![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16553 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fac23840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 123)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 84643,
"osVersion" : {
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"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2025-01-03 18:03:56.0628 -0500",
"codeSigningMonitor" : 1,
"incident" : "777A768E-A8A5-487C-9D86-DE8032EEC181",
"pid" : 23585,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-29 13:32:05.8887 -0500",
"procStartAbsTime" : 27366718813762,
"procExitAbsTime" : 34896976175409,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"777D8A61-C81E-5246-B2B2-49ABC82B8258","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E6A071C4-EA66-FC3F-B912-CA5E01E9CDB6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "CB8C0AC1-90FC-4A08-9DE2-3CB99C8BF141",
"wakeTime" : 2,
"sleepWakeUUID" : "A977EEEF-8B0F-431D-BE84-B01F393AC5C7",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4300111511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1004e8000-1004ec000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23585},
"ktriageinfo" : "VM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\nVM - (arg = 0x1900000016) Filesystem pagein returned an error in vnode_pagein\nVM - (arg = 0x0) Page has error bit set\nCL - (arg = 0x0) cluster_pagein past EOF\n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs
Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level
0.32, step 1, values float32
Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level
0.203, step 1, values float32
Opened J1663_FE as #3, grid size 360,360,360, pixel 2.37, shown at level
0.255, step 1, values float32
Opened J1671_PE z flip as #4, grid size 360,360,360, pixel 2.37, shown at
level 0.0763, step 1, values float32
Opened J1770_FE as #5, grid size 360,360,360, pixel 2.19, shown at level
0.214, step 1, values float32
Log from Tue Dec 24 23:20:40 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs
Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level
0.284, step 1, values float32
Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level
0.159, step 1, values float32
Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level
0.0733, step 1, values float32
Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at
level 0.0913, step 1, values float32
Opened J1748_FE as #3, grid size 588,588,588, pixel 1.34, shown at level
0.0321, step 1, values float32
Log from Tue Dec 24 17:47:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs
Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level
0.284, step 1, values float32
Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level
0.0696, step 1, values float32
Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level
0.0908, step 1, values float32
Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at
level 0.0913, step 1, values float32
Log from Tue Dec 24 14:48:02 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs
Opened emdb35243_ODV as #1, grid size 600,600,600, pixel 1.35, shown at level
0.229, step 1, values float32
Opened emdb43590_BV as #2, grid size 700,700,700, pixel 1.41, shown at level
0.167, step 1, values float32
Opened J1663_FE as #4, grid size 360,360,360, pixel 2.37, shown at level
0.254, step 1, values float32
Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at
level 0.109, step 1, values float32
Log from Tue Dec 24 14:33:25 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P32_J53_002_volume_map.mrc
Opened cryosparc_P32_J53_002_volume_map.mrc as #1, grid size 720,720,720,
pixel 1.06, shown at step 1, values float32
> volume #1 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #1 step 1
> volume #1 change image level -0.02425,0 level 0.1837,0.8 level 0.3523,1
> volume #1 level 0.151
Drag select of 1 cryosparc_P32_J53_002_volume_map.mrc
> select clear
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1668_003_volume_map.mrc
Opened cryosparc_P23_J1668_003_volume_map.mrc as #2, grid size 360,360,360,
pixel 2.37, shown at level 0.334, step 2, values float32
> hide #!1 models
> volume #2 step 1
> volume #2 level 0.2509
> ui mousemode right clip
> ui mousemode right translate
> volume #2 level 0.2417
> volume #2 level 0.2094
> volume #2 level 0.2532
> open emdb:43590\
Fetching url
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590\/map/emd_43590\\.map.gz
failed:
> open emdb:43590
Summary of feedback from opening 43590 fetched from emdb
---
notes | Fetching compressed map 43590 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590/map/emd_43590.map.gz
Fetching map header 43590 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43590/header/emd-43590.xml
Opened emdb 43590 as #3, grid size 700,700,700, pixel 1.41, shown at step 1,
values float32
> volume #3 region 0,0,0,699,699,699 step 4
[Repeated 1 time(s)]
> volume #3 step 1
> volume #3 change image level -0.05584,0 level 0.4551,0.8 level 0.773,1
> hide #!3 models
> show #!3 models
> hide #!2 models
> ui mousemode right clip
> ui mousemode right translate
> open emdb:43591
Summary of feedback from opening 43591 fetched from emdb
---
notes | Fetching compressed map 43591 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43591/map/emd_43591.map.gz
Fetching map header 43591 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-43591/header/emd-43591.xml
Opened emdb 43591 as #4, grid size 384,384,384, pixel 1.41, shown at level
0.225, step 2, values float32
> close #4
> close #1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open emdb:35243
Opened emdb 35243 as #1, grid size 600,600,600, pixel 1.35, shown at level
0.35, step 4, values float32
> close #2
> rename #1 emdb35243_ODV
> rename #3 emdb43590 id #2
> rename #2 emdb43590_BV
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1671_004_volume_map.mrc
Opened cryosparc_P23_J1671_004_volume_map.mrc as #3, grid size 360,360,360,
pixel 2.37, shown at level 0.355, step 2, values float32
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1663_003_volume_map.mrc
Opened cryosparc_P23_J1663_003_volume_map.mrc as #4, grid size 360,360,360,
pixel 2.37, shown at level 0.302, step 2, values float32
> hide #!4 models
> hide #!3 models
> rename #3 J1671_PE
> rename #4 J1663_FE
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #1 inMap #2
Fit map emdb35243_ODV in map emdb43590_BV using 42321 points
correlation = 0.6504, correlation about mean = 0.07068, overlap = 3677
steps = 840, shift = 215, angle = 14.7 degrees
Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates:
Matrix rotation and translation
0.97285467 0.11356563 -0.20163492 106.14728499
-0.13398831 0.98682657 -0.09066670 173.53911084
0.18868208 0.11522224 0.97525530 66.06041994
Axis 0.40690739 -0.77140072 -0.48925178
Axis point 69.18299426 0.00000000 765.33059572
Rotation angle (degrees) 14.65465662
Shift along axis -122.99625756
> fitmap #1 inMap #2
Fit map emdb35243_ODV in map emdb43590_BV using 42321 points
correlation = 0.6504, correlation about mean = 0.07071, overlap = 3677
steps = 104, shift = 0.0146, angle = 0.00468 degrees
Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates:
Matrix rotation and translation
0.97283638 0.11360386 -0.20170163 106.14959138
-0.13402943 0.98682367 -0.09063750 173.53917511
0.18874717 0.11520941 0.97524422 66.03781833
Axis 0.40672513 -0.77147305 -0.48928928
Axis point 69.36205442 0.00000000 764.99261400
Rotation angle (degrees) 14.65831075
Shift along axis -123.01868679
> fitmap #1 inMap #2
Fit map emdb35243_ODV in map emdb43590_BV using 42321 points
correlation = 0.6504, correlation about mean = 0.07066, overlap = 3677
steps = 60, shift = 0.0202, angle = 0.00485 degrees
Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates:
Matrix rotation and translation
0.97285464 0.11356683 -0.20163440 106.14869030
-0.13397976 0.98683234 -0.09061650 173.52336845
0.18868832 0.11517161 0.97526008 66.07751356
Axis 0.40674044 -0.77147333 -0.48927612
Axis point 69.15375523 0.00000000 765.29725022
Rotation angle (degrees) 14.65346616
Shift along axis -123.02383462
> select add #2
4 models selected
> select add #1
6 models selected
> select subtract #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.17627,0.98434,-0.00073339,8.4342,-0.98191,0.17589,0.070127,791.23,0.069158,-0.011641,0.99754,158.34
> fitmap #1 inMap #2
Fit map emdb35243_ODV in map emdb43590_BV using 42321 points
correlation = 0.8508, correlation about mean = 0.2973, overlap = 5847
steps = 124, shift = 16.6, angle = 5.06 degrees
Position of emdb35243_ODV (#1) relative to emdb43590_BV (#2) coordinates:
Matrix rotation and translation
0.22884137 0.97346373 0.00000023 6.56644567
-0.97346373 0.22884137 0.00000059 795.07225194
0.00000052 -0.00000036 1.00000000 179.58410153
Axis -0.00000048 -0.00000015 -1.00000000
Axis point 505.10857801 393.39162659 0.00000000
Rotation angle (degrees) 76.77113185
Shift along axis -179.58422442
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> ui mousemode right rotate
> ui mousemode right translate
> select subtract #1
Nothing selected
> volume #3 level 0.2279
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.62102,0.77799,-0.095165,399.88,0.76736,0.62824,0.12834,-223.39,0.15964,0.0066773,-0.98715,777.94
> ui mousemode right "translate selected models"
Drag select of 1 emdb35243_ODV , 2 emdb43590_BV , 3 J1671_PE
> select clear
> select subtract #3
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,-0.62102,0.77799,-0.095165,386.59,0.76736,0.62824,0.12834,-139.06,0.15964,0.0066773,-0.98715,840.43
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.59828,0.78575,0.15701,265.87,0.79956,0.59829,0.052522,-107.63,-0.05267,0.15696,-0.9862,866.45
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.59828,0.78575,0.15701,346.36,0.79956,0.59829,0.052522,-134.36,-0.05267,0.15696,-0.9862,880.56
> view matrix models
> #3,-0.59828,0.78575,0.15701,-3.4192,0.79956,0.59829,0.052522,-21.834,-0.05267,0.15696,-0.9862,804.23
> vflip #3
Unknown command: vflip #3
> volume flip #3
Opened J1671_PE z flip as #5, grid size 360,360,360, pixel 2.37, shown at step
1, values float32
> close #3
> ui mousemode right "rotate selected models"
> select add #5
2 models selected
> view matrix models
> #5,-0.98925,0.0012409,-0.14622,625.6,0.060453,-0.90704,-0.41668,1132.8,-0.13315,-0.42104,0.89722,289.05
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.98925,0.0012409,-0.14622,983.74,0.060453,-0.90704,-0.41668,1047,-0.13315,-0.42104,0.89722,347.49
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.9746,0.21646,-0.05741,848.26,-0.17632,-0.89974,-0.39923,1137.4,-0.13807,-0.37897,0.91505,324.12
> view matrix models
> #5,0.015509,0.99968,0.019979,59.911,-0.99511,0.013483,0.097818,887.14,0.097517,-0.021399,0.995,37.586
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #5 inMap #1
Fit map J1671_PE z flip in map emdb35243_ODV using 1058456 points
correlation = 0.7675, correlation about mean = 0.06833, overlap = 1.003e+05
steps = 264, shift = 16.4, angle = 7.76 degrees
Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.95303348 0.30286496 0.00002327 -130.17331272
-0.30286496 0.95303348 0.00003703 127.93398000
-0.00001097 -0.00004234 1.00000000 -121.40095851
Axis -0.00013103 0.00005653 -0.99999999
Axis point 347.39215679 483.62545297 0.00000000
Rotation angle (degrees) 17.62976098
Shift along axis 121.42524514
> view matrix models
> #5,0.30902,0.29306,0.90478,-145.34,-0.83128,-0.37894,0.40666,837.38,0.46203,-0.87779,0.12651,604.39
> undo
> select add #5
3 models selected
> select subtract #5
Nothing selected
> ui mousemode right rotate
> ui mousemode right translate
> show #!4 models
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,344.93,0,1,0,0.63352,0,0,1,128.18
> volume #4 level 0.2379
> view matrix models #4,1,0,0,81.692,0,1,0,-19.877,0,0,1,125.49
> view matrix models #4,1,0,0,83.558,0,1,0,70.413,0,0,1,133.11
> view matrix models #4,1,0,0,70.873,0,1,0,70.205,0,0,1,133.5
> fitmap #4 inMap #1
Fit map J1663_FE in map emdb35243_ODV using 99734 points
correlation = 0.83, correlation about mean = 0.228, overlap = 9730
steps = 88, shift = 14.2, angle = 0.0496 degrees
Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22800509 -0.97365994 -0.00000874 722.74511445
0.97365994 0.22800508 0.00010883 -107.11178091
-0.00010397 -0.00003333 0.99999999 -59.46670416
Axis -0.00007300 0.00004890 1.00000000
Axis point 428.91462448 402.21523340 0.00000000
