269053 -0.22554849  
-0.00918563 0.00275177 0.99995401 0.75236792  
Axis 0.23307472 0.78755242 0.57047117  
Axis point 69.56011434 0.00000000 31.22810259  
Rotation angle (degrees) 0.66894456  
Shift along axis 0.19629189  
  

> ui tool show ""Volume Viewer""

> volume #16 level 0.03421

> volume #12 level 0.03982

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> volume #12 level 0.02566

> volume #12 level 0.01837

> volume #12 level 0.01794

> volume #12 level 0.03038

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!16 models

> open /Users/bo1il/Downloads/cryosparc_P13_J1226_003_volume_map_sharp.mrc

Opened cryosparc_P13_J1226_003_volume_map_sharp.mrc as #19, grid size
288,288,288, pixel 0.633, shown at level 0.0836, step 2, values float32  

> volume flip 19#

Missing or invalid ""volumes"" argument: invalid density maps specifier  

> volume flip #19

Opened cryosparc_P13_J1226_003_volume_map_sharp.mrc z flip as #20, grid size
288,288,288, pixel 0.633, shown at step 1, values float32  

> volume #20 level 0.07679

> volume #20 level 0.05332

> surface dust #16 size 7.29

> surface dust #20 size 6.33

> volume #20 level 0.04961

> surface dust #16 size 7.29

> surface dust #20 size 6.33

> ui tool show ""Fit in Map""

> fitmap #20 inMap #12

Fit map cryosparc_P13_J1226_003_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 843988 points  
correlation = 0.5835, correlation about mean = 0.05588, overlap = 1261  
steps = 328, shift = 29.7, angle = 17.1 degrees  
  
Position of cryosparc_P13_J1226_003_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
-0.74444885 0.05237370 -0.66562217 273.89826363  
0.63400447 -0.25715636 -0.72932085 183.38767605  
-0.20936621 -0.96494951 0.15823460 225.47117574  
Axis -0.30369342 -0.58805211 0.74964326  
Axis point 159.66963010 216.10834888 0.00000000  
Rotation angle (degrees) 157.17372033  
Shift along axis -21.99966505  
  

> show #!12 models

> ui mousemode right select

> select #20

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,0.78833,0.60423,-0.11589,-0.34683,-0.093781,0.30418,0.94799,-6.8721,0.60806,-0.73646,0.29646,88.148

> ui mousemode right ""translate selected models""

> view matrix models
> #20,0.78833,0.60423,-0.11589,-10.526,-0.093781,0.30418,0.94799,-8.6809,0.60806,-0.73646,0.29646,97.498

> view matrix models
> #20,0.78833,0.60423,-0.11589,-3.7302,-0.093781,0.30418,0.94799,-8.358,0.60806,-0.73646,0.29646,104.68

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,0.73574,0.65657,0.16613,-28.009,-0.089248,-0.14917,0.98478,26.438,0.67135,-0.73937,-0.051152,129.53

> ui mousemode right ""translate selected models""

> view matrix models
> #20,0.73574,0.65657,0.16613,-34.853,-0.089248,-0.14917,0.98478,27.445,0.67135,-0.73937,-0.051152,135.43

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,0.75644,0.65034,0.069676,-27.8,-0.083775,-0.0093149,0.99644,14.022,0.64868,-0.75958,0.047436,130.62

> ui mousemode right ""translate selected models""

> view matrix models
> #20,0.75644,0.65034,0.069676,-29.663,-0.083775,-0.0093149,0.99644,9.9149,0.64868,-0.75958,0.047436,129.61

> fitmap #20 inMap #12

Fit map cryosparc_P13_J1226_003_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 843988 points  
correlation = 0.8532, correlation about mean = 0.3103, overlap = 3014  
steps = 92, shift = 4.18, angle = 5.16 degrees  
  
Position of cryosparc_P13_J1226_003_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
-0.96440068 0.26346120 -0.02279225 207.07566303  
0.26410874 0.96393600 -0.03277075 31.32955258  
0.01333644 -0.03762377 -0.99920296 235.65219424  
Axis -0.13310918 -0.99094223 0.01776091  
Axis point 100.34534090 0.00000000 119.02596618  
Rotation angle (degrees) 178.95547077  
Shift along axis -54.42405051  
  

> ui mousemode right select

> select clear

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> volume #20 level 0.03232

> volume #20 level 0.03108

> select #17:LIP

32 atoms, 32 bonds, 2 residues, 1 model selected  

> select #17/D:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> view sel

> hide #!20 models

> show #!2 atoms

> hide #!16 models

> show #!16 models

> select #17/D:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> show #17 models

> hide #17 models

> select #17/D:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> show #17 models

> hide #!2 models

> show #!2 models

> hide #17 models

> hide #!2 atoms

> show #17 models

> hide #17 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!5 models

> hide #!5 atoms

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!18 models

> hide #!18 models

> show #!2 models

> hide #!2 models

> show #!2 models

> view

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!12 models

> show #!12 models

> hide #!16 models

> show #!16 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> hide #5 models

> hide #!12 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> ui tool show Matchmaker

> matchmaker #17#!3 to #2/A 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 PusCD1-OC-chainB-Gly.pdb, chain A (#2) with
PusCD1-CC_real_space_refined_008 (1).pdb, chain C (#17), sequence alignment
score = 4113.2  
RMSD between 795 pruned atom pairs is 0.665 angstroms; (across all 860 pairs:
2.284)  
  
Matchmaker PusCD1-OC-chainB-Gly.pdb, chain A (#2) with PusC1.pdb, chain A
(#3), sequence alignment score = 4258.6  
RMSD between 840 pruned atom pairs is 0.334 angstroms; (across all 843 pairs:
0.393)  
  

> ui tool show Matchmaker

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> show #!3 models

> show #17 models

> hide #!16 models

> hide #!18 models

> show #!18 models

> ui tool show Matchmaker

> matchmaker #!18 to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusC1.pdb, chain A (#18), sequence alignment score = 4074.4  
RMSD between 785 pruned atom pairs is 0.713 angstroms; (across all 829 pairs:
1.272)  
  

