![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17780 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-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f43d9f00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, tables._comp_lzo, tables._comp_bzip2, tables.utilsextension, numexpr.interpreter, tables.hdf5extension, tables.linkextension, tables.lrucacheextension, tables.tableextension, tables.indexesextension, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, cython.cimports.libc.math, 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._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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 132)
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"procRole" : "Background",
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"captureTime" : "2025-05-22 10:47:33.5545 +0300",
"codeSigningMonitor" : 1,
"incident" : "C3D0F48A-8190-4D9B-8DFF-6F4B04A8A966",
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"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-21 10:13:25.2605 +0300",
"procStartAbsTime" : 2790824222737,
"procExitAbsTime" : 4135692998601,
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"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "332C7E2F-79A6-E46B-9116-6FCCB179314C",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn","siriAssetIsNotReady"]},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"vmRegionInfo" : "0x3eb70000401e is not in any region. Bytes after previous region: 68474663616543 Bytes before following region: 36597416312802\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":13774},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sahtelis/Downloads/cryosparc_P2_J217_005_volume_map_sharp.mrc
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.828, shown at level 0.0432, step 2, values float32
> open /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_hexamer_startingmodel_isolderelaxed.pdb
Chain information for cx45_hexamer_startingmodel_isolderelaxed.pdb #2
---
Chain | Description
A B C D E F | No description available
> volume #1 level 0.04324
> volume flip #1 axis x
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip as #3, grid size
384,384,384, pixel 0.828, shown at step 1, values float32
> close #1
> volume #3 level 0.1441
> volume #3 level 0.1
> volume #3 level 0.125
> surface dust #3 size 8.28
> hide atoms
> show cartoons
> transparency 50
> volume #3 level 0.1
> volume #3 level 0.15
> volume gaussian #2 sDev 1.2
> volume gaussian #3 sDev 1.2
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #1, grid
size 384,384,384, pixel 0.828, shown at step 1, values float32
> volume #1 level 0.0956
> transparency #1.1 50
> volume #1 level 0.08253
> surface dust #1 size 8.28
> hide #!1 models
> show #!1 models
> help
> cofr showPivot true
> cofr centerOfView showPivot true
> volume #1 level 0.071
> volume #1 level 0.07868
> volume #1 level 0.04716
> volume #1 level 0.06408
> volume #1 level 0.04793
> volume #1 level 0.06946
> for
Unknown command: for
> ~cofr
> show #!3 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.125
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.125
> hide #!3 models
> show #!1 models
> save /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs
> includeMaps true
> set bgColor gray
> set bgColor black
> set bgColor gray
> set bgColor black
> hide #!2 models
> hide #!1 models
> open 31495 fromDatabase emdb format ccp4
Summary of feedback from opening 31495 fetched from emdb
---
notes | Fetching compressed map 31495 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31495/map/emd_31495.map.gz
Fetching map header 31495 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-31495/header/emd-31495.xml
Opened emdb 31495 as #4, grid size 400,400,400, pixel 0.675, shown at level
0.032, step 2, values float32, fit PDB 7f92
> save /Users/sahtelis/Desktop/connexin-str_analysis/Cx43_gjc.mrc models #4
> volume #4 level 0.01019
> volume #4 level 0.02282
> surface dust #4 size 6.75
> volume #4 level 0.03143
> volume #4 level 0.01995
> volume #4 level 0.04348
> volume #4 level 0.02684
> cofr showPivot true
> cofr centerOfView showPivot true
> cofr centerOfView true
Expected 3-tuple of numbers or a keyword
> cofr centerOfView
> cofr showPivot true
> volume gaussian #4 sDev 2
Opened emdb 31495 gaussian as #5, grid size 400,400,400, pixel 0.675, shown at
step 1, values float32
> volume #5 level 0.007418
> volume #5 level 0.009522
> volume #5 level 0.007328
> volume gaussian #4 sDev 1.5
Opened emdb 31495 gaussian as #6, grid size 400,400,400, pixel 0.675, shown at
step 1, values float32
> volume #6 level 0.01301
> volume #6 level 0.01187
> volume #6 level 0.01171
> volume #6 level 0.003536
> close #5
> hide #!6 models
> show #!4 models
> volume #4 level 0.01708
> open /Users/sahtelis/Desktop/connexin-str_analysis/7z1t.pdb
7z1t.pdb title:
CONNEXIN43 gap junction channel structure In digitonin [more info...]
Chain information for 7z1t.pdb #5
---
Chain | Description | UniProt
A B C D E F G H I J K L | gap junction α-1 protein | CXA1_HUMAN 1-382
> select add #5
18492 atoms, 19044 bonds, 12 pseudobonds, 2268 residues, 2 models selected
> ui mousemode right "move picked models"
> view matrix models #5,1,0,0,9.7007,0,1,0,0.82447,0,0,1,8.8541
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms
average map value = 0.004396, steps = 92
shifted from previous position = 2.33
rotated from previous position = 2.86 degrees
atoms outside contour = 14821, contour level = 0.01708
Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates:
Matrix rotation and translation
0.99911797 -0.03108315 -0.02823347 19.53107763
0.03183255 0.99914203 0.02649308 -6.01678294
0.02738576 -0.02736845 0.99925021 8.57024344
Axis -0.53988691 -0.55750536 0.63064245
Axis point 236.20196104 590.63542089 0.00000000
Rotation angle (degrees) 2.85922806
Shift along axis -1.78542516
> view matrix models
> #5,0.99912,-0.031083,-0.028233,15.629,0.031833,0.99914,0.026493,1.1829,0.027386,-0.027368,0.99925,9.071
> fitmap #5 inMap #4
Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms
average map value = 0.00433, steps = 80
shifted from previous position = 1.61
rotated from previous position = 2.14 degrees
atoms outside contour = 14434, contour level = 0.01708
Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates:
Matrix rotation and translation
0.99863289 -0.03577737 -0.03810954 17.40615529
0.03809717 0.99734918 0.06199373 -2.68546053
0.03579054 -0.06336085 0.99734871 13.89840881
Axis -0.76812999 -0.45283441 0.45267793
Axis point 0.00000000 257.17370857 97.13848771
Rotation angle (degrees) 4.68038124
Shift along axis -5.86261816
> hide sel atoms
> show sel cartoons
> fitmap #5 inMap #4
Fit molecule 7z1t.pdb (#5) to map emdb 31495 (#4) using 18492 atoms
average map value = 0.004331, steps = 64
shifted from previous position = 0.00482
rotated from previous position = 0.00986 degrees
atoms outside contour = 14429, contour level = 0.01708
Position of 7z1t.pdb (#5) relative to emdb 31495 (#4) coordinates:
Matrix rotation and translation
0.99863299 -0.03565402 -0.03822237 17.40426607
0.03797983 0.99735590 0.06195763 -2.66259565
0.03591227 -0.06332461 0.99734663 13.88063268
Axis -0.76795946 -0.45443307 0.45136332
Axis point 0.00000000 257.11406366 97.15205153
Rotation angle (degrees) 4.67871556
Shift along axis -5.89059084
> select subtract #5
Nothing selected
> hide #!4 models
> hide #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.15
> show #!1 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> volume #3 level 0.125
> volume #1 level 0.15
> volume #1 level 0.1
> volume #1 level 0.15
> volume #1 level 0.075
> surface dust #1 size 8.28
> volume #1 level 0.095
> show #!3 models
> hide #!1 models
> volume #3 level 0.15
> volume #3 color #88a9bf80
> volume #3 color #73aabf80
> volume #3 color #6c99bf80
> volume #3 color #97b0bf80
> volume #3 color #a9bbbf80
> volume #3 color #9ea8bf80
> volume #3 color #8bb2bf80
> volume #3 color #69b4bf80
> volume #3 color #55aebf80
> volume #3 color #70e5fc80
> volume #3 color #94f0fc80
> volume #3 color #adeafc80
> volume #3 color #8ee5fc80
> volume #3 color #8ee5fca3
> volume #3 color #86d9efa3
> volume #3 level 0.13
> volume #3 level 0.175
> volume #3 step 2
> volume #3 step 1
> show #!1 models
> hide #!3 models
> volume #3 level 0.095
> volume #1 level 0.1
> volume #1 level 0.125
> volume #1 level 0.1
> volume #1 level 0.125
> volume #3 level 0.125
> volume #3 level 0.15
> hide #!1 models
> show #!3 models
> volume #3 level 0.17
> volume #3 level 0.19
> volume #3 level 0.2
> volume #3 level 0.17
> surface dust #3 size 8.28
> surface dust #3 size 15
> surface dust #3 size 8
> surface dust #3 size 15
> surface dust #3 size 8
> surface dust #3 size 15
> surface dust #3 size 8
> surface dust #3 size 5
> surface dust #3 size 10
> surface dust #3 size 15
> surface dust #3 size 20
> surface dust #3 size 15
> surface dust #3 size 20
> surface dust #3 size 30
> surface dust #3 size 25
> surface dust #3 size 20
> surface dust #3 size 25
> surface dust #3 size 15
> surface dust #3 size 20
> show #!1 models
> hide #!3 models
> volume #1 level 0.15
> volume #1 level 0.1
> volume #1 level 0.13
> volume #1 level 0.12
> cofr centerOfView
> cofr off
Expected 3-tuple of numbers or a keyword
> cofr showPivot false
> volume #1 level 0.1
> volume #1 level 0.15
> volume #1 level 0.1
> volume #1 level 0.13
> volume #1 level 0.125
> volume #1 level 0.12
> volume #1 level 0.127
> volume #1 level 0.12
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250421_top.png width 1042 height 722