Rotation angle (degrees) 76.82034903
Shift along axis -59.52470265
> ui mousemode right zoom
> ui mousemode right rotate
> select subtract #4
Nothing selected
> ui mousemode right translate
> volume #2 level 0.2977
> volume #1 level 0.3465
> volume #4 level 0.2335
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
> fitmap #4 inMap #1
Fit map J1663_FE in map emdb35243_ODV using 827535 points
correlation = 0.8296, correlation about mean = 0.234, overlap = 7.948e+04
steps = 44, shift = 0.055, angle = 0.0137 degrees
Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22793154 -0.97367716 0.00001878 722.76413763
0.97367715 0.22793154 -0.00011550 -106.96571476
0.00010818 0.00004462 0.99999999 -59.55985998
Axis 0.00008222 -0.00004590 1.00000000
Axis point 428.83496900 402.26790985 0.00000000
Rotation angle (degrees) 76.82467682
Shift along axis -59.49552349
> fitmap #2 inMap #1
Fit map emdb43590_BV in map emdb35243_ODV using 3024743 points
correlation = 0.7983, correlation about mean = 0.1452, overlap = 3.651e+05
steps = 44, shift = 0.128, angle = 0.0297 degrees
Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22934616 -0.97334492 0.00000038 772.16317142
0.97334492 0.22934616 -0.00000003 -188.52800554
-0.00000006 0.00000038 1.00000000 -179.71258188
Axis 0.00000021 0.00000022 1.00000000
Axis point 505.13813030 393.36165391 0.00000000
Rotation angle (degrees) 76.74141952
Shift along axis -179.71246293
> fitmap #4 inMap #1
Fit map J1663_FE in map emdb35243_ODV using 827535 points
correlation = 0.8296, correlation about mean = 0.234, overlap = 7.948e+04
steps = 36, shift = 0.0126, angle = 0.00531 degrees
Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22793225 -0.97367699 -0.00000066 722.77597776
0.97367699 0.22793225 -0.00002493 -107.00856619
0.00002443 0.00000504 1.00000000 -59.50745513
Axis 0.00001539 -0.00001288 1.00000000
Axis point 428.86473096 402.25276864 0.00000000
Rotation angle (degrees) 76.82463471
Shift along axis -59.49495194
> fitmap #5 inMap #1
Fit map J1671_PE z flip in map emdb35243_ODV using 1058456 points
correlation = 0.7675, correlation about mean = 0.06833, overlap = 1.003e+05
steps = 96, shift = 0.0142, angle = 0.00165 degrees
Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.95302877 0.30287977 0.00000058 -130.16785956
-0.30287977 0.95302877 0.00002874 127.93693847
0.00000815 -0.00002757 1.00000000 -121.42680505
Axis -0.00009296 -0.00001250 -1.00000000
Axis point 347.40797876 483.60691161 0.00000000
Rotation angle (degrees) 17.63065109
Shift along axis 121.43730542
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right clip
> volume #2 color white
> volume #2 color #ff9300
> volume #2 color #942192
> volume #1 color #ff40ff
> volume #1 color white
> volume #2 color white
> ui mousemode right translate
> volume #2 level 0.1926
> volume #1 level 0.2772
> volume #2 level 0.2234
> volume #2 level 0.29
> volume #1 level 0.3743
> volume #2 level 0.3284
> volume #5 color #ff2600
> volume #5 color #00fdff
> volume #5 color #7a81ff
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.2478
> volume #1 level 0.3951
> volume #4 level 0.2535
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!2 models
> set bgColor white
> graphics silhouettes true
> lighting depthCue false
> lighting soft
> graphics bgColor white
> graphics silhouettes width 2.3
> volume #1 level 0.2287
> show #!2 models
> hide #!1 models
> volume #2 level 0.1747
> volume #2 level 0.2541
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #5 level 0.1086
> volume #2 level 0.167
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
——— End of log from Tue Dec 24 14:33:25 2024 ———
opened ChimeraX session
> hide #!5 models
> color #2 #fffb00ff models
> hide #!1 models
> show #!4 models
> volume #4 level 0.1109
> volume #2 level 0.2362
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> volume #1 level 0.2842
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.2669
> show #!4 models
> volume #4 level 0.1666
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #4 level 0.09079
> hide #!4 models
> show #!5 models
> volume #2 level 0.1363
> volume #5 level 0.09125
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> volume #2 level 0.003029
> volume #2 level 0.06965
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
——— End of log from Tue Dec 24 14:48:02 2024 ———
opened ChimeraX session
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> show #!5 models
> show #!4 models
> show #!1 models
> fitmap #2 inMap #1
Fit map emdb43590_BV in map emdb35243_ODV using 14658219 points
correlation = 0.7541, correlation about mean = 0.4206, overlap = 6.34e+05
steps = 44, shift = 0.0918, angle = 0.00815 degrees
Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22948454 -0.97331231 -0.00000019 772.07912980
0.97331231 0.22948454 0.00000002 -188.58027009
0.00000003 -0.00000019 1.00000000 -179.80414440
Axis -0.00000011 -0.00000011 1.00000000
Axis point 505.14652168 393.35360876 0.00000000
Rotation angle (degrees) 76.73327344
Shift along axis -179.80420481
> volume #2 level 0.1593
> fitmap #2 inMap #1
Fit map emdb43590_BV in map emdb35243_ODV using 6420765 points
correlation = 0.788, correlation about mean = 0.2153, overlap = 5.315e+05
steps = 40, shift = 0.0561, angle = 0.0102 degrees
Position of emdb43590_BV (#2) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22965823 -0.97327134 0.00000041 771.97288598
0.97327134 0.22965823 0.00000005 -188.64582157
-0.00000014 0.00000039 1.00000000 -179.74825591
Axis 0.00000018 0.00000028 1.00000000
Axis point 505.15663052 393.34320391 0.00000000
Rotation angle (degrees) 76.72304870
Shift along axis -179.74817265
> fitmap #4 inMap #1
Fit map J1663_FE in map emdb35243_ODV using 3515214 points
correlation = 0.7547, correlation about mean = 0.4947, overlap = 1.23e+05
steps = 44, shift = 1.44, angle = 0.00292 degrees
Position of J1663_FE (#4) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.22797990 -0.97366584 0.00000032 722.75242081
0.97366584 0.22797990 -0.00001052 -107.05172737
0.00001017 0.00000271 1.00000000 -58.05938758
Axis 0.00000679 -0.00000506 1.00000000
Axis point 428.88300196 402.23914637 0.00000000
Rotation angle (degrees) 76.82183100
Shift along axis -58.05393872
> fitmap #5 inMap #1
Fit map J1671_PE z flip in map emdb35243_ODV using 2887742 points
correlation = 0.7439, correlation about mean = 0.3608, overlap = 1.359e+05
steps = 84, shift = 0.0126, angle = 0.0165 degrees
Position of J1671_PE z flip (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.95294192 0.30315291 -0.00002329 -130.23084526
-0.30315291 0.95294192 0.00003337 128.08923520
0.00003231 -0.00002474 1.00000000 -121.44780533
Axis -0.00009584 -0.00009171 -0.99999999
Axis point 347.50822763 483.49288311 0.00000000
Rotation angle (degrees) 17.64707305
Shift along axis 121.44853799
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1748_004_volume_map.mrc
Opened cryosparc_P23_J1748_004_volume_map.mrc as #3, grid size 588,588,588,
pixel 1.34, shown at level 0.129, step 4, values float32
> hide #!4 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #3 step 1
> ui mousemode right clip
> ui mousemode right translate
> select add #3
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.40948,-0.77865,-0.47542,760.83,-0.71746,-0.59673,0.35938,744.31,-0.56353,0.19394,-0.80301,985.38
> view matrix models
> #3,0.32041,-0.69825,0.64014,244.66,-0.90173,-0.43184,-0.019699,928.51,0.2902,-0.57093,-0.768,934.07
> view matrix models
> #3,0.39371,-0.91284,-0.10826,648.9,-0.91524,-0.37831,-0.1386,968.12,0.085564,0.15365,-0.98441,830.02
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.39371,-0.91284,-0.10826,762.28,-0.91524,-0.37831,-0.1386,1064.7,0.085564,0.15365,-0.98441,801.88
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.37861,-0.92556,-0.0013901,723.46,-0.91898,-0.37574,-0.11957,1056.3,0.11015,0.046549,-0.99282,838.31
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.37861,-0.92556,-0.0013901,717.57,-0.91898,-0.37574,-0.11957,1053,0.11015,0.046549,-0.99282,889.03
> view matrix models
> #3,0.37861,-0.92556,-0.0013901,714.64,-0.91898,-0.37574,-0.11957,1041.5,0.11015,0.046549,-0.99282,889.68
> fitmap #3 inMap #1
Fit map cryosparc_P23_J1748_004_volume_map.mrc in map emdb35243_ODV using
2033906 points
correlation = 0.8586, correlation about mean = 0.213, overlap = 1.155e+05
steps = 176, shift = 23, angle = 7.82 degrees
Position of cryosparc_P23_J1748_004_volume_map.mrc (#3) relative to
emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.99578155 0.09175521 0.00000256 -23.45858541
0.09175519 -0.99578156 -0.00000778 761.14443305
0.00000183 0.00000798 -0.99999997 760.15790824
Axis 0.99892332 0.04637151 -0.00137005
Axis point 0.00000000 381.11520699 380.06436878
Rotation angle (degrees) 179.99954802
Shift along axis 10.82063276
> fitmap #3 inMap #1
Fit map cryosparc_P23_J1748_004_volume_map.mrc in map emdb35243_ODV using
2033906 points
correlation = 0.8586, correlation about mean = 0.2131, overlap = 1.155e+05
steps = 36, shift = 0.0092, angle = 0.00079 degrees
Position of cryosparc_P23_J1748_004_volume_map.mrc (#3) relative to
emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.99578150 0.09175583 0.00001530 -23.45998132
0.09175581 -0.99578151 -0.00000256 761.14824253
0.00001500 0.00000396 -0.99999997 760.15889297
Axis 0.99888925 0.04700335 -0.00330788
Axis point 0.00000000 381.12546248 380.04122309
Rotation angle (degrees) 179.99981308
Shift along axis 9.82808080
> select subtract #3
Nothing selected
> volume #3 level 0.03398
> volume #3 level 0.04519
> volume #3 color #3b8fff
> ui mousemode right clip
> ui mousemode right translate
> hide #!1 models
> volume #3 level 0.05546
> volume #4 level 0.1149
> volume #4 level 0.1236
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #3 level 0.05173
> volume #3 level 0.03211
> volume #4 level 0.07328
> hide #!4 models
> show #!4 models
> hide #!4 models
> rename #3 J1748_FE
> show #!5 models
> hide #!5 models
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
——— End of log from Tue Dec 24 17:47:32 2024 ———
opened ChimeraX session
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> volume #3 level 0.04733
> volume #3 level 0.06065
> ui mousemode right clip
> show #!1 models
> show #!2 models
> show #!5 models
> volume #5 level 0.1186
> volume #5 level 0.1111
> volume #2 level 0.1926
> show #!4 models
> volume #4 level 0.1535
> hide #!5 models
> close #4
> volume #2 level 0.2003
> volume #1 level 0.2218
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #1 level 0.1698
> hide #!3 models
> volume #1 level 0.2252
> volume #1 level 0.2703
> hide #!5 models
> show #!3 models
> volume #3 level 0.06804
> volume #3 level 0.07359
> volume #3 level 0.05788
> ui tool show "Hide Dust"
> surface dust #3 size 8.04
> surface dust #3 size 8.8
> surface dust #3 size 18.45
> surface dust #3 size 18.75
> surface dust #3 size 37.37
> volume #1 level 0.2495
> volume #1 level 0.246
> surface dust #3 size 37.37
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #1 size 8.1
> surface dust #1 size 8.02
> surface dust #1 size 20.2
> surface dust #1 size 18.89
> surface dust #1 size 23.12
> volume #2 level 0.2054
> volume #2 color #dfd9fc
> volume #2 color #c2cafd
> volume #2 color #f34d8f
> volume #2 color #3b8fff
> volume #2 color #7a81ff
> volume #2 color #d2d2d3
> volume #2 color #dfd9fc
> volume #2 color #c2cafd
> volume #2 color #f34d8f
> volume #2 color #235091
> volume #2 color #d2d2d3
> volume #2 color #d9776e
> volume #5 level 0.1409
> ui mousemode right rotate
> ui mousemode right translate
> surface dust #2 size 8.46
> surface dust #2 size 8.3
[Repeated 1 time(s)]
> transparency #3 50
> transparency #3 40
> volume #2 level 0.2403
> volume #3 level 0.06527
> volume #1 level 0.2595
> volume #1 color #c2cafd
> ui tool show "Hide Dust"
> surface dust #1 size 1.35
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #5 size 14.2
> surface dust #5 size 15.03
> surface dust #5 size 37.91
> surface dust #1 size 12.83
> surface dust #1 size 13.96
> surface dust #1 size 33.45
> surface dust #1 size 14.19
> surface dust #1 size 27.82
> surface dust #1 size 33.45
> surface dust #1 size 58.26
> ui mousemode right clip
> volume #5 level 0.02913
> volume #5 level 0.1086
> volume #5 level 0.07634
> transparency #3 0
> volume #3 level 0.0158
> volume #3 level 0.03958
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1663_003_volume_map.mrc
Opened cryosparc_P23_J1663_003_volume_map.mrc as #4, grid size 360,360,360,