> show #!16 models

> hide #!16 models

> show #!16 models

> volume #16 level 0.0345

> volume #16 level 0.0348

> volume #16 level 0.035

> volume #16 level 0.036

> volume #16 level 0.037

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume #20 level 0.02429

> surface dust #16 size 7.29

> surface dust #20 size 6.33

> volume #20 level 0.024

> volume #20 level 0.0239

> open /Users/bo1il/Downloads/cryosparc_P13_J1227_002_volume_map_sharp.mrc

Opened cryosparc_P13_J1227_002_volume_map_sharp.mrc as #21, grid size
288,288,288, pixel 0.633, shown at level 0.08, step 2, values float32  

> volume flip #21

Opened cryosparc_P13_J1227_002_volume_map_sharp.mrc z flip as #22, grid size
288,288,288, pixel 0.633, shown at step 1, values float32  

> volume #22 level 0.05821

> select #21

2 models selected  

> select #22

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #22,0.90578,0.34458,0.24661,-45.367,-0.28434,0.062737,0.95667,24.963,0.31418,-0.93666,0.1548,133.89

> ui mousemode right ""translate selected models""

> view matrix models
> #22,0.90578,0.34458,0.24661,-35.379,-0.28434,0.062737,0.95667,15.461,0.31418,-0.93666,0.1548,167.86

> ui mousemode right ""rotate selected models""

> view matrix models
> #22,0.87524,0.46982,-0.11496,-10.853,-0.03689,0.30183,0.95265,-29.333,0.48228,-0.82956,0.28151,130.64

> view matrix models
> #22,0.86537,0.49708,-0.063557,-17.139,0.026941,0.080497,0.99639,-19.035,0.50041,-0.86396,0.056268,152.74

> view matrix models
> #22,0.79611,0.59524,0.10911,-35.467,-0.024033,-0.14906,0.98854,7.5263,0.60468,-0.7896,-0.10437,150.85

> view matrix models
> #22,0.89974,0.41693,0.129,-30.665,-0.093536,-0.10449,0.99012,9.8184,0.42629,-0.90291,-0.055014,173.47

> ui mousemode right ""translate selected models""

> view matrix models
> #22,0.89974,0.41693,0.129,-26.519,-0.093536,-0.10449,0.99012,16.576,0.42629,-0.90291,-0.055014,165.4

> view matrix models
> #22,0.89974,0.41693,0.129,-22.653,-0.093536,-0.10449,0.99012,18.114,0.42629,-0.90291,-0.055014,168.18

> fitmap #22 inMap #12

Fit map cryosparc_P13_J1227_002_volume_map_sharp.mrc z flip in map
cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip using 625829 points  
correlation = 0.8357, correlation about mean = 0.2113, overlap = 2373  
steps = 160, shift = 6.98, angle = 14.6 degrees  
  
Position of cryosparc_P13_J1227_002_volume_map_sharp.mrc z flip (#22) relative
to cryosparc_P13_J1225_003_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
-0.96369808 0.26587732 -0.02439725 207.03458152  
0.26659594 0.96322429 -0.03354884 31.31185148  
0.01458014 -0.03883517 -0.99913924 235.56638889  
Axis -0.13437261 -0.99076250 0.01826647  
Axis point 100.21966844 0.00000000 119.06316579  
Rotation angle (degrees) 178.87289640  
Shift along axis -54.53941919  
  

> volume #22 level 0.05

> volume #22 level 0.045

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> volume #22 level 0.04

> surface dust #16 size 7.29

> surface dust #20 size 6.33

> surface dust #22 size 6.33

> select add #22

2 models selected  

> volume #22 level 0.03637

> surface dust #22 size 6.33

> view matrix models
> #22,0.78896,0.61417,0.018182,-23.989,-0.0081478,-0.01913,0.99978,5.3308,0.61439,-0.78894,-0.010089,142.89

> undo

> ui mousemode right select

> select clear

> hide #!20 models

> hide #!16 models

> select clear

> ui mousemode right translate

> save /Users/bo1il/Desktop/image31.png supersample 3

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume #16 level 0.04585

> hide #17 models

> show #17 models

> hide #17 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> save /Users/bo1il/Desktop/image32.png supersample 3

> save /Users/bo1il/Desktop/image33.png supersample 3

> select #17/D:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> view sel

> show #17 models

> hide #17 models

> show #17 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!22 models

> volume #22 level 0.037

> volume #22 level 0.038

> volume #22 level 0.05

> select #17/B:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> view sel

> hide #!22 models

> show #!22 models

> show sel atoms

> hide #!22 models

> show #!22 models

> hide #!12 models

> hide #!22 models

> show #!22 models

> show #!20 models

> hide #!22 models

> volume #20 level 0.04675

> show #!22 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> view sel

> view

> hide #17 models

> show #17 models

> show #!16 models

> hide #!22 models

> volume #16 level 0.045

> volume #16 level 0.04

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!22 models

> volume #16 level 0.035

> hide #!16 models

> hide #!3 models

> show #!3 models

> hide #!22 models

> show #!18 models

> select #17/A:170-323

957 atoms, 966 bonds, 136 residues, 1 model selected  

> select #17/A:170-323 /C170-323

957 atoms, 966 bonds, 136 residues, 1 model selected  

> select #17/A:170-323 /C170-323

957 atoms, 966 bonds, 136 residues, 1 model selected  

> select add #17

22555 atoms, 23025 bonds, 2897 residues, 1 model selected  

> select add #3

29772 atoms, 29662 bonds, 4 pseudobonds, 4447 residues, 3 models selected  

> select add #18

36989 atoms, 36299 bonds, 8 pseudobonds, 5997 residues, 5 models selected  

> select add #2

57187 atoms, 56854 bonds, 12 pseudobonds, 8890 residues, 7 models selected  

> show sel cartoons

> hide sel cartoons

> select #17/A:170-323 /C170-323

957 atoms, 966 bonds, 136 residues, 1 model selected  

> show sel cartoons

> select #17/A:170-323 /C:170-323

1923 atoms, 1941 bonds, 273 residues, 1 model selected  

> show sel cartoons

> select #2/A:170-323 /C:170-323

2031 atoms, 2050 bonds, 287 residues, 1 model selected  

> show sel cartoons

> select #3

7217 atoms, 6637 bonds, 4 pseudobonds, 1550 residues, 2 models selected  
Alignment identifier is 3/A  

