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Opened 3 weeks ago
Closed 3 weeks ago
#19911 closed defect (duplicate)
Crash destroying OpenGL context on exit
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020560a0c0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 440 in quit
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 805 in closeEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 302 in event
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.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_Daily.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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 100)
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364
> fab and CSP.cxs"
Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level
0.3, step 1, values float32
Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel
0.5, shown at level 3.78, step 1, values float32
Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637,
pixel 0.5, shown at level 4.4, step 1, values float32
Log from Thu Feb 12 17:06:40 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/zrizvi/Downloads/8DZ5.cif
8DZ5.cif title:
Cryo-EM structure of 364 Fab in complex with recombinant shortened Plasmodium
falciparum circumsporozoite protein (rsCSP) [more info...]
Chain information for 8DZ5.cif #1
---
Chain | Description
A C E H M | 364 Fab heavy chain
B D F L N | 364 Fab light chain
I | Circumsporozoite protein
> open EMDB:27789
Opened emdb 27789 as #2, grid size 220,220,220, pixel 1.15, shown at level
0.3, step 1, values float32, fit PDB 8dz5
> hide atoms
> show cartoons
> open /Users/zrizvi/Desktop/J138_005_volume_map_emready2.mrc
Opened J138_005_volume_map_emready2.mrc as #3, grid size 637,637,637, pixel
0.5, shown at level 0.082, step 4, values float32
> volume #3 step 1
> volume #3 level 1.727
> volume #3 level 3.448
> vop flip #3
Opened J138_005_volume_map_emready2.mrc z flip as #4, grid size 637,637,637,
pixel 0.5, shown at step 1, values float32
> hide #1 models
> set bgColor white
> graphics silhouettes true
> lighting shadows false
> lighting soft
> lighting full
> hide #!4 models
> show #!4 models
> select add #4
2 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,327.4,0.067721,-0.96335,-0.25955,350.65,0.057095,-0.25598,0.965,38.156
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,325.57,0.067721,-0.96335,-0.25955,327.43,0.057095,-0.25598,0.965,11.263
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99607,-0.080169,0.037668,297.17,0.067721,-0.96335,-0.25955,331.06,0.057095,-0.25598,0.965,15.212
> ui mousemode right translate
> select up
8950 atoms, 9174 bonds, 1155 residues, 7 models selected
> fitmap #4 inMap #2
Fit map J138_005_volume_map_emready2.mrc z flip in map emdb 27789 using 722271
points
correlation = 0.7375, correlation about mean = 0.04011, overlap = 9.945e+05
steps = 136, shift = 5.32, angle = 14.3 degrees
Position of J138_005_volume_map_emready2.mrc z flip (#4) relative to emdb
27789 (#2) coordinates:
Matrix rotation and translation
-0.99337646 0.10058286 0.05555444 264.91651700
-0.11457169 -0.90384363 -0.41223782 369.68694887
0.00874847 -0.41587231 0.90938094 55.13871083
Axis -0.01650415 0.21254486 -0.97701192
Axis point 142.31803628 183.34485876 0.00000000
Rotation angle (degrees) 173.67843250
Shift along axis 20.33165992
> select subtract #1
6 models selected
> select subtract #2
4 models selected
> hide #!2 models
> show #1 models
> select subtract #3
2 models selected
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.582, steps = 2000
shifted from previous position = 3.12
rotated from previous position = 6.67 degrees
atoms outside contour = 6103, contour level = 3.4477
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99477432 -0.09896582 0.02509620 304.20449803
0.08642159 -0.94707885 -0.30914875 323.81417332
0.05436324 -0.30536439 0.95068251 69.72705585
Axis 0.02015947 -0.15590668 0.98756605
Axis point 143.58853154 174.64329383 0.00000000
Rotation angle (degrees) 174.61424657
Shift along axis 24.50788175
> color #4 #ffffb2ab models
> lighting full
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
Drag select of 2 residues
> select up
280 atoms, 289 bonds, 40 residues, 1 model selected
> color sel black
> select clear
> show #!4 models
> show #!2 models
> hide #!4 models
> color #2 #b2b2b2b1 models
> color #2 #b2b2b2b0 models
> hide #!2 models
> show #!4 models
> volume #3 level 3.781
> hide #!3 models
> volume #4 level 4.397
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.581, steps = 2000
shifted from previous position = 0.242
rotated from previous position = 0.0941 degrees
atoms outside contour = 6767, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99482591 -0.09809147 0.02644767 303.97868662
0.08519576 -0.94730131 -0.30880722 324.17704316
0.05534526 -0.30495620 0.95075687 69.63647307
Axis 0.02075004 -0.15570561 0.98758554
Axis point 143.53604341 174.72210576 0.00000000
Rotation angle (degrees) 174.67554238
Shift along axis 24.60336188
> fitmap #2 inMap #4
Fit map emdb 27789 in map J138_005_volume_map_emready2.mrc z flip using 67102
points
correlation = 0.7187, correlation about mean = 0.1659, overlap = 8.451e+04
steps = 96, shift = 0.377, angle = 0.608 degrees
Position of emdb 27789 (#2) relative to J138_005_volume_map_emready2.mrc z
flip (#4) coordinates:
Matrix rotation and translation
-0.99393761 -0.10858956 0.01721448 303.06956338
0.09152362 -0.90395157 -0.41772596 331.71968624