> supersample 3 transparentBackground true
> save /Users/sahtelis/Desktop/connexin-
> str_analysis/cx45_map_model_20250421_side.png width 1042 height 722
> supersample 3 transparentBackground true
> hide #!1 models
> show #!3 models
> save /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs
> includeMaps true
> close session
> open browser vseries true
'browser' has no suffix
> open browser vseries
'browser' has no suffix
> open browser
'browser' has no suffix
> open browser
Unknown command: vseries open browser
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_000.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_019.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_018.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_017.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_016.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_015.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_014.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_013.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_012.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_011.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_010.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_009.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_008.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_007.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_006.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_005.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_004.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_003.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_002.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_001.mrc
> vseries
Missing "vseries" keyword's argument
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_000.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_019.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_018.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_017.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_016.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_015.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_014.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_013.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_012.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_011.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_010.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_009.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_008.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_007.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_006.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_005.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_004.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_003.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_002.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_001/J241_component_001_frame_001.mrc
> vseries true
Opened map series J241_component_001_frame_000.mrc as #1, 20 images, grid size
384,384,384, pixel 0.828, shown at level 0.0406, step 2, values float32
> volume #1.1 level 0.15
> volume #1.1 level 0.1
> surface dust #1.1 size 8.28
> surface dust #1.1 size 10
> surface dust #1.1 size 11
> surface dust #1.1 size 12
> surface dust #1.1 size 15
> surface dust #1.1 size 13
> surface dust #1.1 size 12
> surface dust #1.1 size 10
> surface dust #1.1 size 8
> volume #1.1 level 0.09
> surface dust #1.1 size 8
> surface dust #1.1 size 10
> surface dust #1.1 size 8
> surface dust #1.1 size 9
> surface dust #1.1 size 5
> volume #1.1 level 0.1
> volume #1.1 level 0.15
> volume #1.1 level 0.1
> surface dust #1.1 size 5
> surface dust #1.1 size 0
> surface dust #1.1 size 2
> surface dust #1.1 size 5
> surface dust #1.1 size 7
> vseries play #1 loop true direction oscilate
Invalid "direction" argument: Should be one of 'backward', 'forward', or
'oscillate'
> vseries play #1 loop true direction oscillate pauseFrames frame 5 cache
> frame 50
Invalid "pauseFrames" argument: Expected an integer
> vseries play #1 loop true direction oscillate
> vseries stop
Missing or invalid "series" argument: empty atom specifier
>
Unknown command: vseries #1 stop
> movie record
> movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0
Error processing trigger "new frame":
Movie encoding failed because no images were recorded.
> pause
Unknown command: vseries pause
> vseries stop
Missing or invalid "series" argument: empty atom specifier
> vseries stop #1
> volume #1.1 level 0.125
> surface dust #1 10
Expected a keyword
> surface dust #1.1 10
Expected a keyword
> surface dust #1.1 size 10
> close #1
> open browser vseries true
'browser' has no suffix
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_000.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_019.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_018.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_017.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_016.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_015.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_014.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_013.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_012.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_011.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_010.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_009.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_008.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_007.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_006.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_005.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_004.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_003.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_002.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_002/J241_component_002_frame_001.mrc
> vseries true
Opened map series J241_component_002_frame_000.mrc as #1, 20 images, grid size
384,384,384, pixel 0.828, shown at level 0.0418, step 2, values float32
> volume #1.1 level 0.18
> volume #1.1 level 0.1
> volume #1.1 level 0.12
> surface dust #1.1 size 8.28
> volume #1.1 level 0.1
> volume #1.1 level 0.09
> volume #1.1 step 1
> volume #1.1 step 4
> volume #1.1 step 1
> volume #1.1 level 0.12
> volume #1.1 step 2
> volume #1.1 step 1
> volume #1.1 level 0.1
> volume #1.1 level 0.11
> volume #1.1 level 0.115
> volume #1.1 level 0.105
> vseries play #1 loop true direction oscillate pauseFrames frame 5 cache
> frame 50
Invalid "pauseFrames" argument: Expected an integer
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 10 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 2 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 7 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries stop #1
> surface dust #1.7 size 8.28
> surface dust #1 size 10
> movie record
> movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie2.mp4
> close session
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_019.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_018.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_017.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_016.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_015.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_014.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_013.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_012.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_011.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_010.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_009.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_008.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_007.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_006.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_005.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_004.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_003.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_002.mrc
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_001.mrc
> vseries true
Opened map series J241_component_000_frame_000.mrc as #1, 20 images, grid size
384,384,384, pixel 0.828, shown at level 0.0404, step 2, values float32
> volume #1.1 level 0.125
> volume #1.1 step 1
> volume #1.1 level 0.15
> volume #1.1 level 0.1
> volume #1.1 level 0.09
> volume #1.1 level 0.17
> volume #1.1 level 0.125
> volume #1.1 step 2
> volume #1.1 step 1
> volume #1.1 step 2
> volume #1.1 step 1
> volume #1.1 step 2
> surface dust #1.1 size 8.28
> volume #1.1 level 0.1
> volume #1.1 level 0.11
> surface dust #1 size 12
> surface dust #1 size 8
> surface dust #1 size 7
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheframe30
Expected a keyword
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 30
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 25
> movie record
> movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 10 cacheFrames 25
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 2 cacheFrames 25
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 100
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries stop #1
> movie record supersample 3 size 1920 1080
Invalid "size" argument: Need exactly 2 ','-separated 2-tuple of integers
> for i in range(1, 21):
Unknown command: for i in range(1, 21):
> set #1 index $i
Unknown command: vseries set #1 index $i
> wait 2 # Adjust to control speed (e.g., wait 2 = ~0.07 sec per frame at 30
> fps)
Expected a keyword
> movie stop
No movie being recorded.