> select #3/A:202

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:202-319

844 atoms, 853 bonds, 118 residues, 1 model selected  

> show sel cartoons

> select #3/A:320

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:320-323

30 atoms, 29 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #3/A:324

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:324-330

45 atoms, 44 bonds, 7 residues, 1 model selected  

> show sel cartoons

> select #3/A:331-332

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/A:331-345

105 atoms, 105 bonds, 15 residues, 1 model selected  

> show sel cartoons

> select #3/A:346

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:346-349

28 atoms, 27 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #3/A:351

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:350-351

13 atoms, 12 bonds, 2 residues, 1 model selected  

> show sel cartoons

> select #3/A:209

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #18/A:209

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #18

7217 atoms, 6637 bonds, 4 pseudobonds, 1550 residues, 2 models selected  
Alignment identifier is 18/A  

> select #18/A:202

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #18/A:202-351

1065 atoms, 1075 bonds, 150 residues, 1 model selected  

> show sel cartoons

> select #18/A:567

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #18/A:567

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #17/A:566

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel cartoons

> select #17/A:568-570

25 atoms, 25 bonds, 3 residues, 1 model selected  

> show sel cartoons

> select #17/A:569-570

18 atoms, 18 bonds, 2 residues, 1 model selected  

> show sel cartoons

> select #17/A:565-570

55 atoms, 57 bonds, 6 residues, 1 model selected  

> show sel cartoons

> select #17/A:562-570

80 atoms, 82 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select #18/A:320-321

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #18/A:320-331

83 atoms, 82 bonds, 12 residues, 1 model selected  

> select #18/A:465

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #18/A:465-480

108 atoms, 108 bonds, 16 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #18/A:481-482

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #18/A:481-493

92 atoms, 92 bonds, 13 residues, 1 model selected  

> show sel cartoons

> select #18/A:452

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #18/A:452-462

97 atoms, 97 bonds, 11 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #18

7217 atoms, 6637 bonds, 4 pseudobonds, 1550 residues, 2 models selected  

> select #18:473

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #18:478

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #18:480

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #18/A:480

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #18/A:488

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #18/A:489-495

53 atoms, 54 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> select #18/A:487-495

68 atoms, 69 bonds, 9 residues, 1 model selected  

> select #18/A:487-490

32 atoms, 32 bonds, 4 residues, 1 model selected  

> select #18/A:487-490

32 atoms, 32 bonds, 4 residues, 1 model selected  

> select #18/A:480-490

75 atoms, 75 bonds, 11 residues, 1 model selected  

> select #18/A:479-488

66 atoms, 65 bonds, 10 residues, 1 model selected  

> show sel cartoons

> select #18/A:479-487

59 atoms, 58 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> select up

138 atoms, 139 bonds, 20 residues, 1 model selected  

> select #18/A:479-488

66 atoms, 65 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> select down

59 atoms, 58 bonds, 9 residues, 1 model selected  

> select #18/A:479-487

59 atoms, 58 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select #17/A:450-460

74 atoms, 73 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #18/A:478-486

59 atoms, 58 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select #2/A:478-486

77 atoms, 79 bonds, 9 residues, 1 model selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #17/A to #2/A 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 PusCD1-OC-chainB-Gly.pdb, chain A (#2) with
PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17), sequence alignment
score = 4077.3  
RMSD between 792 pruned atom pairs is 0.656 angstroms; (across all 859 pairs:
2.282)  
  

> hide #17 models

> show #17 models

> select #18/A:478-486

59 atoms, 58 bonds, 9 residues, 1 model selected  

> select #2/A:478-486

77 atoms, 79 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> select #2/A:450-460

74 atoms, 73 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #3/A:478-486

59 atoms, 58 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select #2/C:450-460

74 atoms, 73 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #17/C:450-460

74 atoms, 73 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #17/C:562-570

80 atoms, 82 bonds, 9 residues, 1 model selected  

> show sel cartoons

> save /Users/bo1il/Documents/PusCD_PI_paper/PusCD1_OC_plug.cxs

> select #17/C:454,455

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #17/A:454,455

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #2/A:454,455

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #2/C:454,455

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #3/A:482,483

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> ui mousemode right distance

> distance #17/A:454@OG #3/A:482@OG

Distance between PusCD1-CC_real_space_refined_008 (1).pdb #17/A SER 454 OG and
PusC1.pdb #3/A SER 482 OG: 4.165Å  

> show #!13 models

> show #!10 models

> ui tool show Matchmaker

> matchmaker #10/A to #2/A 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 PusCD1-OC-chainB-Gly.pdb, chain A (#2) with
PusCD1-CC_real_space_refined_008.pdb, chain A (#10), sequence alignment score
= 4077.3  
RMSD between 792 pruned atom pairs is 0.656 angstroms; (across all 859 pairs:
2.282)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusCD1-OC-chainB-Gly.pdb, chain A (#2), sequence alignment score = 4077.3  
RMSD between 792 pruned atom pairs is 0.656 angstroms; (across all 859 pairs:
2.282)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusCD1-OC-chainB-Gly.pdb, chain A (#2), sequence alignment score = 4077.3  
RMSD between 792 pruned atom pairs is 0.656 angstroms; (across all 859 pairs:
2.282)  
  

> hide #!10 models

> show #!10 models

> distance #17/A:454@OG #2/C:454@OG

Distance between PusCD1-CC_real_space_refined_008 (1).pdb #17/A SER 454 OG and
PusCD1-OC-chainB-Gly.pdb #2/C SER 454 OG: 56.884Å  

> distance #2/C:454@OG #17/A:454@OG

Distance already exists; modify distance properties with 'distance style'  

> ~distance #10/C:454@OG #3/A:482@OG

> ~distance #17/A:454@OG #2/C:454@OG

> ui mousemode right translate

> select #10/C

6775 atoms, 6909 bonds, 880 residues, 1 model selected  

> hide sel cartoons

> select #10/C:300-305

41 atoms, 41 bonds, 6 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> select #2/C:300-305

41 atoms, 41 bonds, 6 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> hide sel atoms

> select #10/C:300-305

41 atoms, 41 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #10/C:LA

Nothing selected  

> select #10/C:ALA

265 atoms, 217 bonds, 53 residues, 1 model selected  

> hide sel atoms

> select #10/C:LEU

609 atoms, 537 bonds, 76 residues, 1 model selected  

> hide sel atoms

> select #3/C:209

Nothing selected  

> select #3/C:209

Nothing selected  

> select #3/C:209

Nothing selected  

> select #17/C:566

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/C:566

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:566

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel cartoons

> select #2/A:560-566

61 atoms, 62 bonds, 7 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #2/A:562-570