pixel 2.37, shown at level 0.302, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
> volume #4 level 0.09233
> volume #4 level 0.1146
> ui mousemode right translate
> volume #4 level 0.0901
> ui mousemode right clip
> select add #4
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,65.037,0,1,0,-9.76,0,0,1,122.44
> ui tool show "Fit in Map"
> surface dust #1 size 58.3
> surface dust #1 size 58.42
> surface dust #1 size 58.58
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #4 inMap #3
Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 3557522
points
correlation = 0.4347, correlation about mean = -0.02198, overlap = 1.693e+04
steps = 188, shift = 24, angle = 3.93 degrees
Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE
(#3) coordinates:
Matrix rotation and translation
0.33050798 -0.94178203 0.06173458 681.45164000
-0.94275723 -0.33251334 -0.02537203 979.22027943
0.04442248 -0.04981506 -0.99777009 818.62961298
Axis -0.81561934 0.57767311 -0.03254049
Axis point 0.00000000 734.69129100 391.17873063
Rotation angle (degrees) 179.14142847
Shift along axis -16.77451928
> view matrix models
> #4,0.99891,0.016612,0.043643,30.823,-0.014401,0.99862,-0.050483,34.399,-0.044421,0.049799,0.99777,106.43
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99791,-0.016664,-0.062458,89.788,0.016304,0.99985,-0.0062726,2.309,0.062553,0.0052411,0.99803,79.721
> fitmap #4 inMap #3
Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 3557522
points
correlation = 0.4361, correlation about mean = -0.01796, overlap = 1.701e+04
steps = 152, shift = 17, angle = 1.78 degrees
Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE
(#3) coordinates:
Matrix rotation and translation
0.31830062 -0.94776499 -0.02064779 722.74851077
-0.94395812 -0.31887832 0.08520406 917.64991711
-0.08733756 -0.00762985 -0.99614958 857.77294072
Axis -0.81170878 0.58311312 0.03328592
Axis point 0.00000000 733.56123549 427.29369258
Rotation angle (degrees) 176.72179560
Shift along axis -23.01584556
> volume #4 level 0.1302
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99618,0.0017832,-0.087354,122.51,-0.0024414,0.99997,-0.0074289,67.89,0.087338,0.0076138,0.99615,82.111
> view matrix models
> #4,0.99618,0.0017832,-0.087354,111.55,-0.0024414,0.99997,-0.0074289,66.848,0.087338,0.0076138,0.99615,83.851
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99989,-0.012706,0.0079521,78.608,0.012717,0.99992,-0.0013316,58.009,-0.0079345,0.0014326,0.99997,125.58
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99989,-0.012706,0.0079521,73.359,0.012717,0.99992,-0.0013316,57.418,-0.0079345,0.0014326,0.99997,127
> fitmap #4 inMap #3
Fit map cryosparc_P23_J1663_003_volume_map.mrc in map J1748_FE using 1934742
points
correlation = 0.9722, correlation about mean = 0.8889, overlap = 4.877e+04
steps = 72, shift = 7.35, angle = 0.83 degrees
Position of cryosparc_P23_J1663_003_volume_map.mrc (#4) relative to J1748_FE
(#3) coordinates:
Matrix rotation and translation
0.31655931 -0.94857276 -0.00000334 663.27925709
-0.94857276 -0.31655929 -0.00000757 933.06974962
0.00000612 0.00000557 -1.00000003 819.98524864
Axis 0.81162632 -0.58417690 0.00025913
Axis point 0.00000000 705.23406850 409.88905627
Rotation angle (degrees) 179.99953615
Shift along axis -6.53039807
> select subtract #4
Nothing selected
> ui mousemode right translate
> volume #3 level 0.05385
> transparency #3 50
> transparency #3 0
> volume #3 level 0.051
> ui mousemode right clip
> volume #3 level 0.03007
> volume #3 level 0.04434
> volume #3 level 0.03958
> volume #3 level 0.04
> volume #3 level 0.042
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.2422
> volume #1 level 0.25
> volume #2 level 0.248
> ui mousemode right translate
> volume #2 level 0.275
> volume #1 level 0.24
> volume #2 level 0.28
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui tool show "Side View"
> ui mousemode right translate
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> volume #4 level 0.1035
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> volume #4 level 0.1146
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!3 models
> transparency #2 50
> transparency #2 40
> volume #1 level 0.2712
> show #!5 models
> hide #!5 models
> color #2 #d2d2d3ff models
> color #2 #c2cafdff models
> color #1 #f34d8fff models
> color #1 #c1153cff models
> color #1 #f34d8fff models
> color #1 white models
> color #1 #5f90e2ff models
> color #1 #74fad9ff models
> color #1 white models
> color #1 #71ed4eff models
> color #1 white models
> color #1 #6057e0ff models
> transparency #2 40
> transparency #2 0
> transparency #1 40
> transparency #2 40
> transparency #1 0
> color #1 #7f51e0ff models
> color #1 #5573e1ff models
> color #1 #4e5ce0ff models
> color #2 #c3b2e9ff models
> color #2 #c9b8eaff models
> color #2 #7a81ffff models
> color #2 #fefefeff models
> color #2 white models
> transparency #2 0
> color #2 #f6f0e1ff models
> color #2 #d2d2d3ff models
> color #2 #d2d2d366 models
> transparency #2 0
> transparency #1 40
> transparency #2 40
> transparency #1 40
> transparency #1 0
> lighting gentle
> lighting soft
> lighting gentle
> lighting flat
> lighting gentle
> lighting soft
> lighting gentle
> lighting soft
> color #1 #d2d2d3ff models
> color #2 #3b8fffff models
> color #2 #c2cafdff models
> color #2 #7a81ffff models
> transparency #1 40
> transparency #1 0
> transparency #2 40
> color #1 #fafcfbff models
> color #1 #f7eef5ff models
> color #1 #f1dcedff models
> color #1 #f9f3f0ff models
> color #1 #f8f7ebff models
> color #1 #edf8caff models
> color #1 #f0f8cbff models
> color #1 #f8f1d9ff models
> color #1 #f8efd7ff models
> color #1 #e1d8c3ff models
> color #1 #f2e9d2ff models
> color #1 #dfd7c2ff models
> color #1 #dbd3beff models
> color #1 #7a81ffff models
> color #2 #dbd3beff models
> transparency #2 40
> transparency #2 0
> transparency #1 40
> color #2 #d2e2d7ff models
> color #2 #c9e2c2ff models
> color #2 #dcd9e2ff models
> color #2 #f8f4ffff models
> color #2 #e4e0eaff models
> transparency #1 50
> transparency #1 35
> name view front
"front": invalid atom specifier
> view name front
> save /Users/ConstantinePetridis/Desktop/BV_ODV.png width 3000 height 1962
> supersample 4
> color #2 #8d8b91ff models
> color #2 #a3a1a8ff models
> transparency #1 35
> transparency #2 0
> color #2 #f7f5ffff models
> color #2 #cbc9d1ff models
> color #2 #cbc9d2ff models
> lighting soft
> lighting gentle
> lighting soft
> ui mousemode right rotate
> ui mousemode right zoom
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right translate
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #1 level 0.3024
> color #1 #7a81ffff models
> color #1 #7a81ff00 models
> color #1 #7a81ff34 models
> color #1 #7a81ffff models
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right translate
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.2885
> volume #1 level 0.2469
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #2 level 0.2031
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> volume #1 level 0.3197
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.05913
> volume #3 level 0.05722
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.07815
> volume #3 level 0.08481
> volume #3 level 0.08
> hide #!1 models
> volume #3 level 0.1009
> show #!4 models
> volume #4 level 0.2261
> volume #4 level 0.235
> volume #3 level 0.09998
> volume #3 level 0.08856
> volume #4 level 0.2551
> volume #3 level 0.1019
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #3
> rename #4 J1663_FE
> rename #4 J1663_FE id #3
> rename #5 id #4
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1770_003_volume_map.mrc
Opened cryosparc_P23_J1770_003_volume_map.mrc as #5, grid size 360,360,360,
pixel 2.19, shown at level 0.277, step 2, values float32
> hide #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 step 1
> volume #5 level 0.1721
> show #!3 models
> hide #!4 models
> volume #5 level 0.2115
> volume #5 level 0.2174
> ui mousemode right "rotate selected models"
> select add #5
3 models selected
> view matrix models
> #5,0.95745,0.28858,0.0043312,-98.953,0.28414,-0.93989,-0.18942,741.06,-0.050591,0.18259,-0.98189,876.7
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95745,0.28858,0.0043312,-4.1809,0.28414,-0.93989,-0.18942,804.6,-0.050591,0.18259,-0.98189,869.49
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.9971,0.066566,0.037008,52.351,0.073264,-0.97107,-0.22728,917.7,0.020808,0.22933,-0.97313,818.85
> view matrix models
> #5,0.99854,-0.036256,0.040116,90.834,-0.024169,-0.96292,-0.26869,972.29,0.048371,0.26733,-0.96239,787.99
> view matrix models
> #5,0.99559,-0.055166,-0.07586,153.79,-0.070768,-0.97259,-0.22149,972.33,-0.061562,0.22588,-0.97221,852.22
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99559,-0.055166,-0.07586,138.73,-0.070768,-0.97259,-0.22149,972.47,-0.061562,0.22588,-0.97221,837.2
> fitmap #5 inMap #3
Fit map cryosparc_P23_J1770_003_volume_map.mrc in map J1663_FE using 822201
points
correlation = 0.9965, correlation about mean = 0.9334, overlap = 9.029e+04
steps = 208, shift = 47.2, angle = 16.4 degrees
Position of cryosparc_P23_J1770_003_volume_map.mrc (#5) relative to J1663_FE
(#3) coordinates:
Matrix rotation and translation
0.99517678 0.09809776 0.00003947 -4.57853809
0.09809776 -0.99517678 -0.00003620 779.53497612
0.00003573 0.00003990 -1.00000000 819.70376405
Axis 0.99879463 0.04908453 0.00003744
Axis point 0.00000000 389.87217475 409.85938563
Rotation angle (degrees) 179.99781716
Shift along axis 33.72077697
[deleted to fit within ticket limits]
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> volume #1 level 0.2885
> volume #1 level 0.2469
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #2 level 0.2031
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> volume #1 level 0.3197
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.05913
> volume #3 level 0.05722
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.07815
> volume #3 level 0.08481
> volume #3 level 0.08
> hide #!1 models
> volume #3 level 0.1009
> show #!4 models
> volume #4 level 0.2261
> volume #4 level 0.235
> volume #3 level 0.09998
> volume #3 level 0.08856
> volume #4 level 0.2551
> volume #3 level 0.1019
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #3
> rename #4 J1663_FE
> rename #4 J1663_FE id #3
> rename #5 id #4
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1770_003_volume_map.mrc
Opened cryosparc_P23_J1770_003_volume_map.mrc as #5, grid size 360,360,360,
pixel 2.19, shown at level 0.277, step 2, values float32
> hide #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 step 1
> volume #5 level 0.1721
> show #!3 models
> hide #!4 models
> volume #5 level 0.2115
> volume #5 level 0.2174
> ui mousemode right "rotate selected models"
> select add #5
3 models selected
> view matrix models
> #5,0.95745,0.28858,0.0043312,-98.953,0.28414,-0.93989,-0.18942,741.06,-0.050591,0.18259,-0.98189,876.7
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95745,0.28858,0.0043312,-4.1809,0.28414,-0.93989,-0.18942,804.6,-0.050591,0.18259,-0.98189,869.49
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.9971,0.066566,0.037008,52.351,0.073264,-0.97107,-0.22728,917.7,0.020808,0.22933,-0.97313,818.85
> view matrix models
> #5,0.99854,-0.036256,0.040116,90.834,-0.024169,-0.96292,-0.26869,972.29,0.048371,0.26733,-0.96239,787.99
> view matrix models
> #5,0.99559,-0.055166,-0.07586,153.79,-0.070768,-0.97259,-0.22149,972.33,-0.061562,0.22588,-0.97221,852.22
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99559,-0.055166,-0.07586,138.73,-0.070768,-0.97259,-0.22149,972.47,-0.061562,0.22588,-0.97221,837.2
> fitmap #5 inMap #3
Fit map cryosparc_P23_J1770_003_volume_map.mrc in map J1663_FE using 822201
points
correlation = 0.9965, correlation about mean = 0.9334, overlap = 9.029e+04
steps = 208, shift = 47.2, angle = 16.4 degrees
Position of cryosparc_P23_J1770_003_volume_map.mrc (#5) relative to J1663_FE
(#3) coordinates:
Matrix rotation and translation
0.99517678 0.09809776 0.00003947 -4.57853809
0.09809776 -0.99517678 -0.00003620 779.53497612
0.00003573 0.00003990 -1.00000000 819.70376405
Axis 0.99879463 0.04908453 0.00003744
Axis point 0.00000000 389.87217475 409.85938563
Rotation angle (degrees) 179.99781716
Shift along axis 33.72077697
> select subtract #5
Nothing selected
> ui mousemode right translate
> volume #5 level 0.2155
> volume #5 level 0.2135
> ui mousemode right clip
> ui mousemode right translate