> movie encode output cx45_vseries.mp4 bitrate 15000
No frames have been recorded
> movie record supersample 3 size 1920 1080
Invalid "size" argument: Need exactly 2 ','-separated 2-tuple of integers
> for i in range(1, 21):
Unknown command: for i in range(1, 21):
> set #1 index $i
Unknown command: vseries set #1 index $i
> wait 2 # Adjust to control speed (e.g., wait 2 = ~0.07 sec per frame at 30
> fps)
Expected a keyword
> movie stop
No movie being recorded.
> movie encode output cx45_vseries.mp4 bitrate 15000
No frames have been recorded
> movie record supersample 3 size 1920 1080
Invalid "size" argument: Need exactly 2 ','-separated 2-tuple of integers
> for i in range(1, 21):
Unknown command: for i in range(1, 21):
> hide #1.1-1.20
> show #1.$i
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> wait 2
> movie stop
No movie being recorded.
> movie encode output cx45_frames.mp4 bitrate 15000
No frames have been recorded
> vseries save #1 ~/Desktop/test.cmap subregion 100,0,0,200,511,150 threshold
> 140 valueType uint8
> open /Users/sahtelis/Desktop/test.cmap
Opened map series test.cmap as #2, 20 images, grid size 101,512,151, pixel
0.828, shown at level 0.0002, step 1, values uint8
> select add #2
22 models selected
> view clip false
> close #2.1
> close #2
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> record
Expected a keyword
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> recordmovie
Expected a keyword
> vseries stop #1
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50
> vseries stop #1
> vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50
> lighting full
> lighting soft
> lighting simple
> volume #1.1 color #82a9bf
> volume #1.1 color #8cb6cf
> transparency #1.1#!1 0
> vseries play #1 loop false direction oscillate pauseFrames 5 cacheFrames 50
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/sahtelis/Desktop/movie1.mp4
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> vseries stop #1
> vseries play #1 loop true direction oscillate normalize true pauseFrames 5
> cacheFrames 50
> vseries stop #1
> vseries play #1 loop true direction oscillate normalize false pauseFrames 5
> cacheFrames 50
> vseries stop #1
> vseries play #1 loop true direction oscillate normalize true pauseFrames 5
> cacheFrames 50
> vseries stop #1
> vseries play #1 loop true direction oscillate normalize true pauseFrames 5
> cacheFrames 50
> vseries stop #1
> vseries slider #1
> vseries play #1 loop true direction oscillate normalize true pauseFrames 5
> cacheFrames 50
> vseries slider #1
> vseries stop #1
> movie record supersample 3 size 1920 1080
Invalid "size" argument: Need exactly 2 ','-separated 2-tuple of integers
> movie record supersample 3 size 1920,1080
> vseries play #1 loop false direction forward normalize true pauseFrames 5
> cacheFrames 50
> wait 40
> movie stop
> movie encode output cx45_vseries_play.mp4 bitrate 15000
Movie saved to cx45_vseries_play.mp4
> movie record supersample 3 size 1920,1080
> vseries play #1 loop false direction oscillate normalize true pauseFrames 5
> cacheFrames 50
> wait 80 # 40 forward + 40 backward
Expected a keyword
> wait 80 #1 40 forward + 40 backward
Expected a keyword
> wait 80 40 forward + 40 backward
Expected a keyword
> wait 80
> movie stop
> movie encode output cx45_vseries_play2.mp4 bitrate 15000
Movie saved to cx45_vseries_play2.mp4
> vseries play #1 loop true direction oscillate pauseFrames 5 cacheFrames 50
> vseries stop #1
> record #1 loop true direction oscillate pauseframe 5 cacheframe 50
Unknown command: vseries record #1 loop true direction oscillate pauseframe 5
cacheframe 50
> movie record supersample 3 size 1920,1080
> set #1 index $i
Unknown command: vseries set #1 index $i
> hide #1.1-1.20
> movie record supersample 3 size 1920,1080
Already recording a movie
> for i in range(1, 21):
Unknown command: for i in range(1, 21):
> show #1.$i
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> wait
Unknown command: ui wait
> wait 2
> hide #1.$i
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> movie stop
> hide #1.1-1.20
> movie record supersample 3 size 1920,1080
> show #1.$i
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> movie stop
> hide #1.1-1.20
> movie record supersample 3 size 1920,1080
> eval("show #1.%d" % i)
Unknown command: eval("show #1.%d" % i)
> show #1.1
> wait 2
> hide #1.1
> show #1.2
> wait 2
> hide #1.2
> show #1.3
> wait 2
> hide #1.3
> show #1.4
> wait 2
> hide #1.4
> show #1.5
> wait 2
> hide #1.5
> show #1.6
> wait 2
> hide #1.6
> show #1.7
> wait 2
> hide #1.7
> show #1.8
> wait 2
> hide #1.8
> show #1.9
> wait 2
> hide #1.9
> show #1.10
> wait 2
> hide #1.10
> show #1.11
> wait 2
> hide #1.11
> show #1.12
> wait 2
> hide #1.12
> show #1.13
> wait 2
> hide #1.13
> show #1.14
> wait 2
> hide #1.14
> show #1.15
> wait 2
> hide #1.15
> show #1.16
> wait 2
> hide #1.16
> show #1.17
> wait 2
> hide #1.17
> show #1.18
> wait 2
> hide #1.18
> show #1.19
> wait 2
> hide #1.19
> show #1.20
> wait 2
> hide #1.20
> movie stop
> movie encode output cx45_frames_movie.mp4 bitrate 15000
Movie saved to cx45_frames_movie.mp4
> hide #1.1-1.20
> movie record supersample 3 size 1920,1080
> show #1.1
> wait; wait 2; hide #1.1
Unknown command: ui wait; wait 2; hide #1.1
> show #1.2
> wait; wait 2; hide #1.2
Unknown command: ui wait; wait 2; hide #1.2
> show #1.3
> wait; wait 2; hide #1.3
Unknown command: ui wait; wait 2; hide #1.3
> show #1.4
> wait; wait 2; hide #1.4
Unknown command: ui wait; wait 2; hide #1.4
> show #1.5
> wait; wait 2; hide #1.5
Unknown command: ui wait; wait 2; hide #1.5
> show #1.6
> wait; wait 2; hide #1.6
Unknown command: ui wait; wait 2; hide #1.6
> show #1.7
> wait; wait 2; hide #1.7
Unknown command: ui wait; wait 2; hide #1.7
> show #1.8
> wait; wait 2; hide #1.8