80 atoms, 82 bonds, 9 residues, 1 model selected  

> show sel cartoons

> select #10/C:289

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel atoms

> ui mousemode right distance

> select #17/A:320-330

73 atoms, 72 bonds, 11 residues, 1 model selected  

> select #17/A:350-370

171 atoms, 176 bonds, 21 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #17/A:340-350

88 atoms, 89 bonds, 11 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #17/A:320-330

73 atoms, 72 bonds, 11 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #18/A:859

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #18/A:859-894

258 atoms, 260 bonds, 36 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:792

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #3/A:792-830

275 atoms, 284 bonds, 1 pseudobond, 32 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:660

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:660-692

268 atoms, 273 bonds, 33 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:503-504

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #3/A:503-543

340 atoms, 347 bonds, 41 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:557

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #3/A:557-588

258 atoms, 261 bonds, 32 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:604-605

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #3/A:604-613

79 atoms, 81 bonds, 10 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:517

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:517-540

193 atoms, 195 bonds, 24 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:553

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:553-563

86 atoms, 85 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select
> #3/A:204-207,210-213,221-225,248-252,261-265,278-281,317-323,340-345,352-366,403-415,419-431,438-452,458-472,524-544,547-566,578-601,604-628,646-648,652-671,675-686,695-706,719-733,778-791,796-808,811-814,825-828,832-848,852-862,864-868,875-877,891-893,902-905,907-910,916-918,932-935,942-952,955-965,968-970,1011-1013,1016-1027,1038-1046,1049-1052,1083-1093

3340 atoms, 3364 bonds, 416 residues, 1 model selected  

> hide sel cartoons

> select #3/A:547-548

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:548-554

58 atoms, 58 bonds, 7 residues, 1 model selected  

> show sel cartoons

> select #17/A:553

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3A:553

Expected an objects specifier or a keyword  

> show sel atoms

> hide sel cartoons

> select #3/A:553

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/A:554

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:556-557

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #3/A:543-557

120 atoms, 120 bonds, 15 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #3/A:564

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/A:564-590

214 atoms, 217 bonds, 27 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:602

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:602-623

180 atoms, 184 bonds, 22 residues, 1 model selected  

> select #3/A:650-651

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select #3/A:650-658

65 atoms, 65 bonds, 9 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:602-603

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #3/A:602-628

217 atoms, 222 bonds, 27 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #18/A:900

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #18/A:900-939

308 atoms, 312 bonds, 40 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #18/A:409

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #18/A:409-508

763 atoms, 772 bonds, 100 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:602

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:602-792

1210 atoms, 1241 bonds, 2 pseudobonds, 151 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:452

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:452-602

1198 atoms, 1218 bonds, 151 residues, 1 model selected  

> show sel cartoons

> select #3/A:551

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select ~sel & ##selected

7209 atoms, 6630 bonds, 4 pseudobonds, 1549 residues, 2 models selected  

> select #3/A:549-555

57 atoms, 57 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #3/A:549-595

384 atoms, 390 bonds, 47 residues, 1 model selected  

> select #3/A:594

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:590

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:590

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A:452-590

1096 atoms, 1113 bonds, 139 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #18/A:661

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #18/A:661-708

393 atoms, 405 bonds, 48 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:603

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:603-710

797 atoms, 818 bonds, 1 pseudobond, 101 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select #3/A:610-615

46 atoms, 47 bonds, 6 residues, 1 model selected  

> show sel cartoons

> select #3/A:612

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:614

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select #3/A:611

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:612

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:612

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:PHE

462 atoms, 462 bonds, 42 residues, 1 model selected  

> select #3/A:612

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:612

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:606

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:606

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:PHE

462 atoms, 462 bonds, 42 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> hide sel cartoons

> select #3/A:664

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> select #3/A:tyr

480 atoms, 483 bonds, 40 residues, 1 model selected  

> select #3/A:614

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/A:tyr

480 atoms, 483 bonds, 40 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/A:332

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> undo

> hide sel atoms

> select #3/A:332,594

24 atoms, 24 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #3/A:332,594, 209

36 atoms, 36 bonds, 3 residues, 1 model selected  

> show sel atoms

> select #17/A:302,556

13 atoms, 11 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel atoms

> select #17/A:304

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> close #15

> close #12

> hide #17#!3,10,13,18 target m

> show #!22 target m

> hide #!2 target m

> show #!21 target m

> hide #!22 target m

> show #!22 target m

> hide #!21 target m

> show #!21 models

> close #19-20

> close #21-22

> open /Users/bo1il/Downloads/cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc

Opened cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc as #12, grid size
384,384,384, pixel 0.729, shown at level 0.0365, step 2, values float32  

> open
> ""/Users/bo1il/Library/CloudStorage/GoogleDrive-i.lidbury@sheffield.ac.uk/My
> Drive/cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc""

Opened cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc as #15, grid size
384,384,384, pixel 0.729, shown at level 0.035, step 2, values float32  

> open
> ""/Users/bo1il/Library/CloudStorage/GoogleDrive-i.lidbury@sheffield.ac.uk/My
> Drive/cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc""

Opened cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc as #19, grid size
384,384,384, pixel 0.729, shown at level 0.035, step 2, values float32  

> show #17 models

> hide #17 models

> show #17 models

> hide #!19 models

> close #15

> show #!19 models

> hide #!19 models

> show #!19 models

> volume flip #1224

> volume flip #19

Opened cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc z flip as #15, grid
size 384,384,384, pixel 0.729, shown at step 1, values float32  

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume flip #12

Opened cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip as #20, grid
size 384,384,384, pixel 0.729, shown at step 1, values float32  

> close #19

> hide #!16 models

> show #!16 models

> close #12

> close #6

> close #9

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #17 models

> show #17 models

> show #!18 models

> hide #!18 models

> show #!18 models

> show #!16 models

> volume #16 level 0.04

> hide #!20 models

> show #!20 models

> hide #!15 models

> show #!15 models

> hide #!18 models

> hide #17 models

> hide #!16 models

> hide #!2 models

> ui mousemode right translate

> ui mousemode right select

> select #15

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #15,1,0,0,-15.465,0,1,0,-20.659,0,0,1,22.999

> view matrix models #15,1,0,0,-33.431,0,1,0,-42.405,0,0,1,36.447

> ui mousemode right select

> select #20

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #20,1,0,0,-23.096,0,1,0,-31.534,0,0,1,38.358

