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Opened 3 months ago
Closed 3 months ago
#18479 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 0x00000001ffc5df00 (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, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, 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, markupsafe._speedups, 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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast (total: 104)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "Mac15,6",
"coalitionID" : 5204,
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"captureTime" : "2025-08-19 13:58:53.7766 +0100",
"codeSigningMonitor" : 1,
"incident" : "0C44634B-401C-4ADF-9840-17D174F79C95",
"pid" : 18623,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-18 09:38:08.9811 +0100",
"procStartAbsTime" : 29190577273962,
"procExitAbsTime" : 30923824389099,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"24620DA0-5988-5B23-9E82-940A82D06194","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E13F26CC-2B73-1C1F-F7BF-9C3A2414B42E",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 15609,
"sleepWakeUUID" : "16577EF3-D695-479B-B46A-DA7BEEC6D40D",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4304846487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10096c000-100970000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":18623},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4304846487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10096c000-100970000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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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/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/StrAnalysis-M26709(BRD9).cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.5, step 1, values float32
opened ChimeraX session
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> show #!1.6 models
> hide #!5 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2 models
> show #!1.7 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.7 models
> color #1.6 #d6d6d6ff models
> color #1.6 #ebebebff models
> color #1.6 #d6d6d6ff models
> lighting flat
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> volume #1.6 level 0.02726
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263
> supersample 4
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!1.6 models
> hide #!2.1 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.7 models
> hide #!2 models
> show #!1.6 models
> hide #!1.7 models
> fitmap #5.2 inMap#1.6
Expected a keyword
> fitmap #5.2 inMap #1.6
Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map
Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms
average map value = 2.48e-19, steps = 652
shifted from previous position = 32.3
rotated from previous position = 22.2 degrees
atoms outside contour = 16233, contour level = 0.027265
Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to
Gaussian_local_filtered_map.mrc (#1.6) coordinates:
Matrix rotation and translation
0.93565187 -0.15830921 -0.31542632 64.40958566
0.11186587 0.98069697 -0.16037296 -107.24352394
0.33472615 0.11476782 0.93530035 -87.17093173
Axis 0.36398764 -0.86009595 0.35741846
Axis point 357.21288153 -0.00000000 33.78486496
Rotation angle (degrees) 22.20697265
Shift along axis 84.52751343
> show #!5 models
> fitmap #5.2 inMap #1.6
Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map
Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms
average map value = 2.48e-19, steps = 144
shifted from previous position = 0.00707
rotated from previous position = 0.121 degrees
atoms outside contour = 16233, contour level = 0.027265
Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to
Gaussian_local_filtered_map.mrc (#1.6) coordinates:
Matrix rotation and translation
0.93530406 -0.15724230 -0.31698764 64.48169295
0.11038925 0.98079281 -0.16080942 -107.06117498
0.33618525 0.11541368 0.93469736 -87.32017575
Axis 0.36441148 -0.86170815 0.35307695
Axis point 355.38830202 0.00000000 33.25914596
Rotation angle (degrees) 22.27168615
Shift along axis 84.92261543
> show #!5.2 models
> hide #!5.1 models
> show #!5.1 models
> show #!2 models
> hide #!2 models
> hide #!5.2 models
> show #!5.2 models
> select add #5.2
16233 atoms, 16405 bonds, 8 pseudobonds, 1020 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #5.2,0.9353,-0.15724,-0.31699,12.334,0.11039,0.98079,-0.16081,85.765,0.33619,0.11541,0.9347,-9.9527
> view matrix models
> #5.2,0.9353,-0.15724,-0.31699,31.751,0.11039,0.98079,-0.16081,79.217,0.33619,0.11541,0.9347,-5.824
> view matrix models
> #5.2,0.9353,-0.15724,-0.31699,30.154,0.11039,0.98079,-0.16081,85.427,0.33619,0.11541,0.9347,-3.5056
> fitmap #5.2 inMap #1.6
Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map
Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms
average map value = 0.02531, steps = 208
shifted from previous position = 10.6
rotated from previous position = 22.4 degrees
atoms outside contour = 10058, contour level = 0.027265
Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to
Gaussian_local_filtered_map.mrc (#1.6) coordinates:
Matrix rotation and translation
0.99999867 -0.00036713 0.00159068 -0.08863738
0.00036638 0.99999982 0.00047471 -0.07580690
-0.00159085 -0.00047412 0.99999862 0.18892049
Axis -0.27906254 0.93572596 0.21573369
Axis point 119.44333269 0.00000000 56.77798040
Rotation angle (degrees) 0.09740463
Shift along axis -0.00544259
> hide sel atoms
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> color sel orange
> color zone #1.6 near #5.2@C /I distance 5
> color zone #1.6 near #5.2@C /I distance 6
> hide #!5.1 models
> hide #!5.2 models
> color zone #1.6 near #5.2@C /I distance 4
> color zone #1.6 near #5.2@C /I distance 5
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> color zone #1.6 near #5.2@C /I distance 5.5
> color zone #1.6 near #5.2@C /I distance 6
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263
> supersample 3
> show #!5.1 models
> hide #!1.6 models
> show #!2 models
> hide #!2.2 models
> show #!2.2 models
> volume #2.2 level 2.064
> undo
> volume #2.2 level 4.28
> volume #2.2 color white
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> show #!5.2 models
> show #!1.6 models
> color #1.6 #d6d6d6ff models
> ui mousemode right select
> select clear
> hide #5.1.4 models
> hide #5.1.5 models
> hide #5.1.3 models
> ui windowfill toggle
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> hide sel h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> hide sel H