Unknown command: ui wait; wait 2; hide #1.8
> show #1.9
> wait; wait 2; hide #1.9
Unknown command: ui wait; wait 2; hide #1.9
> show #1.10
> wait; wait 2; hide #1.10
Unknown command: ui wait; wait 2; hide #1.10
> show #1.11
> wait; wait 2; hide #1.11
Unknown command: ui wait; wait 2; hide #1.11
> show #1.12
> wait; wait 2; hide #1.12
Unknown command: ui wait; wait 2; hide #1.12
> show #1.13
> wait; wait 2; hide #1.13
Unknown command: ui wait; wait 2; hide #1.13
> show #1.14
> wait; wait 2; hide #1.14
Unknown command: ui wait; wait 2; hide #1.14
> show #1.15
> wait; wait 2; hide #1.15
Unknown command: ui wait; wait 2; hide #1.15
> show #1.16
> wait; wait 2; hide #1.16
Unknown command: ui wait; wait 2; hide #1.16
> show #1.17
> wait; wait 2; hide #1.17
Unknown command: ui wait; wait 2; hide #1.17
> show #1.18
> wait; wait 2; hide #1.18
Unknown command: ui wait; wait 2; hide #1.18
> show #1.19
> wait; wait 2; hide #1.19
Unknown command: ui wait; wait 2; hide #1.19
> show #1.20
> wait; wait 2; hide #1.20
Unknown command: ui wait; wait 2; hide #1.20
> movie stop
> movie encode output cx45_frames_movie.mp4 bitrate 15000
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/sahtelis/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie2.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie2.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie3.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie3.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie3.mp4 framerate 50.0
Movie encoding failed because no images were recorded.
> movie record
> movie encode /Users/sahtelis/Desktop/movie4.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie4.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie5.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie5.mp4
> volume #1.1 step 1
> volume #1.1 level 0.1
> volume #1.1 level 0.11
> volume #1.1 level 0.1131
> movie record
> movie encode /Users/sahtelis/Desktop/movie6.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie6.mp4
> movie record
> movie encode /Users/sahtelis/Desktop/movie7.mp4 framerate 25.0
Movie saved to /Users/sahtelis/Desktop/movie7.mp4
> view
> ui tool show "Side View"
> view
> close session
> open browse
Unknown command: vseries open browse
> browse open
Unknown command: vseries browse open
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc
> vseries
Missing "vseries" keyword's argument
> open
> /Users/sahtelis/Downloads/cryosparc_P2_J241_component_000/J241_component_000_frame_000.mrc
> vseries true
Opened J241_component_000_frame_000.mrc as #1, grid size 384,384,384, pixel
0.828, shown at level 0.0404, step 2, values float32
> volume #1 level 0.12
> volume #1 level 0.15
> volume #1 level 0.1
> surface dust #1 size 8.28
> close session
> open /Users/sahtelis/Desktop/connexin-str_analysis/cx45map_20250521.cxs
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip as #3, grid size
384,384,384, pixel 0.828, shown at level 0.17, step 1, values float32
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #1, grid
size 384,384,384, pixel 0.828, shown at level 0.12, step 1, values float32
Opened emdb 31495 as #4, grid size 400,400,400, pixel 0.675, shown at level
0.0171, step 2, values float32
Opened emdb 31495 gaussian as #6, grid size 400,400,400, pixel 0.675, shown at
level 0.00354, step 1, values float32
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/sahtelis/Desktop/movie1.mp4
Movie saved to /Users/sahtelis/Desktop/movie1.mp4
> show #!6 models
> volume #6 level 0.009791
> hide #!6 models
> show #!5 models
> select add #5
18492 atoms, 19044 bonds, 12 pseudobonds, 2268 residues, 2 models selected
> view matrix models
> #5,0.99863,-0.035654,-0.038222,43.731,0.03798,0.99736,0.061958,18.394,0.035912,-0.063325,0.99735,-2.4187
> hide #!2 models
> select subtract #5
Nothing selected
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #3 level 0.17
> volume #1 level 0.07947
> hide #!1 models
> show #!3 models
> volume #3 level 0.1182
> transparency #3,5 90
> transparency #3,5 20
> transparency #3,5 30
> volume gaussian #3 sDev 1
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #7, grid
size 384,384,384, pixel 0.828, shown at step 1, values float32
> volume #7 level 0.1004
> volume #7 level 0.12
> surface dust #7 size 8.28
> volume #7 level 0.09955
> transparency #5,7 40
> hide #!5 models
> volume #7 level 0.08023
> show #!5 models
> volume #7 level 0.0825
> hide #!5 models
> hide #!7 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 cartoons
> show #!5 surfaces
> hide #!5 surfaces
> show #!5 atoms
> hide #!5 atoms
> style #!5 stick
Changed 18492 atom styles
> show #!5 cartoons
> rainbow #!5
> undo
> coulombic #!5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7z1t.pdb_A SES surface #5.2: minimum, -15.68, mean 0.27,
maximum 14.86
Coulombic values for 7z1t.pdb_B SES surface #5.3: minimum, -13.61, mean 0.24,
maximum 13.31
Coulombic values for 7z1t.pdb_C SES surface #5.4: minimum, -13.13, mean 0.24,
maximum 13.52
Coulombic values for 7z1t.pdb_D SES surface #5.5: minimum, -13.79, mean 0.29,
maximum 19.64
Coulombic values for 7z1t.pdb_E SES surface #5.6: minimum, -13.19, mean 0.25,
maximum 14.62
Coulombic values for 7z1t.pdb_F SES surface #5.7: minimum, -13.54, mean 0.26,
maximum 15.60
Coulombic values for 7z1t.pdb_G SES surface #5.8: minimum, -13.19, mean 0.27,
maximum 16.26
Coulombic values for 7z1t.pdb_H SES surface #5.9: minimum, -13.15, mean 0.28,
maximum 12.99
Coulombic values for 7z1t.pdb_I SES surface #5.10: minimum, -17.63, mean 0.28,
maximum 14.83
Coulombic values for 7z1t.pdb_J SES surface #5.11: minimum, -17.52, mean 0.27,
maximum 15.83
Coulombic values for 7z1t.pdb_K SES surface #5.12: minimum, -13.56, mean 0.28,
maximum 15.36
Coulombic values for 7z1t.pdb_L SES surface #5.13: minimum, -16.14, mean 0.24,