> view matrix models #20,1,0,0,-39.202,0,1,0,-47.455,0,0,1,29.378

> view matrix models #20,1,0,0,-36.361,0,1,0,-42.812,0,0,1,37.625

> show #!16 models

> hide #!16 models

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,0.93889,0.043919,0.34141,-82.662,-0.34368,0.064004,0.9369,1.7857,0.019296,-0.99698,0.075187,305.7

> ui mousemode right select

> select #15

3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.84797,-0.16213,0.50464,-70.655,-0.53001,-0.27013,0.80382,74.189,0.0059933,-0.94908,-0.31499,371.85

> view matrix models
> #15,0.88284,-0.07126,0.46423,-81.285,-0.46927,-0.093096,0.87813,30.338,-0.019358,-0.9931,-0.11563,349.82

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.88284,-0.07126,0.46423,-74.633,-0.46927,-0.093096,0.87813,56.291,-0.019358,-0.9931,-0.11563,343.83

> view matrix models
> #15,0.88284,-0.07126,0.46423,-73.599,-0.46927,-0.093096,0.87813,54.868,-0.019358,-0.9931,-0.11563,336.37

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.90249,-0.022903,0.43009,-77.411,-0.42868,0.048839,0.90213,26.389,-0.041667,-0.99854,0.034259,316.47

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.90249,-0.022903,0.43009,-80.081,-0.42868,0.048839,0.90213,19.969,-0.041667,-0.99854,0.034259,318.87

> view matrix models
> #15,0.90249,-0.022903,0.43009,-83.646,-0.42868,0.048839,0.90213,20.61,-0.041667,-0.99854,0.034259,323

> view matrix models
> #15,0.90249,-0.022903,0.43009,-84.421,-0.42868,0.048839,0.90213,19.548,-0.041667,-0.99854,0.034259,319.81

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.93735,-0.020074,0.34781,-76.475,-0.3461,0.060611,0.93624,1.6185,-0.039876,-0.99796,0.049866,317.04

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.93735,-0.020074,0.34781,-75.932,-0.3461,0.060611,0.93624,3.8825,-0.039876,-0.99796,0.049866,315.72

> ui mousemode right translate

> show #!16 models

> hide #!16 models

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.93735,-0.020074,0.34781,-59.616,-0.3461,0.060611,0.93624,-7.2058,-0.039876,-0.99796,0.049866,257.97

> ui mousemode right select

> select #20

3 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #20,0.93889,0.043919,0.34141,-65.538,-0.34368,0.064004,0.9369,-8.0735,0.019296,-0.99698,0.075187,244.78

> show #!16 models

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,0.79744,0.53211,0.2845,-106.06,-0.33324,-0.004681,0.94283,-0.77248,0.50303,-0.84666,0.17359,143.13

> ui mousemode right ""translate selected models""

> view matrix models
> #20,0.79744,0.53211,0.2845,-110.22,-0.33324,-0.004681,0.94283,-0.15413,0.50303,-0.84666,0.17359,148.74

> ui tool show ""Volume Viewer""

> ui tool show ""Fit in Map""

> fitmap #20 inMap #16

Fit map cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip in map
cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 565159 points  
correlation = 0.791, correlation about mean = 0.4019, overlap = 1349  
steps = 324, shift = 12, angle = 20.7 degrees  
  
Position of cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip (#20)
relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.96402116 0.26578351 -0.00472603 239.65998384  
0.26573144 0.96305472 -0.04373107 -25.87984848  
-0.00707157 -0.04341354 -0.99903216 289.25808771  
Axis 0.13412356 0.99072058 -0.02199097  
Axis point 121.66820179 0.00000000 144.27023386  
Rotation angle (degrees) 179.93217587  
Shift along axis 0.14328714  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,-0.083298,0.45349,-0.88736,178.46,0.99183,-0.048587,-0.11794,-20.716,-0.096597,-0.88994,-0.44574,326.39

> view matrix models
> #20,-0.5541,0.71666,-0.42352,140.6,0.31886,-0.28724,-0.90323,217.12,-0.76896,-0.63552,-0.069353,329.99

> ui mousemode right select

> select #15

3 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,0.076018,0.62168,-0.77957,144.88,0.90677,-0.36828,-0.20527,64.636,-0.41471,-0.69129,-0.59172,367

> view matrix models
> #15,-0.060964,0.72845,-0.68238,133.22,0.76,-0.40931,-0.50484,136.87,-0.64706,-0.54939,-0.52867,368.6

> fitmap #20 inMap #16

Fit map cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip in map
cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 565159 points  
correlation = 0.987, correlation about mean = 0.9186, overlap = 2036  
steps = 420, shift = 6.42, angle = 24.2 degrees  
  
Position of cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip (#20)
relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
0.99999903 -0.00105896 -0.00090771 0.29528933  
0.00105907 0.99999943 0.00010997 -0.01207684  
0.00090759 -0.00011093 0.99999958 -0.06543684  
Axis -0.07894304 -0.64872749 0.75691522  
Axis point 51.36957060 273.95399060 0.00000000  
Rotation angle (degrees) 0.08016365  
Shift along axis -0.06500660  
  

> view matrix models
> #15,-0.39058,0.72358,-0.5691,159.79,0.49205,-0.35839,-0.79337,210.93,-0.77804,-0.5899,-0.21606,342.27

> view matrix models
> #15,-0.63373,0.76689,-0.10136,112.51,-0.16624,-0.26298,-0.95037,310.02,-0.75548,-0.58543,0.29414,258.33

> ui mousemode right ""translate selected models""

> view matrix models
> #15,-0.63373,0.76689,-0.10136,106.39,-0.16624,-0.26298,-0.95037,280.66,-0.75548,-0.58543,0.29414,272.83

> ui mousemode right ""rotate selected models""

> view matrix models
> #15,-0.49636,0.84824,-0.18471,90.215,0.051512,-0.18362,-0.98165,245.89,-0.86659,-0.49677,0.047446,314.36

> fitmap #15 inMap #16

Fit map cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc z flip in map
cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 565312 points  
correlation = 0.9811, correlation about mean = 0.8882, overlap = 1866  
steps = 204, shift = 6.63, angle = 10.7 degrees  
  