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> select sel H
Expected a keyword
> select clear
> select #5.2/I:1@H521
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #5.2/I:1@H522
1 atom, 1 residue, 1 model selected
> select #5.2/I:1@H523
1 atom, 1 residue, 1 model selected
> select add #5.2/I:1@H522
2 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H541
3 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H542
4 atoms, 1 residue, 1 model selected
> select #5.2/I:1@H541
1 atom, 1 residue, 1 model selected
> select add #5.2/I:1@H542
2 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H523
3 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H522
4 atoms, 1 residue, 1 model selected
> hide sel atoms
> ui windowfill toggle
> hide #!2 models
> hide #!1.6 models
> select clear
> select #5.2/I:1@H531
1 atom, 1 residue, 1 model selected
> select add #5.2/I:1@H532
2 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H1_2
3 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H1_3
4 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H1_1
5 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H533
6 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC49
7 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC40
8 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H442
9 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H433
10 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H431
11 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H432
12 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC42
13 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H441
14 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H372
15 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H371
16 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H382
17 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H381
18 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H8_2
19 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H153
20 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H9_2
21 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H8_1
22 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H6_2
23 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H6_1
24 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC4
25 atoms, 1 residue, 1 model selected
> hide sel atoms
> select add #5.2/I:1@HC46
26 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H211
27 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H213
28 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H212
29 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H311
30 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H313
31 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H312
32 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC18
33 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC16
34 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H293
35 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H292
36 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H291
37 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H253
38 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@C25
39 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H251
40 atoms, 1 residue, 1 model selected
> select subtract #5.2/I:1@C25
39 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H252
40 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H112
41 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H321
42 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H341
43 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H342
44 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H351
45 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H443
46 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H9_1
47 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H151
48 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H152
49 atoms, 1 residue, 1 model selected
> hide sel atoms
> select add #5.2/I:1@HC23
50 atoms, 1 residue, 1 model selected
> hide sel atoms
> select add #5.2/I:1@H111
51 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H322
52 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@HC50
53 atoms, 1 residue, 1 model selected
> select add #5.2/I:1@H352
54 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #!1.6 models
> show #!2 models
> ui windowfill toggle
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!2 models
> hide #!2.2 models
> show #!1.3 models
> hide #!1.4 models
> hide #!1.6 models
> hide #!1.3 models
> show #!1.3 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> show #!1.7 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.7 models
> show #!2.2 models
> hide #!1.3 models
> volume #1.6 level 0.02546
> volume #2.2 level 4.161
> ui windowfill toggle
Drag select of 1.6 Gaussian_local_filtered_map.mrc , 36 residues
Drag select of 1.6 Gaussian_local_filtered_map.mrc , 2.2 EMready_Maps , 1020
residues, 56 atoms, 61 bonds
Drag select of 2.2 EMready_Maps , 172 atoms, 1018 residues, 26 pseudobonds,
167 bonds
Drag select of 2.2 EMready_Maps , 172 atoms, 1016 residues, 26 pseudobonds,
167 bonds
> select clear
Drag select of 2.2 EMready_Maps , 172 atoms, 1018 residues, 26 pseudobonds,
167 bonds
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
Drag select of 1.6 Gaussian_local_filtered_map.mrc , 56 atoms, 1018 residues,
61 bonds
> ui mousemode right "translate selected models"
> view matrix models
> #1.6,1,0,0,-16.312,0,1,0,90.607,0,0,1,47.123,#5.2,1,-0.00036713,0.0015907,-16.401,0.00036638,1,0.00047471,90.531,-0.0015908,-0.00047412,1,47.312
> ui mousemode right select
> select clear
> ui windowfill toggle
> hide #!1 models
> hide #!5.2 models
> undo
> hide #!5.2 models
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850
> supersample 4
> ui windowfill toggle
> hide #!2 models
> hide #!5.1 models
> show #!5.2 models
> show #!1 models
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850
> supersample 4
> ui windowfill toggle
> show #!5.1 models
> hide #!5.2 models
> hide #!1.6 models
> show #!2 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #3 models
> volume #2.2 level 3.939
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting flat
> lighting soft
> volume #2.1 level 4.777
> volume #2.2 step 2
> volume #2.2 step 1
> select #5.1/I:1@N57
1 atom, 1 residue, 1 model selected
> select clear
> select #2.2
2 models selected
> select clear
> select #5.1/B:62@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5.1/B
1337 atoms, 1376 bonds, 42 pseudobonds, 171 residues, 4 models selected