maximum 12.69
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> hide #!5 surfaces
Alignment identifier is 1
Alignment identifier is 2
> select #5/A-L:2
48 atoms, 36 bonds, 12 residues, 1 model selected
> select #5/A-L:2-16
1344 atoms, 1356 bonds, 180 residues, 1 model selected
> surface (#!5 & sel)
> style (#!5 & sel) stick
Changed 1344 atom styles
> surface hidePatches (#!5 & sel)
> style (#!5 & sel) stick
Changed 1344 atom styles
> surface style #5 dot
> surface (#!5 & sel)
> surface hidePatches (#!5 & sel)
> surface (#!5 & sel)
> surface style #5 dot
> surface style #5 mesh
> surface style #5 solid
> transparency (#!5 & sel) 50
> select #5/A-L:2
48 atoms, 36 bonds, 12 residues, 1 model selected
> select #5/A-L:2-17
1488 atoms, 1512 bonds, 192 residues, 1 model selected
> ui tool show "Selection Inspector"
> style sel ball
Changed 1488 atom styles
> surface hidePatches (#!5 & sel)
> cartoon hide (#!5 & sel)
> show (#!5 & sel) target ab
> style (#!5 & sel) ball
Changed 1488 atom styles
> style (#!5 & sel) stick
Changed 1488 atom styles
> style (#!5 & sel) sphere
Changed 1488 atom styles
> style (#!5 & sel) ringFill thin
Changed 192 residue ring styles
> style (#!5 & sel) ringFill off
Changed 192 residue ring styles
> style (#!5 & sel) ball
Changed 1488 atom styles
> style (#!5 & sel) stick
Changed 1488 atom styles
> view sel
> hide #* target a
> show (#!5 & sel) target ab
> hide (#!5 & sel) target a
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon hide (#!5 & sel)
> cartoon style (#!5 & sel) xsection oval modeHelix default
> cartoon hide (#!5 & sel)
> cartoon (#!5 & sel)
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> cartoon style (#!5 & sel) xsection oval modeHelix default
> cartoon style (#!5 & sel) modeHelix tube sides 20
> select protein
34962 atoms, 35784 bonds, 18 pseudobonds, 3276 residues, 4 models selected
> select clear
> select #5/A-L:2-17
1488 atoms, 1512 bonds, 192 residues, 1 model selected
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> cartoon style (#!5 & sel) xsection rectangle modeHelix default
> cartoon style (#!5 & sel) xsection oval modeHelix default
> surface style #5 mesh
> surface (#!5 & sel)
> select ~sel
33474 atoms, 34260 bonds, 18 pseudobonds, 3084 residues, 14 models selected
> undo
> select clear
> select #5/A-L:2-16
1344 atoms, 1356 bonds, 180 residues, 1 model selected
> surface (#!5 & sel)
> surface style #5 solid
> color (#!5 & sel) red
> color (#!5 & sel) lime
> color (#!5 & sel) cyan
> color (#!5 & sel) gray
> select clear
> transparency #5 10
> select clear
> select #5/A-L:2-16
1344 atoms, 1356 bonds, 180 residues, 1 model selected
> surface hidePatches (#!5 & sel)
> select clear
> show #!7 models
> transparency #5,7 20
> volume #7 color #c0faffcc
> volume #7 color #a6f2ffcc
> volume #7 color #9dfff8cc
Alignment identifier is 1
Alignment identifier is 2
> select clear
> select #5/A-L:2-17
1488 atoms, 1512 bonds, 192 residues, 1 model selected
> color (#!5 & sel) orange
> select clear
> select #5/A-L:2-17
1488 atoms, 1512 bonds, 192 residues, 1 model selected
> color (#!5 & sel) orange red
> select clear
Drag select of 6 emdb 31495 gaussian
> undo
Drag select of 6 emdb 31495 gaussian
> undo
> hide #!5 models
> show #!7 models
> tile
2 models tiled
> transparency #6-7 0
> volume #7 color #c9fbe7
> volume #7 color #adfbc8
> volume #7 color #a5fbd2
> volume #7 color #abfbf3
> volume #7 color #9feffb
> lighting full
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> view matrix models
> #7,0.99342,-0.025082,0.11175,-4.22,-0.03759,0.85027,0.525,11.66,-0.10819,-0.52574,0.84373,48.43
> volume #6 level 0.009165
> volume gaussian #3 sDev 1.2
Opened cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian as #8, grid
size 384,384,384, pixel 0.828, shown at step 1, values float32
> volume #8 level 0.08688
> select add #8
2 models selected
> view matrix models #8,1,0,0,51.534,0,1,0,39.283,0,0,1,-27.73
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.99936,-0.012202,0.033733,48.268,-0.0085695,0.83194,0.5548,-19.938,-0.034834,-0.55473,0.8313,92.511
> view matrix models
> #8,0.99977,-0.018173,0.011388,52.668,0.010042,0.86588,0.50015,-19.678,-0.01895,-0.49992,0.86586,75.847
> ui mousemode right "move picked models"
> view matrix models
> #8,0.99846,-0.030417,0.046301,71.565,-0.0037266,0.79701,0.60395,-53.061,-0.055272,-0.6032,0.79567,124.56
> volume #8 level 0.07847
> surface dust #8 size 8.28
> select subtract #8
Nothing selected
> volume #6 level 0.009556
> show #!3 models
> show #!1 models
> tile
5 models tiled
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.99643,-0.036804,0.076014,128.36,0.0026097,0.91304,0.40786,261.2,-0.084415,-0.4062,0.90987,-73.946
> select subtract #6
Nothing selected
> select add #1
2 models selected
> view matrix models
> #1,0.98773,-0.0064489,0.15604,33.423,-0.064652,0.89263,0.44612,97.527,-0.14217,-0.45074,0.88126,25.126
> select subtract #1
Nothing selected
> select add #3
2 models selected
> view matrix models
> #3,0.98329,-0.012796,0.18159,-23.78,-0.094051,0.81838,0.56693,-45.095,-0.15587,-0.57454,0.8035,146.78
> select subtract #3
Nothing selected
> tile
5 models tiled
> transparency #1,3,6-8 0
> lighting full
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume #7 level 0.08023
> volume gaussian #4 sDev 1.5
Opened emdb 31495 gaussian as #9, grid size 400,400,400, pixel 0.675, shown at
step 1, values float32
> volume #9 level 0.008522
> select add #9
2 models selected
> view matrix models
> #9,0.8467,0.4658,-0.25716,-7.4711,-0.45329,0.88458,0.10977,61.957,0.27861,0.02362,0.96011,-35.416
> view matrix models
> #9,0.90232,0.37633,-0.21022,-9.2384,-0.36837,0.92645,0.077404,49.209,0.22389,0.0075955,0.97459,-27.819
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.81074,0.5133,-0.28148,-5.7456,-0.49786,0.8575,0.12974,68.934,0.30796,0.034952,0.95076,-39.645