Position of cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc z flip (#15)
relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
0.99999703 -0.00140761 -0.00199200 0.51510023  
0.00140580 0.99999860 -0.00091167 0.09254971  
0.00199328 0.00090887 0.99999760 -0.35012209  
Axis 0.34963692 -0.76538014 0.54032144  
Axis point 154.31612719 0.00000000 272.38094663  
Rotation angle (degrees) 0.14916770  
Shift along axis -0.07991612  
  

> surface dust #15 size 7.29

> select add #20

6 models selected  

> surface dust #15 size 7.29

> surface dust #20 size 7.29

> ui mousemode right translate

> ui mousemode right select

> select clear

> ui mousemode right translate

> volume #15 level 0.038

> volume #15 level 0.035

> volume #15 level 0.04

> volume #15 level 0.03

> volume #20 level 0.03

> volume #20 level 0.025

> volume #20 level 0.03

> volume #20 level 0.035

> volume #15 level 0.035

> volume #16 level 0.035

> show #17 models

> show #!7 models

> ui mousemode right select

> select #7

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.68228,0.72955,-0.047492,-85.297,0.090968,-0.020259,0.99565,-55.934,0.72541,-0.68363,-0.080188,140.62

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.68228,0.72955,-0.047492,-83.923,0.090968,-0.020259,0.99565,-55.642,0.72541,-0.68363,-0.080188,134.38

> view matrix models
> #7,0.68228,0.72955,-0.047492,-83.577,0.090968,-0.020259,0.99565,-57.466,0.72541,-0.68363,-0.080188,135

> ui mousemode right select

> select clear

> fitmap #7 inMap #16

Fit map cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian in
map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 88016 points  
correlation = 0.652, correlation about mean = -0.03597, overlap = 1182  
steps = 184, shift = 2.7, angle = 11.1 degrees  
  
Position of cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian
(#7) relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.95964865 0.28083048 -0.01444694 237.80269282  
0.28116503 0.95908717 -0.03313654 -28.62481924  
0.00455012 -0.03586142 -0.99934641 286.73033292  
Axis -0.14196181 -0.98971868 0.01742912  
Axis point 120.25913548 0.00000000 143.68947468  
Rotation angle (degrees) 179.45011222  
Shift along axis -0.43092299  
  
Drag select of 7 cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip
gaussian , 16 cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip , 15
cryosparc_P13_J1224_map_aligned_0_map_sharp.mrc z flip , 20
cryosparc_P13_J1222_map_aligned_0_map_sharp.mrc z flip  

> select clear

> ui mousemode right ""translate selected models""

> select ~sel & ##selected

Nothing selected  

> select #17/A:LIP

Nothing selected  

> select #17/B:LIP

16 atoms, 16 bonds, 1 residue, 1 model selected  

> view sel

> ui mousemode right select

> select #17/B:602@O2

1 atom, 1 residue, 1 model selected  

> ui mousemode right ""translate selected atoms""

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> volume #15 level 0.04

> volume #20 level 0.04

> volume #16 level 0.04

> select #17/B:858-870

Nothing selected  

> select #17/A:858-870

94 atoms, 95 bonds, 13 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> hide #!16 models

> hide #!20 models

> hide #!15 models

> hide sel cartoons

> select #17/A:858-870

94 atoms, 95 bonds, 13 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #17/A:854-865

82 atoms, 83 bonds, 12 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> show #!15 models

> hide #!15 models

> show #!15 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> show #!20 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!20 models

> hide #!15 models

> open /Users/bo1il/Downloads/PusCD1-CC_real_space_refined_008.pdb

Chain information for PusCD1-CC_real_space_refined_008.pdb #6  
---  
Chain | Description  
A | No description available  
B D | No description available  
C | No description available  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #6/A to #17/A 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 PusCD1-CC_real_space_refined_008 (1).pdb, chain A (#17) with
PusCD1-CC_real_space_refined_008.pdb, chain A (#6), sequence alignment score =
4538.6  
RMSD between 879 pruned atom pairs is 0.000 angstroms; (across all 879 pairs:
0.000)  
  

> show #!20 models

> hide #!20 models

> show #!20 models

> ui mousemode right translate

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> show #!15 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> hide #!15 models

> select #2/A:865

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show #6,17 atoms

> hide #6,17 atoms

> show #!2 models

> select #2/A:865

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #!2 models

> show #!2 models

> select #17/A:865

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #!2 models

> show #!2 models

> hide #17 models

> show #17 models

> view sel

> show #!20 models

> hide #!20 models

> hide #6 models

> view

> select #17/A:302,556

13 atoms, 11 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #17/A:304

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #2/A:181

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #3/A:332,594, 209

36 atoms, 36 bonds, 3 residues, 1 model selected  

> show #17#!2 atoms

> undo

> show #!3 models

> save /Users/bo1il/Desktop/image34.png supersample 3

> select #17/A

6766 atoms, 6900 bonds, 879 residues, 1 model selected  
Alignment identifier is 17/A  

> select #17/A:550

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #17/A:550-564

123 atoms, 123 bonds, 15 residues, 1 model selected  

> select #17/A:639

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #17/A:639-651

110 atoms, 112 bonds, 13 residues, 1 model selected  

> select #17/A:635

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #17/A:635-636

23 atoms, 24 bonds, 2 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> select #17/A:635

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #17/A:635

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/A:610-615

46 atoms, 47 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #3/A:599-603

39 atoms, 38 bonds, 5 residues, 1 model selected  

> hide sel cartoons

> select #3/A:202-209

62 atoms, 62 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select #3/A:202-323

874 atoms, 883 bonds, 122 residues, 1 model selected  

> show sel cartoons

> select #3/A:202-343

1010 atoms, 1020 bonds, 142 residues, 1 model selected  

> select #3/A:202-353

1078 atoms, 1088 bonds, 152 residues, 1 model selected  

> show sel cartoons

> select
> #17/A:193-197,220-224,233-237,250-253,289-295,312-317,326-338,375-387,392-403,410-424,430-445,496-514,519-538,550-571,578-599,623-643,647-658,667-678,691-705,717-720,736-739,750-763,768-780,782-787,796-801,804-816,824-833,836-840,847-849,863-865,874-877,879-882,888-890,904-907,914-924,927-937,940-942,983-985,988-1000,1010-1018,1022-1024,1055-1066

3264 atoms, 3292 bonds, 405 residues, 1 model selected  

> select #17/A:698

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #17/A:698-702

38 atoms, 39 bonds, 5 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select #17/A:824