> select #5.1/B
1337 atoms, 1376 bonds, 42 pseudobonds, 171 residues, 4 models selected
> hide sel atoms
> select #5.1/C
825 atoms, 847 bonds, 109 pseudobonds, 101 residues, 3 models selected
> hide sel atoms
> select clear
> ui windowfill toggle
> select #2.2
2 models selected
> select clear
> save /Users/tarunnarwani/Pictures/Image1.jpg width 1920 height 850
> supersample 4
> ui windowfill toggle
> fitmap #5.2 inMap #1.6
Fit molecule schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) to map
Gaussian_local_filtered_map.mrc (#1.6) using 16233 atoms
average map value = 0.02531, steps = 28
shifted from previous position = 0.00877
rotated from previous position = 0.0068 degrees
atoms outside contour = 9226, contour level = 0.025461
Position of schrodinger_relaxed_with_rotamer_corrected.pdb (#5.2) relative to
Gaussian_local_filtered_map.mrc (#1.6) coordinates:
Matrix rotation and translation
0.99999881 -0.00040674 0.00148637 -0.07764102
0.00040609 0.99999982 0.00043444 -0.06917223
-0.00148654 -0.00043383 0.99999880 0.17950003
Axis -0.27116477 0.92845541 0.25385077
Axis point 120.29893784 0.00000000 51.89437557
Rotation angle (degrees) 0.09173041
Shift along axis 0.00239640
> show #!5.2 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.3 models
> fitmap #5.1 inMap #1.3
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc (#1.3) using 8099
atoms
average map value = 0.04491, steps = 40
shifted from previous position = 0.0244
rotated from previous position = 0.0515 degrees
atoms outside contour = 1826, contour level = 0.024647
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc (#1.3) coordinates:
Matrix rotation and translation
0.99999975 -0.00041862 -0.00056256 0.08661369
0.00041881 0.99999985 0.00035071 -0.08006894
0.00056241 -0.00035095 0.99999978 -0.02480425
Axis -0.44743420 -0.71737671 0.53401620
Axis point 49.33028395 0.00000000 158.26863156
Rotation angle (degrees) 0.04492490
Shift along axis 0.00543979
> fitmap #5.1 inMap #1.5
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms
average map value = 0.1535, steps = 28
shifted from previous position = 0.0166
rotated from previous position = 0.0267 degrees
atoms outside contour = 1204, contour level = 0.033787
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.99999969 -0.00029605 -0.00073344 0.08979761
0.00029600 0.99999995 -0.00006562 -0.01650503
0.00073346 0.00006540 0.99999973 -0.07136704
Axis 0.08254430 -0.92415452 0.37299445
Axis point 95.33653629 0.00000000 122.83775369
Rotation angle (degrees) 0.04547248
Shift along axis -0.00395404
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.4 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> show #!1.4 models
> show #!1.5 models
> volume #1.5 level 0.05162
> fitmap #5.1 inMap #1.5
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms
average map value = 0.1535, steps = 40
shifted from previous position = 0.013
rotated from previous position = 0.0195 degrees
atoms outside contour = 1959, contour level = 0.051617
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.99999978 0.00000255 -0.00066430 0.05792100
-0.00000250 1.00000000 0.00008443 -0.01270232
0.00066430 -0.00008443 0.99999978 -0.05454194
Axis -0.12607893 -0.99201304 -0.00377292
Axis point 82.10293260 0.00000000 88.20845195
Rotation angle (degrees) 0.03836801
Shift along axis 0.00550403
> measure mapstats #1.5
Map DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc #1.5, minimum -0.618,
maximum 0.9837, mean -0.0002284, SD 0.01979, RMS 0.01979
> measure mapstats #1.4
Map DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc #1.4, minimum
-0.06459, maximum 0.1527, mean -0.0002284, SD 0.004562, RMS 0.004568
> fitmap #5.1 inMap #1.5
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) using 8099 atoms
average map value = 0.1535, steps = 44
shifted from previous position = 0.01
rotated from previous position = 0.00612 degrees
atoms outside contour = 1959, contour level = 0.051617
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc (#1.5) coordinates:
Matrix rotation and translation
0.99999976 -0.00009341 -0.00069344 0.06935420
0.00009344 0.99999999 0.00004760 -0.01070345
0.00069343 -0.00004766 0.99999976 -0.05495719
Axis -0.06791780 -0.98875810 0.13320880
Axis point 79.01021253 0.00000000 99.84512464
Rotation angle (degrees) 0.04018274
Shift along axis -0.00144804
> fitmap #5.1 inMap #1.4
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc (#1.4) using 8099 atoms
average map value = 0.04366, steps = 44
shifted from previous position = 0.0167
rotated from previous position = 0.0238 degrees
atoms outside contour = 2489, contour level = 0.028037
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc (#1.4) coordinates:
Matrix rotation and translation
0.99999973 -0.00041544 -0.00060533 0.09005454
0.00041562 0.99999987 0.00029471 -0.07560695
0.00060521 -0.00029496 0.99999977 -0.03497916
Axis -0.37265894 -0.76503607 0.52520960
Axis point 62.98367676 0.00000000 152.38017056
Rotation angle (degrees) 0.04533038
Shift along axis 0.00591103
> fitmap #5.1 inMap #2.2
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
EMready_Maps (#2.2) using 8099 atoms
average map value = 5.396, steps = 40
shifted from previous position = 0.0258
rotated from previous position = 0.0492 degrees
atoms outside contour = 1841, contour level = 3.939
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
EMready_Maps (#2.2) coordinates:
Matrix rotation and translation
0.99999873 -0.00095513 -0.00127197 0.20736724
0.00095547 0.99999951 0.00026985 -0.12373672
0.00127171 -0.00027106 0.99999915 -0.07722232
Axis -0.16762293 -0.78825778 0.59207452
Axis point 68.77375787 0.00000000 165.20808818
Rotation angle (degrees) 0.09244556
Shift along axis 0.01705556
> fitmap #5.1 inMap #2.1
Fit molecule DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) to map
final_unsharp_EMreadyOUT.mrc (#2.1) using 8099 atoms
average map value = 8.94, steps = 36
shifted from previous position = 0.0103
rotated from previous position = 0.0193 degrees
atoms outside contour = 1568, contour level = 4.7773
Position of DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb (#5.1) relative to
final_unsharp_EMreadyOUT.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99999874 -0.00067755 -0.00143404 0.20192690
0.00067809 0.99999970 0.00037363 -0.11415728
0.00143379 -0.00037460 0.99999890 -0.08365712
Axis -0.22957660 -0.87993219 0.41594943
Axis point 64.05481872 0.00000000 143.84235556
Rotation angle (degrees) 0.09336790
Shift along axis 0.01929585
> measure mapstats #2.1
Map final_unsharp_EMreadyOUT.mrc #2.1, minimum -0.1337, maximum 18.67, mean