> view matrix models
> #9,0.79247,0.53518,-0.29252,-4.743,-0.51825,0.84375,0.13967,72.204,0.32156,0.040918,0.946,-41.645
> hide #!6 models
> close #9
> close #7
> hide #!1 models
> show #!1 models
> close #8
> volume gaussian #4 sDev 2
Opened emdb 31495 gaussian as #7, grid size 400,400,400, pixel 0.675, shown at
step 1, values float32
> volume #7 level 0.007722
> select add #7
2 models selected
> view matrix models
> #7,0.70254,0.62659,-0.33737,1.113,-0.60233,0.77603,0.18702,86.302,0.379,0.071821,0.92261,-50.412
> view matrix models
> #7,0.84957,0.46171,-0.25504,-7.5924,-0.44944,0.88674,0.10815,61.364,0.27609,0.022743,0.96086,-35.059
> ui mousemode right "move picked models"
> view matrix models
> #7,0.84957,0.46171,-0.25504,113.46,-0.44944,0.88674,0.10815,292.73,0.27609,0.022743,0.96086,-181.28
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.86188,0.50323,0.062579,63.318,-0.47261,0.75237,0.45889,266.64,0.18385,-0.42509,0.88629,-98.298
> select subtract #7
Nothing selected
> tile
2 models tiled
> volume #1 color #97b9fe
> lighting full
> select add #7
2 models selected
> view matrix models
> #7,0.85105,0.51632,0.095564,73.555,-0.5108,0.7719,0.37848,360.87,0.12165,-0.37092,0.92066,-112.53
> ui mousemode right "move picked models"
> view matrix models
> #7,0.85105,0.51632,0.095564,58.366,-0.5108,0.7719,0.37848,295.35,0.12165,-0.37092,0.92066,-76.808
> view matrix models
> #7,0.85105,0.51632,0.095564,58.867,-0.5108,0.7719,0.37848,296.81,0.12165,-0.37092,0.92066,-77.626
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.85365,0.50785,0.11567,56.945,-0.50123,0.7406,0.44753,290.43,0.14161,-0.44001,0.88676,-66.418
> volume #7 level 0.0069
> select subtract #7
Nothing selected
> close #7
> select add #6
2 models selected
> view matrix models
> #6,0.99449,0.027048,0.10126,112.8,-0.066163,0.91132,0.40635,261.24,-0.081293,-0.41081,0.90809,-67.508
> ui mousemode right "move picked models"
> view matrix models
> #6,0.99449,0.027048,0.10126,101.47,-0.066163,0.91132,0.40635,219.12,-0.081293,-0.41081,0.90809,-44.317
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.9921,0.023665,0.1232,99.293,-0.075799,0.89559,0.43838,218.22,-0.099958,-0.44426,0.89031,-34.882
> select subtract #6
Nothing selected
> surface dust #1 size 8.28
> surface dust #6 size 6.75
> volume #1 level 0.0833
> select add #1
2 models selected
> view matrix models
> #1,0.98604,0.046183,0.15998,22.809,-0.12511,0.83948,0.52879,97.689,-0.10988,-0.54143,0.83354,44.946
> select subtract #1
Nothing selected
> set bgColor gray
> set bgColor #80808000
> open /Users/sahtelis/Downloads/emd_14452.map
Opened emd_14452.map as #7, grid size 384,384,384, pixel 0.654, shown at level
0.00226, step 2, values float32
> open /Users/sahtelis/Downloads/emd_14455.map
Opened emd_14455.map as #8, grid size 384,384,384, pixel 0.654, shown at level
0.00389, step 2, values float32
> open /Users/sahtelis/Downloads/emd_14456.map
Opened emd_14456.map as #9, grid size 384,384,384, pixel 0.654, shown at level
0.00296, step 2, values float32
> open /Users/sahtelis/Downloads/emd_9116.map
Opened emd_9116.map as #10, grid size 320,320,320, pixel 0.665, shown at level
0.0238, step 2, values float32
> open /Users/sahtelis/Downloads/emd_0826.map
Opened emd_0826.map as #11, grid size 320,320,320, pixel 0.673, shown at level
0.0162, step 2, values float32
> tile
7 models tiled
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> select add #7
2 models selected
> color #7 #f77bb6ff models
> view matrix models
> #7,0.98363,0.0055776,0.1801,172.05,-0.064184,0.9448,0.32129,431.81,-0.16836,-0.32759,0.9297,-144.65
> volume #7 level 0.004092
> select subtract #7
Nothing selected
> volume gaussian #7 sDev 2
Opened emd_14452.map gaussian as #12, grid size 384,384,384, pixel 0.654,
shown at step 1, values float32
> volume #12 level 0.00227
> volume gaussian #7 sDev 1.5
Opened emd_14452.map gaussian as #13, grid size 384,384,384, pixel 0.654,
shown at step 1, values float32
> close #12
> volume #13 level 0.002471
> show #!7 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.99511,0.068185,0.071465,232.86,-0.097711,0.78543,0.61119,73.863,-0.014457,-0.61518,0.78825,59.236
> select subtract #8
Nothing selected
> volume #8 level 0.00631
> volume gaussian #8 sDev 1.5
Opened emd_14455.map gaussian as #12, grid size 384,384,384, pixel 0.654,
shown at step 1, values float32
> hide #!12 models
> show #!12 models
> volume #12 level 0.004649
> hide #!9 models
> show #!9 models
> volume #9 level 0.005524
> select add #9
2 models selected
> view matrix models
> #9,0.99792,-0.056479,-0.030994,314.94,-0.0067944,0.38614,-0.92242,451.8,0.064065,0.92071,0.38495,-174.45
> view matrix models
> #9,0.9663,-0.25737,0.004827,339.54,-0.21522,-0.81804,-0.53337,579.25,0.14122,0.51436,-0.84587,24.848
> view matrix models
> #9,0.96561,-0.2584,0.028699,336.69,-0.20798,-0.83398,-0.5111,577.48,0.156,0.48756,-0.85904,28.048
> select subtract #9
Nothing selected
> volume #9 level 0.005258
> volume #9 level 0.003842
> volume #9 level 0.00517
> volume gaussian #9 sDev 1.5
Opened emd_14456.map gaussian as #14, grid size 384,384,384, pixel 0.654,
shown at step 1, values float32
> volume #14 level 0.003542
> select add #10
2 models selected
> view matrix models
> #10,0.93907,-0.16538,0.30134,368.57,0.09229,0.96577,0.24243,386.75,-0.33112,-0.19985,0.92218,-125.33
> volume gaussian #10 sDev 1.5
Opened emd_9116.map gaussian as #15, grid size 320,320,320, pixel 0.665, shown
at step 1, values float32
> volume #15 level 0.01634
> view matrix models
> #10,0.93907,-0.16538,0.30134,368.57,0.09229,0.96577,0.24243,386.75,-0.33112,-0.19985,0.92218,-125.33
> select add #15
4 models selected
> view matrix models
> #10,0.95661,-0.052457,0.28662,356.25,-0.022612,0.96733,0.25251,397.73,-0.2905,-0.24803,0.92417,-124.73,#15,0.98484,-0.1246,0.12069,378.58,0.070855,0.924,0.37577,379.29,-0.15834,-0.36152,0.91882,-126.15
> view matrix models
> #10,0.95134,0.16204,0.26211,336.6,-0.23469,0.93221,0.27552,421.59,-0.19969,-0.32363,0.92487,-126.43,#15,0.98791,0.091283,0.12527,354.79,-0.13679,0.89352,0.42768,399.1,-0.072894,-0.43965,0.89521,-124.42
> view matrix models
> #10,0.53428,-0.74217,0.40464,462.02,0.72956,0.64664,0.22273,354.99,-0.42696,0.17621,0.88694,-151.39,#15,0.54764,-0.80873,0.21459,487.9,0.79028,0.5842,0.18486,359.21,-0.27486,0.06835,0.95905,-163.77
> view matrix models
> #10,0.5971,-0.69875,0.39398,451.85,0.67642,0.7026,0.22096,354.88,-0.4312,0.13456,0.89217,-147.07,#15,0.61041,-0.76649,0.19972,478.31,0.74073,0.6417,0.19885,356.87,-0.28058,0.026554,0.95946,-158.76
> view matrix models
> #10,0.071132,-0.88378,0.46246,520.21,0.94417,0.20918,0.25453,375.32,-0.32169,0.41854,0.84932,-184.37,#15,0.091689,-0.94058,0.32696,538.48,0.98233,0.13924,0.12509,392.47,-0.16319,0.30971,0.93672,-198.96
> view matrix models
> #10,0.39164,-0.8156,0.42592,482.74,0.82526,0.51607,0.2294,357.99,-0.4069,0.26165,0.8752,-161.37,#15,0.40607,-0.87934,0.24874,506.84,0.87838,0.45066,0.15919,366.77,-0.25208,0.15385,0.9554,-174.9
> view matrix models
> #10,0.05033,-0.88421,0.46437,522.27,0.94792,0.18871,0.25658,376.88,-0.3145,0.42727,0.84766,-185.89,#15,0.14129,-0.93871,0.31442,534.34,0.9734,0.18959,0.12861,387.69,-0.18034,0.28789,0.94053,-195.22
> view clip false
> view matrix models
> #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38,#15,0.09464,-0.94839,0.30267,541.59,0.95051,0.17646,0.25573,378,-0.29594,0.26349,0.91815,-177.94
> select subtract #15
2 models selected
> view matrix models
> #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> volume #11 level 0.03407
> view matrix models
> #10,0.0057552,-0.89467,0.4467,530,0.90469,0.19497,0.37884,367.81,-0.42603,0.40195,0.81052,-167.38
> ui mousemode right "move picked models"
> view matrix models
> #11,0.9935,0.020734,0.1119,299.76,-0.00697,0.9925,-0.12202,334.12,-0.11359,0.12044,0.9862,-82.241
> view matrix models
> #11,0.9935,0.020734,0.1119,225.16,-0.00697,0.9925,-0.12202,475.79,-0.11359,0.12044,0.9862,-110.02
> select add #11
4 models selected
> view matrix models
> #11,0.9935,0.020734,0.1119,214.38,-0.00697,0.9925,-0.12202,479.68,-0.11359,0.12044,0.9862,-107.11
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.15789,-0.84389,0.51276,524.54,0.92257,-0.3112,-0.22809,590.23,0.35205,0.43704,0.82768,-263.93,#11,0.96122,-0.074588,0.2655,210.24,0.25572,0.6015,-0.75684,567.39,-0.10325,0.79538,0.59725,-135.63
> view matrix models
> #10,0.16906,-0.9389,0.2998,544.43,0.24941,-0.25352,-0.93462,741.02,0.95353,0.23278,0.19131,-186.38,#11,0.99143,0.078188,-0.10466,233.62,-0.077078,-0.29676,-0.95184,722.65,-0.10548,0.95174,-0.28819,-49.158
> view matrix models
> #10,0.23301,-0.96817,-0.091409,597.94,-0.59439,-0.067393,-0.80135,761.94,0.76968,0.24105,-0.59117,-64.491,#11,0.88531,-0.063107,-0.4607,301.71,-0.24508,-0.90529,-0.34696,735.86,-0.39517,0.42008,-0.81693,100.83
> view matrix models
> #10,0.16904,-0.98414,-0.053825,604.39,-0.67894,-0.07668,-0.73018,764.24,0.71447,0.15997,-0.68114,-23.535,#11,0.91032,-0.10269,-0.40097,296.32,-0.21559,-0.94459,-0.24753,725.34,-0.35333,0.31178,-0.88202,115.56
> select subtract #11
2 models selected
> volume #11 level 0.06705
> volume gaussian #11 sDev 1.5
Opened emd_0826.map gaussian as #16, grid size 320,320,320, pixel 0.673, shown
at step 1, values float32
> volume #16 level 0.00762
> close #11
> close #10
> close #9
> close #8
> close #7
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!6 models
> show #!6 models
> hide #!16 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> tile
7 models tiled
> volume #16 color #91f762
> close #14
> tile
6 models tiled
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!13 models
> show #!13 models
> hide #!6 models
> close #6
> close #4
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> tile
4 models tiled
> select add #12
2 models selected
> view matrix models
> #12,0.94659,-0.016676,0.322,103.7,-0.071205,0.96319,0.25921,311.1,-0.31447,-0.26829,0.91057,-45.418
> ui mousemode right "move picked models"
> view matrix models
> #12,0.94659,-0.016676,0.322,99.005,-0.071205,0.96319,0.25921,261.54,-0.31447,-0.26829,0.91057,-25.076
> select subtract #12
Nothing selected
> select add #15
2 models selected
> view matrix models
> #15,0.18591,-0.97442,0.1263,456.2,0.93853,0.21416,0.27074,78.732,-0.29086,0.0682,0.95433,-35.489
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.1397,-0.95899,0.24663,446.68,0.87937,0.23465,0.4143,67.571,-0.45518,0.159,0.87609,-19.342
> ui mousemode right "move picked models"
> view matrix models
> #15,0.1397,-0.95899,0.24663,380.14,0.87937,0.23465,0.4143,84.864,-0.45518,0.159,0.87609,-5.0209
> select subtract #15
Nothing selected
> select add #16
2 models selected
> view matrix models
> #16,0.75684,-0.12353,-0.64182,371.63,-0.27645,-0.95031,-0.14309,517.96,-0.59226,0.28573,-0.75339,115.59
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.97016,-0.06985,-0.23218,295.61,-0.14137,-0.94094,-0.30763,521.39,-0.19698,0.33128,-0.92274,87.666
> view matrix models
> #16,0.95588,-0.089003,-0.27995,304.72,-0.16303,-0.9535,-0.25351,518.83,-0.24436,0.28796,-0.92594,97.801
> view matrix models
> #16,0.95374,-0.078568,-0.2902,305.01,-0.16825,-0.93942,-0.29863,523.08,-0.24916,0.33364,-0.90918,91.464
> select subtract #16
Nothing selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!12 models
> hide #!15 models
> hide #!16 models
> ui mousemode right "move picked models"
> view #2 clip false
No displayed objects specified.
> select add #1
2 models selected
> view #2 clip false
No displayed objects specified.
> view #1 clip false
> select subtract #1
Nothing selected
> volume #1 level 0.08482
> volume #1 level 0.07718
> show #!2 models
> select add #2
16470 atoms, 16740 bonds, 6 pseudobonds, 1008 residues, 2 models selected
> hide #!1 models
> show #!1 models
> view matrix models
> #2,0.99706,-0.0055579,0.076461,43.4,0.00071027,0.998,0.063281,133.14,-0.07666,-0.06304,0.99506,-42.485
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.9773,-0.04743,0.2065,33.392,-0.0078424,0.96586,0.25896,109.82,-0.21173,-0.2547,0.94356,17.186
> view matrix models
> #2,0.97873,-0.04646,0.19984,34.024,-0.0063833,0.96666,0.25599,109.91,-0.20507,-0.25182,0.9458,15.334
> view matrix models
> #2,0.93521,-0.054235,0.34992,19.302,-0.027504,0.97409,0.22448,116.87,-0.35303,-0.21956,0.90948,39.132
> ui mousemode right "move picked models"
> view matrix models
> #1,0.046692,0.28593,-0.95711,310.46,0.40412,0.87084,0.27987,46.331,0.91351,-0.39985,-0.07489,3.8185
> view matrix models
> #2,0.20307,0.20581,-0.95729,296.89,0.45813,0.84408,0.27865,46.929,0.86538,-0.49515,0.077114,17.619
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.90772,0.36596,-0.20523,332.64,0.41612,0.84787,-0.32858,145.39,0.053762,-0.38366,-0.92191,280.3
> view matrix models
> #2,-0.90497,0.37688,-0.19744,329.28,0.42113,0.85955,-0.28952,136.79,0.060594,-0.34516,-0.93659,275.33
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470
atoms
average map value = 0.0483, steps = 60
shifted from previous position = 1.36
rotated from previous position = 3.57 degrees
atoms outside contour = 12449, contour level = 0.077178
Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates:
Matrix rotation and translation
0.99747380 -0.07098521 -0.00266685 12.07098320
0.07098654 0.99747719 0.00040881 -10.84033065
0.00263110 -0.00059709 0.99999636 -10.96426753
Axis -0.00708009 -0.03729010 0.99927940
Axis point 164.09589031 163.14848416 0.00000000
Rotation angle (degrees) 4.07355508
Shift along axis -10.63759339
> fitmap #2 inMap #1
Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470
atoms
average map value = 0.0483, steps = 64
shifted from previous position = 0.00134
rotated from previous position = 0.00645 degrees
atoms outside contour = 12446, contour level = 0.077178
Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates:
Matrix rotation and translation
0.99746582 -0.07109717 -0.00266791 12.09011924
0.07109848 0.99746922 0.00040101 -10.85542717
0.00263265 -0.00058968 0.99999636 -10.96436038
Axis -0.00696204 -0.03724973 0.99928174
Axis point 164.06189377 163.16131742 0.00000000
Rotation angle (degrees) 4.07998058
Shift along axis -10.63629515
> show #!3 models
> hide #!3 models
> view matrix models
> #2,0.58214,0.75996,0.28909,-41.72,-0.81284,0.53523,0.22983,305.43,0.019929,-0.36878,0.9293,2.0517
> fitmap #2 inMap #1
Fit molecule cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) to map
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) using 16470
atoms
average map value = 0.05138, steps = 104
shifted from previous position = 10.7
rotated from previous position = 9.49 degrees
atoms outside contour = 12134, contour level = 0.077178
Position of cx45_hexamer_startingmodel_isolderelaxed.pdb (#2) relative to
cryosparc_P2_J217_005_volume_map_sharp.mrc x flip gaussian (#1) coordinates:
Matrix rotation and translation
0.99743047 0.07164049 -0.00029854 -10.94311791
-0.07164063 0.99743038 -0.00049075 11.77748300
0.00026261 0.00051087 0.99999983 10.32977683
Axis 0.00699041 -0.00391627 -0.99996790
Axis point 158.17955418 157.40401107 0.00000000
Rotation angle (degrees) 4.10835301
Shift along axis -10.45206592
> select subtract #2
Nothing selected
> hide #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> volume #3 level 0.1252
> volume #1 level 0.08129
> select add #1
2 models selected
> select subtract #1
Nothing selected
> save /Users/sahtelis/Downloads/cx45_NTD_pore.png width 954 height 637
> supersample 3 transparentBackground true
> hide #!3 models
> hide #!1 models
> show #!12 models
> view #12 clip false
> save /Users/sahtelis/Downloads/cx43_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> hide #!12 models
> show #!13 models
> close #13
> show #!15 models
> view #15 clip false
> save /Users/sahtelis/Downloads/cx46_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> show #!16 models
> hide #!15 models
> view #16 clip false
> color #16 #b9f2a7ff models
> lighting full
> surface dust #16 size 6.73
> volume #16 level 0.008334
> volume #16 level 0.006191
> volume #16 level 0.00762
> volume #16 level 0.008334
> save /Users/sahtelis/Downloads/cx31.3_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> show #!15 models
> hide #!16 models
> view #15 clip false
> save /Users/sahtelis/Downloads/cx46_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> lighting full
> hide #!15 models
> show #!12 models
> view #12 clip false
> save /Users/sahtelis/Downloads/cx43_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> hide #!12 models
> show #!1 models
> view #1 clip false
> volume #1 level 0.0828
> save /Users/sahtelis/Downloads/cx45_NTD_pore.png width 867 height 637
> supersample 3 transparentBackground true
> hide #!1 models
> show #!16 models
> view #16 clip false
> ui mousemode right "tape measure"
> marker segment #4 position 366.2,377.7,25.6 toPosition 381.1,376.4,21.94
> color yellow radius 0.1682 label 15.35 labelHeight 1.535 labelColor yellow
> hide #!16 models
> show #!15 models
> close #4
> show #!12 models
> show #!16 models
> show #!3 models
> hide #!3 models
> show #!1 models
> view clip false
> ui mousemode right "tape measure"
> ui mousemode right "rotate slab"
> ui mousemode right "tape measure"
> marker segment #4 position 370,370.3,31.76 toPosition 376.6,383.8,20.46
> color yellow radius 0.1682 label 18.79 labelHeight 1.879 labelColor yellow
> marker segment #4 position 334.4,261.2,99.77 toPosition 322.8,275.2,94.87
> color yellow radius 0.1663 label 18.81 labelHeight 1.881 labelColor yellow
> marker segment #4 position 199.4,288.3,83.42 toPosition 217.6,294.5,73.04
> color yellow radius 0.207 label 21.78 labelHeight 2.178 labelColor yellow
> marker segment #4 position 254.2,422,41.15 toPosition 265.7,422.3,31.3 color
> yellow radius 0.1635 label 15.16 labelHeight 1.516 labelColor yellow
> close #4
> show #!2 models
> hide #!12 models
> hide #!15 models
> hide #!16 models
> view clip false
> show #!3 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> view #3 clip false
> show #!1 models
> view #3 clip false
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,12
Model Number: MC8G4KS/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 4 days, 11 hours, 35 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 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 , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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