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #17/A:824-834

86 atoms, 88 bonds, 11 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show #6 models

> select #6/A:657-667

88 atoms, 89 bonds, 11 residues, 1 model selected  

> show sel atoms

> open
> ""/Users/bo1il/Library/CloudStorage/GoogleDrive-i.lidbury@sheffield.ac.uk/My
> Drive/PusC1.pdb""

Chain information for PusC1.pdb #9  
---  
Chain | Description  
A | No description available  
  
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #9/A to #6/A 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 PusCD1-CC_real_space_refined_008.pdb, chain A (#6) with PusC1.pdb,
chain A (#9), sequence alignment score = 4074.4  
RMSD between 785 pruned atom pairs is 0.713 angstroms; (across all 829 pairs:
1.272)  
  

> hide #!2 models

> show #!2 models

> select #2/A:657-667

89 atoms, 90 bonds, 11 residues, 1 model selected  

> hide sel cartoons

> select #2/A:657-667

89 atoms, 90 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #17/A:657-667

88 atoms, 89 bonds, 11 residues, 1 model selected  

> show sel cartoons

> select #17/A:777

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select #17/A:749

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> select #3/A:777

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> select #3/A:689

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> select #17/A:661

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> open /Users/bo1il/Downloads/PusCD1-OC-chainB-Gly.pdb

Chain information for PusCD1-OC-chainB-Gly.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> save /Users/bo1il/Documents/PusCD_PI_paper/PusCD1_OC_plug.cxs

> select #17/A:657

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #17/A:657

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #17/A:658

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui tool show Matchmaker

> matchmaker #12/A to #6/A 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 PusCD1-CC_real_space_refined_008.pdb, chain A (#6) with PusCD1-OC-
chainB-Gly.pdb, chain A (#12), sequence alignment score = 4077.3  
RMSD between 792 pruned atom pairs is 0.656 angstroms; (across all 859 pairs:
2.282)  
  

> hide #!3 models

> hide #!2 models

> hide #17 models

> ui mousemode right select

> hide sel atoms

> select #6/A:687

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/A:667

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> ui mousemode right translate

> select #6/A:785

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #9/A:813

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> view sel

> select #6/A:709

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #12/A:785

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> ui tool show ""Side View""

> select #12/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> select #6/B

4497 atoms, 4601 bonds, 566 residues, 1 model selected  

> select #12/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> select #12/A:686

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #9/A:686

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #12/A:686

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #12/A:667

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #12/A:661

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #17 models

> show #!2 models

> hide #6 models

> show #!3 models

> select #2/A:749

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> show #!20 models

> hide #!20 models

> show #!20 models

> volume #20 level 0.04149

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> show #!15 models

> hide #!15 models

> hide #!16 models

> show #!16 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!4 models

> hide #!4 models

> close #4

> open /Users/bo1il/Downloads/cryosparc_P13_J1223_002_volume_map_sharp.mrc

Opened cryosparc_P13_J1223_002_volume_map_sharp.mrc as #4, grid size
384,384,384, pixel 0.729, shown at level 0.0367, step 2, values float32  

> hide #!4 models

> show #!4 models

> volume flip #4

Opened cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip as #19, grid size
384,384,384, pixel 0.729, shown at step 1, values float32  

> view

> ui mousemode right select

> select #19

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #19,-0.2823,0.28185,-0.91699,271.76,0.9388,0.27783,-0.20362,-5.7505,0.19738,-0.91835,-0.34304,285.91

> view matrix models
> #19,-0.22174,0.67045,-0.70804,180.03,0.29493,-0.646,-0.70406,284.43,-0.92943,-0.36494,-0.054494,330.27

> ui mousemode right ""translate selected models""

> view matrix models
> #19,-0.22174,0.67045,-0.70804,235.14,0.29493,-0.646,-0.70406,335.09,-0.92943,-0.36494,-0.054494,395.05

> close #4

> hide #!19 models

> show #!19 models

> close #19

> open ""/Users/bo1il/Downloads/cryosparc_P13_J1050_006_volume_map_sharp
> (1).mrc""

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc as #4, grid size
384,384,384, pixel 0.729, shown at level 0.109, step 2, values float32  

> open ""/Users/bo1il/Downloads/cryosparc_P13_J1044_004_volume_map_sharp
> (1).mrc""

Opened cryosparc_P13_J1044_004_volume_map_sharp (1).mrc as #19, grid size
384,384,384, pixel 0.729, shown at level 0.101, step 2, values float32  

> surface dust #7 size 7.29

> surface dust #16 size 7.29

> surface dust #20 size 7.29

> surface dust #4 size 7.29

> surface dust #19 size 7.29

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!11 models

> hide #!11 models

> hide #!4 models

> show #!4 models

> show #!11 models

> hide #!11 models

> close #11

> volume flip #4

Opened cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip as #11, grid
size 384,384,384, pixel 0.729, shown at step 1, values float32  

> surface dust #7 size 7.29

> surface dust #16 size 7.29

> surface dust #20 size 7.29

> surface dust #11 size 7.29

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> ui mousemode right ""rotate selected models""

> select add #7

2 models selected  

> view matrix models
> #7,0.96907,-0.2386,-0.062977,2.156,0.069597,0.019417,0.99739,-61.342,-0.23675,-0.97092,0.035422,286.17

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> undo

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.96907,-0.2386,-0.062977,-9.092,0.069597,0.019417,0.99739,-58.475,-0.23675,-0.97092,0.035422,307.35

> view matrix models
> #7,0.96907,-0.2386,-0.062977,-10.155,0.069597,0.019417,0.99739,-58.675,-0.23675,-0.97092,0.035422,308.2

> volume flip #12

> fitmap #7 inMap #16

Fit map cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian in
map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 88016 points  
correlation = 0.5738, correlation about mean = 0.04118, overlap = 620.3  
steps = 260, shift = 5.82, angle = 12.8 degrees  
  
Position of cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian
(#7) relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.42598234 0.90473038 0.00140631 75.61592991  
0.90115525 0.42415994 0.08948499 -78.78009647  
0.08036329 0.03938633 -0.99598718 270.44771744  
Axis -0.53536736 -0.84375481 -0.03820479  
Axis point 59.04151955 0.00000000 138.17254917  
Rotation angle (degrees) 177.31820550  
Shift along axis 15.65638749  
  