0.0002461, SD 0.702, RMS 0.702
> measure mapstats #2.2
Map EMready_Maps #2.2, minimum -0.1027, maximum 9.086, mean 0.0006311, SD
0.5525, RMS 0.5525
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> hide #5.1.5 models
> hide #5.1.4 models
> hide #5.1.3 models
> hide #3 models
> show #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> color #2.2 #ffffff79 models
> color #2.2 #ffffff78 models
> open /Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/PreQC-
> Proteros_SMARCA2_40272set.cxs format session
Opened AMPH-38945-001_screening.mrc as #1.1, grid size 256,256,256, pixel
0.914, shown at level 0.127, step 1, values float32
Opened AMPH-39541-001_screening.mrc as #1.2, grid size 256,256,256, pixel
0.914, shown at level 0.203, step 1, values float32
Opened AMPH-39576-003_screening.mrc as #1.3, grid size 256,256,256, pixel
0.914, shown at level 0.121, step 1, values float32
Opened AMPH-40272-003_screening.mrc as #1.4, grid size 256,256,256, pixel
0.914, shown at level 0.224, step 1, values float32
Opened AMPH-38945-001_screening.mrc gaussian as #5, grid size 256,256,256,
pixel 0.914, shown at step 1, values float32
Opened AMPH-39541-001_screening.mrc gaussian as #6, grid size 256,256,256,
pixel 0.914, shown at level 0.173, step 1, values float32
Opened AMPH-39576-003_screening.mrc gaussian as #7, grid size 256,256,256,
pixel 0.914, shown at step 1, values float32
Opened AMPH-40272-003_screening.mrc gaussian as #8, grid size 256,256,256,
pixel 0.914, shown at step 1, values float32
opened ChimeraX session
> show #!8 models
> hide #!7 models
> show #!7 models
> volume #!7-8 style surface
> volume #!7-8 showOutlineBox false
> hide #!8 models
> show #!3 models
> hide #!3 models
> volume #7 level 0.2814
> volume #8 change image level -0.01811,0 level 0.1172,0.8 level 0.6057,1
> volume #8 level 0.05563
> volume #8 level 0.05659
> volume #1.4 level 0.3053
> volume #1.4 level 0.2353
Drag select of 1.4 AMPH-40272-003_screening.mrc
> select clear
> volume #5 level -0.01558,0 level 0.09931,0.8 level 0.5854,1
> volume #5 style surface
> volume #5 level 0.3267
> volume #5 level 0.1177
> show #2 models
> show #!6 models
> hide #!5 models
> hide #2 models
> volume #6 level 0.2989
> volume #6 level 0.1818
> volume #6 level 0.1669
> volume #6 level 0.1699
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> hide #5.1.3 models
> hide #5.1.4 models
> hide #5.1.5 models
> hide #3 models
> select #5.1/I
56 atoms, 61 bonds, 1 residue, 1 model selected
> surface zone #2.2 nearAtoms sel distance 5
> surface zone #2.2 nearAtoms sel distance 3.5
> volume gaussian #2.2 bfactor 200
Opened EMready_Maps gaussian as #4, grid size 300,300,300, pixel 0.65, shown
at step 1, values float32
> surface zone #3 nearAtoms sel distance 3.5
No surfaces specified
> hide #!4 models
> show #!4 models
> surface zone #4 nearAtoms sel distance 3.5
> show #!2.2 models
> hide #!4 models
> close #4
> color #2.2 #ffffff80 models
> color #2.2 #ffffff5d models
> color #2.2 #ffffff5e models
> select #5.1/B:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5.1/B:175
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #5.1/B:174
19 atoms, 16 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> surface zone #4 nearAtoms sel distance 3
No surfaces specified
> surface zone #2.2 nearAtoms sel distance 3
No atoms specified
> select #5.1/I
56 atoms, 61 bonds, 1 residue, 1 model selected
> surface zone #2.2 nearAtoms sel distance 3
> select #5.1/B,C
2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected
> select #5.1/B,C
2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected
> color sel light gray
> select #5.1/B,C
2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected
> color sel gray
> select #5.1/B,C
2162 atoms, 2223 bonds, 173 pseudobonds, 272 residues, 4 models selected
> color sel light gray
> color #5.1 darkgrey
> color #5.1 #929292ff
> color #5.1 #929292a4
> color #5.1 #929292ff
> select #5.1/I
56 atoms, 61 bonds, 1 residue, 1 model selected
> color sel orange
> select #5.1/I
56 atoms, 61 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel
> label sel bgColor yellow
> show #5.1.4 models
> ui mousemode right label
> label delete residues
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel
> label sel bgColor yellow
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885
> supersample 4
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/StrAnalysis-M26709(BRD9).cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.5, step 1, values float32
opened ChimeraX session
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> hide #3 models
> hide #5.1.5 models
> hide #5.1.3 models
> ui mousemode right "move label"
> label bgColor color gray
Invalid "bgColor" argument: Expected 'none' or a color
> label bgColor gray
> label bgColor light gray
> select #5.1/B:173,191
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #5.1/B:173,191 /C:216,188
33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected
> select #5.1/B:173,191 /C:216,188
33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected
> color sel maroon
> select #5.1/B:173,191 /C:216,188
33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected
> color sel byhetero
> select #5.1/B:173,191 /C:216,188
33 atoms, 29 bonds, 12 pseudobonds, 4 residues, 3 models selected
> label sel bgColor light yellow
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel bgColor yellow
> ui mousemode right select
> select clear
> select #2.2
2 models selected
> select #5.1/I:1@C15
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 61 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select add #5.1/I:1@C21
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@N57
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@C44
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel maroon
> color sel byhetero
> select clear
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1263
> supersample 3
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> ui tool show "Model-map Q-Score"
> style #5.2 stick
Changed 16233 atom styles
> color #5.2 byhetero
> transparency #2.2 60
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
> assignAttr false
Overall mean Q-Score: 0.64
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
> assignAttr false
Overall mean Q-Score: 0.64
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
> assignAttr false
Overall mean Q-Score: 0.64
> qscore #5.2/C toVolume #2.2
When the "qscore" command is called with "useGui True", the analysis will be
run on the entire model.
> ui tool show "Model-map Q-Score"
> transparency #2.2 60
Overall mean Q-Score: 0.64
> select #5.1/C:140
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #5.1/C:171
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5.1/C:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #5.1/C:239
10 atoms, 9 bonds, 1 residue, 1 model selected
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 5 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false
> assignAttr false
Overall mean Q-Score: 0.65
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 5 shellRadiusStep
> 0.100 maxShellRadius 2.50 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.74
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 4 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 4 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.50 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.74
> qscore #5.2 toVolume #2.2 useGui false pointsPerShell 8 shellRadiusStep
> 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.75 logDetails false
> assignAttr false
Overall mean Q-Score: 0.69
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> ui tool show "Ramachandran Plot"
> hide #3 models
> show #3 models
> hide #5.1.5 models
> hide #5.1.3 models
> show #5.1.5 models
> hide #5.1.5 models
Drag select of 1 atoms, 1 bonds
> select clear
> hide #!2.2 models
> ui mousemode right label
> label #5.1/C:157
> label #5.1/C:156
> label #5.1/B:62
> label #5.1/C:160
> label #5.1/C:157
> show #!2.2 models
> hide #!2.2 models
> undo
> hide #!2.2 models
> ui mousemode right "move label"
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel color green
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel bgColor yellow
> show #!2.2 models
> ui mousemode right select
> select clear
> hide #3 models
> show #3 models
> show #5.1.5 models
> hide #5.1.5 models
> show #5.1.5 models
> hide sel
> ui mousemode right label
> label #5.1/C:167
> label #5.1/B:196
> select #5.1/C:167 /B:196
16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected
> select #5.1/C:167 /B:196
16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected
> label sel color orange
> select #5.1/C:167 /B:196
16 atoms, 14 bonds, 4 pseudobonds, 2 residues, 2 models selected
> label sel bgColor light yellow
> ui mousemode right "move label"
> ui mousemode right select
> select clear
Drag select of 2.2 EMready_Maps
> select clear
> ui mousemode right "move label"
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885
> supersample 4
> ui windowfill toggle
> open /Users/tarunnarwani/Library/CloudStorage/OneDrive-
> AmphistaLTD/Proteros/SOW-8_C1943/AMPH-26709/DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb
DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb title:
DDB1-DCAF16-BRD9 In complex with ligand AMPH-26709-010-04 [more info...]
Chain information for DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
Non-standard residues in DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #4
---
INX — (INX)
ZN — (ZN)
21 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> color #4 #ff9300ff
> color #4 #ff2600ff
> select #4
8099 atoms, 8271 bonds, 8 pseudobonds, 1020 residues, 3 models selected
> hide sel atoms
> select #4/I
56 atoms, 61 bonds, 1 residue, 1 model selected
> show sel atoms
> color #4 bychain
> select #4/B:191
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:191,62
23 atoms, 22 bonds, 2 residues, 1 model selected
> select #4/B:191,54
25 atoms, 25 bonds, 2 residues, 1 model selected
> select #4/B:191,52
19 atoms, 17 bonds, 2 residues, 1 model selected
> select #4/B:191,53
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #5.1/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color #4 mediumslateblue
> color #4 #7b68ee3a
> color #4 #7b68ee8b
> color #4 #7b68ee74
> color #4 #7b68ee73
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right select
> ui mousemode right "move label"
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> color #4 bychain
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right label
> hide #!2.2 models
> label #5.1/B:55
> ui mousemode right "move label"
> ui mousemode right label
> label delete residues
> label sel color orange
> label sel bgColor gray
> ui mousemode right "move label"
> ui mousemode right select
> select clear
Drag select of 1 pseudobonds
> select add #5.1/C:163@CZ
1 atom, 7 pseudobonds, 1 residue, 3 models selected
> select subtract #5.1/C:163
1 pseudobond, 1 model selected
Drag select of 2 pseudobonds
Drag select of 6 pseudobonds
> hide sel
> select clear
> hide sel
> select clear
> hide sel
> select clear
Drag select of 1 pseudobonds
> hide sel
> select clear
> hide sel
> ui mousemode right label
> ui mousemode right "move label"
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel
> select clear
> select #5.1/B:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5.1/C:166
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #5.1/C:167@CG
1 atom, 1 residue, 1 model selected
> select #5.1/C:166
7 atoms, 6 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
8092 atoms, 8265 bonds, 257 pseudobonds, 1019 residues, 6 models selected
> select up
8094 atoms, 8265 bonds, 257 pseudobonds, 1020 residues, 6 models selected
> select ~sel & ##selected
5 atoms, 6 bonds, 1 residue, 1 model selected
> select #5.1/C:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5.1/B:196
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel
> select #5.1/C:163
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel
> select #5.1/B:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #5.1/B:174
13 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel
> show #!2.2 models
> select clear
> hide sel
> select #4/B:55@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
8090 atoms, 8263 bonds, 8 pseudobonds, 1019 residues, 3 models selected
> select ~sel & ##selected
9 atoms, 8 bonds, 1 residue, 1 model selected
> color #4 mediumslateblue
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> color #4 bychain
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> select #4/B:191,55
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> color #2.2 #ffffff00 models
> color #2.2 #ffffff14 models
> color #2.2 #ffffff20 models
> color #2.2 #ffffff1f models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> lighting flat
> lighting soft
> select #2.2
2 models selected
> hide #!2.2 models
> select #5.1/B:180
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel
> select #4/B:55@NE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5.1/B:191
20 atoms, 18 bonds, 2 residues, 2 models selected
> select subtract #5.1/B:191
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
11 atoms, 9 bonds, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> show #!2.2 models
> ui mousemode right "move label"
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.1/B:58