> rename #5 J1770_FE
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
——— End of log from Tue Dec 24 23:20:40 2024 ———
opened ChimeraX session
> ui mousemode right clip
> show #!4 models
> volume #4 level 0.29
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.28
> show #!1 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit map J1770_FE in map emdb35243_ODV using 851116 points
correlation = 0.8483, correlation about mean = 0.2293, overlap = 8e+04
steps = 48, shift = 0.243, angle = 0.0164 degrees
Position of J1770_FE (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.13132850 0.99133890 -0.00006754 -37.26648368
0.99133890 -0.13132851 -0.00003051 66.19760087
-0.00003911 -0.00006295 -1.00000000 760.18993780
Axis -0.75209153 -0.65905867 0.00001272
Axis point 0.00000000 49.43258156 380.09425290
Rotation angle (degrees) 179.99876430
Shift along axis -15.59062842
> fitmap #5 inMap #1
Fit map J1770_FE in map emdb35243_ODV using 851116 points
correlation = 0.8483, correlation about mean = 0.2294, overlap = 8e+04
steps = 36, shift = 0.00413, angle = 0.0029 degrees
Position of J1770_FE (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.13135235 0.99133574 -0.00002496 -37.29061767
0.99133574 -0.13135236 -0.00001744 66.20215683
-0.00002057 -0.00002245 -1.00000000 760.16825748
Axis -0.75201734 -0.65914331 -0.00013191
Axis point 0.00000000 49.44453715 380.08733738
Rotation angle (degrees) 179.99980896
Shift along axis -15.69379233
> volume #1 level 0.3717
> fitmap #5 inMap #1
Fit map J1770_FE in map emdb35243_ODV using 851116 points
correlation = 0.8483, correlation about mean = 0.2294, overlap = 8e+04
steps = 36, shift = 0.0043, angle = 0.000951 degrees
Position of J1770_FE (#5) relative to emdb35243_ODV (#1) coordinates:
Matrix rotation and translation
0.13135135 0.99133588 -0.00003949 -37.28663274
0.99133587 -0.13135136 -0.00002539 66.20350274
-0.00003036 -0.00003581 -1.00000000 760.17965366
Axis -0.75206738 -0.65908623 -0.00004758
Axis point 0.00000000 49.44186881 380.09087758
Rotation angle (degrees) 179.99960320
Shift along axis -15.62792528
> volume #1 level 0.3405
> view front
> volume #5 color #7a81ff
> volume #4 level 0.2677
> volume #5 level 0.1741
> volume #3 level 0.1949
> volume #1 color #d2d2d3
> volume #1 color #7a81ff
> volume #5 color #dfd9fc
> volume #5 color #c2cafd
> volume #5 color #dbd3be
> volume #5 color #d2d2d3
> volume #5 color #d2d2d37f
> view front
> volume #5 color #d2d2d3cb
> volume #5 color #d2d2d3bf
> volume #4 color #c1153c
> view front
> ui mousemode right "clip rotate"
> ui mousemode right clip
> volume #1 level 0.3058
> hide #!1 models
> volume #5 color #d2d2d3
> volume #5 color #7a81ff
> volume #5 color #dbd3be
> volume #5 color #f34d8f
> volume #5 color #c2cafd
> volume #5 color #75ff79
> volume #5 color #c1153c
> volume #5 color #7a81ff
> volume #5 level 0.2135
> volume #5 level 0.22
> volume #1 level 0.3301
> volume #1 color #c1153c
> volume #1 level 0.357
> volume #5 level 0.2296
> volume #2 level 0.3571
> volume #3 level 0.275
> volume #5 level 0.22
> fitmap #2 inMap #5
Fit map emdb43590_BV in map J1770_FE using 1970231 points
correlation = 0.7092, correlation about mean = 0.03558, overlap = 1.518e+05
steps = 132, shift = 5.67, angle = 0.682 degrees
Position of emdb43590_BV (#2) relative to J1770_FE (#5) coordinates:
Matrix rotation and translation
0.99488447 0.10096665 -0.00326011 -145.50060887
0.10099751 -0.99482187 0.01135595 832.26782874
-0.00209666 -0.01162712 -0.99993021 951.49886823
Axis -0.99872025 -0.05055749 0.00134102
Axis point 0.00000000 422.55694258 473.23931095
Rotation angle (degrees) 179.34072539
Shift along axis 104.51300645
> fitmap #2 inMap #5
Fit map emdb43590_BV in map J1770_FE using 1970231 points
correlation = 0.7092, correlation about mean = 0.03558, overlap = 1.518e+05
steps = 48, shift = 0.00365, angle = 0.0012 degrees
Position of emdb43590_BV (#2) relative to J1770_FE (#5) coordinates:
Matrix rotation and translation
0.99488316 0.10097978 -0.00325450 -145.50768201
0.10101054 -0.99482072 0.01134053 832.26735347
-0.00209248 -0.01161124 -0.99993040 951.48602193
Axis -0.99871992 -0.05056405 0.00133857
Axis point 0.00000000 422.55359730 473.23634432
Rotation angle (degrees) 179.34162287
Shift along axis 104.51223978
> select add #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,1,0.002004,-0.0020819,-1.4849,-0.0020281,0.99993,-0.011639,4.0605,0.0020584,0.011643,0.99993,-6.8056
> fitmap #2 inMap #5
Fit map emdb43590_BV in map J1770_FE using 1970231 points
correlation = 0.7093, correlation about mean = 0.03518, overlap = 1.518e+05
steps = 56, shift = 4.96, angle = 0.332 degrees
Position of emdb43590_BV (#2) relative to J1770_FE (#5) coordinates:
Matrix rotation and translation
0.99484759 0.10105423 -0.00814346 -144.38287979
0.10112086 -0.99484008 0.00823324 833.24382317
-0.00726943 -0.00901429 -0.99993295 952.76155498
Axis -0.99871104 -0.05061005 0.00385835
Axis point 0.00000000 422.33880063 474.28921584
Rotation angle (degrees) 179.50525064
Shift along axis 105.70234875
> select subtract #2
Nothing selected
> select add #2
3 models selected
> view matrix models
> #2,0.99997,0.0020761,-0.0072544,4.7579,-0.0021416,0.99996,-0.009031,6.2994,0.0072354,0.0090463,0.99993,-13.222
> fitmap #2 inMap #5
Fit map emdb43590_BV in map J1770_FE using 1970231 points
correlation = 0.7092, correlation about mean = 0.03557, overlap = 1.518e+05
steps = 92, shift = 4.21, angle = 0.327 degrees
Position of emdb43590_BV (#2) relative to J1770_FE (#5) coordinates:
Matrix rotation and translation
0.99488426 0.10096572 -0.00335336 -145.47747429
0.10099761 -0.99482217 0.01132865 832.27857560
-0.00219219 -0.01160938 -0.99993021 951.53886178
Axis -0.99872020 -0.05055728 0.00138827
Axis point 0.00000000 422.55644599 473.26057510
Rotation angle (degrees) 179.34201733
Shift along axis 104.53454580
> view matrix models
> #2,1,0.0019899,-0.0021815,1.6101,-0.0020151,0.99993,-0.011637,7.3811,0.0021581,0.011641,0.99993,-12.102
> select subtract #2
Nothing selected
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right zone
> ui mousemode right clip
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> volume #2 level 0.3298
> volume #1 level 0.3739
> show #!1 models
> hide #!5 models
> view front
[Repeated 1 time(s)]
> volume #2 color #cbc9d261
> volume #2 color #cbc9d292
> volume #2 color #cbc9d280
> save /Users/ConstantinePetridis/Desktop/BV_ODV_front.png width 3000 height
> 1873 supersample 4
> name view diagonal
"diagonal": invalid atom specifier
> view name diagonal
> save /Users/ConstantinePetridis/Desktop/BV_ODV_diag.png width 3000 height
> 1873 supersample 4
> view name top
> save /Users/ConstantinePetridis/Desktop/BV_ODV_top.png width 3000 height
> 1873 supersample 4
> view front
> save /Users/ConstantinePetridis/Desktop/BV_ODV_slice.png width 3000 height
> 1873 supersample 4
> lighting gentle
> lighting soft
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> volume #1 level 0.3635
> volume #1 level 0.369
> volume #1 level 0.368
> volume #1 level 0.367
> volume #1 level 0.366
> volume #1 level 0.365
> volume #1 level 0.363
> volume #1 level 0.364
> volume #1 level 0.365
> save /Users/ConstantinePetridis/Desktop/BV_ODV_slice.png width 3000 height
> 1873 supersample 4
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.369
> volume #1 level 0.37
> volume #1 level 0.371
> volume #1 level 0.37
> volume #1 level 0.372
> volume #1 level 0.37
> volume #1 level 0.371
> volume #1 level 0.37
> volume #1 level 0.371
> volume #1 level 0.37
> volume #1 level 0.371
> volume #1 level 0.37
> save /Users/ConstantinePetridis/Desktop/BV_ODV_slice.png width 3000 height
> 1873 supersample 4
> show #!5 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #2 #cbc9d2ff models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #5 level 0.218
> ui tool show "Hide Dust"
> surface dust #2 size 1.41
> surface dust #5 size 13.13
> surface dust #5 size 12.94
> surface dust #5 size 14.56
[Repeated 1 time(s)]
> surface dust #5 size 13.84
> surface dust #5 size 24.07
> surface dust #1 size 58.58
> surface dust #2 size 1.41
> surface dust #2 size 1.53
> surface dust #2 size 7.02
> volume #2 color #cbc9d280
> surface dust #2 size 7.9
> surface dust #2 size 13.04
> volume #2 color #cbc9d2
> surface dust #1 size 58.26
> surface dust #1 size 23.5
[Repeated 1 time(s)]
> volume #2 color #6f7073
> undo
> volume #2 color #d2d2d3
> volume #2 color #d2d2d37f
> volume #2 level 0.328
> volume #2 level 0.329
> volume #2 level 0.33
> volume #2 level 0.329
> surface dust #1 size 23.91
> surface dust #2 size 12.41
> surface dust #2 size 13.27
> volume #2 level 0.3136
> volume #2 level 0.315
> surface dust #2 size 13.71
> surface dust #2 size 7.26
> surface dust #1 size 22.74
> surface dust #1 size 24.72
> volume #5 level 0.2003
> volume #5 level 0.2042
> volume #5 level 0.2022
> save /Users/ConstantinePetridis/Desktop/BV_ODV_slice2.png width 3000 height
> 1873 supersample 4
> name view slice
"slice": invalid atom specifier
> view name slice
[Repeated 1 time(s)]
> volume #2 color #d2d2d3
> view name slice
[Repeated 1 time(s)]
> volume #5 level 0.203
> volume #5 level 0.205
> volume #5 level 0.215
> volume #5 level 0.213
> surface dust #5 size 11.7
> surface dust #5 size 11.51
> surface dust #5 size 15.31
> surface dust #5 size 15.57
> surface dust #5 size 22.14
> surface dust #5 size 21.05
> surface dust #5 size 14.56
> surface dust #5 size 15
> surface dust #5 size 15.5
[Repeated 1 time(s)]
> volume #5 level 0.215
> volume #5 level 0.22
> volume #5 level 0.215
> volume #5 level 0.214
> volume #5 level 0.21
> volume #5 level 0.212
> volume #2 color #d2d2d382
> volume #2 color #d2d2d381
> volume #2 color #d2d2d380
> volume #5 color #7a81ff82
> volume #5 color #7a81ff80
> volume #5 color #7a81ff
> volume #5 color #7d82ff
> volume #5 color #9096ff
> volume #5 color #8b90ff
> volume #5 color #8186ee
> volume #5 color #928cee
> volume #5 color #8687ee
> volume #5 color #7a81ff
> volume #5 color #8687ee
> volume #5 color #7a81ff
> volume #5 color #8687ee
> volume #5 color #7a81ff
> volume #5 color #8687ee
> volume #5 color #8d8efd
> volume #5 color #8c8dfc
> save /Users/ConstantinePetridis/Desktop/FE_slice.png width 3000 height 1873
> supersample 4
> view front
> save /Users/ConstantinePetridis/Desktop/FE_front.png width 3000 height 1873
> supersample 4
> view side
Expected an objects specifier or a view name or a keyword
> view top
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save /Users/ConstantinePetridis/Desktop/FE_top.png width 3000 height 1873
> supersample 4
> view diagonal
[Repeated 1 time(s)]
> save /Users/ConstantinePetridis/Desktop/FE_diag.png width 3000 height 1873
> supersample 4
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1558_003_volume_map.mrc
Opened cryosparc_P23_J1558_003_volume_map.mrc as #6, grid size 256,256,256,
pixel 3.33, shown at level 0.217, step 1, values float32
> hide #!5 models
> volume #6 level 0.3811
> volume #6 level 0.3328
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1556_003_volume_map.mrc
Opened cryosparc_P23_J1556_003_volume_map.mrc as #7, grid size 256,256,256,
pixel 3.33, shown at level 0.21, step 1, values float32
> volume #7 level 0.4989
> show #!5 models
> select add #7
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-16.351,0,1,0,47.951,0,0,1,138.25
> view matrix models #7,1,0,0,29.518,0,1,0,46.948,0,0,1,111.17
> view matrix models #7,1,0,0,25.184,0,1,0,58.062,0,0,1,121.54
> view matrix models #7,1,0,0,26.356,0,1,0,61.724,0,0,1,120.42
> volume #7 level 1.549
> view matrix models #7,1,0,0,-5.8723,0,1,0,212.92,0,0,1,115.91
> view matrix models #7,1,0,0,21.885,0,1,0,66.685,0,0,1,255.9
> view matrix models #7,1,0,0,51.063,0,1,0,63.802,0,0,1,118.77
> view matrix models #7,1,0,0,62.627,0,1,0,64.199,0,0,1,115.71
> volume #5 level 0.145
> show #!2 models
> volume #2 level 0.192
> volume #5 level 0.212
> view matrix models #7,1,0,0,62.623,0,1,0,64.137,0,0,1,124.05
> volume #7 level 1.238
> volume #2 level 0.2791
> volume #2 level 0.2433
> volume #2 color #d2d2d3
> select subtract #7
Nothing selected
> show #!5 models
> hide #!2 models
> close #6-7
> view slice
> ui mousemode right clip
> open /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1772_map_locres.mrc
Opened cryosparc_P23_J1772_map_locres.mrc as #6, grid size 360,360,360, pixel
2.19, shown at level 15.3, step 2, values float32
> ui tool show "Surface Color"
> open /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1772_map_locres.mrc