> hide #!2 models

> hide #!3 models

> hide #!9 models

> hide #!20 models

> hide #17 models

> hide #!16 models

> ui mousemode right ""map eraser""

> volume erase #7 center 105.31,89.451,143 radius 26.519

> volume erase #7 center 88.073,61.39,115.26 radius 26.519

> volume erase #7 center 76.59,67.105,124.48 radius 26.519

> volume erase #7 center 66.224,59.799,131.01 radius 26.519

> volume erase #7 center 52.233,69.261,135.49 radius 26.519

> volume erase #7 center 46.151,39.189,147.48 radius 26.519

> volume erase #7 center 41.293,52.902,146.74 radius 26.519

> volume erase #7 center 74.364,27.477,133.72 radius 26.519

> volume erase #7 center 99.433,82.895,87.639 radius 26.519

> volume erase #7 center 80.956,91.784,134.01 radius 26.519

> ui mousemode right translate

> fitmap #7 inMap #16

Fit map cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian in
map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 49060 points  
correlation = 0.7785, correlation about mean = 0.1275, overlap = 529.9  
steps = 68, shift = 0.262, angle = 1.61 degrees  
  
Position of cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian
(#7) relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.40403612 0.91472729 -0.00536713 72.13160032  
0.91187219 0.40322564 0.07679972 -76.78657459  
0.07241497 0.02613572 -0.99703209 273.06195232  
Axis -0.54553014 -0.83752717 -0.03074257  
Axis point 57.27958640 0.00000000 139.06593753  
Rotation angle (degrees) 177.33848085  
Shift along axis 16.56625363  
  

> fitmap #7 inMap #16

Fit map cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian in
map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 49060 points  
correlation = 0.7784, correlation about mean = 0.1274, overlap = 529.9  
steps = 28, shift = 0.0103, angle = 0.0026 degrees  
  
Position of cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian
(#7) relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.40401148 0.91473802 -0.00539170 72.12714848  
0.91188030 0.40320216 0.07682674 -76.77832975  
0.07245028 0.02612229 -0.99702988 273.05699257  
Axis -0.54554089 -0.83752001 -0.03074692  
Axis point 57.27246372 0.00000000 139.06429335  
Rotation angle (degrees) 177.33640750  
Shift along axis 16.55941739  
  

> fitmap #7 inMap #16

Fit map cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian in
map cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip using 49060 points  
correlation = 0.7784, correlation about mean = 0.1273, overlap = 529.9  
steps = 40, shift = 0.00705, angle = 0.00711 degrees  
  
Position of cryosparc_P13_J1050_006_volume_map_sharp (1).mrc z flip gaussian
(#7) relative to cryosparc_P13_J1223_002_volume_map_sharp.mrc z flip (#16)
coordinates:  
Matrix rotation and translation  
-0.40408784 0.91470438 -0.00537718 72.13940036  
0.91185371 0.40327961 0.07673577 -76.76583480  
0.07235905 0.02610479 -0.99703696 273.07387965  
Axis -0.54550684 -0.83754341 -0.03071362  
Axis point 57.27741269 0.00000000 139.06947644  
Rotation angle (degrees) 177.34010314  
Shift along axis 16.55509569  
  

> select #12/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 2

> volume zone #7 nearAtoms sel range 5

> volume zone #7 nearAtoms sel range 8

> volume zone #7 nearAtoms sel range 6

> volume zone #7 nearAtoms sel range 5

> show #6 models

> select #6/B

4497 atoms, 4601 bonds, 566 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #6/B to #12/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 PusCD1-OC-chainB-Gly.pdb, chain B (#12) with
PusCD1-CC_real_space_refined_008.pdb, chain B (#6), sequence alignment score =
209.2  
RMSD between 546 pruned atom pairs is 0.428 angstroms; (across all 564 pairs:
2.646)  
  

> select #12

20198 atoms, 20555 bonds, 4 pseudobonds, 2893 residues, 2 models selected  

> select #6

22555 atoms, 23025 bonds, 2897 residues, 1 model selected  

> hide sel cartoons

> select #6/B

4497 atoms, 4601 bonds, 566 residues, 1 model selected  

> show sel cartoons

> volume flip #6/B

> volume flip #12/B

> select #12/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 5

> volume zone #7 nearAtoms sel range 4

> volume #7 style surface

> volume #7 color #808bc3bb

> volume #7 color #808bc3e3

> volume #7 color #808bc3

> ui mousemode right select

> select clear

> volume zone #7 nearAtoms sel range 5

no atoms specified for zone  

> select #12/B

2261 atoms, 2260 bonds, 565 residues, 1 model selected  

> volume zone #7 nearAtoms sel range 5

> volume zone #7 nearAtoms sel range 7

> ui mousemode right ""map eraser""

> volume erase #7 center 59.326,54.994,151.9 radius 11.301

> volume erase #7 center 62.301,56.816,162.98 radius 3.6795

> volume erase #7 center 57.017,59.639,164.63 radius 3.6795

> volume erase #7 center 71.271,60.058,158.31 radius 3.6795

> volume erase #7 center 67.837,50.247,158.58 radius 3.6795

> volume erase #7 center 69.612,48.655,159.8 radius 3.6795

> volume erase #7 center 64.742,49.364,162.79 radius 3.6795

> volume erase #7 center 61.588,49.94,164.93 radius 3.6795

> volume erase #7 center 64.603,45.356,164.82 radius 3.6795

> volume erase #7 center 69.31,45.82,163.96 radius 3.6795

> volume erase #7 center 66.58,52.135,161.01 radius 3.6795

> volume erase #7 center 73.176,55.865,154.75 radius 3.6795

> show #!16 models

> show #!15 models

> hide #!12 models

> volume #16 level 0.036

> close #4

> show #!20 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-24.5.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: en_US.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: 2103.100.6.0.0 (iBridge: 23.16.15067.0.0,0)
      OS Loader Version: 583~5707

Software:

    System Software Overview:

      System Version: macOS 26.5.1 (25F80)
      Kernel Version: Darwin 25.5.0
      Time since boot: 1 day, 5 hours, 2 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


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
    narwhals: 2.16.0
    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: 2.4.2
    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
    plotly: 6.5.2
    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
    pyKVFinder: 0.9.0
    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
    tomlkit: 0.14.0
    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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX