Opened 2 months ago

Last modified 2 months ago

#18479 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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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  "uptime" : 1200000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,6",
  "coalitionID" : 5204,
  "osVersion" : {
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    "build" : "24F74",
    "releaseType" : "User"
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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=="},
  "bootSessionUUID" : "41822CB7-AF07-4630-B09D-445210611061",
  "wakeTime" : 15609,
  "sleepWakeUUID" : "16577EF3-D695-479B-B46A-DA7BEEC6D40D",
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  "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},
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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

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