Opened cryosparc_P23_J1772_map_locres.mrc as #7, grid size 360,360,360, pixel
2.19, shown at level 15.3, step 2, values float32
> close #7
> ui tool show "Color Zone"
> volume #6 level 34.88
> color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> color sample #5.1 map #6 palette 4,#0000ff:8,#00ff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 3.268, maximum 84.67
Map values for surface "cap front": minimum 0, mean 3.597, maximum 75.98
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 13.26
> select add #6
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,40.565,0,1,0,120.88,0,0,1,-18.957
> view matrix models #6,1,0,0,41.114,0,1,0,127.8,0,0,1,-119.02
> volume #6 level 8.559
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.79891,-0.6006,-0.0319,370.49,-0.60062,-0.79947,0.010071,1069.1,-0.031552,0.011114,-0.99944,738.08
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.79891,-0.6006,-0.0319,372.71,-0.60062,-0.79947,0.010071,1065,-0.031552,0.011114,-0.99944,940.36
> view matrix models
> #6,0.79891,-0.6006,-0.0319,414.56,-0.60062,-0.79947,0.010071,1058.5,-0.031552,0.011114,-0.99944,943.96
> view matrix models
> #6,0.79891,-0.6006,-0.0319,407.83,-0.60062,-0.79947,0.010071,1047.6,-0.031552,0.011114,-0.99944,923.68
> color sample #5.1 map #6 palette 4,#0000ff:8,#00ff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 5.765, maximum 74.22
Map values for surface "cap front": minimum 0, mean 6.344, maximum 14.45
> show #!6 models
> select add #6
3 models selected
> select subtract #6
Nothing selected
> volume #6 level 11.07
> ui tool show "Fit in Map"
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 235274 points
correlation = 0.622, correlation about mean = -0.02491, overlap = 3.607e+05
steps = 176, shift = 31.5, angle = 3.74 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.72829231 -0.67899329 -0.09251157 390.10224659
0.67932068 0.73310920 -0.03277637 -151.45118045
0.09007602 -0.03897424 0.99517199 -23.78717197
Axis -0.00452220 -0.13322261 0.99107582
Axis point 388.57482759 419.00286192 0.00000000
Rotation angle (degrees) 43.25704092
Shift along axis -5.16228847
> volume #6 level 5.917
> select add #6
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.70474,-0.70639,-0.06603,498.29,-0.70626,-0.70735,0.029181,1038.5,-0.067319,0.026069,-0.99739,960.59
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.7101,-0.70395,0.014309,461.1,-0.70409,-0.71001,0.01201,1046,0.0017056,-0.018603,-0.99983,952.03
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7101,-0.70395,0.014309,466.45,-0.70409,-0.71001,0.01201,1044.9,0.0017056,-0.018603,-0.99983,952.74
> view matrix models
> #6,0.7101,-0.70395,0.014309,469.04,-0.70409,-0.71001,0.01201,1051.1,0.0017056,-0.018603,-0.99983,951.55
> view matrix models
> #6,0.7101,-0.70395,0.014309,476.39,-0.70409,-0.71001,0.01201,1047.6,0.0017056,-0.018603,-0.99983,951.57
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 713538 points
correlation = 0.42, correlation about mean = -0.02124, overlap = 6.456e+05
steps = 96, shift = 10.1, angle = 0.907 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.62551415 -0.78013599 0.01094819 439.41706404
0.78021115 0.62548012 -0.00671941 -153.86127727
-0.00160582 0.01274498 0.99991748 -2.24018364
Axis 0.01247302 0.00804476 0.99988985
Axis point 380.02074921 380.80499582 0.00000000
Rotation angle (degrees) 51.28434410
Shift along axis 2.00314369
> color sample #5.1 map #6 palette 4,#0000ff:8,#00ff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.769, maximum 84.46
Map values for surface "cap front": minimum 4.775, mean 6.84, maximum 14.92
> color sample #5.1 map #6 palette #0000ff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 6.769, maximum 84.46
Map values for surface "cap front": minimum 4.775, mean 6.84, maximum 14.92
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.769, maximum 84.46
Map values for surface "cap front": minimum 4.775, mean 6.84, maximum 14.92
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 713538 points
correlation = 0.42, correlation about mean = -0.02125, overlap = 6.456e+05
steps = 40, shift = 0.194, angle = 0.0295 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.62537365 -0.78024819 0.01097844 439.53472662
0.78032286 0.62534576 -0.00623573 -153.90759639
-0.00199990 0.01246638 0.99992028 -1.94177383
Axis 0.01198287 0.00831552 0.99989363
Axis point 380.09000393 380.79996395 0.00000000
Rotation angle (degrees) 51.29433191
Shift along axis 2.04549844
> volume #6 level 11.86
> view matrix models
> #6,0.69955,-0.71451,0.010273,486.54,-0.71458,-0.69951,0.0073239,1048.3,0.0019532,-0.012465,-0.99992,942.21
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 194529 points
correlation = 0.6868, correlation about mean = -0.005782, overlap = 3.239e+05
steps = 176, shift = 6.12, angle = 3.47 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.60157471 -0.79878007 -0.00763050 470.20395732
0.79733311 0.60101206 -0.05517589 -133.26339412
0.04865942 0.02710837 0.99844748 -32.85683310
Axis 0.05145263 -0.03519828 0.99805496
Axis point 369.71797118 404.49193271 0.00000000
Rotation angle (degrees) 53.09305594
Shift along axis -3.90905469
> view matrix models
> #6,0.67755,-0.73536,-0.013089,520.23,-0.73386,-0.67713,0.054182,1032.8,-0.048706,-0.027105,-0.99845,972.09
> view matrix models
> #6,0.67755,-0.73536,-0.013089,519.12,-0.73386,-0.67713,0.054182,1029.5,-0.048706,-0.027105,-0.99845,972.47
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.738, maximum 83.65
Map values for surface "cap front": minimum 0, mean 6.805, maximum 12.79
> volume #6 level 7.105
> view matrix models
> #6,0.67755,-0.73536,-0.013089,514.54,-0.73386,-0.67713,0.054182,1021.4,-0.048706,-0.027105,-0.99845,972.32
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.674,-0.73835,-0.023878,521.69,-0.73736,-0.67436,0.039227,1028,-0.045066,-0.0088322,-0.99894,963.9
> undo
> view matrix models
> #6,0.67655,-0.73609,-0.021086,518.61,-0.735,-0.67676,0.042162,1026.8,-0.045305,-0.013027,-0.99889,965.63
> view matrix models
> #6,0.67863,-0.73447,0.0027947,507.02,-0.73431,-0.6784,0.023716,1035,-0.015523,-0.018147,-0.99971,956.26
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.67863,-0.73447,0.0027947,508.2,-0.73431,-0.6784,0.023716,1038.3,-0.015523,-0.018147,-0.99971,956.19
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 556136 points
correlation = 0.4654, correlation about mean = 0.004979, overlap = 5.607e+05
steps = 192, shift = 9.81, angle = 10.6 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.44852051 -0.89365997 -0.01418363 570.85480520
0.89242120 0.44865831 -0.04785486 -120.70874369
0.04912958 0.00880612 0.99875358 -24.87285560
Axis 0.03168780 -0.03540807 0.99887044
Axis point 383.75107879 402.05737701 0.00000000
Rotation angle (degrees) 63.38672762
Shift along axis -2.48156606
> undo
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.734, maximum 83.39
Map values for surface "cap front": minimum 3.706, mean 6.824, maximum 13.41
> ui mousemode right clip
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.734, maximum 83.39
Map values for surface "cap front": minimum 4.775, mean 6.985, maximum 41.66
> volume #6 level 11.2
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.67863,-0.73447,0.0027947,509.23,-0.73431,-0.6784,0.023716,1035.7,-0.015523,-0.018147,-0.99971,956.19
> volume #6 level 7.105
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.704, maximum 83.63
> ui mousemode right clip
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.7012,-0.71296,0.00026846,492.93,-0.71283,-0.70106,0.019856,1037.8,-0.013968,-0.014114,-0.9998,954.02
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.687, maximum 83.62
Map values for surface "cap front": minimum 4.775, mean 5.637, maximum 9.86
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.7012,-0.71296,0.00026846,498.59,-0.71283,-0.70106,0.019856,1042.5,-0.013968,-0.014114,-0.9998,954.59
> ui mousemode right clip
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.63, maximum 83.86
> color sample #5.1 map #6 palette 3,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.63, maximum 83.86
Map values for surface "cap front": minimum 4.775, mean 6.806, maximum 13.48
> color sample #5.1 map #6 palette 4,#0000ff:6,#00ff00:9,#ff0000
Map values for surface "surface": minimum 0, mean 6.63, maximum 83.86
Map values for surface "cap front": minimum 4.775, mean 6.806, maximum 13.48
> color sample #5.1 map #6 palette 4,#0000ff:7,#00ff00:10,#ff0000
Map values for surface "surface": minimum 0, mean 6.63, maximum 83.86
Map values for surface "cap front": minimum 4.775, mean 6.806, maximum 13.48
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.63, maximum 83.86
Map values for surface "cap front": minimum 4.775, mean 6.806, maximum 13.48
> ui mousemode right "rotate selected models"
> ui mousemode right clip
> fitmap #6 inMap #5
Fit map cryosparc_P23_J1772_map_locres.mrc in map J1770_FE using 556136 points
correlation = 0.4654, correlation about mean = 0.004986, overlap = 5.607e+05
steps = 232, shift = 10.9, angle = 12.3 degrees
Position of cryosparc_P23_J1772_map_locres.mrc (#6) relative to J1770_FE (#5)
coordinates:
Matrix rotation and translation
0.44843477 -0.89370215 -0.01423684 570.92176745
0.89245986 0.44857475 -0.04791714 -120.66744478
0.04920994 0.00878190 0.99874983 -24.85908666
Axis 0.03170755 -0.03548105 0.99886722
Axis point 383.73998016 402.08218830 0.00000000
Rotation angle (degrees) 63.39227213
Shift along axis -2.44698898
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.53458,-0.84491,-0.018944,623.91,-0.84368,-0.53484,0.046304,1016.7,-0.049255,-0.0087703,-0.99875,965.32
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.3124,-0.94994,0.0049256,742.68,-0.9477,-0.3113,0.070378,959.43,-0.065321,-0.026654,-0.99751,978.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.3124,-0.94994,0.0049256,742.74,-0.9477,-0.3113,0.070378,959.02,-0.065321,-0.026654,-0.99751,978.19
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.29215,-0.95632,0.010024,751.07,-0.95409,-0.29071,0.072135,952.67,-0.06607,-0.030638,-0.99734,979.99
> view matrix models
> #6,0.31166,-0.95014,-0.010037,749.47,-0.94798,-0.31163,0.065024,961.53,-0.06491,-0.010751,-0.99783,971.9
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31166,-0.95014,-0.010037,750.23,-0.94798,-0.31163,0.065024,964.57,-0.06491,-0.010751,-0.99783,969.55
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.704, maximum 81.87
Map values for surface "cap front": minimum 0.1064, mean 5.961, maximum 10.3
> ui mousemode right clip
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.704, maximum 81.87
Map values for surface "cap front": minimum 2.423, mean 6.735, maximum 13.35
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.31249,-0.94992,-0.00018017,745.63,-0.94992,-0.31248,-0.0036285,994.83,0.0033905,0.001305,-0.99999,938.81
> view matrix models
> #6,0.31248,-0.94989,-0.0084239,749.12,-0.9499,-0.31241,-0.0092514,997.18,0.0061561,0.010893,-0.99992,933.91
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.609, maximum 84.34
> ui mousemode right clip
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.609, maximum 84.34
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.29
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.31248,-0.94989,-0.0084239,749.68,-0.9499,-0.31241,-0.0092514,996.07,0.0061561,0.010893,-0.99992,934.92
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.608, maximum 84.13
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.43
> color sample #5.1 map #6 palette 5,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.608, maximum 84.13
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.43
> color sample #5.1 map #6 palette 4,#0000ff:8,#00ff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.608, maximum 84.13
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.43
> color sample #5.1 map #6 palette
> 3,#0000ff:5,#00ffff:7,#00ff00:9,#ffff00:11,#ff0000
Map values for surface "surface": minimum 0, mean 6.608, maximum 84.13
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.43
> color sample #5.1 map #6 palette
> 4,#0000ff:6,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.608, maximum 84.13
Map values for surface "cap front": minimum 4.775, mean 6.786, maximum 13.43
> view slice
> view matrix models
> #6,0.31248,-0.94989,-0.0084239,749.68,-0.9499,-0.31241,-0.0092514,995.13,0.0061561,0.010893,-0.99992,938.88
> color sample #5.1 map #6 palette