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel color green
> label sel bgColor yellow
> ui mousemode right select
> select clear
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 885
> supersample 4
> ui windowfill toggle
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> color #2.2 #ffffff00 models
> hide #!2.2 models
> hide #3 models
> hide #5.1.3 models
> hide #5.1.4 models
> hide #5.1.5 models
> select #5.1/I:1@C25
1 atom, 1 residue, 1 model selected
> select up
56 atoms, 61 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select add #5.1/I:1@O27
2 atoms, 2 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@C28
3 atoms, 8 bonds, 1 residue, 1 model selected
> select add #5.1/C:222@OH
4 atoms, 16 bonds, 2 residues, 1 model selected
> select add #5.1/C:160
15 atoms, 27 bonds, 3 residues, 1 model selected
> select add #5.1/I:1@C19
16 atoms, 27 bonds, 3 residues, 1 model selected
> select add #5.1/I:1@C21
17 atoms, 28 bonds, 3 residues, 1 model selected
> select subtract #5.1/I:1@C19
16 atoms, 28 bonds, 3 residues, 1 model selected
> select add #5.1/I:1@C12
17 atoms, 29 bonds, 3 residues, 1 model selected
> select add #5.1/I:1@C15
18 atoms, 32 bonds, 3 residues, 1 model selected
> select add #5.1/I:1@C18
19 atoms, 37 bonds, 3 residues, 1 model selected
> select add #5.1/C:161
30 atoms, 50 bonds, 4 residues, 1 model selected
> contacts sel distanceOnly 3.4
9 distances
> contacts sel distanceOnly 3.5
18 distances
> show #3 models
> undo
> select add #5.1/C:215
42 atoms, 62 bonds, 5 residues, 1 model selected
> contacts sel distanceOnly 3.5
23 distances
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> color #2.2 #ffffff00 models
> ui mousemode right label
> ui mousemode right select
> select #2.2
2 models selected
> select #2.2
2 models selected
> select clear
> hide #!2.2 models
> select #5.1/B:174
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> color sel teal
> select clear
> color sel teal
> select #5.1/C:169@CD1
1 atom, 1 residue, 1 model selected
> color sel teal
> select clear
> ui tool show "Side View"
> ui mousemode right "move label"
> ui mousemode right select
> select ~sel & ##selected
139 pseudobonds, 1 model selected
> select ~sel
24332 atoms, 24676 bonds, 265 pseudobonds, 2040 residues, 31 models selected
> select clear
> color sel yellow
> color sel light yellow
> color sel palegreen yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> color sel darkred yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel orange
> color sel light yellow
> show #!2.2 models
> select clear
> ui windowfill toggle
> ui mousemode right "move label"
> ui windowfill toggle
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> view
> hide #!2.2 models
> ui mousemode right label
> label #5.1/C:158
> undo
> ui mousemode right "move label"
> hide #3 models
> hide #5.1.5 models
> show #5.1.5 models
> hide #5.1.3 models
> show #5.1.3 models
> hide #!2.2 models
> ui mousemode right label
> ui mousemode right select
> select clear
> ui mousemode right "move label"
> ui mousemode right label
> ui mousemode right select
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> label sel bgColor lightblue white
Expected a keyword
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> label sel bgColor white
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> label sel light yellow
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> label sel bgColor light yellow
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> label sel color green
> ui mousemode right "move label"
> ui mousemode right select
> select clear
> hide sel
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select #5.1/B:173
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5.1/B:178
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right "tape measure"
> marker segment #4 position 101.6,120.9,65.37 toPosition 106,122,63.79 color
> yellow radius 0.1 label 4.839 labelHeight 0.4839 labelColor yellow
> marker segment #4 position 101.6,120.9,65.37 toPosition 105.9,122.2,65.29
> color yellow radius 0.1 label 4.542 labelHeight 0.4542 labelColor yellow
> marker segment #4 position 101.6,120.9,65.37 toPosition 105.2,122,64.93
> color yellow radius 0.1 label 3.836 labelHeight 0.3836 labelColor yellow
> show #!2.2 models
> hide #!4 models
> ui mousemode right "move label"
> ui mousemode right select
> hide #!2.2 models
> select #5.1/I:1@C40
1 atom, 1 residue, 1 model selected
> select add #5.1/I:1@N39
2 atoms, 1 residue, 1 model selected
> select add #5.1/I:1@C38
3 atoms, 1 residue, 1 model selected
> select add #5.1/I:1@O48
4 atoms, 4 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@N57
5 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@C54
6 atoms, 10 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@C52
7 atoms, 11 bonds, 1 residue, 1 model selected
> select add #5.1/I:1@F55
8 atoms, 11 bonds, 1 residue, 1 model selected
> contacts sel distanceOnly 3.5
No distances
> contacts sel distanceOnly 4
2 distances
> contacts sel distanceOnly 4
2 distances
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #5.1.5 models
> hide #5.1.3 models
> show #3 models
> hide #3 models
> show #3 models
> show #5.1.3 models
> hide #5.1.3 models
> show #5.1.3 models
> select clear
> select #5.1/B:54
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5.1/B:54
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select #5.1/B:55
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> ui mousemode right "move label"
> ui mousemode right select
> select clear
Drag select of 2 residues
> select clear
> ui mousemode right "move label"
> show #!2.2 models
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> ui mousemode right select
> select #2.2
2 models selected
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.1/C:158
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> save /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs
Taking snapshot of stepper: DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture
> Sandbox- BRD9 images.cxs"
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
3.28, step 1, values float32
opened ChimeraX session
> graphics silhouettes false
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection sil
Expected a keyword
> graphics selection silhoutte
Expected a keyword
> select clear
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics silhouettes true
> graphics silhouettes false
> graphics selection silhoutte true
Expected a keyword
> graphics selection silhouettes true
Expected a keyword
> graphics silhouettes true color orange depthJump 1.5
> select clear
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color black width 5
> graphics selection color black width 1
> graphics selection color black width 1.5
> graphics selection color black width 3
