![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 10 months ago
Closed 10 months ago
#16542 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-14.4.1-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 0x00000001f540fac0 (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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, 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, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, PIL._webp, psutil._psutil_osx, psutil._psutil_posix (total: 124)
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{
"uptime" : 71000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,9",
"coalitionID" : 2735,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-12-30 17:37:13.2966 -0800",
"codeSigningMonitor" : 1,
"incident" : "56F0AC51-8F78-4063-9EA9-F2D1E6959A2E",
"pid" : 90614,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-30 15:56:08.2614 -0800",
"procStartAbsTime" : 1563443327568,
"procExitAbsTime" : 1709001829284,
"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":"AAF5F10B-ACEB-5840-A970-8CE5D4DE2A10","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4050AB06-83DF-3B8B-48D6-B07A49291BA3",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 6563,
"sleepWakeUUID" : "3A8CDE3C-9D8E-401B-8861-89CB8683291F",
"sip" : "enabled",
"vmRegionInfo" : "0x466479941348 is not in any region. Bytes after previous region: 76916314084169 Bytes before following region: 28155765845176\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 ",
"exception" : {"codes":"0x0000000000000001, 0x0000c66479941348","rawCodes":[1,218134838776648],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000c66479941348 -> 0x0000466479941348 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":90614},
"vmregioninfo" : "0x466479941348 is not in any region. Bytes after previous region: 76916314084169 Bytes before following region: 28155765845176\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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"faultingThread" : 0,
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Address size fault"},"pc":{"value":6667885856},"far":{"value":0}}},{"id":1262310,"frames":[{"imageOffset":7456,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":232}],"threadState":{"x":[{"value":13253341184},{"value":150423},{"value":13252804608},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13253341184},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6667885856},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6663421952,
"size" : 4189880320,
"uuid" : "a53b7d2f-a773-3524-8828-248b33ef0b4e"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=19.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=19.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 704K 40 \nColorSync 656K 31 \nCoreAnimation 2096K 129 \nCoreGraphics 48K 3 \nCoreUI image data 5184K 43 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 18.2G 297 \nMALLOC guard page 384K 24 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 1072K 67 \nStack 170.8M 68 \nStack Guard 56.0M 1 \nVM_ALLOCATE 557.2M 349 \nVM_ALLOCATE (reserved) 832.0M 8 reserved VM address space (unallocated)\n__AUTH 2679K 439 \n__AUTH_CONST 32.9M 661 \n__CTF 824 1 \n__DATA 26.0M 891 \n__DATA_CONST 45.2M 892 \n__DATA_DIRTY 2050K 240 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 562.5M 232 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2195K 1 \n__TEXT 1.0G 909 \ndyld private memory 592K 7 \nmapped file 238.8M 61 \nshared memory 3760K 30 \n=========== ======= ======= \nTOTAL 21.7G 5442 \nTOTAL, minus reserved VM space 20.9G 5442 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "3e007e65458b363b257d358c43eb0e3be033561d",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
},
{
"rolloutId" : "648a2601f74c42732876cb5b",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "66b55f4e9142fa69576cb851"
},
"deploymentId" : 240000272
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],
"experiments" : [
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== 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/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs"
Log from Sat Dec 21 19:42:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 1/Chimera Session V2/HSa.cxs"
Log from Sat Dec 21 18:53:40 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_HSA.cxs"
Log from Fri Dec 20 14:57:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs" format
> session
Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.0026, step 1, values float32
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32
Opened 041924-global-resampleonapo.mrc as #11, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32
Opened 041924-global-resampleonapo.mrc 0 as #12.1, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 1 as #12.2, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 2 as #12.3, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 3 as #12.4, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 4 as #12.5, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 5 as #12.6, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 6 as #12.7, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 7 as #12.8, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 8 as #12.9, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 9 as #12.10, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Opened 041924-global-resampleonapo.mrc 10 as #12.11, grid size 480,480,480,
pixel 0.835, shown at level 0.105, step 1, values float32
Log from Thu Dec 12 17:07:10 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 1/Version 2-resubmission/Chimera Session/Figure1_noRvbs'.cxs" format
> session
Opened 121124-a8-split_xl080.mrc as #1, grid size 480,480,480, pixel 0.835,
shown at level 0.00375, step 1, values float32
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 0.348, step 1, values float32
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.238, step 1, values float32
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.235, step 1, values float32
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.174, step 1, values float32
Opened 041924-nuc-resampleonapo_xl080.mrc as #6, grid size 480,480,480, pixel
0.835, shown at level 1.44, step 1, values float32
Opened 121124-a8-split_Xl040.mrc as #4, grid size 448,448,448, pixel 0.831,
shown at level 0.0026, step 1, values float32
Opened onlyies2-lowres-Xl040.mrc as #7, grid size 448,448,448, pixel 0.831,
shown at level 0.0519, step 1, values float32
Opened onlynuc_Xl040.mrc as #8, grid size 448,448,448, pixel 0.831, shown at
level 0.411, step 1, values float32
Opened inocore_Xl040.mrc as #9, grid size 448,448,448, pixel 0.831, shown at
level 0.218, step 1, values float32
Log from Thu Dec 12 15:35:36 2024 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/121124-a8-split.mrc"
Opened 121124-a8-split.mrc as #1, grid size 512,512,512, pixel 0.819, shown at
level 0.000444, step 2, values float32
> set bgColor white
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-inocore-nuc-3.16A.mrc"
Opened 120524-inocore-nuc-3.16A.mrc as #2, grid size 512,512,512, pixel 0.819,
shown at level 0.0802, step 2, values float32
> volume #1 step 1
> volume #2 step 1
> volume #1 level 0.001846
> surface dust #1 size 8.19
> surface dust #2 size 8.19
> volume #2 level 0.1187
> volume #1 level 0.002828
> volume #2 level 0.1524
> volume #2 level 0.1596
> volume #2 level 0.1741
> color #2 silver models
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Yeast-Apo/120524-final-ino80-0y80-apo-512box.pdb"
Chain information for 120524-final-ino80-0y80-apo-512box.pdb #3
---
Chain | Description
A E | No description available
B F | No description available
C | No description available
D H | No description available
G | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
O | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> volume #1 level 0.003126
> hide #!1 models
> hide #!2 models
> hide atoms
> show cartoons
> select #3/A-H,T-Y
26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light gray
> select #3/I,J
7702 atoms, 8638 bonds, 1 pseudobond, 376 residues, 2 models selected
> color sel slate gray
> show sel atoms
> hide sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 7702 atom styles
> nucleotides sel ladder
> show sel atoms
> select #3/Q
6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected
> color sel fire brick
> select #3/Z
464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected
> color sel fire brick
> color sel orange
> select #3/R,S
4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected
> color sel medium sea green
> select #3/K
5092 atoms, 5206 bonds, 628 residues, 1 model selected
> color sel medium blue
> select #3/L
2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected
> color sel gold
> select #3/M
3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected
> color sel deep sky blue
> select #3/N
Nothing selected
> color dim gray
> undo
> select #3/O
287 atoms, 296 bonds, 34 residues, 1 model selected
> color sel dim gray
> select clear
> show #!2 models
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #3 distance 4.91
> color zone #1 near #3 distance 4.81
> color zone #1 near #3 distance 4.71
> color zone #1 near #3 distance 4.61
> color zone #1 near #3 distance 4.51
> color zone #1 near #3 distance 4.41
> color zone #1 near #3 distance 4.31
> color zone #1 near #3 distance 4.21
> color zone #1 near #3 distance 4.11
> color zone #1 near #3 distance 4.01
> color zone #1 near #3 distance 3.91
> color zone #1 near #3 distance 3.81
> color zone #1 near #3 distance 3.71
> color zone #1 near #3 distance 3.61
> color zone #1 near #3 distance 3.51
> color zone #1 near #3 distance 3.41
> color zone #1 near #3 distance 3.83
> color zone #1 near #3 distance 9.39
> color zone #1 near #3 distance 1
> color zone #1 near #3 distance 10
[Repeated 1 time(s)]
> volume #1 level 0.00344
> color zone #2 near #3 distance 4.91
> volume #1 level 0.003283
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Side View"
> hide #!3 models
> color #1 #b2b2b224 models
> color #1 #b2b2b297 models
> color #1 #b2b2b296 models
> undo
[Repeated 4 time(s)]
> color zone #1 near #3 distance 10
> volume #2 level 0.1046
> volume #2 level 0.1313
> volume #2 level 0.1607
> volume #2 level 0.118
> volume #2 level 0.1287
> volume #2 level 0.15
> volume #2 level 0.1634
No map chosen to save
> save /Users/upneet/Desktop/test.png width 3600 height 2697 supersample 3
> transparentBackground true
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc"
Opened 121124-a8-split.mrc as #4, grid size 480,480,480, pixel 0.835, shown at
level 0.000837, step 2, values float32
> volume #4 level 0.003553
> volume #4 step 1
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> volume #4 level 0.003726
> volume #4 level 0.003661
> color #4 silver models
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40yeastnuc-ADPBeF/121124-a8-split.mrc"
Opened 121124-a8-split.mrc as #5, grid size 480,480,480, pixel 0.835, shown at
level 4.83e-07, step 2, values float32
> volume #5 level 0.003775
> volume #5 level 0.003851
> hide #!4 models
> hide #!5 models
> show #!3 models
> select ::name="ARG"
3893 atoms, 3559 bonds, 362 residues, 1 model selected
> ui mousemode right select
> select clear
Drag select of 1 residues
> show sel surfaces
> hide sel surfaces
> style sel stick
Changed 11 atom styles
> show sel atoms
> color sel byhetero
> hide #!3 models
> show #!1 models
> show #!2 models
> close #1-5
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-a8-split.mrc"
Opened 121124-a8-split.mrc as #1, grid size 480,480,480, pixel 0.835, shown at
level 4.88e-06, step 2, values float32
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/121124-0n80-xe-wt-adpbef-final-coot-0-pymol-
> shortdna.pdb"
Chain information for 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb
#2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
O | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> hide atoms
> show cartoons
> volume #1 step 1
> volume #1 level 0.004082
> hide #!2 models
> show #!2 models
> hide #!1 models
> color #2/Q firebrick
> color #2/Q firebrick, #2/R,S seagreen
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/Q firebrick
> color #2/R,S medium seagreen
> color #2/T-Y, A-H grey
> color #2/T-Y, A-H lightr grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/T-Y, A-H light grey
> color #2/Z orange
> color #2/k medium blue
> color #2/L gold
> color #2/N deep skyblue
> color #2/M deep skyblue
[Repeated 1 time(s)]
> color #2/O grey
> color #2/I,J slate blue
> color #2/I,J slate grey
> select #2/I,J
7787 atoms, 8735 bonds, 380 residues, 1 model selected
> nucleotides sel ladder
> show sel atoms
> select clear
[Repeated 2 time(s)]
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 5.01
> color zone #1 near #2 distance 5.19
> color zone #1 near #2 distance 11.56
> color zone #1 near #2 distance 11.7
[Repeated 1 time(s)]
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 10
[Repeated 1 time(s)]
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 15
[Repeated 1 time(s)]
> volume #1 level 0.004276
> volume #1 level 0.004216
> volume #1 level 0.003992
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/ies2-x80-lowres.mrc"
Opened ies2-x80-lowres.mrc as #3, grid size 480,480,480, pixel 0.835, shown at
level 5.64e-05, step 2, values float32
> volume #3 step 1
> volume #3 level 0.3484
> hide #!3 models
> volume #1 level 0.003664
> surface dust #1 size 8.35
> volume #1 level 0.003843
> volume #1 level 0.003873
> ui tool show "Side View"
> volume #1 level 0.003754
> volume #1 level 0.003664
> surface dust #1 size 8.35
> volume #1 level 0.003754
> select #2/L
2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected
> ui tool show "Color Actions"
> color sel sandy brown
> color zone #1 near #2 distance 15
> color sel navajo white
> color zone #1 near #2 distance 15
> hide #!1 models
> show #!1 models
> color sel goldenrod
> color zone #1 near #2 distance 15
> color sel orange
> color zone #1 near #2 distance 15
> color (#!2 & sel) #ffd479ff
> color zone #1 near #2 distance 15
> color (#!2 & sel) #ffd778ff
> color (#!2 & sel) #ffd87aff
> color (#!2 & sel) #ffdb82ff
> color (#!2 & sel) #ffdc89ff
> color (#!2 & sel) #ffe296ff
> color (#!2 & sel) #ffe396ff
> color (#!2 & sel) #ffea91ff
> color (#!2 & sel) #ffe482ff
> color (#!2 & sel) #ffe077ff
> color (#!2 & sel) #ffe370ff
> color (#!2 & sel) #ffea6cff
> color (#!2 & sel) #fff26aff
> color (#!2 & sel) #fff36aff
> color (#!2 & sel) #fff36dff
> color (#!2 & sel) #fff475ff
> color zone #1 near #2 distance 15
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2/O
347 atoms, 356 bonds, 40 residues, 1 model selected
> color sel #011993ff
> color zone #1 near #2 distance 15
> color sel #9437ffff
> color zone #1 near #2 distance 15
> color sel #76d6ffff
> color zone #1 near #2 distance 15
> color sel #79b8ffff
> color zone #1 near #2 distance 15
> color sel #00fdffff
> color sel #73fdffff
> color zone #1 near #2 distance 15
> color sel #ffd479ff
> color zone #1 near #2 distance 15
> color sel #011993ff
> color sel #005493ff
> color zone #1 near #2 distance 15
> select clear
> select #2/Z
467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected
> color (#!2 & sel) #ff2600ff
> color (#!2 & sel) #ff7e79ff
> select clear
> select #2/M
3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected
> select #2/L
2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected
> select #2/L
2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected
> select #2/K
5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color zone #1 near #2 distance 15
> color sel royal blue
> color zone #1 near #2 distance 15
> select #2/M
3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light pink
> color zone #1 near #2 distance 15
> color sel plum
> color zone #1 near #2 distance 15
> color sel pink
> color zone #1 near #2 distance 15
> color sel light pink
> color zone #1 near #2 distance 15
> hide #!1 models
> cartoon style (#!2 & sel) modeHelix tube sides 20
> cartoon style modeHelix tube radius 1.5
> select clear
> show #!1 models
> select #2/L
2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected
> select #2/K
5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel blue
> color zone #1 near #2 distance 15
> color sel medium blue
> color zone #1 near #2 distance 15
> select #2/M
3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected
> ui tool show "Color Actions"
> color sel deep sky blue
> color zone #1 near #2 distance 15
> select clear
> hide #!1 models
> show #!1 models
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-global-resampleonapo.mrc"
Opened 041924-global-resampleonapo.mrc as #4, grid size 480,480,480, pixel
0.835, shown at level 0.105, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1559
> volume #4 level 0.2387
> volume #4 level 0.3295
> volume #4 level 0.2569
> volume #4 level 0.2205
> color zone #4 near #2 distance 5.01
> hide #!2 models
> lighting soft
> lighting simple
> lighting soft
> volume splitbyzone #4
Opened 041924-global-resampleonapo.mrc 0 as #5.1, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 1 as #5.2, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 2 as #5.3, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 3 as #5.4, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 4 as #5.5, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 5 as #5.6, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 6 as #5.7, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 7 as #5.8, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 8 as #5.9, grid size 480,480,480, pixel
0.835, shown at level 0.221, step 1, values float32
Opened 041924-global-resampleonapo.mrc 9 as #5.10, grid size 480,480,480,
pixel 0.835, shown at level 0.221, step 1, values float32
> hide #!5 models
> show #!5 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.3 models
> hide #5.2.1 models
> show #5.2.1 models
> volume #5.2 level 0.2383
> volume #5.8 level 0.2205
> volume #5.9 level 0.2241
> volume #5.10 level 0.164
> volume #5.10 level 0.174
> surface dust #1 size 8.35
> surface dust #5.1 size 8.35
> surface dust #5.2 size 8.35
> surface dust #5.4 size 8.35
> surface dust #5.5 size 8.35
> surface dust #5.6 size 8.35
> surface dust #5.7 size 8.35
> surface dust #5.8 size 8.35
> surface dust #5.9 size 8.35
> surface dust #5.10 size 8.35
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/WT-0N80Xe-ADPBeF/041924-nuc-resampleonapo.mrc"
Opened 041924-nuc-resampleonapo.mrc as #6, grid size 480,480,480, pixel 0.835,
shown at level 0.188, step 2, values float32
> color zone #6 near #2 distance 5.01
> surface dust #1 size 8.35
> surface dust #5.1 size 8.35
> surface dust #5.2 size 8.35
> surface dust #5.4 size 8.35
> surface dust #5.5 size 8.35
> surface dust #5.6 size 8.35
> surface dust #5.7 size 8.35
> surface dust #5.8 size 8.35
> surface dust #5.9 size 8.35
> surface dust #5.10 size 8.35
> surface dust #6 size 8.35
> volume #6 step 1
> volume #6 level 0.7474
> volume #6 level 0.9057
> color zone #6 near #2 distance 5.01
[Repeated 1 time(s)]
> volume #6 level 1.127
> volume #6 level 1.233
> color zone #6 near #2 distance 5.11
> color zone #6 near #2 distance 5.21
> color zone #6 near #2 distance 5.31
> color zone #6 near #2 distance 5.41
> color zone #6 near #2 distance 5.51
> color zone #6 near #2 distance 5.61
> color zone #6 near #2 distance 5.71
> color zone #6 near #2 distance 5.81
> color zone #6 near #2 distance 5.91
> color zone #6 near #2 distance 6.01
> color zone #6 near #2 distance 6.11
> color zone #6 near #2 distance 6.21
> volume #6 level 1.444
> volume #5.9 level 0.2348
> show #!3 models
> color zone #3 near #2 distance 5.01
> select clear
> save /Users/upneet/Desktop/test.png width 3600 height 2671 supersample 3
> transparentBackground true
> close #4
> rename #5 "041924-global-resampleonapo_xl080.mrc split"
> rename #6 041924-nuc-resampleonapo_xl080.mrc
> rename #1 121124-a8-split_xl080.mrc
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/INO-40Xenuc-ADPBe/121124-a8-split.mrc"
Opened 121124-a8-split.mrc as #4, grid size 448,448,448, pixel 0.831, shown at
level 0.0002, step 2, values float32
[deleted to fit within ticket limits]
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-histone-resample.mrc"
Opened 122324-x80-apo-histone-resample.mrc as #17, grid size 480,480,480,
pixel 0.835, shown at level 0.000232, step 2, values float32
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-i2highres-resample.mrc"
Opened 122324-x80-apo-i2highres-resample.mrc as #18, grid size 480,480,480,
pixel 0.835, shown at level 3.03e-06, step 2, values float32
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-resample.pdb"
Chain information for 122324-x80-apo-resample.pdb #19
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
O | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
f | No description available
h | No description available
k | No description available
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-apo-rvb-resample.mrc"
Opened 122324-x80-apo-rvb-resample.mrc as #20, grid size 480,480,480, pixel
0.835, shown at level 7.73e-05, step 2, values float32
> open "/Users/upneet/Library/CloudStorage/Box-Box/INO-yeastNCP/Map and
> Model/wtINO80-0N80-Xe-Apo/122324-x80-ies2lowres-resample.mrc"
Opened 122324-x80-ies2lowres-resample.mrc as #21, grid size 480,480,480, pixel
0.835, shown at level 2.62e-07, step 2, values float32
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!4 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!8 models
> hide #!9 atoms
> show #!9 atoms
> hide #!9 atoms
> show #!9 cartoons
> show #!2 models
> ui tool show Matchmaker
> matchmaker #9/A to #2/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb, chain A
(#2) with 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb, chain A (#9), sequence
alignment score = 421.7
RMSD between 90 pruned atom pairs is 0.778 angstroms; (across all 94 pairs:
1.004)
> ui tool show "Fit in Map"
> hide #!10 models
> hide #!2 models
> hide #!9 models
> show #!2 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #11
3 models selected
> view matrix models
> #11,0.46801,-0.5411,-0.6987,391.67,0.76816,0.63998,0.018915,-119.95,0.43692,-0.54557,0.71516,64.823
> view matrix models
> #11,-0.46811,-0.17111,-0.86695,584.39,0.81301,0.30101,-0.4984,53.015,0.34624,-0.93814,-0.0017941,326.48
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.46811,-0.17111,-0.86695,548.45,0.81301,0.30101,-0.4984,96.499,0.34624,-0.93814,-0.0017941,342.22
> hide #!2 models
> show #!9 models
> view matrix models
> #11,-0.46811,-0.17111,-0.86695,569.09,0.81301,0.30101,-0.4984,71.249,0.34624,-0.93814,-0.0017941,328.15
> fitmap #2 inMap #11
Fit molecule 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb (#2) to
map 120524-inocore-nuc-3.16A.mrc (#11) using 58339 atoms
average map value = 0.04758, steps = 196
shifted from previous position = 14.4
rotated from previous position = 7.46 degrees
atoms outside contour = 42985, contour level = 0.080218
Position of 121124-0n80-xe-wt-adpbef-final-coot-0-pymol-shortdna.pdb (#2)
relative to 120524-inocore-nuc-3.16A.mrc (#11) coordinates:
Matrix rotation and translation
-0.45865907 0.76124611 0.45840617 66.04130277
-0.26224952 0.37693123 -0.88834004 373.23224661
-0.84903300 -0.52766202 0.02675350 515.57895222
Axis 0.21227268 0.76947747 -0.60236595
Axis point 165.83506426 0.00000000 379.29198569
Rotation angle (degrees) 121.83582990
Shift along axis -9.35463366
> fitmap #9 inMap #11
Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms
average map value = 0.2017, steps = 1708
shifted from previous position = 35.3
rotated from previous position = 75 degrees
atoms outside contour = 17523, contour level = 0.080218
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:
Matrix rotation and translation
1.00000000 -0.00006074 0.00005427 0.01055650
0.00006074 1.00000000 0.00000568 -0.02064744
-0.00005427 -0.00000568 1.00000000 0.01686760
Axis -0.06958774 0.66463915 0.74391689
Axis point 319.03804700 171.59046789 0.00000000
Rotation angle (degrees) 0.00467819
Shift along axis -0.00190961
> ui tool show "Side View"
> show #!5 models
> select subtract #11
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!7 models
> hide #!9 models
> hide #!11 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> surface dust #7 size 8.35
> surface dust #11 size 8.19
> select add #11
2 models selected
> view matrix models
> #11,-0.46811,-0.17111,-0.86695,549.14,0.81301,0.30101,-0.4984,69.47,0.34624,-0.93814,-0.0017941,317.54
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.8341,0.48974,-0.25383,367.01,0.26446,-0.048787,-0.96316,370.59,-0.48408,-0.8705,-0.088827,517.57
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.8341,0.48974,-0.25383,360.21,0.26446,-0.048787,-0.96316,375.41,-0.48408,-0.8705,-0.088827,530.18
> view matrix models
> #11,-0.8341,0.48974,-0.25383,358.84,0.26446,-0.048787,-0.96316,383.34,-0.48408,-0.8705,-0.088827,519.86
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.82246,0.54164,-0.17371,327.61,0.20486,-0.0028233,-0.97879,392.41,-0.53064,-0.8406,-0.10864,529.86
> view matrix models
> #11,-0.69285,0.68006,0.23976,174.05,-0.18361,0.15515,-0.97068,451.29,-0.69732,-0.71655,0.01737,515.69
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.69285,0.68006,0.23976,166.8,-0.18361,0.15515,-0.97068,441.71,-0.69732,-0.71655,0.01737,521.17
> view matrix models
> #11,-0.69285,0.68006,0.23976,174.07,-0.18361,0.15515,-0.97068,439.89,-0.69732,-0.71655,0.01737,504.12
> view matrix models
> #11,-0.69285,0.68006,0.23976,169.03,-0.18361,0.15515,-0.97068,443.43,-0.69732,-0.71655,0.01737,503.91
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.72409,0.58246,0.36937,163.26,-0.37781,0.11308,-0.91895,483.65,-0.57702,-0.80496,0.13818,463.57
> view matrix models
> #11,-0.90807,0.26406,0.32508,274.47,-0.3083,0.10391,-0.9456,475.62,-0.28348,-0.95889,-0.012948,459.88
> view matrix models
> #11,-0.93735,0.33746,0.086626,324.52,-0.03972,0.14351,-0.98885,416.66,-0.34613,-0.93034,-0.12112,494.85
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.93735,0.33746,0.086626,330.67,-0.03972,0.14351,-0.98885,410.13,-0.34613,-0.93034,-0.12112,506.84
> ui tool show "Fit in Map"
> fitmap #11 inMap #5.8
Fit map 120524-inocore-nuc-3.16A.mrc in map 041924-global-resampleonapo.mrc 7
using 167598 points
correlation = 0.2717, correlation about mean = 0.05944, overlap = 682.8
steps = 236, shift = 3.15, angle = 11.2 degrees
Position of 120524-inocore-nuc-3.16A.mrc (#11) relative to 041924-global-
resampleonapo.mrc 7 (#5.8) coordinates:
Matrix rotation and translation
-0.88632457 0.45950295 -0.05732199 331.62490500
0.11024555 0.08916261 -0.98989694 386.02823887
-0.44974958 -0.88368947 -0.12968517 520.47184865
Axis 0.19816062 0.73218669 -0.65164025
Axis point 162.64429754 0.00000000 401.27755246
Rotation angle (degrees) 164.45570404
Shift along axis 9.19933237
> show #!10 models
> hide #!10 models
> show #!9 models
> fitmap #9 inMap #11
Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms
average map value = 0.06358, steps = 524
shifted from previous position = 21.4
rotated from previous position = 23.6 degrees
atoms outside contour = 39139, contour level = 0.080218
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:
Matrix rotation and translation
0.60709616 0.65538577 0.44933700 -150.63587196
-0.57100015 0.75305562 -0.32690373 245.95812177
-0.55262381 -0.05810950 0.83140255 171.50849007
Axis 0.16733755 0.62376959 -0.76348520
Axis point 265.73463114 388.45394890 0.00000000
Rotation angle (degrees) 53.43194556
Shift along axis -2.73003438
> show #!10 models
> select subtract #11
Nothing selected
> select add #10
3 models selected
> view matrix models #10,1,0,0,-42.69,0,1,0,28.059,0,0,1,10.168
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.62,0.55054,-0.55902,487.63,0.71305,0.69264,-0.10869,-115.76,0.32736,-0.466,-0.822,391.76
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.62,0.55054,-0.55902,412.65,0.71305,0.69264,-0.10869,-19.792,0.32736,-0.466,-0.822,461.07
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.80313,0.46625,-0.37093,434.96,0.55878,0.80549,-0.19737,30.687,0.20676,-0.36578,-0.90744,502.6
> view matrix models
> #10,-0.73853,-0.32286,-0.59189,572.19,0.51443,0.2976,-0.80423,250.23,0.43581,-0.89844,-0.053698,312
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.73853,-0.32286,-0.59189,575.43,0.51443,0.2976,-0.80423,233.34,0.43581,-0.89844,-0.053698,323.6
> view matrix models
> #10,-0.73853,-0.32286,-0.59189,576.08,0.51443,0.2976,-0.80423,235.18,0.43581,-0.89844,-0.053698,321.07
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> view matrix models
> #10,-0.73853,-0.32286,-0.59189,525.98,0.51443,0.2976,-0.80423,242.04,0.43581,-0.89844,-0.053698,302.07
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.96781,-0.019089,0.25096,360.53,-0.18592,0.72632,-0.66174,358.14,-0.16964,-0.6871,-0.70648,600.72
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.96781,-0.019089,0.25096,334.89,-0.18592,0.72632,-0.66174,295.54,-0.16964,-0.6871,-0.70648,587.83
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.99457,0.10342,-0.011745,386.22,0.021508,0.093791,-0.99536,395.41,-0.10184,-0.99021,-0.095506,469.24
> view matrix models
> #10,-0.99331,0.099471,-0.058607,397.07,0.057616,-0.012807,-0.99826,399.75,-0.10005,-0.99496,0.0069906,445.98
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.99331,0.099471,-0.058607,405.04,0.057616,-0.012807,-0.99826,411.07,-0.10005,-0.99496,0.0069906,440.48
> fitmap #10 inMap #1
Fit map 121124-a8-split.mrc in map 121124-a8-split_xl080.mrc using 167748
points
correlation = 0.9841, correlation about mean = 0.987, overlap = 2.479
steps = 264, shift = 35.9, angle = 17.3 degrees
Position of 121124-a8-split.mrc (#10) relative to 121124-a8-split_xl080.mrc
(#1) coordinates:
Matrix rotation and translation
-0.93714444 0.33750899 0.08858891 329.85593650
-0.05354817 0.11177048 -0.99229026 416.63699329
-0.34480851 -0.93466307 -0.08667210 498.17344367
Axis 0.09824214 0.73885064 -0.66666949
Axis point 188.32785546 0.00000000 403.66415364
Rotation angle (degrees) 162.94487597
Shift along axis 8.12122851
> show #!9 models
> rename #7 y0_80_ADPBeF_Core.mrc
> rename #8 y0_80_ADPBeF_Core-filter.mrc
> select add #9
57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 4 models selected
> select add #10
57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 5 models selected
> view matrix models
> #9,-0.76878,-0.23152,-0.59613,525.04,0.56306,0.19692,-0.80261,228,0.30321,-0.95269,-0.021028,338.17,#10,-0.93714,0.33751,0.088589,286.57,-0.053548,0.11177,-0.99229,423.06,-0.34481,-0.93466,-0.086672,487.71
> undo
> select subtract #10
57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.94202,0.26393,0.20722,343.39,-0.02008,0.57211,-0.81993,335.43,-0.33496,-0.77656,-0.53363,631.23
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.94202,0.26393,0.20722,313.8,-0.02008,0.57211,-0.81993,324.18,-0.33496,-0.77656,-0.53363,633.54
> show #!2 models
> fitmap #9 inMap #11
Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
120524-inocore-nuc-3.16A.mrc (#11) using 57717 atoms
average map value = 0.2017, steps = 772
shifted from previous position = 72
rotated from previous position = 31.2 degrees
atoms outside contour = 17524, contour level = 0.080218
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
120524-inocore-nuc-3.16A.mrc (#11) coordinates:
Matrix rotation and translation
1.00000000 -0.00006501 0.00004475 0.00518918
0.00006501 1.00000000 0.00002173 -0.01831902
-0.00004475 -0.00002172 1.00000000 0.01687531
Axis -0.26537272 0.54669131 0.79416997
Axis point 298.68209806 88.00700545 0.00000000
Rotation angle (degrees) 0.00469039
Shift along axis 0.00200995
> hide #!1 models
> hide #!2 models
> hide #!7 models
> fitmap #9 inMap #10
Fit molecule 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) to map
121124-a8-split.mrc (#10) using 57717 atoms
average map value = 0.001464, steps = 376
shifted from previous position = 6.79
rotated from previous position = 11.8 degrees
atoms outside contour = 40556, contour level = 0.00044382
Position of 121124-0n80-ye-wt-apo-final-coot-0-pymol.pdb (#9) relative to
121124-a8-split.mrc (#10) coordinates:
Matrix rotation and translation
0.99996889 0.00779041 0.00123500 -0.92235426
-0.00779156 0.99996921 0.00092843 2.92489776
-0.00122773 -0.00093803 0.99999880 0.56357269
Axis -0.11749503 0.15503124 -0.98089767
Axis point 374.74059597 119.75654981 0.00000000
Rotation angle (degrees) 0.45508845
Shift along axis 0.00901544
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
> hide #!9 models
> select subtract #9
Nothing selected
> hide #!10 models
> hide #!11 models
> rename #1 x0_80_ADPBeF_A8-Split.mrc
> rename #2 x0_80_ADPBeF.pdb
> rename #3 x0_80_ADPBeF_Ies21.mrc
> rename #3 x0_80_ADPBeF_Ies2.mrc
> rename #4 y0_80_ADPBeF
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> rename #5 "x0_80_ADPBeF_core.mrc split"
> rename #6 x0_80_ADPBeF_nuc.mrc
> rename #9 y0_80_Apo.pdb
> show #!10 models
> hide #!10 models
> rename #10 x0_80_Apo_A8-split.mrc
> rename #11 x0_80_Apo_core_nuc.mrc
> rename #10 y0_80_Apo_A8-split.mrc
> rename #11 y0_80_Apo_core_nuc.mrc
> show #!4 models
> show #!8 models
> show #!7 models
> hide #!7 models
> rename #4 y0_80_ADPBeF.pdb
> hide #!1 models
> hide #!4 models
> hide #!8 models
> ui favorite true "Model Panel"
> log metadata #4
No models had metadata
> log chains #4
Chain information for y0_80_ADPBeF.pdb #4
---
Chain | Description
C | No description available
D | No description available
E h | No description available
F j | No description available
G | No description available
H | No description available
K | No description available
L | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> hide #!5.2,4-10 target m
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!6 models
> show #!7 models
> show #!4 models
> show #!8 models
> hide #!4 atoms
> show #!4 cartoons
> select #4/A-H,T-Y
24941 atoms, 25248 bonds, 3218 residues, 1 model selected
> color sel light gray
> select #4/Q
5289 atoms, 5407 bonds, 3 pseudobonds, 660 residues, 2 models selected
> ui tool show "Color Actions"
> color sel fire brick
> select #4/R,S
4562 atoms, 4675 bonds, 2 pseudobonds, 567 residues, 2 models selected
> color sel sea green
> select #4/Z
248 atoms, 254 bonds, 28 residues, 1 model selected
> color sel indian red
> hide #!7 models
> hide #!8 models
> select #4/I,J
Nothing selected
> ui tool show "Color Actions"
> color light slate gray
> nucleotides #!4 ladder
> show #!4 atoms
> undo
[Repeated 3 time(s)]
> select #4/I,J
Nothing selected
> ui mousemode right select
Drag select of 2 residues
> select up
2969 atoms, 3334 bonds, 144 residues, 1 model selected
> select up
42356 atoms, 43634 bonds, 4935 residues, 1 model selected
> select down
2969 atoms, 3334 bonds, 144 residues, 1 model selected
> select #4/K,L
5904 atoms, 6622 bonds, 288 residues, 1 model selected
> color sel light slate gray
> nucleotides sel ladder
> show sel atoms
Drag select of 5 residues
> select up
194 atoms, 197 bonds, 22 residues, 1 model selected
> select up
785 atoms, 794 bonds, 95 residues, 1 model selected
> color sel light gray
> select clear
> show #!7 models
> ui tool show "Color Zone"
> color zone #7 near #4 distance 5.01
> hide #!7 models
Drag select of 17 residues
> select up
733 atoms, 737 bonds, 91 residues, 1 model selected
> color sel light gray
> select clear
Drag select of 22 residues
Drag select of 21 residues
> select up
580 atoms, 586 bonds, 68 residues, 1 model selected
> select up
3578 atoms, 3635 bonds, 449 residues, 1 model selected
> select down
580 atoms, 586 bonds, 68 residues, 1 model selected
Drag select of 63 residues
> select up
1514 atoms, 1521 bonds, 196 residues, 1 model selected
> color sel light gray
Drag select of 82 residues
> select up
1870 atoms, 1889 bonds, 232 residues, 1 model selected
> select down
673 atoms, 82 residues, 1 model selected
> color sel light gray
Drag select of 291 residues
> color sel light gray
Drag select of 20 residues
> color sel light gray
> select clear
> show #!7 models
> color zone #7 near #4 distance 5.01
[Repeated 2 time(s)]
> color zone #7 near #4 distance 8
[Repeated 1 time(s)]
> show #!8 models
> hide #!8 models
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
> hide #!4 models
> hide #!7 models
> show #!9 models
> select #9/A-H,T-Y
26415 atoms, 26739 bonds, 2 pseudobonds, 3403 residues, 2 models selected
> color (#!9 & sel) light gray
> select #9/Q
6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected
> ui tool show "Color Actions"
> color sel fire brick
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
——— End of log from Sun Dec 29 17:47:13 2024 ———
opened ChimeraX session
> select #9/I,K
9286 atoms, 9879 bonds, 835 residues, 1 model selected
> select #9/I,J
8481 atoms, 9512 bonds, 414 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light slate gray
> nucleotides sel atoms
> style nucleic & sel stick
Changed 8481 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 8481 atom styles
> nucleotides sel ladder
> show sel atoms
> select #9/K
5092 atoms, 5206 bonds, 628 residues, 1 model selected
> color sel medium blue
> select #9/L
2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected
> color sel khaki
> select #9/M
3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected
> color sel royal blue
> color sel deep sky blue
> select #9/O
287 atoms, 296 bonds, 34 residues, 1 model selected
> color sel dark blue
> select #9/Z
464 atoms, 469 bonds, 1 pseudobond, 72 residues, 2 models selected
> color sel indian red
> select clear
> show #!10 models
> show #!11 models
> volume #10 level 0.00122
> volume #10 step 1
> volume #10 level 0.0006063
> volume #11 level 0.08901
> volume #11 step 1
> volume #11 level 0.1187
> ui tool show "Fit in Map"
> fitmap #9 inMap #11
Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_core_nuc.mrc (#11) using
57717 atoms
average map value = 0.2017, steps = 312
shifted from previous position = 6.79
rotated from previous position = 11.8 degrees
atoms outside contour = 20896, contour level = 0.11874
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_core_nuc.mrc (#11)
coordinates:
Matrix rotation and translation
1.00000000 -0.00003537 -0.00001420 0.01261198
0.00003537 1.00000000 0.00006454 -0.02167371
0.00001419 -0.00006454 1.00000000 0.01098547
Axis -0.86107623 -0.18938758 0.47188990
Axis point 0.00000000 181.69642546 340.45423658
Rotation angle (degrees) 0.00429427
Shift along axis -0.00157121
> fitmap #9 inMap #10
Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_A8-split.mrc (#10) using
57717 atoms
average map value = 0.001464, steps = 340
shifted from previous position = 6.79
rotated from previous position = 11.8 degrees
atoms outside contour = 40619, contour level = 0.00060625
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_A8-split.mrc (#10)
coordinates:
Matrix rotation and translation
0.99996906 0.00776652 0.00124346 -0.90713737
-0.00776759 0.99996946 0.00085491 2.93731787
-0.00123678 -0.00086454 0.99999886 0.55705285
Axis -0.10865733 0.15673404 -0.98164557
Axis point 377.44174395 118.13477585 0.00000000
Rotation angle (degrees) 0.45334497
Shift along axis 0.01211637
> fitmap #9 inMap #11
Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_core_nuc.mrc (#11) using
57717 atoms
average map value = 0.2017, steps = 332
shifted from previous position = 6.78
rotated from previous position = 11.8 degrees
atoms outside contour = 20891, contour level = 0.11874
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_core_nuc.mrc (#11)
coordinates:
Matrix rotation and translation
1.00000000 -0.00003686 0.00002583 0.00303389
0.00003686 1.00000000 0.00002713 -0.01803754
-0.00002583 -0.00002713 1.00000000 0.01936458
Axis -0.51626765 0.49144166 0.70139348
Axis point 531.38843357 126.43530707 0.00000000
Rotation angle (degrees) 0.00301099
Shift along axis 0.00315149
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.90529,0.42058,0.059653,315.92,-0.07551,-0.021135,-0.99692,442,-0.41803,-0.90701,0.050891,484.68
> view matrix models
> #10,-0.92895,0.36988,-0.015398,346.82,-0.038145,-0.137,-0.98984,444.9,-0.36823,-0.91892,0.14138,450.95
> view matrix models
> #10,-0.90265,0.42501,0.067688,312.71,-0.067158,0.01625,-0.99761,434.68,-0.4251,-0.90504,0.013875,494.95
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.90265,0.42501,0.067688,326.32,-0.067158,0.01625,-0.99761,446.02,-0.4251,-0.90504,0.013875,489.37
> view matrix models
> #10,-0.90265,0.42501,0.067688,307.93,-0.067158,0.01625,-0.99761,452.76,-0.4251,-0.90504,0.013875,484.21
> select clear
> select add #10
2 models selected
> select subtract #10
Nothing selected
> ui tool show "Color Zone"
> color zone #10 near #9 distance 4.91
> color zone #10 near #9 distance 1
> color zone #10 near #9 distance 15
> color zone #10 near #9 distance 2
> color zone #10 near #9 distance 20
> color zone #10 near #9 distance 3
> color zone #10 near #9 distance 30
> color zone #11 near #9 distance 4.91
> color zone #11 near #9 distance 7
> color zone #11 near #9 distance 9
> surface dust #10 size 8.19
> surface dust #11 size 8.19
> select #9/R,S
4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected
> color sel medium sea green
> color zone #11 near #9 distance 9
[Repeated 1 time(s)]
> volume #11 level 0.1329
> volume #10 level 0.000744
> volume #10 level 0.0008301
> volume #10 level 0.000899
> volume #11 level 0.1471
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
> hide #!9 models
> hide #!10 models
> hide #!11 models
> select add #19
62823 atoms, 64722 bonds, 17 pseudobonds, 7408 residues, 4 models selected
> select subtract #19
4527 atoms, 4639 bonds, 2 pseudobonds, 570 residues, 2 models selected
> show #!19 models
> show #!18 models
> hide #!18 models
> hide #!19 cartoons
> hide #!19 atoms
> show #!19 cartoons
> select #19/A-H,T-Y
32178 atoms, 32645 bonds, 6 pseudobonds, 4174 residues, 2 models selected
> select #19/A-H,T-Y
32178 atoms, 32645 bonds, 6 pseudobonds, 4174 residues, 2 models selected
> select
216708 atoms, 223413 bonds, 55 pseudobonds, 25307 residues, 61 models selected
> color sel light gray
> select clear
> ui mousemode right select
Drag select of 6 residues
> select up
209 atoms, 208 bonds, 42 residues, 1 model selected
> select up
219 atoms, 218 bonds, 44 residues, 1 model selected
> select up
58296 atoms, 60083 bonds, 6838 residues, 1 model selected
> select up
216708 atoms, 223413 bonds, 25307 residues, 37 models selected
> select down
58296 atoms, 60083 bonds, 6838 residues, 1 model selected
> select down
219 atoms, 218 bonds, 44 residues, 1 model selected
> select #19/F
219 atoms, 218 bonds, 44 residues, 1 model selected
> color sel indian red
Drag select of 5 residues
> select up
412 atoms, 416 bonds, 52 residues, 1 model selected
> select up
957 atoms, 969 bonds, 118 residues, 1 model selected
> select up
58296 atoms, 60083 bonds, 6838 residues, 1 model selected
> select down
957 atoms, 969 bonds, 118 residues, 1 model selected
> color sel fire brick
Drag select of 9 residues
> select up
228 atoms, 231 bonds, 29 residues, 1 model selected
> select up
2056 atoms, 2112 bonds, 247 residues, 1 model selected
> select up
58296 atoms, 60083 bonds, 6838 residues, 1 model selected
> select down
2056 atoms, 2112 bonds, 247 residues, 1 model selected
> select #19/K
2056 atoms, 2112 bonds, 247 residues, 1 model selected
> color sel fire brick
> select #19/Q
3409 atoms, 3474 bonds, 5 pseudobonds, 421 residues, 2 models selected
> color sel fire brick
Drag select of 14 residues
> select up
235 atoms, 234 bonds, 47 residues, 1 model selected
> select up
404 atoms, 403 bonds, 81 residues, 1 model selected
> select up
412 atoms, 410 bonds, 82 residues, 1 model selected
> select up
651 atoms, 649 bonds, 130 residues, 1 model selected
> select up
771 atoms, 768 bonds, 154 residues, 1 model selected
> select up
58296 atoms, 60083 bonds, 6838 residues, 1 model selected
> select down
771 atoms, 768 bonds, 154 residues, 1 model selected
> color sel medium sea green
Drag select of 21 residues
> select up
643 atoms, 663 bonds, 79 residues, 1 model selected
> select up
2626 atoms, 2693 bonds, 327 residues, 1 model selected
> select up
3029 atoms, 3109 bonds, 376 residues, 1 model selected
> select up
4561 atoms, 4674 bonds, 570 residues, 1 model selected
> color sel medium sea green
Drag select of 25 residues
> select up
690 atoms, 696 bonds, 82 residues, 1 model selected
> select up
5060 atoms, 5173 bonds, 626 residues, 1 model selected
> color sel medium blue
Drag select of 7 residues
> select up
195 atoms, 201 bonds, 22 residues, 1 model selected
> select up
2570 atoms, 2628 bonds, 325 residues, 1 model selected
> color sel khaki
Drag select of 13 residues
> select up
381 atoms, 388 bonds, 47 residues, 1 model selected
> select up
2540 atoms, 2602 bonds, 318 residues, 1 model selected
> color sel deep sky blue
Drag select of 8 residues
> select up
235 atoms, 241 bonds, 27 residues, 1 model selected
> select up
1205 atoms, 1228 bonds, 149 residues, 1 model selected
> color sel dark blue
> undo
> select #19/C
347 atoms, 356 bonds, 40 residues, 1 model selected
> color sel dark blue
> select #19/B
3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel deep sky blue
Drag select of 6 residues
> select up
7828 atoms, 8781 bonds, 382 residues, 1 model selected
> color sel light slate gray
> nucleotides sel ladder
> show sel cartoons
> show sel atoms
> select clear
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!16 models
> show #!17 models
> show #!18 models
> show #!20 models
> show #!21 models
> volume #21 step 1
> volume #21 level 0.0003197
> volume #20 step 1
> volume #20 level 0.241
> volume #20 level 0.2214
> volume #18 step 1
> volume #18 level 0.1038
> volume #17 step 1
> volume #17 level 0.4374
> volume #17 level 1.484
> volume #17 level 1.289
> volume #16 step 1
> volume #16 level 0.06124
> volume #16 level 0.1099
> volume #15 step 1
> volume #15 level 0.6283
> volume #15 level 0.8467
> volume #14 step 1
> volume #14 level 0.02117
> volume #13 step 1
> volume #13 level 0.04944
> volume #13 level 0.08318
> volume #12 step 1
> volume #12 level 0.001063
> color zone #12 near #19 distance 5.01
> color zone #12 near #19 distance 5.1
> color zone #12 near #19 distance 40.94
> color zone #12 near #19 distance 2
> color zone #12 near #19 distance 25
> color zone #12 near #19 distance 3
> color zone #12 near #19 distance 30
> volume #12 level 0.001206
> volume #12 level 0.001414
> volume #12 level 0.001297
> volume #12 level 0.001219
> color zone #13 near #19 distance 5.01
> color zone #14 near #19 distance 5.01
> color zone #15 near #19 distance 5.01
> color zone #16 near #19 distance 5.01
> color zone #17 near #19 distance 5.01
> color zone #18 near #19 distance 5.01
> color zone #21 near #19 distance 5.01
> surface dust #12 size 8.35
> surface dust #13 size 8.35
> surface dust #14 size 8.35
> surface dust #15 size 8.35
> surface dust #16 size 8.35
> surface dust #17 size 8.35
> surface dust #18 size 8.35
> surface dust #20 size 8.35
> surface dust #21 size 8.35
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> color zone #1 near #19 distance 5.01
> color zone #1 near #19 distance 2
> color zone #1 near #19 distance 20
> hide #!12 models
> hide #!2 models
> volume #1 level 0.003197
> volume #1 level 0.002949
> volume #1 level 0.002501
> volume #1 level 0.002609
> hide #!21 models
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!13 models
> show #!2 models
> hide #!6 models
> hide #!5 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> select #2/Q
6141 atoms, 6266 bonds, 8 pseudobonds, 758 residues, 2 models selected
> color sel fire brick
> select #2/R,S
5315 atoms, 5425 bonds, 5 pseudobonds, 726 residues, 2 models selected
> color sel medium sea green
> select #2/z
467 atoms, 472 bonds, 1 pseudobond, 72 residues, 2 models selected
> color sel indian red
> select #2/K
5614 atoms, 5735 bonds, 1 pseudobond, 692 residues, 2 models selected
> color sel medium blue
> select #2/l
2862 atoms, 2925 bonds, 1 pseudobond, 364 residues, 2 models selected
> color sel deep sky blue
> color sel khaki
> select #2/m
3430 atoms, 3507 bonds, 1 pseudobond, 429 residues, 2 models selected
> color sel deep sky blue
[Repeated 1 time(s)]
> select #2/o
347 atoms, 356 bonds, 40 residues, 1 model selected
> color sel dark blue
> select #2/i,j
7787 atoms, 8735 bonds, 380 residues, 1 model selected
> color sel light slate gray
> select clear
> show #!1 models
> color zone #1 near #2 distance 20
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule x0_80_ADPBeF.pdb (#2) to map x0_80_ADPBeF_A8-Split.mrc (#1) using
58339 atoms
average map value = 0.001452, steps = 1000
shifted from previous position = 15.1
rotated from previous position = 7.37 degrees
atoms outside contour = 42857, contour level = 0.0026092
Position of x0_80_ADPBeF.pdb (#2) relative to x0_80_ADPBeF_A8-Split.mrc (#1)
coordinates:
Matrix rotation and translation
0.99994014 0.00694600 -0.00845407 0.33822171
-0.00700867 0.99994801 -0.00740623 3.05230247
0.00840219 0.00746504 0.99993684 -1.18934593
Axis 0.56207240 -0.63709731 -0.52742927
Axis point 213.16300362 0.00000000 113.44077700
Rotation angle (degrees) 0.75798549
Shift along axis -1.12721276
> color zone #1 near #2 distance 20
> show #!3 models
> color zone #1 near #2 distance 20
> color zone #3 near #2 distance 5.01
> show #!4 models
> hide #!4 models
> show #!5 models
> select add #5
21 models selected
> select subtract #5
Nothing selected
> color zone #5.1 near #2 distance 5.01
[Repeated 1 time(s)]
> color zone #5.2 near #2 distance 5.01
> color zone #5.3 near #2 distance 5.01
> color zone #5.4 near #2 distance 5.01
> color zone #5.5 near #2 distance 5.01
> color zone #5.6 near #2 distance 5.01
> color zone #5.7 near #2 distance 5.01
> color zone #5.8 near #2 distance 5.01
> color zone #5.9 near #2 distance 5.01
> color zone #5.10 near #2 distance 5.01
> color zone #6 near #2 distance 5.01
> surface dust #1 size 8.35
> surface dust #3 size 8.35
> surface dust #5.1 size 8.35
> surface dust #5.2 size 8.35
> surface dust #5.3 size 8.35
> surface dust #5.4 size 8.35
> surface dust #5.5 size 8.35
> surface dust #5.6 size 8.35
> surface dust #5.7 size 8.35
> surface dust #5.8 size 8.35
> surface dust #5.9 size 8.35
> surface dust #5.10 size 8.35
> surface dust #6 size 8.35
> show #!12 models
> show #!13 models
> show #!14 models
> show #!15 models
> show #!16 models
> show #!18 models
> show #!17 models
> show #!19 models
> show #!20 models
> show #!21 models
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
——— End of log from Mon Dec 30 10:34:25 2024 ———
opened ChimeraX session
Cell requested for row 0 is out of bounds for table with 31 rows! Resizing
table model.
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> show #!4 models
> select #4/Q
5289 atoms, 5407 bonds, 3 pseudobonds, 660 residues, 2 models selected
> show #!9 models
> select #4,9/Q
11430 atoms, 11673 bonds, 11 pseudobonds, 1418 residues, 4 models selected
> ui tool show "Color Actions"
> color sel fire brick
> select #4,9/Z
712 atoms, 723 bonds, 1 pseudobond, 100 residues, 3 models selected
> color sel indian red
> select #4,9/R,S
9089 atoms, 9314 bonds, 4 pseudobonds, 1137 residues, 4 models selected
> color sel medium sea green
> select #4,9/I,J
8481 atoms, 9512 bonds, 414 residues, 1 model selected
> select #9/I,J
8481 atoms, 9512 bonds, 414 residues, 1 model selected
> color sel light slate gray
> ui mousemode right select
Drag select of 5 residues, 14 shapes
> select up
5904 atoms, 6622 bonds, 288 residues, 1 model selected
> color sel light slate gray
> select #9/K
5092 atoms, 5206 bonds, 628 residues, 1 model selected
> color sel medium blue
> select #9/L
2856 atoms, 2919 bonds, 1 pseudobond, 363 residues, 2 models selected
> color sel khaki
> select #9/M
3454 atoms, 3531 bonds, 1 pseudobond, 433 residues, 2 models selected
> color sel royal blue
> color sel deep sky blue
> select #9/O
287 atoms, 296 bonds, 34 residues, 1 model selected
> color sel dark blue
> select clear
> hide #!9 models
> show #!7 models
> ui tool show "Color Zone"
> color zone #7 near #4 distance 5.01
> color zone #7 near #4 distance 9
> color zone #7 near #4 distance 9.1
> color zone #7 near #4 distance 9.2
> color zone #7 near #4 distance 9.3
> color zone #7 near #4 distance 9.4
> color zone #7 near #4 distance 9.5
> color zone #7 near #4 distance 9.6
> color zone #7 near #4 distance 9.7
> color zone #7 near #4 distance 9.8
> color zone #7 near #4 distance 9.9
> color zone #7 near #4 distance 10
> color zone #7 near #4 distance 11
> color zone #7 near #4 distance 12
> color zone #7 near #4 distance 13
> color zone #7 near #4 distance 14
> color zone #7 near #4 distance 15
> color zone #7 near #4 distance 16
> color zone #7 near #4 distance 17
> color zone #7 near #4 distance 18
> color zone #7 near #4 distance 19
> color zone #7 near #4 distance 20
> color zone #7 near #4 distance 21
> color zone #7 near #4 distance 1
> color zone #7 near #4 distance 15
[Repeated 1 time(s)]
> volume #7 step 1
> volume #7 level 0.2222
> volume #7 level 0.2028
> volume #7 level 0.1861
> surface dust #7 size 8.35
> coulombic #!4
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
y0_80_ADPBeF.pdb #4/G ILE 63
y0_80_ADPBeF.pdb #4/G ILE 88
y0_80_ADPBeF.pdb #4/Q LYS 707
y0_80_ADPBeF.pdb #4/Q ARG 802
y0_80_ADPBeF.pdb #4/Q ASN 804
y0_80_ADPBeF.pdb #4/Q VAL 824
y0_80_ADPBeF.pdb #4/Q ARG 863
y0_80_ADPBeF.pdb #4/Q ARG 865
y0_80_ADPBeF.pdb #4/Q ASP 896
y0_80_ADPBeF.pdb #4/Q GLU 897
y0_80_ADPBeF.pdb #4/Q LYS 947
y0_80_ADPBeF.pdb #4/Q ARG 959
y0_80_ADPBeF.pdb #4/Q ARG 1293
y0_80_ADPBeF.pdb #4/Q LYS 1300
y0_80_ADPBeF.pdb #4/Q ASP 1305
y0_80_ADPBeF.pdb #4/Q ARG 1317
y0_80_ADPBeF.pdb #4/Q LYS 1326
y0_80_ADPBeF.pdb #4/Q MET 1327
y0_80_ADPBeF.pdb #4/Q GLN 1403
y0_80_ADPBeF.pdb #4/Q ARG 1407
y0_80_ADPBeF.pdb #4/Q LEU 1423
y0_80_ADPBeF.pdb #4/Q ILE 1428
y0_80_ADPBeF.pdb #4/Q ARG 1431
y0_80_ADPBeF.pdb #4/Q ARG 1433
y0_80_ADPBeF.pdb #4/Q ARG 1435
y0_80_ADPBeF.pdb #4/Q LYS 1437
y0_80_ADPBeF.pdb #4/Q LYS 1439
y0_80_ADPBeF.pdb #4/T LYS 161
y0_80_ADPBeF.pdb #4/T THR 162
y0_80_ADPBeF.pdb #4/T ILE 163
y0_80_ADPBeF.pdb #4/U GLU 137
y0_80_ADPBeF.pdb #4/U GLU 182
y0_80_ADPBeF.pdb #4/W GLU 137
y0_80_ADPBeF.pdb #4/Y GLU 137
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of y0_80_ADPBeF.pdb #/Q PRO 1289 H bonded to atom that should
not have hydrogens (copy of y0_80_ADPBeF.pdb #/Q PRO 1289 C)
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
Cell requested for row 3 is out of bounds for table with 22 rows! Resizing
table model.
> hide #!4 models
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/Sc_0N80_ADP.png" width 3600 height 3121
> supersample 3 transparentBackground true
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> ui tool show "Fit in Map"
> fitmap #9 inMap #10
Fit molecule y0_80_Apo.pdb (#9) to map y0_80_Apo_A8-split.mrc (#10) using
57717 atoms
average map value = 0.001464, steps = 336
shifted from previous position = 10.2
rotated from previous position = 11.2 degrees
atoms outside contour = 40732, contour level = 0.000899
Position of y0_80_Apo.pdb (#9) relative to y0_80_Apo_A8-split.mrc (#10)
coordinates:
Matrix rotation and translation
0.99996930 0.00773960 0.00121901 -0.89960346
-0.00774083 0.99996953 0.00100630 2.88667355
-0.00121118 -0.00101571 0.99999875 0.56591299
Axis -0.12797580 0.15381035 -0.97977782
Axis point 372.35967518 117.63351086 0.00000000
Rotation angle (degrees) 0.45263969
Shift along axis 0.00465875
> fitmap #9 inMap #7
Fit molecule y0_80_Apo.pdb (#9) to map y0_80_ADPBeF_Core.mrc (#7) using 57717
atoms
average map value = 0.2218, steps = 356
shifted from previous position = 14.9
rotated from previous position = 9.23 degrees
atoms outside contour = 28944, contour level = 0.18614
Position of y0_80_Apo.pdb (#9) relative to y0_80_ADPBeF_Core.mrc (#7)
coordinates:
Matrix rotation and translation
-0.94309943 0.33155029 0.02525599 343.62268043
0.01465608 0.11733048 -0.99298477 400.56032429
-0.33218769 -0.93611322 -0.11551354 502.14203310
Axis 0.11822041 0.74302773 -0.65873647
Axis point 181.59334510 0.00000000 400.47979006
Rotation angle (degrees) 166.08206693
Shift along axis 7.47137295
> select add #10
2 models selected
Drag select of 31 residues, 6 shapes, 10 y0_80_Apo_A8-split.mrc
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.9431,0.33155,0.025256,343.47,0.014656,0.11733,-0.99298,395.9,-0.33219,-0.93611,-0.11551,507.18,#10,-0.90265,0.42501,0.067688,307.78,-0.067158,0.01625,-0.99761,448.1,-0.4251,-0.90504,0.013875,489.25
> undo
> select add #9
57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 4 models selected
> select subtract #9
2 models selected
> view matrix models
> #10,-0.90265,0.42501,0.067688,305.68,-0.067158,0.01625,-0.99761,444.26,-0.4251,-0.90504,0.013875,492.99
> view matrix models
> #10,-0.90265,0.42501,0.067688,305.86,-0.067158,0.01625,-0.99761,442.74,-0.4251,-0.90504,0.013875,492.92
> select subtract #10
Nothing selected
> color zone #10 near #9 distance 4.91
> color zone #10 near #9 distance 1
> color zone #10 near #9 distance 15
> color zone #10 near #9 distance 3
> color zone #10 near #9 distance 30
> select add #9
57717 atoms, 59577 bonds, 15 pseudobonds, 6675 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #10
2 models selected
> view matrix models
> #10,-0.90265,0.42501,0.067688,309.18,-0.067158,0.01625,-0.99761,438.01,-0.4251,-0.90504,0.013875,493.14
> color zone #10 near #9 distance 30
> volume #10 level 0.001061
> volume #10 level 0.001224
> volume #10 level 0.001477
> volume #10 level 0.001603
> surface dust #10 size 8.19
> color zone #11 near #9 distance 4.91
> color zone #11 near #9 distance 1
> color zone #11 near #9 distance 10
> select clear
> hide #!9 models
> volume #11 level 0.1719
> volume #11 level 0.1669
> volume #11 level 0.1644
> volume #11 level 0.157
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/Sc_0N80_Apo.png" width 3600 height 3121
> supersample 3 transparentBackground true
> save "/Users/upneet/Desktop/Narlilkar Lab/Manuscript_INO80_AutoInib/Figures
> /Figure 2/Version 2- Resubmission/0_80_ApovsADPBeF_Maps.cxs" includeMaps
> true
——— End of log from Mon Dec 30 10:55:42 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Max
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: Mac15,9
Model Number: Z1CM000M6LL/A
Chip: Apple M3 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 2 days, 23 hours, 34 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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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