> 4,#0000ff:6,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> view slice
> key rainbow :4 :6 :8 :10 :12 showTool true
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> undo
> view slice
> undo
> view slice
> color sample #5.1 map #6 palette
> 5,#0000ff:6,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> color sample #5.1 map #6 palette
> 4,#0000ff:5,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> color sample #5.1 map #6 palette
> 4,#0000ff:5,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> color sample #5.1 map #6 palette
> 5,#0000ff:7,#00ffff:9,#00ff00:11,#ffff00:13,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> color sample #5.1 map #6 palette
> 4,#0000ff:6,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.65, maximum 83.6
Map values for surface "cap front": minimum 4.775, mean 6.723, maximum 12.76
> save /Users/ConstantinePetridis/Desktop/localres.png width 3000 height 2655
> supersample 4
> view slice
> ui mousemode right rotate
> save /Users/ConstantinePetridis/Desktop/localres.png width 3000 height 2655
> supersample 4
> close #7
> close #6
> color #5 #8c8dfcff
> open /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1772_map_locres.mrc
Opened cryosparc_P23_J1772_map_locres.mrc as #6, grid size 360,360,360, pixel
2.19, shown at level 15.3, step 2, values float32
> volume #6 level 4.338
> view slice
> select add #6
3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.73792,-0.65748,-0.15229,426.93,-0.65684,-0.7515,0.06169,922.6,-0.15501,0.054508,-0.98641,883.06
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.73792,-0.65748,-0.15229,481.25,-0.65684,-0.7515,0.06169,1044.3,-0.15501,0.054508,-0.98641,976.95
> view matrix models
> #6,0.73792,-0.65748,-0.15229,521.56,-0.65684,-0.7515,0.06169,1039.7,-0.15501,0.054508,-0.98641,983.22
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.77527,-0.63157,0.0082957,428.45,-0.63144,-0.77464,0.034901,1050.2,-0.015616,-0.032296,-0.99936,968
> view matrix models
> #6,0.57957,-0.8149,0.005019,579.17,-0.81492,-0.57955,0.0047301,1058.4,-0.0009458,-0.0068316,-0.99998,952.45
> view matrix models
> #6,0.56528,-0.82392,0.040091,573.46,-0.82321,-0.56657,-0.036471,1074,0.052763,-0.012386,-0.99853,932.87
> view matrix models
> #6,0.59292,-0.80379,0.048658,551,-0.80287,-0.59474,-0.041117,1079.1,0.061988,-0.014687,-0.99797,929.9
> view matrix models
> #6,0.64649,-0.7621,0.035332,519.13,-0.75938,-0.64726,-0.066303,1093.4,0.073399,0.016034,-0.99717,912.96
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.64649,-0.7621,0.035332,530.48,-0.75938,-0.64726,-0.066303,1094.8,0.073399,0.016034,-0.99717,896.38
> ui mousemode right clip
> volume #6 level 8.563
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.64649,-0.7621,0.035332,526.11,-0.75938,-0.64726,-0.066303,1077.4,0.073399,0.016034,-0.99717,897.09
> view matrix models
> #6,0.64649,-0.7621,0.035332,519.94,-0.75938,-0.64726,-0.066303,1083,0.073399,0.016034,-0.99717,897.33
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.64806,-0.75633,-0.089372,570,-0.75997,-0.64987,-0.011,1060.8,-0.049761,0.075049,-0.99594,922.08
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.64806,-0.75633,-0.089372,576.4,-0.75997,-0.64987,-0.011,1054.9,-0.049761,0.075049,-0.99594,921.37
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.6425,-0.75609,-0.12456,593.44,-0.75795,-0.65097,0.041827,1032.1,-0.11271,0.067537,-0.99133,947.17
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.6425,-0.75609,-0.12456,593.72,-0.75795,-0.65097,0.041827,1031.3,-0.11271,0.067537,-0.99133,947.14
> volume #6 level 6.847
> view matrix models
> #6,0.6425,-0.75609,-0.12456,592.38,-0.75795,-0.65097,0.041827,1030.9,-0.11271,0.067537,-0.99133,947.42
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.64591,-0.75866,-0.085075,575.28,-0.75837,-0.65043,0.042488,1030.5,-0.087569,0.037075,-0.99547,951.28
> view matrix models
> #6,0.72579,-0.68433,-0.070145,508.19,-0.68645,-0.72712,-0.0089347,1054.3,-0.04489,0.054635,-0.9975,928.4
> view matrix models
> #6,0.72509,-0.685,-0.070781,509,-0.686,-0.72748,0.012928,1044.9,-0.060348,0.039182,-0.99741,940.54
> view matrix models
> #6,0.66079,-0.74786,-0.063795,556.13,-0.74283,-0.66378,0.087132,1010.7,-0.10751,-0.010187,-0.99415,977.19
> volume #6 level 8.827
> transparency #6
Missing or invalid "percent" argument: Expected a number
> transparency #6 50
> volume #6 level 8.167
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66079,-0.74786,-0.063795,560.77,-0.74283,-0.66378,0.087132,1001.6,-0.10751,-0.010187,-0.99415,976.52
> view matrix models
> #6,0.66079,-0.74786,-0.063795,568.86,-0.74283,-0.66378,0.087132,1002.1,-0.10751,-0.010187,-0.99415,976.76
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.60104,-0.76193,-0.24127,673.3,-0.7084,-0.64766,0.28054,900.01,-0.37001,0.0022994,-0.92902,1047.6
> view matrix models
> #6,0.6286,-0.74356,-0.22801,649.58,-0.74019,-0.66195,0.11807,987.15,-0.23872,0.094554,-0.96647,975.44
> view matrix models
> #6,0.65931,-0.74084,-0.12833,594.08,-0.74854,-0.66281,-0.019335,1049.1,-0.070734,0.10881,-0.99154,914.29
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.65931,-0.74084,-0.12833,584.52,-0.74854,-0.66281,-0.019335,1056.8,-0.070734,0.10881,-0.99154,917.83
> view matrix models
> #6,0.65931,-0.74084,-0.12833,584.07,-0.74854,-0.66281,-0.019335,1055.8,-0.070734,0.10881,-0.99154,917.84
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.65065,-0.75059,-0.1152,585.75,-0.75,-0.65894,0.05741,1022.3,-0.119,0.049046,-0.99168,960.46
> view matrix models
> #6,0.66794,-0.73266,-0.1306,578.41,-0.73646,-0.67599,0.025754,1037.1,-0.10715,0.078978,-0.9911,943.76
> view matrix models
> #6,0.67045,-0.73938,-0.061804,550.86,-0.74121,-0.67117,-0.011271,1052.8,-0.033148,0.053367,-0.99802,927.63
> view matrix models
> #6,0.67828,-0.73209,-0.063063,545.43,-0.73394,-0.67915,-0.0098613,1052.5,-0.035609,0.052973,-0.99796,928.73
> view matrix models
> #6,0.66893,-0.74053,-0.064409,553.01,-0.74248,-0.66978,-0.010479,1052.4,-0.03538,0.054832,-0.99787,927.87
> volume #6 level 7.507
> ui mousemode right clip
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66911,-0.74205,-0.04069,543.47,-0.74285,-0.66942,-0.0076748,1051.2,-0.021544,0.035362,-0.99914,930.63
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66911,-0.74205,-0.04069,536.2,-0.74285,-0.66942,-0.0076748,1050.5,-0.021544,0.035362,-0.99914,931.48
> view matrix models
> #6,0.66911,-0.74205,-0.04069,533.53,-0.74285,-0.66942,-0.0076748,1051.2,-0.021544,0.035362,-0.99914,931.93
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66873,-0.74274,-0.03382,531.04,-0.74335,-0.66884,-0.0094975,1051.9,-0.015566,0.031491,-0.99938,931.21
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66873,-0.74274,-0.03382,532.76,-0.74335,-0.66884,-0.0094975,1051.4,-0.015566,0.031491,-0.99938,931.66
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66744,-0.74437,-0.020672,528.32,-0.74465,-0.66731,-0.013922,1053.2,-0.0034315,0.024686,-0.99969,929.69
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.66744,-0.74437,-0.020672,534.92,-0.74465,-0.66731,-0.013922,1054.9,-0.0034315,0.024686,-0.99969,929.71
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.66683,-0.74518,0.0062522,524.05,-0.74518,-0.66686,-0.0035196,1050.6,0.006792,-0.002312,-0.99997,936.44
> ui tool show "Surface Color"
> color sample #5.1 map #6 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000
Map values for surface "surface": minimum 0, mean 6.678, maximum 84.54
> hide #!6 models
> select subtract #6
Nothing selected
> view slice
> color sample #5.1 map #6 palette
> 4,#0000ff:6,#00ffff:8,#00ff00:10,#ffff00:12,#ff0000
Map values for surface "surface": minimum 0, mean 6.678, maximum 84.54
Map values for surface "cap front": minimum 4.775, mean 6.72, maximum 12.62
> view slice
> ui mousemode right rotate
> save /Users/ConstantinePetridis/Desktop/localres.png width 3000 height 2655
> supersample 4
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1586_003_volume_map.mrc
Opened cryosparc_P23_J1586_003_volume_map.mrc as #7, grid size 256,256,256,
pixel 3.33, shown at level 0.585, step 1, values float32
> hide #!5 models
> volume #7 level 0.7706
> ui mousemode right clip
> open
> /Users/ConstantinePetridis/Downloads/cryosparc_P23_J1577_001_volume_map.mrc
Opened cryosparc_P23_J1577_001_volume_map.mrc as #8, grid size 636,636,636,
pixel 1.34, shown at level 0.041, step 4, values float32
> volume #8 level 0.072
> volume #8 step 1
> volume #8 step 2
> volume #8 step 4
> volume #8 level 0.06093
> ui mousemode right rotate
> close #7-8
> show #!3 models
> show #!2 models
> view front
> color #3 #8c8dfcff models
> color #3 #8c8dfc80 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> volume #2 level 0.3359
> volume #3 level 0.2475
> volume #2 level 0.1906
> volume #2 level 0.1716
> volume #2 level 0.336
> volume #3 level 0.212
> volume #2 level 0.3002
> ui tool show "Hide Dust"
> surface dust #2 size 1.41
> surface dust #3 size 14.2
> surface dust #3 size 14.43
> surface dust #3 size 65.43
> hide #!2 models
> surface dust #3 size 68.1
> surface dust #3 size 8.53
> ui mousemode right clip
> surface dust #3 size 8.64
> surface dust #3 size 2.37
> surface dust #3 size 6
> surface dust #3 size 63
[Repeated 1 time(s)]
> surface dust #3 size 6
> surface dust #3 size 60
[Repeated 1 time(s)]
> show #!2 models
> view front
> volume #3 color #8687ee
> volume #3 color #8c8dfc
> volume #3 color #7a81ff
> volume #3 color #8687ee
> volume #3 color #8c8dfc
> volume #3 color #8c8dfc80
> volume #3 color #8c8dfc8c
> volume #2 level 0.2462
> volume #2 level 0.24
> volume #2 level 0.26
> volume #2 level 0.2125
> volume #2 level 0.2773
> volume #2 level 0.2902
> volume #3 level 0.21
> volume #3 level 0.208
> surface dust #2 size 3.56
> surface dust #2 size 3.42
> surface dust #2 size 8.43
> surface dust #3 size 6
> surface dust #3 size 62
[Repeated 2 time(s)]
> surface dust #3 size 6
> surface dust #3 size 64
[Repeated 1 time(s)]
> surface dust #3 size 6
> surface dust #3 size 62
[Repeated 1 time(s)]
> surface dust #3 size 67.21
> surface dust #3 size 57.94
> surface dust #3 size 6
> surface dust #3 size 60
[Repeated 1 time(s)]
> view front
> volume #3 level 0.212
> volume #3 level 0.21
> volume #3 level 0.209
> volume #3 level 0.211
> view front
> save /Users/ConstantinePetridis/Desktop/BV_FE_front.png width 3000 height
> 1974 supersample 4
> view side
Expected an objects specifier or a view name or a keyword
> view diagonal
> save /Users/ConstantinePetridis/Desktop/BV_FE_diag.png width 3000 height
> 1974 supersample 4
> view top
> save /Users/ConstantinePetridis/Desktop/BV_FE_top.png width 3000 height 1974
> supersample 4
> view slice
> save /Users/ConstantinePetridis/Desktop/BV_FE_slice.png width 3000 height
> 1974 supersample 4
> view front
> volume #3 color #8c8dfc80
> view slice
> ui tool show "Side View"
> view name slice
> undo
> view name slice
[Repeated 3 time(s)]
> ui mousemode right rotate
> ui mousemode right clip
> view name slice
> view matrix
view matrix camera
-0.94831,0.019789,-0.31672,-111.3,-0.31734,-0.059575,0.94644,2298.4,-0.00014037,0.99803,0.062776,594.4
view matrix models
#1,0.22884,0.97346,2.2675e-07,6.5664,-0.97346,0.22884,5.8736e-07,795.07,5.199e-07,-3.5514e-07,1,179.58,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0.00083921,3.6674e-07,-0.41412,-0.00083921,1,1.9537e-07,0.41458,-3.6657e-07,-1.9568e-07,1,-0.16369,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,-0.00067234,5.3385e-06,67.653,0.00067234,1,2.164e-05,67.085,-5.353e-06,-2.1636e-05,1,119.77,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,-0.077036,0.99703,2.7381e-05,101.45,-0.99703,-0.077036,3.09e-05,951.16,3.2916e-05,-2.4918e-05,1,58.136,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99509,0.098993,-3.3983e-05,62.481,0.098993,-0.99509,3.2042e-05,846.52,-3.0643e-05,-3.5249e-05,-1,939.76,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.66683,-0.74518,0.0062522,524.05,-0.74518,-0.66686,-0.0035196,1050.6,0.006792,-0.002312,-0.99997,936.44,#6.1,1,0,0,0,0,1,0,0,0,0,1,0
> save /Users/ConstantinePetridis/Desktop/BV_FE_slice.png width 3000 height
> 1974 supersample 4
> volume #2 color #d2d2d3f4
> volume #2 color #d2d2d3
> volume #2 color #d2d2d3f3
> volume #2 color #d2d2d3
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> open 8I8B
8i8b title:
Outer shell and inner layer structures of Autographa californica multiple
nucleopolyhedrovirus (AcMNPV) [more info...]