> graphics selection color black width 2
> graphics selection color black width 1
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> graphics selection color black width 1
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color black width 1
> select clear
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture
> Sandbox- BRD9 images.cxs" format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
3.28, step 1, values float32
opened ChimeraX session
> graphics silhouettes false
> show #!1.7 models
> hide #!1.7 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.5 models
> hide #!1.5 models
> show #!2 models
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel black
> color zone #2.2 near #5.2@C /I distance 7
> select #5.2/A
11759 atoms, 11864 bonds, 4 pseudobonds, 747 residues, 2 models selected
> color sel purple
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> color sel orange
> color zone #2.2 near #5.2@C /I distance 7
> select clear
> color zone #2.2 near #5.2@C /I distance 10
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> color zone #2.2 near #5.2@C /I distance 15
> hide #!5.2 models
> volume #2.2 level 3.388
> volume #2.2 level 4.279
> surface dust #2.2 size 6.5
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> graphics silhouettes false
> graphics silhouettes true
> open /Users/tarunnarwani/Documents/StructurePG_TJR/CryoEM-
> QC/DATA/BRD9/M-26709/CryoEM_QC-M26709.cxs format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
4.08, step 1, values float32
opened ChimeraX session
> hide #!2.2 models
> hide #3 models
> hide #!5.1 models
> show #!5.2 models
> select #5.2/B:178
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> show #!5.1 models
> hide #!5.2 models
> hide #5.1.3 models
> ui mousemode right label
> label #5.1/B:178
> ui mousemode right "move label"
> label bgColor yellow
> label bgColor light gray
> ui mousemode right distance
> distance #5.1/B:178@SG #5.1/I:1@C34
Distance between DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #5.1/B CYS 178
SG and /I INX 1 C34: 4.542Å
> distance #5.1/B:178@SG #5.1/I:1@C35
Distance between DDB1-DCAF16-BRD9_AMPH-26709-010-04_model.pdb #5.1/B CYS 178
SG and /I INX 1 C35: 4.256Å
> ui mousemode right "move label"
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture
> Sandbox- BRD9 images.cxs" format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
3.28, step 1, values float32
opened ChimeraX session
> graphics silhouettes false
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select #5.1/B
1337 atoms, 1376 bonds, 29 pseudobonds, 171 residues, 3 models selected
> select #5.1/B
1337 atoms, 1376 bonds, 29 pseudobonds, 171 residues, 3 models selected
> show #!5.1 models
> hide #!5.2 models
> hide #!5.1 models
> show #!5.2 models
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> color sel white
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> undo
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel white
> ui mousemode right select
> select clear
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel light yellow
> select clear
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel yellow
> select clear
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel darkred yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #5.2/C
1660 atoms, 1682 bonds, 101 residues, 1 model selected
> color sel orange
> select clear
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> color sel pink
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> color sel purple
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> color #5.2/B:58 byhetero
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color black
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray width
Missing "width" keyword's argument
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray width 1.4
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray width 2
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray width 1
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color gray width 1
> select #5.2/B: black
Nothing selected
> select #5.2/B: color sel black
Expected a keyword
> select #5.2/B
2699 atoms, 2738 bonds, 4 pseudobonds, 171 residues, 2 models selected
> color sel black
> color byhetero
> color #5.2/I white
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> graphics selection color black width 1
> select #5.2/I
115 atoms, 120 bonds, 1 residue, 1 model selected
> color byhetero
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> color #5.2/B dark green
> color byhetero
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> select clear
> select add #5.2/B:179@SG
1 atom, 3 bonds, 1 residue, 1 model selected
> label sel
> select clear
> select #5.2/B:177@SG
1 atom, 1 residue, 1 model selected
> ui mousemode right label
> label #5.2/B:100
> label #5.2/B:103
> label delete residues
> label #5.2/B:177
> label #5.2/B:179
> label #5.2/B:100
> label #5.2/B:103
> select #5.2/I /B:58,100,103,177,179
165 atoms, 166 bonds, 6 residues, 1 model selected
> label delete residues
> select #5.2/I /B:58,100,103,177,179 Zn
Expected a keyword
> hide #5.2.2 models
> select #5.2/I /B:58,100,103,177,179
165 atoms, 166 bonds, 6 residues, 1 model selected
> color #5.2/I black
> color #5.2/I byhetero
> color #5.2/B light green
> color #5.2/B byhetero
> select #5.2/I /B:58,100,103,177,179 @CG
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @CB
120 atoms, 120 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @CG
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @CN
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @C
120 atoms, 120 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @CG
115 atoms, 120 bonds, 1 residue, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @CB
120 atoms, 120 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @SG
120 atoms, 121 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58,100,103,177,179 @C,SG
125 atoms, 121 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58,100,103,177,179
165 atoms, 166 bonds, 6 residues, 1 model selected
> select #5.2/I /B:58
125 atoms, 130 bonds, 2 residues, 1 model selected
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> show #!1.7 models
> hide #!1.7 models
> show #!1.6 models
> show #!1.7 models
> hide #!1.7 models
> show #!1.7 models
> hide #!1.6 models
> hide #!1.7 models
> show #!2 models
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/I orange
> color #5.2/C light gray
> color zone #2.2 near #5.2@C /I distance 15
> graphics silhouettes true
> hide #!5.2 models
> select up
352 atoms, 360 bonds, 15 residues, 1 model selected
> select down
125 atoms, 130 bonds, 2 residues, 1 model selected
> color #5.2/B black
> color #5.2/C dark green
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/B purple
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/C purple
> color #5.2/B yellow
> color #5.2/C light green
> color #5.2/I black
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/I dark gray
> color #5.2/A purple
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/I purple
> color #5.2/C pink
> color #5.2/A pink
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/C green
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/C light green
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color zone #2.2 near #5.2@C /I distance 15
> select #2.2
2 models selected
> color zone #2.2 near #5.2@C /I distance 15
> open "/Users/tarunnarwani/Documents/StructurePG_TJR/ChimeraX/Picture
> Sandbox- BRD9 images.cxs" format session
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half1_map.mrc as #1.1, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_half2_map.mrc as #1.2, grid size
300,300,300, pixel 0.65, shown at level 0.0309, step 2, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_local_filtered_map.mrc as #1.3, grid
size 300,300,300, pixel 0.65, shown at level 0.0246, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_unsharpened_map.mrc as #1.4, grid
size 300,300,300, pixel 0.65, shown at level 0.028, step 1, values float32
Opened DDB1-DCAF16-BRD9_AMPH-26709-010-04_final_map.mrc as #1.5, grid size
300,300,300, pixel 0.65, shown at level 0.0338, step 1, values float32
Opened Gaussian_local_filtered_map.mrc as #1.6, grid size 300,300,300, pixel
0.65, shown at level 0.0285, step 1, values float32
Opened Gaussian_unsharpened_map.mrc as #1.7, grid size 300,300,300, pixel
0.65, shown at level 0.0282, step 1, values float32
Opened final_unsharp_EMreadyOUT.mrc as #2.1, grid size 300,300,300, pixel
0.65, shown at level 4.81, step 1, values float32
Opened EMready_Maps as #2.2, grid size 300,300,300, pixel 0.65, shown at level
3.28, step 1, values float32
opened ChimeraX session
> show #!2 models
> hide #!5 models
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/C green
> color zone #2.2 near #5.2@C /I distance 15
> undo
> color #5.2/I orange
> color #5.2/C green
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/A purple
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/B purple
> color #5.2/C gem
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5.2/C light blue
> color #5.2/B light green
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 3
> color #5.2/I purple
> color #5.2/A orange
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/B light green
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/B light pink
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/I light green
> color #5.2/B purple
> color #5.2/C red
> color zone #2.2 near #5.2@C /I distance 15
> color #5.2/B purple
> color #5.2/C yellow
> color #5.2/C red
> color #5.2/A yellow
> color zone #2.2 near #5.2@C /I distance 15
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> hide #!5.2 models
> show #!5.2 models
> hide #!2 models
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> graphics silhouettes false
> color byhetero
> hide #5.2.2 models
> select #5.2/I /B:58
125 atoms, 130 bonds, 2 residues, 1 model selected
> select #5.2/I /B:58
125 atoms, 130 bonds, 2 residues, 1 model selected
> graphics selection color black width 1
> ui mousemode right select
> select #5.2/B:1001@ZN
1 atom, 1 residue, 1 model selected
> select #5.2/I /B:58
125 atoms, 130 bonds, 2 residues, 1 model selected
> graphics selection color black width 1
> select add #5.2/B:1001@ZN
126 atoms, 130 bonds, 3 residues, 1 model selected
> select subtract #5.2/B:1001@ZN
125 atoms, 130 bonds, 2 residues, 1 model selected
> select add #5.2/B:1001@ZN
126 atoms, 130 bonds, 3 residues, 1 model selected
> select add #5.2/B:100@SG
127 atoms, 132 bonds, 4 residues, 1 model selected
> select subtract #5.2/B:100@SG
126 atoms, 131 bonds, 3 residues, 1 model selected
> select add #5.2/B:100@SG
127 atoms, 131 bonds, 4 residues, 1 model selected
> select subtract #5.2/B:100@SG
126 atoms, 131 bonds, 3 residues, 1 model selected
> select add #5.2/B:177@SG
127 atoms, 132 bonds, 4 residues, 1 model selected
> select subtract #5.2/B:177@SG
126 atoms, 132 bonds, 3 residues, 1 model selected
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/I orange
> color #5.2/I byhetero
> color #5.2/I white byhet
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5.2/I white
> color #5.2/I byhetero
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/C pink
> color #5.2/C darkred pink
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5.2/C salmon
> color #5.2/I orange
> color #5.2/I black
> color #5.2/I byhetero
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> color #5.2/A light green
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
> graphics silhouettes true
> save /Users/tarunnarwani/Pictures/Image1.jpg width 2000 height 1301
> supersample 4
===== 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 Pro
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 Pro
Model Identifier: Mac15,6
Model Number: Z1AY0010LB/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 36 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: 39 days, 21 hours, 49 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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
biopython: 1.83
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-Cytoscape: 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-EMalign: 0.1.3
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-LigandRecognizer: 0.2
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-OpenCommands: 1.2
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-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-PICKLUSTER: 2.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
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-StarMap: 1.2.15
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-TugLigands: 1.1
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
DiffFit: 0.7.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
fsspec: 2025.3.2
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: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
more-itertools: 10.3.0
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
narwhals: 1.34.1
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: 2.2.4
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
plotly: 6.0.1
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
pyKVFinder: 0.7.3
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
pyqtgraph: 0.13.7
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
Send2Trash: 1.8.3
SEQCROW: 1.8.21
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
sympy: 1.13.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tomli: 2.0.1
torch: 2.2.1
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 , 3 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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