Chain information for 8i8b #7
---
Chain | Description | UniProt
A B C | Viral capsid associated protein | A0A0N7CTI8_9ABAC 1-691
D | AcOrf-109 peptide | A0A0N7CRZ7_9ABAC 1-390
E | Early 49 Daa protein | A0A0N7CTL8_9ABAC 1-477
F G | P40 | A0A0N7CQX9_9ABAC 1-361
H I | Occlusion-derived virus envelope/capsid protein | A0A0N7CT36_9ABAC 1-290
J | 38K | A0A0N7CSX4_9ABAC 1-320
W X Y Z | Major viral capsid protein | A0A0N6WHR0_9ABAC 1-347
> select add #7
30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select subtract #7
Nothing selected
> sequence chain #7/A#7/B#7/C
Alignment identifier is 1
> hide cartoons
> show surfaces
> hide surfaces
> show #7/A-C
> show #7/A-C cartoons
> hide surfaces
> hide #7/A-C surfaces
> hide atoms
> select add #7
30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.55519,-0.77651,0.29799,690.82,0.76662,-0.3388,0.54544,-241.77,-0.32258,0.53127,0.78339,103.57
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.55519,-0.77651,0.29799,664.48,0.76662,-0.3388,0.54544,-203.22,-0.32258,0.53127,0.78339,294.77
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.90677,0.38864,0.16346,-123.03,-0.24069,0.79549,-0.55612,374.79,-0.34616,0.46493,0.81487,306.61
> view matrix models
> #7,0.5346,0.83963,0.096021,-35.653,-0.77475,0.53231,-0.34119,571.6,-0.33759,0.10801,0.93508,331.78
> view matrix models
> #7,0.57975,0.79531,0.17713,-74.058,-0.81452,0.56002,0.15147,408.62,0.021266,-0.23209,0.97246,238.4
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.57975,0.79531,0.17713,-33.385,-0.81452,0.56002,0.15147,460.61,0.021266,-0.23209,0.97246,248.01
> view matrix models
> #7,0.57975,0.79531,0.17713,-53.863,-0.81452,0.56002,0.15147,465.73,0.021266,-0.23209,0.97246,233.23
> hide #!2 models
> view matrix models
> #7,0.57975,0.79531,0.17713,-34.001,-0.81452,0.56002,0.15147,475.16,0.021266,-0.23209,0.97246,227.42
> view matrix models
> #7,0.57975,0.79531,0.17713,-42.007,-0.81452,0.56002,0.15147,472.25,0.021266,-0.23209,0.97246,239.31
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.57983,0.78956,-0.20099,92.537,-0.7095,0.6106,0.35181,348.17,0.4005,-0.061389,0.91424,69.47
> view matrix models
> #7,0.91297,0.39972,-0.081914,-9.1552,-0.35383,0.87556,0.32894,156.79,0.2032,-0.27133,0.94079,183.29
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.91297,0.39972,-0.081914,-18.147,-0.35383,0.87556,0.32894,159.95,0.2032,-0.27133,0.94079,183.5
> ui tool show "Fit in Map"
> fitmap #7 inMap #3
Fit molecule 8i8b (#7) to map J1663_FE (#3) using 30015 atoms
average map value = 0.2814, steps = 96
shifted from previous position = 10.8
rotated from previous position = 16.1 degrees
atoms outside contour = 8860, contour level = 0.211
Position of 8i8b (#7) relative to J1663_FE (#3) coordinates:
Matrix rotation and translation
0.90246535 0.42993054 0.02675881 -121.96814063
-0.43063237 0.89892384 0.08057105 209.56352313
0.01058582 -0.08423580 0.99638962 74.38816054
Axis -0.18806028 0.01845492 -0.98198409
Axis point 396.19186388 393.80100387 0.00000000
Rotation angle (degrees) 25.98753426
Shift along axis -46.24314981
> select clear
> hide #!3 models
> select #7/A-C/485
5049 atoms, 5151 bonds, 2 pseudobonds, 605 residues, 2 models selected
> select #7/A-C:485
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/A-C:480
9 atoms, 8 bonds, 1 residue, 1 model selected
> rainbow sel
> select add #7
30015 atoms, 30679 bonds, 10 pseudobonds, 3660 residues, 3 models selected
> rainbow sel
> select clear
> show #!5 models
> color #5 #8c8dfc70 models
> color #5 #8c8dfc7e models
> color #5 #8c8dfc46 models
> color #5 #8c8dfc58 models
> show #!2 models
> hide #!2 models
> open
> /Users/ConstantinePetridis/Downloads/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_model_0.cif
Chain information for fold_2025_01_03_16_08_vp80x1_model_0.cif #8
---
Chain | Description
A | .
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> show #!7 models
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,414.74,0,1,0,29.281,0,0,1,615.06
> view matrix models #8,1,0,0,376.64,0,1,0,25.149,0,0,1,578.93
> open
> /Users/ConstantinePetridis/Downloads/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_model_1.cif
Chain information for fold_2025_01_03_16_08_vp80x1_model_1.cif #9
---
Chain | Description
A | .
> select add #9
11218 atoms, 11396 bonds, 1382 residues, 2 models selected
> select subtract #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> view matrix models #9,1,0,0,127.72,0,1,0,53.916,0,0,1,531.41
> view matrix models #9,1,0,0,243.93,0,1,0,-8.1051,0,0,1,567.78
> hide #9 models
> select subtract #9
Nothing selected
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> view matrix models #8,1,0,0,584.9,0,1,0,192.74,0,0,1,569.87
> view matrix models #8,1,0,0,568.66,0,1,0,323.29,0,0,1,503.74
> view matrix models #8,1,0,0,437.31,0,1,0,247.49,0,0,1,572.67
> view matrix models #8,1,0,0,460.65,0,1,0,249.63,0,0,1,580.54
> ui tool show Matchmaker
> matchmaker #8/A to #7/C 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 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_0.cif,
chain A (#8), sequence alignment score = 2774.4
RMSD between 179 pruned atom pairs is 0.767 angstroms; (across all 229 pairs:
13.472)
> hide #8 models
> volume #3 level 0.1697
> volume #3 level 0.211
> show #8 models
> matchmaker #8 to #7/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 8i8b, chain A (#7) with fold_2025_01_03_16_08_vp80x1_model_0.cif,
chain A (#8), sequence alignment score = 2745
RMSD between 126 pruned atom pairs is 0.835 angstroms; (across all 188 pairs:
8.377)
> matchmaker #8 to #7/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 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_0.cif,
chain A (#8), sequence alignment score = 2774.4
RMSD between 179 pruned atom pairs is 0.767 angstroms; (across all 229 pairs:
13.472)
> matchmaker #9 to #7/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 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_1.cif,
chain A (#9), sequence alignment score = 2787
RMSD between 180 pruned atom pairs is 0.786 angstroms; (across all 229 pairs:
11.833)
> show #9 models
> hide #8 models
> select subtract #8
Nothing selected
> open
> /Users/ConstantinePetridis/Downloads/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_model_2.cif
Chain information for fold_2025_01_03_16_08_vp80x1_model_2.cif #10
---
Chain | Description
A | .
> open
> /Users/ConstantinePetridis/Downloads/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_model_3.cif
Chain information for fold_2025_01_03_16_08_vp80x1_model_3.cif #11
---
Chain | Description
A | .
> open
> /Users/ConstantinePetridis/Downloads/fold_2025_01_03_16_08_vp80x1/fold_2025_01_03_16_08_vp80x1_model_4.cif
Chain information for fold_2025_01_03_16_08_vp80x1_model_4.cif #12
---
Chain | Description
A | .
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #8-12 to #7/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 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_0.cif,
chain A (#8), sequence alignment score = 2774.4
RMSD between 179 pruned atom pairs is 0.767 angstroms; (across all 229 pairs:
13.472)
Matchmaker 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_1.cif,
chain A (#9), sequence alignment score = 2787
RMSD between 180 pruned atom pairs is 0.786 angstroms; (across all 229 pairs:
11.833)
Matchmaker 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_2.cif,
chain A (#10), sequence alignment score = 2775
RMSD between 178 pruned atom pairs is 0.812 angstroms; (across all 229 pairs:
3.873)
Matchmaker 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_3.cif,
chain A (#11), sequence alignment score = 2781
RMSD between 181 pruned atom pairs is 0.820 angstroms; (across all 229 pairs:
12.164)
Matchmaker 8i8b, chain C (#7) with fold_2025_01_03_16_08_vp80x1_model_4.cif,
chain A (#12), sequence alignment score = 2775
RMSD between 179 pruned atom pairs is 0.784 angstroms; (across all 229 pairs:
5.761)
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #11 models
> show #10 models
> hide #11 models
> show #9 models
> hide #9 models
> show #8 models
> hide #10 models
> close #9-12
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> view matrix models
> #8,-0.33087,0.92677,0.17782,239.4,0.17859,-0.12354,0.97614,420.91,0.92662,0.35474,-0.12464,625.24
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.96976,0.18739,-0.15635,229.57,-0.1066,0.90154,0.41935,414.16,0.21953,-0.39001,0.89426,642.41
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.96976,0.18739,-0.15635,320.18,-0.1066,0.90154,0.41935,268.06,0.21953,-0.39001,0.89426,613.06
> view matrix models
> #8,0.96976,0.18739,-0.15635,366.43,-0.1066,0.90154,0.41935,253.63,0.21953,-0.39001,0.89426,618.23
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.23162,-0.971,0.059244,378.67,0.93761,0.23906,0.25248,246.88,-0.25932,-0.0029305,0.96579,620.94
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.23162,-0.971,0.059244,390.01,0.93761,0.23906,0.25248,355.44,-0.25932,-0.0029305,0.96579,590.38
> view matrix models
> #8,0.23162,-0.971,0.059244,431.94,0.93761,0.23906,0.25248,332.25,-0.25932,-0.0029305,0.96579,584.9
> view matrix models
> #8,0.23162,-0.971,0.059244,425.8,0.93761,0.23906,0.25248,336.21,-0.25932,-0.0029305,0.96579,585.13
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.3126,-0.94721,-0.071286,428.77,0.93721,-0.31977,0.13921,337.52,-0.15465,-0.023295,0.98769,584.59
> view matrix models
> #8,-0.27615,-0.92399,-0.26454,426.74,0.90243,-0.34398,0.25941,338.91,-0.33069,-0.16709,0.92883,586.03
> view matrix models
> #8,0.24386,-0.89807,-0.36607,421.77,0.92524,0.10232,0.36533,337.82,-0.29064,-0.42779,0.85588,586.16
> view matrix models
> #8,0.3086,-0.94876,-0.067985,424.03,0.90394,0.27027,0.33144,337.01,-0.29609,-0.16374,0.94102,585.85
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.3086,-0.94876,-0.067985,424.13,0.90394,0.27027,0.33144,335.13,-0.29609,-0.16374,0.94102,591.48
> view matrix models
> #8,0.3086,-0.94876,-0.067985,422.75,0.90394,0.27027,0.33144,337.64,-0.29609,-0.16374,0.94102,594.67
> fitmap #8 inMap #3
Fit molecule fold_2025_01_03_16_08_vp80x1_model_0.cif (#8) to map J1663_FE
(#3) using 5609 atoms
average map value = 0.2021, steps = 276
shifted from previous position = 37.8
rotated from previous position = 62.6 degrees
atoms outside contour = 2697, contour level = 0.211
Position of fold_2025_01_03_16_08_vp80x1_model_0.cif (#8) relative to J1663_FE
(#3) coordinates:
Matrix rotation and translation
0.07597177 -0.98817675 -0.13317281 374.71403761
0.19670877 -0.11608066 0.97356609 277.83676812
-0.97751417 -0.10015980 0.18556418 443.06936938
Axis -0.59379417 0.46693945 0.65526790
Axis point 298.40216197 218.87930806 0.00000000
Rotation angle (degrees) 115.29458126
Shift along axis 197.55907340
> select subtract #8
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #8 models
> ui mousemode right clip
> show #!2 models
> volume #5 level 0.21
> hide #!5 models
> show #!5 models
> color #5 #00000058 models
> undo
> color #5 #a3a7ff58 models
> color #5 #8c8dfcff models
> color #5 #c1153cff models
> volume #5 level 0.1967
> volume #5 level 0.1901
> volume #5 level 0.1818
> volume #2 level 0.2924
> volume #5 level 0.1801
> volume #5 color #8c8dfc80
> show #8 models
> hide #!5 models
> hide #8/A:470-691
> hide #8/A:470-691 cartoons
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> select clear
> ui mousemode right "translate selected models"
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.784,-0.58956,0.19434,449.97,0.5852,-0.80637,-0.085449,335.96,0.20709,0.046738,0.9772,559.89
> view matrix models
> #8,-0.7894,0.25957,-0.5563,440.13,-0.31772,-0.94815,0.0084374,344.28,-0.52526,0.1834,0.83094,563.71
> view matrix models
> #8,-0.89125,-0.39728,0.21872,450.22,0.45335,-0.79308,0.40682,341.13,0.011841,0.46174,0.88694,558.93
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.89125,-0.39728,0.21872,457.51,0.45335,-0.79308,0.40682,329.37,0.011841,0.46174,0.88694,551.89
> view matrix models
> #8,-0.89125,-0.39728,0.21872,455.73,0.45335,-0.79308,0.40682,324,0.011841,0.46174,0.88694,552.62
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.87984,-0.43916,0.1817,455.5,0.47518,-0.80567,0.3537,323.43,-0.0089451,0.39754,0.91754,553.31
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.87984,-0.43916,0.1817,453.6,0.47518,-0.80567,0.3537,325.37,-0.0089451,0.39754,0.91754,554.25
> show #!5 models
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.45511,-0.88406,0.10639,451.5,0.83548,-0.38264,0.3944,321.22,-0.30797,0.26838,0.91276,557.03
> open 8I8B
8i8b title:
Outer shell and inner layer structures of Autographa californica multiple
nucleopolyhedrovirus (AcMNPV) [more info...]
Chain information for 8i8b #9
---
Chain | Description | UniProt
A B C | Viral capsid associated protein | A0A0N7CTI8_9ABAC 1-691
D | AcOrf-109 peptide | A0A0N7CRZ7_9ABAC 1-390
E | Early 49 Daa protein | A0A0N7CTL8_9ABAC 1-477
F G | P40 | A0A0N7CQX9_9ABAC 1-361
H I | Occlusion-derived virus envelope/capsid protein | A0A0N7CT36_9ABAC 1-290
J | 38K | A0A0N7CSX4_9ABAC 1-320
W X Y Z | Major viral capsid protein | A0A0N6WHR0_9ABAC 1-347
> ui tool show Matchmaker
> matchmaker #9/A#9/B#9/C to #7/A#7/B#7/C 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 8i8b, chain A (#7) with 8i8b, chain A (#9), sequence alignment
score = 2761.8
Matchmaker 8i8b, chain B (#7) with 8i8b, chain B (#9), sequence alignment
score = 2761.8
Matchmaker 8i8b, chain C (#7) with 8i8b, chain C (#9), sequence alignment
score = 2822.4
RMSD between 605 pruned atom pairs is 0.000 angstroms; (across all 605 pairs:
0.000)
> hide sel atoms
> select add #9
35624 atoms, 36377 bonds, 10 pseudobonds, 4351 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> color #9 #0d1c2cff
> select subtract #9
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #8 models
> ui mousemode right clip
> show #!2 models
> hide #!2 models
> color #9 #0d1c2cff
> color #9 #d2d2d3ff
> show #8 models
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.45511,-0.88406,0.10639,491.36,0.83548,-0.38264,0.3944,332.76,-0.30797,0.26838,0.91276,581.52
> open 8VWI
Summary of feedback from opening 8VWI fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /N:1
Atom H1 is not in the residue template for MET /i:1
note | Fetching compressed mmCIF 8vwi from http://files.rcsb.org/download/8vwi.cif
8vwi title:
The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised
reconstruction) [more info...]
Chain information for 8vwi #10
---
Chain | Description | UniProt
A B C D E F V W X Y Z a | Major capsid protein | MCP_NPVAC 1-347
G H I b c d | Capsid-associated protein VP80 | VP80_NPVAC 1-691
J M Q S e h | Occlusion-derived virus envelope protein E27 | E27_NPVAC 1-290
K L R T f g | Protein C42 | C42_NPVAC 1-361
N i | Protein AC109 | AC109_NPVAC 1-390
O j | Protein AC142 | AC142_NPVAC 1-477
P k | 38K (AC98) protein in P143-LEF5 intergenic region | 38K_NPVAC 1-320
Non-standard residues in 8vwi #10
---
ZN — zinc ion
> select add #10
161875 atoms, 163633 bonds, 77 pseudobonds, 10305 residues, 4 models selected
> select subtract #8
156266 atoms, 157935 bonds, 77 pseudobonds, 9614 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select #10/b:472-668
3289 atoms, 3323 bonds, 197 residues, 1 model selected
> select #10/c:477-682
3452 atoms, 3488 bonds, 206 residues, 1 model selected
> select #10/d:460-688
3743 atoms, 3780 bonds, 1 pseudobond, 223 residues, 2 models selected
> select #10/I:460-688
3740 atoms, 3777 bonds, 1 pseudobond, 224 residues, 2 models selected
> select #10/H:473-682
3513 atoms, 3549 bonds, 210 residues, 1 model selected
> select #10/G:475-668
3228 atoms, 3263 bonds, 194 residues, 1 model selected
> matchmaker #10/G#10/H#10/I to #7/A#7/B#7/C 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 8i8b, chain A (#7) with 8vwi, chain G (#10), sequence alignment
score = 2652.6
Matchmaker 8i8b, chain B (#7) with 8vwi, chain H (#10), sequence alignment
score = 2649.6
Matchmaker 8i8b, chain C (#7) with 8vwi, chain I (#10), sequence alignment
score = 2731.8
RMSD between 311 pruned atom pairs is 1.250 angstroms; (across all 581 pairs:
4.160)
> select clear
> hide #!9 models
> hide #!7 models
> color #10 #d2d2d3ff
> hide #8 models
> rainbow #!10
> color #10 #dfd9fcff
> show #8 models
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> view matrix models
> #8,-0.45511,-0.88406,0.10639,543.02,0.83548,-0.38264,0.3944,283.99,-0.30797,0.26838,0.91276,617.35
> view matrix models
> #8,-0.45511,-0.88406,0.10639,444.98,0.83548,-0.38264,0.3944,459.45,-0.30797,0.26838,0.91276,600.64
> view matrix models
> #8,-0.45511,-0.88406,0.10639,331.15,0.83548,-0.38264,0.3944,410.32,-0.30797,0.26838,0.91276,602.64
> ui mousemode right clip
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.45511,-0.88406,0.10639,354.2,0.83548,-0.38264,0.3944,388.46,-0.30797,0.26838,0.91276,579.93
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.33008,-0.94352,-0.02851,352.33,0.70873,-0.26766,0.65273,391.17,-0.62349,0.19525,0.75706,581.32
> view matrix models
> #8,-0.22548,-0.95818,-0.17623,350.32,0.80248,-0.28523,0.52408,389.43,-0.55243,-0.023249,0.83323,582.32
> view matrix models
> #8,-0.3036,-0.95103,-0.058011,351.91,0.88451,-0.30396,0.35391,387.42,-0.35421,0.056136,0.93348,581.33
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.3036,-0.95103,-0.058011,359.35,0.88451,-0.30396,0.35391,385.58,-0.35421,0.056136,0.93348,586.37
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.32482,-0.9245,0.19946,361.6,0.9278,-0.27055,0.25688,384.28,-0.18352,0.2685,0.94564,584.3
> view matrix models
> #8,-0.27759,-0.95214,0.12796,360.74,0.94212,-0.24373,0.23025,383.83,-0.18804,0.18446,0.96468,584.84
> view matrix models
> #8,-0.052316,-0.98479,0.16568,359.47,0.9806,-0.019274,0.19508,382.32,-0.18892,0.17267,0.96669,584.91
> volume #5 level 0.05217
> ui mousemode right clip
[Repeated 1 time(s)]
> volume #5 level 0.1153
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.052316,-0.98479,0.16568,434.57,0.9806,-0.019274,0.19508,331.79,-0.18892,0.17267,0.96669,566.71
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.3051,-0.91518,-0.26338,427.88,0.85205,0.1388,0.50472,334.78,-0.42535,-0.3784,0.82213,569.54
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.3051,-0.91518,-0.26338,429.63,0.85205,0.1388,0.50472,338.7,-0.42535,-0.3784,0.82213,590.77
> view matrix models
> #8,0.3051,-0.91518,-0.26338,427.92,0.85205,0.1388,0.50472,341.73,-0.42535,-0.3784,0.82213,595.28
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.41522,-0.90379,-0.10372,428.39,0.74173,0.27033,0.6138,342.97,-0.52671,-0.33179,0.78262,595.53
> view matrix models
> #8,0.41891,-0.90352,-0.090411,428.48,0.73123,0.27664,0.62352,343.11,-0.53835,-0.32731,0.77656,595.55
> view matrix models
> #8,0.35537,-0.93028,-0.091064,429.07,0.73966,0.22031,0.6359,343.38,-0.5715,-0.29334,0.76638,595.58
> view matrix models
> #8,0.47009,-0.86177,-0.1907,427.06,0.77137,0.29613,0.56329,342.21,-0.42895,-0.4119,0.80395,595.29
> view matrix models
> #8,0.42451,-0.88862,-0.17364,427.66,0.77195,0.25499,0.5823,342.53,-0.47317,-0.38123,0.79421,595.42
> view matrix models
> #8,0.4645,-0.88458,0.041929,429.18,0.73537,0.41167,0.5383,341.8,-0.49342,-0.21921,0.84171,595.32
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.4645,-0.88458,0.041929,426.69,0.73537,0.41167,0.5383,340.14,-0.49342,-0.21921,0.84171,595.5
> volume #5 level 0.03555
> volume #5 level 0.018
> volume #5 level 0.18
> hide #10/Q
> hide #10/Q cartoons
> hide #10/R cartoons
> hide #10/S cartoons
> hide #10/T cartoons
> show #!7 models
> select subtract #8
Nothing selected
> hide #8 models
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
> graphics silhouettes width 2.3
> cartoon style protein modeHelix tube radius 1.9 sides 24
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!5 models
> select add #10
156266 atoms, 157935 bonds, 77 pseudobonds, 9614 residues, 3 models selected
> rainbow sel
> select subtract #10
Nothing selected
> show #!5 models
> close #7
> close #9
> fitmap #10 inMap #5
Fit molecule 8vwi (#10) to map J1770_FE (#5) using 156266 atoms
average map value = 0.1952, steps = 68
shifted from previous position = 1.47
rotated from previous position = 0.601 degrees
atoms outside contour = 69289, contour level = 0.18
Position of 8vwi (#10) relative to J1770_FE (#5) coordinates:
Matrix rotation and translation
-0.95114419 0.30851336 0.01201014 507.01050285
0.30844994 0.95121582 -0.00686308 171.49398090
-0.01354159 -0.00282325 -0.99990432 663.94584373
Axis 0.15616368 0.98772815 -0.00245184
Axis point 242.12403205 0.00000000 330.65209235
Rotation angle (degrees) 179.25888171
Shift along axis 246.93816886
> graphics silhouettes width 2
> cartoon style protein modeHelix tube radius 1.9 sides 24
> graphics silhouettes width 1.8
> cartoon style protein modeHelix tube radius 1.9 sides 24
> graphics silhouettes width 2
> cartoon style protein modeHelix tube radius 1.9 sides 24
> rainbow #!10
> color #10 #dfd9fcff
> color #10 #d2d2d3ff
> rainbow #10/G-I
> rainbow #10/G-I, a-c
> color #10 #d2d2d3ff
> rainbow #10/G-I, b-d
> show #8 models
> select add #8
5609 atoms, 5698 bonds, 691 residues, 1 model selected
> save /Users/ConstantinePetridis/Desktop/AcMNPV_Caps.cxs includeMaps true
——— End of log from Fri Jan 3 17:12:52 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 30 days, 5 hours, 1 minute
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
XV272U V3:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 180.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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