0.06092174 -0.41361801 0.90840997 87.47175308
Axis 0.02005131 -0.21333946 0.97677235
Axis point 141.80065823 183.36819890 0.00000000
Rotation angle (degrees) 174.12053987
Shift along axis 20.74803338
> show #!2 models
> hide #1 models
> show #1 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/Ward lab work/364
> fab and CSP.cxs" includeMaps true
——— End of log from Thu Feb 12 17:06:40 2026 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> show #1 models
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 2.582, steps = 2000
shifted from previous position = 0.108
rotated from previous position = 0.145 degrees
atoms outside contour = 6785, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
-0.99459702 -0.10017085 0.02724993 304.11905575
0.08699560 -0.94749088 -0.30772195 323.74569560
0.05664383 -0.30368871 0.95108603 69.18569866
Axis 0.02128319 -0.15511012 0.98766790
Axis point 143.44028428 174.60330984 0.00000000
Rotation angle (degrees) 174.56297062
Shift along axis 24.58888421
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #1
8950 atoms, 9174 bonds, 1155 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.6314,-0.73868,-0.23597,167.23,0.74572,0.49495,0.44601,-94.609,-0.21267,-0.45758,0.86336,102.65
> view matrix models
> #1,-0.98558,-0.15069,0.077003,272.57,-0.010092,0.50657,0.86214,-47.02,-0.16892,0.84893,-0.50079,108.09
> view matrix models
> #1,-0.94088,-0.28361,-0.18525,316.03,-0.28544,0.36925,0.88441,4.0657,-0.18242,0.885,-0.42837,96.327
> fitmap #1 inMap #4
Fit molecule 8DZ5.cif (#1) to map J138_005_volume_map_emready2.mrc z flip (#4)
using 8950 atoms
average map value = 4.14, steps = 540
shifted from previous position = 2.77
rotated from previous position = 11.8 degrees
atoms outside contour = 4982, contour level = 4.3974
Position of 8DZ5.cif (#1) relative to J138_005_volume_map_emready2.mrc z flip
(#4) coordinates:
Matrix rotation and translation
0.99019989 0.13963739 -0.00236196 11.48961637
0.08976090 -0.64928916 -0.75522616 342.31421032
-0.10699140 0.74761285 -0.65546004 161.48976063
Axis 0.99703892 0.06941504 -0.03308991
Axis point 0.00000000 133.70365955 158.52805012
Rotation angle (degrees) 131.09235241
Shift along axis 29.87366836
> hide #1 models
> show #1 models
> volume #4 level 4.141
> hide #!4 models
> show #!4 models
> hide #1 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 6.81, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 6.34, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 6.71, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 5.88, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 4.06, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 5.07, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.33, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.11, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 7.44, step 1, values float32
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at level 1.65, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel
0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300,
pixel 0.74, shown at level 0.00288, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300,
pixel 0.74, shown at level 0.00217, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300,
pixel 0.74, shown at level 0.00284, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300,
pixel 0.74, shown at level 0.00903, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300,
pixel 0.74, shown at level 0.00381, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size
300,300,300, pixel 0.731, shown at level 0.0175, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size
300,300,300, pixel 0.731, shown at level 0.0363, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size
300,300,300, pixel 0.731, shown at level 0.0168, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.00917, step 1, values float32
Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300,
pixel 0.74, shown at level 0.00274, step 1, values float32
Log from Fri Feb 27 10:44:17 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 5.05, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 6.34, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 6.71, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 5.88, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 4.06, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 5.07, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.33, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.11, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 7.44, step 1, values float32
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at level 1.65, step 1, values float32
Log from Thu Feb 26 15:13:55 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 9.26, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 3.48, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy as #16, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 0 as #14.1, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 1 as #14.2, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 2 as #14.3, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 3 as #14.4, grid size
443,443,443, pixel 0.5, shown at level 4.95, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 4 as #14.5, grid size
443,443,443, pixel 0.5, shown at level 3.46, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 5 as #14.6, grid size
443,443,443, pixel 0.5, shown at level 4.45, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 6 as #14.7, grid size
443,443,443, pixel 0.5, shown at level 6.02, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 7 as #14.8, grid size
443,443,443, pixel 0.5, shown at level 2.27, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 0 as #17.1, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 1 as #17.2, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 2 as #17.3, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 3 as #17.4, grid size
443,443,443, pixel 0.5, shown at level 2.89, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 4 as #17.5, grid size
443,443,443, pixel 0.5, shown at level 2.84, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 5 as #17.6, grid size
443,443,443, pixel 0.5, shown at level 2.85, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 6 as #17.7, grid size
443,443,443, pixel 0.5, shown at level 2.17, step 1, values float32
Opened 6b. combination of 2526 and 2540 emready2 copy 7 as #17.8, grid size
443,443,443, pixel 0.5, shown at level 2.11, step 1, values float32
Opened 10. int1 vvd+imid NU J2527_map_emready2.mrc as #18, grid size
443,443,443, pixel 0.5, shown at level 0.9, step 1, values float32
Opened 11. int1 vvd+imid local J2541_004_volume_map_emready2.mrc as #19, grid
size 443,443,443, pixel 0.5, shown at level 1.16, step 1, values float32
Opened 12. combination of 10 and 11 as #20, grid size 443,443,443, pixel 0.5,
shown at level 5.05, step 1, values float32
Opened 14. int2 vvd+imid NU J2612_map_emready2.mrc as #21, grid size
438,438,438, pixel 0.5, shown at level 3.83, step 1, values float32
Opened 15. int2 vvd+imid local J2614_004_volume_map_emready2.mrc as #23, grid
size 438,438,438, pixel 0.5, shown at level 1.74, step 1, values float32
Opened 16. combination of 2612 and 2614 as #24, grid size 438,438,438, pixel
0.5, shown at level 5.92, step 1, values float32
Opened 18. frustrated vvd+imid NU J2438_map_emready2.mrc as #26, grid size
443,443,443, pixel 0.5, shown at level 1.18, step 1, values float32
Opened 19. frustrated vvd+imid local J2456_004_volume_map_emready2.mrc as #27,
grid size 443,443,443, pixel 0.5, shown at level 0.895, step 1, values float32
Opened 20 combination of 18 and 19 as #28, grid size 443,443,443, pixel 0.5,
shown at level 6.9, step 1, values float32
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.67, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.87, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.62, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 3.84, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 4.7, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 1.29, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 0.584, step 1, values float32
Opened 22. intT NU J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel
0.5, shown at level 1.39, step 1, values float32
Opened 23. intT local J2619_004_volume_map_emready2.mrc as #32, grid size
438,438,438, pixel 0.5, shown at level 1.71, step 1, values float32
Opened combination of 22 and 23 as #33, grid size 438,438,438, pixel 0.5,
shown at level 4.67, step 1, values float32
Log from Thu Feb 26 14:52:15 2026UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
Opened 2. cryosparc_P341_J1614_localrefine. selected.mrc as #4, grid size
300,300,300, pixel 0.833, shown at level 0.304, step 1, values float32
Opened 1. cryosparc_P341_J1735_NUrefine selected.mrc as #9, grid size
300,300,300, pixel 0.833, shown at level 0.158, step 1, values float32
Opened 3a. composite_map on EMReady2 maps of 1735 and 1614.ccp4 as #10, grid
size 300,300,300, pixel 0.833, shown at level 14, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 0 as #13.1, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 1 as #13.2, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 2 as #13.3, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 3 as #13.4, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 4 as #13.5, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 5 as #13.6, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 6 as #13.7, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 7 as #13.8, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 8 as #13.9, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 9 as #13.10, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 10 as #13.11, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened composite_map on EMReady2 maps of 1735 and 1614.ccp4 11 as #13.12, grid
size 300,300,300, pixel 0.833, shown at level 9.96, step 1, values float32
Opened 4. open- vvd+imid NU J2526_map_emready2.mrc as #1, grid size
443,443,443, pixel 0.5, shown at level 1.01, step 1, values float32
Opened 5. open- vvd+imid local J2540_005_volume_map_emready2.mrc as #2, grid
size 443,443,443, pixel 0.5, shown at level 1.2, step 1, values float32
Opened 6a. combination of 2526 and 2540 emready2 as #3, grid size 443,443,443,
pixel 0.5, shown at level 6.02, step 1, values float32
Opened 7. Clsoed- vvd+imid NU J2528_map_emready2.mrc as #5, grid size
443,443,443, pixel 0.5, shown at level 2.31, step 1, values float32
Opened 8. Closed- vvd+imid local J2544_007_volume_map_emready2.mrc as #7, grid
size 443,443,443, pixel 0.5, shown at level 2.03, step 1, values float32
Opened 9a. combination of 2528 and 2544 emready2 as #8, grid size 443,443,443,
pixel 0.5, shown at level 5.07, step 1, values float32
[deleted to fit within ticket limits]
> fitmap sel inMap #28
Fit molecule copy of 9b. 5v3o- closed vvd+imid C (#29.2) to map 20 combination
of 18 and 19 (#28) using 2902 atoms
average map value = 4.105, steps = 100
shifted from previous position = 1.88
rotated from previous position = 4.04 degrees
atoms outside contour = 2438, contour level = 7.4224
Position of copy of 9b. 5v3o- closed vvd+imid C (#29.2) relative to 20
combination of 18 and 19 (#28) coordinates:
Matrix rotation and translation
0.27233221 0.52177145 0.80844897 123.48841484
-0.49550931 -0.64417995 0.58266862 177.43691566
0.82480646 -0.55927342 0.08311166 122.12419648
Axis -0.74664500 -0.01069515 -0.66513672
Axis point 0.00000000 89.54887059 -48.61646436
Rotation angle (degrees) 130.11830986
Shift along axis -175.32900958
> select clear
> select add #29
8879 atoms, 9055 bonds, 16 pseudobonds, 1140 residues, 6 models selected
> combine sel
> close #29
> rename #30 "21. model for frustrated"
> color zone #28 near #30 distance 10
> hide #!30 models
> color zone #28 near #30 distance 15
> select clear
> volume #28 level 6.67
> volume #28 level 6.933
> volume #28 level 6.896
> ui mousemode right "map eraser"
> volume erase #28 center 146.05,96.223,129.13 radius 3.8053
> view
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/frustrated/frustrated.png"
> width 1800 height 1592 supersample 4 transparentBackground true
> hide #!28 models
> show #!28 models
> show #!24 models
> show #!20 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!8 models
> show #!20 models
> volume #20 level 4.956
> show #!16 models
> hide #!16 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:06:42 2026 ———
> view name session-start
opened ChimeraX session
> show #!14 models
> hide #!8 models
> hide #!24 models
> hide #!28 models
> hide #!20 models
> show #!3 models
> hide #!3 models
> show #!14.4 models
> show #!14.5 models
> show #!14.6 models
> show #!14.7 models
> show #!14.8 models
> volume #14.4 level 4.654
> volume #14.8 level 2.274
> volume #14.6 level 4.453
> volume #14.5 level 3.458
> volume #14.4 level 4.954
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/open/fig2b.open.png" width
> 1800 height 1532 supersample 4 transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:20:52 2026 ———
> view name session-start
opened ChimeraX session
> hide #!14 models
> show #!20 models
> hide #!20 models
> show #!18 models
> show #!19 models
> show #!20 models
> hide #!19 models
> hide #!18 models
> show #!22 models
> hide #!22 models
> volume #20 level 0.9846
> volume #20 level 5.052
> show #!22 models
> fitmap #22 inMap #20
Fit molecule 13. vvd+iberdo int1.pdb (#22) to map 12. combination of 10 and 11
(#20) using 8572 atoms
average map value = 10.26, steps = 80
shifted from previous position = 2.39
rotated from previous position = 0.5 degrees
atoms outside contour = 1849, contour level = 5.0525
Position of 13. vvd+iberdo int1.pdb (#22) relative to 12. combination of 10
and 11 (#20) coordinates:
Matrix rotation and translation
0.45290121 -0.60806549 0.65202519 66.30022263
0.65359924 -0.27095091 -0.70667789 185.29085499
0.60637325 0.74621844 0.27471715 -70.50773735
Axis 0.75483642 0.02371797 0.65548413
Axis point 0.00000000 129.65147482 28.74738650
Rotation angle (degrees) 105.76344401
Shift along axis 8.22384205
> ui tool show "Color Zone"
> volume splitbyzone #20
Opened 12. combination of 10 and 11 0 as #29.1, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 1 as #29.2, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 2 as #29.3, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 3 as #29.4, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 4 as #29.5, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 5 as #29.6, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 6 as #29.7, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
Opened 12. combination of 10 and 11 7 as #29.8, grid size 443,443,443, pixel
0.5, shown at level 5.05, step 1, values float32
> volume #29.2 level 5.983
> volume #29.2 level 5.673
> volume #29.3 level 5.872
> hide #!22 models
> volume #29.4 level 5.623
> volume #29.5 level 3.84
> volume #29.6 level 4.849
> volume #29.7 level 1.294
> volume #29.8 level 0.5091
> volume #29.6 level 4.704
> volume #29.8 level 0.5836
[Repeated 1 time(s)]
> surface dust #29.1 size 5
> surface dust #29.2 size 5
> surface dust #29.3 size 5
> surface dust #29.4 size 5
> surface dust #29.5 size 5
> surface dust #29.6 size 5
> surface dust #29.7 size 5
> surface dust #29.8 size 5
> view
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1.png" width 1800
> height 1536 supersample 4 transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Wed Feb 25 16:39:20 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/zrizvi/Desktop/J2618_map_emready2.mrc
Opened J2618_map_emready2.mrc as #31, grid size 438,438,438, pixel 0.5, shown
at level 1.39, step 2, values float32
> open /Users/zrizvi/Desktop/J2619_004_volume_map_emready2.mrc
Opened J2619_004_volume_map_emready2.mrc as #32, grid size 438,438,438, pixel
0.5, shown at level 1.71, step 2, values float32
> volume #31 step 1
> volume #32 step 1
> hide #!29 models
> vop max #31 #32
Opened volume maximum as #33, grid size 438,438,438, pixel 0.5, shown at step
1, values float32
> rename #31 "22. intT NU J2618_map_emready2.mrc"
> rename #32 "23. intT local J2619_004_volume_map_emready2.mrc"
> rename #33 "combination of 22 and 23"
> volume #33 level 2.381
> show #!22 models
> color #33 darkgrey models
> color #33 #a9a9a9c7 models
> volume #33 level 5.874
> volume #33 level 4.545
> show #!20 models
> hide #!22 models
> volume #33 level 2.913
> fitmap #33 inMap #20
Fit map combination of 22 and 23 in map 12. combination of 10 and 11 using
652899 points
correlation = 0.9014, correlation about mean = 0.6876, overlap = 3.196e+07
steps = 68, shift = 1.94, angle = 2.29 degrees
Position of combination of 22 and 23 (#33) relative to 12. combination of 10
and 11 (#20) coordinates:
Matrix rotation and translation
0.99985638 0.01511052 -0.00767438 -0.38329162
-0.01537770 0.99923205 -0.03603929 7.26333600
0.00712391 0.03615212 0.99932091 -4.77174349
Axis 0.90521734 -0.18555763 -0.38229561
Axis point 0.00000000 134.36592659 199.34294276
Rotation angle (degrees) 2.28528549
Shift along axis 0.12948695
> show #!22 models
> hide #!20 models
> fitmap #13 inMap #33
Multiple maps for #13
> fitmap #22 inMap #33
Fit molecule 13. vvd+iberdo int1.pdb (#22) to map combination of 22 and 23
(#33) using 8572 atoms
average map value = 7.743, steps = 48
shifted from previous position = 0.0492
rotated from previous position = 0.175 degrees
atoms outside contour = 1479, contour level = 2.9126
Position of 13. vvd+iberdo int1.pdb (#22) relative to combination of 22 and 23
(#33) coordinates:
Matrix rotation and translation
0.44794773 -0.59759499 0.66499854 63.25832983
0.68016505 -0.25496860 -0.68728925 177.00102643
0.58027436 0.76017843 0.29225062 -72.48259428
Axis 0.74896737 0.04383907 0.66115506
Axis point 0.00000000 126.28354268 26.48493941
Rotation angle (degrees) 104.91496081
Shift along axis 7.21575224
> volume #33 level 2.799
> combine #22 close false modelId #34
> hide #!22 models
> split #34
Split copy of 13. vvd+iberdo int1.pdb (#34) into 3 models
Chain information for copy of 13. vvd+iberdo int1.pdb F #34.1
---
Chain | Description
F | No description available
Chain information for copy of 13. vvd+iberdo int1.pdb G #34.2
---
Chain | Description
G | No description available
> select add #34
8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected
> select subtract #34
Nothing selected
> select add #34.1
6318 atoms, 6434 bonds, 824 residues, 1 model selected
> fitmap sel inMap #33
Fit molecule copy of 13. vvd+iberdo int1.pdb F (#34.1) to map combination of
22 and 23 (#33) using 6318 atoms
average map value = 8.754, steps = 48
shifted from previous position = 0.0938
rotated from previous position = 0.438 degrees
atoms outside contour = 663, contour level = 2.7987
Position of copy of 13. vvd+iberdo int1.pdb F (#34.1) relative to combination
of 22 and 23 (#33) coordinates:
Matrix rotation and translation
0.44720607 -0.59287065 0.66970973 62.36924831
0.68026524 -0.26069452 -0.68503838 177.34741034
0.58072880 0.76193357 0.28672512 -72.18123785
Axis 0.74996599 0.04611884 0.65986671
Axis point 0.00000000 125.96199032 26.58252675
Rotation angle (degrees) 105.27081321
Shift along axis 7.32387673
> select subtract #34.1
Nothing selected
> select add #34.2
2236 atoms, 2278 bonds, 4 pseudobonds, 351 residues, 2 models selected
> fitmap sel inMap #33
Fit molecule copy of 13. vvd+iberdo int1.pdb G (#34.2) to map combination of
22 and 23 (#33) using 2236 atoms
average map value = 5.896, steps = 76
shifted from previous position = 1.14
rotated from previous position = 2.85 degrees
atoms outside contour = 589, contour level = 2.7987
Position of copy of 13. vvd+iberdo int1.pdb G (#34.2) relative to combination
of 22 and 23 (#33) coordinates:
Matrix rotation and translation
0.44344600 -0.63389462 0.63366652 71.75468851
0.67511779 -0.22879669 -0.70133305 176.58897148
0.58955205 0.73880287 0.32649456 -74.75561140
Axis 0.73980171 0.02266172 0.67244321
Axis point 0.00000000 129.64772120 24.41606470
Rotation angle (degrees) 103.26340176
Shift along axis 6.81714860
> select subtract #34.2
Nothing selected
> select add #34.3
18 atoms, 20 bonds, 1 residue, 1 model selected
> select subtract #34.3
Nothing selected
> volume #33 level 4.263
> select add #34
8572 atoms, 8732 bonds, 4 pseudobonds, 1176 residues, 5 models selected
> combine sel
> rename #35 "vvd+iberdo intT.pdb"
> close #34
> color zone #33 near #35 distance 8
> hide #!35 models
> volume #33 level 5.801
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!13 models
> hide #!20 models
> hide #!33 models
> show #!33 models
> show #!20 models
> hide #!13 models
> show #!10 models
> show #!11 models
> show #!13 models
> hide #!20 models
> hide #!33 models
> volume #10 level 9.255
> hide #!10 models
> show #!10 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!20 models
> show #!35 models
> hide #!35 models
> show #!33 models
> show #!3 models
> hide #!20 models
> hide #!33 models
> show #!33 models
> hide #!33 models
> show #!20 models
> hide #!20 models
> volume #3 level 4.554
> show #!14 models
> hide #!3 models
> show #!35 models
> hide #!35 models
> show #!33 models
> hide #!14 models
> volume #33 level 4.52
> volume #33 level 4.007
> volume #33 level 4.373
> volume #33 level 4.666
> show #!15 models
> hide #!15 models
> volume copy #33 modelId #36
Opened combination of 22 and 23 copy as #36, grid size 438,438,438, pixel 0.5,
shown at step 1, values float32
> show #!35 models
> color zone #36 near #35 distance 8
> hide #!35 models
> show #!16 models
> hide #!36 models
> show #!14 models
> hide #!16 models
> show #!36 models
> select add #36
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #36,0.97911,-0.16791,0.11466,13.358,0.15621,0.26023,-0.95283,192.83,0.13015,0.95083,0.28103,-63.585
> select subtract #36
Nothing selected
> color #36 darkgrey models
> color #36 #a9a9a9b1 models
> color #36 #a9a9a9b0 models
> select add #36
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #36,0.97911,-0.16791,0.11466,31.329,0.15621,0.26023,-0.95283,187.23,0.13015,0.95083,0.28103,-64.985
Must specify one map, got 8
> hide #!14 models
> show #!3 models
> fitmap #36 inMap #3
Fit map combination of 22 and 23 copy in map 6a. combination of 2526 and 2540
emready2 using 414467 points
correlation = 0.9261, correlation about mean = 0.6457, overlap = 2.816e+07
steps = 204, shift = 12.5, angle = 7.94 degrees
Position of combination of 22 and 23 copy (#36) relative to 6a. combination of
2526 and 2540 emready2 (#3) coordinates:
Matrix rotation and translation
0.99962918 0.02226516 -0.01567676 -0.49377100
-0.02233593 0.99974104 -0.00435423 4.75196594
0.01557575 0.00470277 0.99986763 -1.11245630
Axis 0.16405010 -0.56607901 -0.80786269
Axis point 165.16995213 11.13270144 0.00000000
Rotation angle (degrees) 1.58181509
Shift along axis -1.87227942
> select clear
> volume #3 level 3.39
> volume #3 level 4.252
> hide #!36 models
> volume #3 level 3.476
> show #!36 models
> volume #36 level 3.48
> hide #!36 models
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!3 models
> show #!35 models
> hide #!35 models
> show #!6 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> close #36
> show #!33 models
> show #!35 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Thu Feb 26 14:52:15 2026 ———
> view name session-start
opened ChimeraX session
> hide #!35 models
> show #!35 models
> ui tool show "Color Zone"
> volume #33 level 3.679
> volume splitbyzone #33
Opened combination of 22 and 23 0 as #34.1, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 1 as #34.2, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 2 as #34.3, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 3 as #34.4, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 4 as #34.5, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 5 as #34.6, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 6 as #34.7, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
Opened combination of 22 and 23 7 as #34.8, grid size 438,438,438, pixel 0.5,
shown at level 3.68, step 1, values float32
> hide #!35 models
> volume #34.1 level 6.344
> volume #34.2 level 5.958
> volume #34.3 level 5.16
> volume #34.4 level 3.856
> volume #34.5 level 4.357
> volume #34.6 level 4.173
> volume #34.7 level 3.106
> volume #34.8 level 0.8963
> split #34.8
> hide #34.8.1 models
> show #34.8.1 models
> hide #!34.8 models
> show #!34.8 models
> volume #34.8 level 2.434
> volume #34.6 level 3.308
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> hide #!34.1 models
> hide #!34 models
> show #!34 models
> volume erase #34.8 center 120.33,109.23,128.57 radius 1.8615
> show #!34.1 models
> hide #!34.1 models
> show #!34.2 models
> show #!34.3 models
> show #!34.4 models
> show #!34.5 models
> show #!34.6 models
> show #!34.7 models
Can only have one displayed volume when erasing
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> volume erase #34.8 center 119.25,108.39,128.28 radius 1.2045
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> hide #!34.4 models
> hide #!34.5 models
> show #!34.5 models
> hide #!34.7 models
> hide #!34.5 models
> hide #!34.6 models
> volume erase #34.8 center 121.8,109.59,127.84 radius 1.2045
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> volume erase #34.8 center 121.22,109.7,127.61 radius 1.2045
> hide #36 models
> show #!34.2 models
> show #!34.3 models
> show #!34.4 models
> show #!34.5 models
> show #!34.6 models
> show #!34.7 models
> show #36 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> volume erase #34.8 center 115.77,109.2,129.16 radius 1.2045
> show #!34.5 models
> show #!34.4 models
> hide #!34.4 models
> show #!34.6 models
> hide #!34.5 models
Can only have one displayed volume when erasing
> hide #!34.6 models
> volume erase #34.8 center 114.83,108.58,128.85 radius 0.438
> hide #36 models
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> show #!34.3 models
> show #!34.2 models
> volume #34.8 level 5.949
> volume #34.8 level 7.438
> show #!35 models
> hide #!35 models
> volume #34.6 level 2.123
> volume #34.6 level 2.716
> volume copy #34.8 modelId #37
Opened combination of 22 and 23 7 copy as #37, grid size 438,438,438, pixel
0.5, shown at step 1, values float32
> volume #34.6 level 3.531
> hide #!37 models
> show #!37 models
> show #!34.8 models
> hide #!34.8 models
> hide #34.8.1 models
> hide #!34.7 models
> hide #!34.6 models
> hide #!34.5 models
> show #!34.5 models
> show #!34.6 models
> show #!34.7 models
> volume #37 level 1.653
> hide #!34.6 models
> hide #!34.7 models
> hide #!34.5 models
> hide #!34.4 models
> hide #!34.3 models
> hide #!34.2 models
> show #36 models
> volume erase #37 center 118.25,112.1,126.67 radius 10.731
> show #!34.8 models
> show #34.8.1 models
> show #!34.7 models
> show #!34.6 models
> show #!34.5 models
> show #!34.4 models
> show #!34.3 models
> show #!34.2 models
> volume #34.4 level 4.063
> volume #34.2 level 6.366
> volume #34.2 level 6.706
> volume #34.3 level 5.881
> volume #34.5 level 5.067
> volume #34.6 level 3.333
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/intT.png" width 1800
> height 1541 supersample 4 transparentBackground true
Cell requested for row 35 is out of bounds for table with 47 rows! Resizing
table model.
> close #36
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
——— End of log from Thu Feb 26 15:13:55 2026 ———
> view name session-start
opened ChimeraX session
> hide #!34 models
> hide #!37 models
> show #!20 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened cryosparc_P341_J2527_map (3).mrc as #36, grid size 300,300,300, pixel
0.74, shown at level 0.00925, step 2, values float32
> volume #36 step 1
> show #!22 models
> volume #36 level 0.003026
> color #36 #b2b2b2ab models
> hide #!22 models
> show #!21 models
> hide #!20 models
> show #!22 models
> hide #!21 models
> ui tool show "Color Zone"
Need to color zone map before it can be split
> color zone #36 near #22 distance 4.44
> color zone #36 near #22 distance 4.54
> color zone #36 near #22 distance 4.64
> color zone #36 near #22 distance 4.74
> color zone #36 near #22 distance 1
> color zone #36 near #22 distance 10
[Repeated 1 time(s)]
> color zone #36 near #22 distance 11
> color zone #36 near #22 distance 12
> color zone #36 near #22 distance 13
> color zone #36 near #22 distance 14
> color zone #36 near #22 distance 15
> color zone #36 near #22 distance 16
> color zone #36 near #22 distance 17
> color zone #36 near #22 distance 18
> color zone #36 near #22 distance 19
[Repeated 1 time(s)]
> volume splitbyzone #36
Opened cryosparc_P341_J2527_map (3).mrc 0 as #38.1, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 1 as #38.2, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 2 as #38.3, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 3 as #38.4, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 4 as #38.5, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 5 as #38.6, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 6 as #38.7, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
Opened cryosparc_P341_J2527_map (3).mrc 7 as #38.8, grid size 300,300,300,
pixel 0.74, shown at level 0.00303, step 1, values float32
> hide #!22 models
> hide #!38.2 models
> hide #!38.3 models
> color #38.4 darkgrey models
> color #38.5 darkgrey models
> color #38.6 darkgrey models
> color #38.6 #a9a9a9ae models
> hide #!38.7 models
> color #38.6 #a9a9a9ad models
> color #38.5 #a9a9a9ad models
> color #38.4 #a9a9a9ad models
> show #!20 models
> volume #20 level 6.805
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> hide #!38.8 models
> show #!38.8 models
> hide #!38.8 models
> show #!38.8 models
> hide #!38.6 models
> show #!38.6 models
> hide #!38.5 models
> show #!38.5 models
> hide #!38.4 models
> show #!38.4 models
> volume #38.8 level 0.009034
> volume copy #38.8 modelId #39
Opened cryosparc_P341_J2527_map (3).mrc 7 copy as #39, grid size 300,300,300,
pixel 0.74, shown at step 1, values float32
> volume #39 level 0.009534
> volume #39 level 0.004671
> show #!38.8 models
> hide #!38 models
> hide #!20 models
> show #!20 models
> volume #39 level 0.003813
> hide #!20 models
> ui mousemode right "map eraser"
> volume erase #39 center 101.4,96.436,134.1 radius 9.6285
> volume erase #39 center 98.503,100.69,141.99 radius 9.6285
> volume erase #39 center 103.91,97.962,145.36 radius 9.6285
> show #!38 models
> show #!38.8 models
> show #!20 models
> volume #38.6 level 0.002838
> volume #38.5 level 0.001958
> volume #38.4 level 0.002883
> volume #38.5 level 0.002171
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"
> width 1800 height 1643 supersample 4 transparentBackground true
> hide #!38 models
> hide #!39 models
> hide #!20 models
> show #!24 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2574_006_volume_map (4).mrc"
Opened cryosparc_P341_J2574_006_volume_map (4).mrc as #40, grid size
300,300,300, pixel 0.731, shown at level 0.0255, step 2, values float32
> select add #40
2 models selected
> show #!39 models
> show #!38 models
> select subtract #40
Nothing selected
> hide #!40 models
> hide #!24 models
> show #!20 models
> color #38.4 #d6d6d6ff models
> color #38.5 #d6d6d6ff models
> color #38.6 #d6d6d6ff models
> color #38.4 #d6d6d680 models
> color #38.5 #d6d6d680 models
> color #38.6 #d6d6d680 models
> select clear
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 1/int1withLOWRES.png"
> width 1800 height 1643 supersample 4 transparentBackground true
> hide #!38 models
> hide #!39 models
> hide #!20 models
> show #!40 models
> show #!24 models
> volume #40 step 1
> volume #40 level 0.08603
> select add #40
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #40,1,0,0,0.29592,0,1,0,38.019,0,0,1,1.4105
> ui mousemode right translate
> fitmap #40 inMap #24
Fit map cryosparc_P341_J2574_006_volume_map (4).mrc in map 16. combination of
2612 and 2614 using 76567 points
correlation = 0.9704, correlation about mean = 0.6325, overlap = 1.003e+05
steps = 76, shift = 1.78, angle = 0.0636 degrees
Position of cryosparc_P341_J2574_006_volume_map (4).mrc (#40) relative to 16.
combination of 2612 and 2614 (#24) coordinates:
Matrix rotation and translation
0.99999997 -0.00011331 -0.00020616 0.84203922
0.00011353 0.99999940 0.00108507 36.29613778
0.00020603 -0.00108510 0.99999939 0.89143909
Axis -0.97729698 -0.18562141 0.10215333
Axis point 0.00000000 1542.77868389 -32171.78243850
Rotation angle (degrees) 0.06361512
Shift along axis -7.46919917
> select clear
> volume #40 level 0.03029
> show #!25 models
> hide #!24 models
> color zone #40 near #25 distance 20
> volume splitbyzone #40
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 0 as #41.1, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 1 as #41.2, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 2 as #41.3, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 3 as #41.4, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 4 as #41.5, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 5 as #41.6, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 6 as #41.7, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 7 as #41.8, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
Opened cryosparc_P341_J2574_006_volume_map (4).mrc 8 as #41.9, grid size
300,300,300, pixel 0.731, shown at level 0.0303, step 1, values float32
> hide #!41.2 models
> hide #!41.3 models
> hide #!25 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!41.7 models
> hide #!41.8 models
> hide #!41.9 models
> color #41.4 #d6d6d6ff models
> color #41.5 #d6d6d6ff models
> color #41.6 #d6d6d6ff models
> color #41.4 #d6d6d680 models
> color #41.5 #d6d6d680 models
> color #41.6 #d6d6d680 models
> volume #41.4 level 0.02525
> volume #41.5 level 0.03192
> volume #41.6 level 0.02225
> volume #41.6 level 0.01654
> volume #41.5 level 0.02215
> volume #41.4 level 0.0175
> volume #41.6 level 0.01676
> volume #41.5 level 0.03626
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/int 2/int2withLOWRES.png"
> width 1800 height 2071 supersample 4 transparentBackground true
> hide #!41.4 models
> show #!41.4 models
> hide #!41.1 models
> show #!41.1 models
> hide #!41 models
> hide #!24 models
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.0102, step 2, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300, pixel
0.74, shown at level 0.00925, step 2, values float32
> rename #42 "OPEN cryosparc_P341_J2526_map (3).mrc"
> rename #43 "INT1 cryosparc_P341_J2527_map (3).mrc"
> volume #42 step 1
> volume #43 step 1
> volume #42 level 0.008174
> volume #43 level 0.003606
> volume #43 level 0.004475
> fitmap #42 inMap #43
Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map INT1
cryosparc_P341_J2527_map (3).mrc using 302851 points
correlation = 0.9587, correlation about mean = 0.8943, overlap = 311.4
steps = 84, shift = 0.372, angle = 1.93 degrees
Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to INT1
cryosparc_P341_J2527_map (3).mrc (#43) coordinates:
Matrix rotation and translation
0.99994514 -0.00782905 0.00695917 0.32141175
0.00804782 0.99945593 -0.03198565 2.52472465
-0.00670496 0.03203990 0.99946410 -3.99736918
Axis 0.95042634 0.20283696 0.23568399
Axis point 0.00000000 125.14400802 77.59405627
Rotation angle (degrees) 1.93023280
Shift along axis -0.12453025
> volume #42 level 0.009173
> ui tool show "Side View"
> volume #42 color #d6d6d6
> volume #43 color #797979
> color #43 khaki
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> volume #43 color #f0e68c68
> volume #43 color #f0e68c69
> volume #42 color #d6d6d6
> volume #42 color silver
> volume #42 color darkgrey
> volume #42 color #a9a9a980
> volume #43 color khaki
> volume #43 level 0.003606
> volume #43 color #f0e68c80
> volume #42 color #d6d6d6
> volume #42 level 0.007674
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!43 models
> ui mousemode right "rotate selected models"
> hide #!43 models
> select add #42
4 models selected
> view matrix models
> #42,0.74119,-0.63871,-0.20662,142.23,0.12355,0.43232,-0.89322,164.37,0.65983,0.63651,0.39934,-98.741
> view matrix models
> #42,0.74119,-0.63871,-0.20662,144.66,0.12355,0.43232,-0.89322,143.85,0.65983,0.63651,0.39934,-102.15
> view matrix models
> #42,0.44408,-0.89568,0.023216,189.36,0.37521,0.16238,-0.91261,154.39,0.81364,0.41398,0.40818,-89.996
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.91023,-0.37692,-0.17151,84.578,-0.039193,0.33389,-0.9418,181.92,0.41225,0.86397,0.28915,-92.763
> view matrix models
> #42,0.91023,-0.37692,-0.17151,95.55,-0.039193,0.33389,-0.9418,183.8,0.41225,0.86397,0.28915,-76.869
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.91023,-0.37692,-0.17151,99.112,-0.039193,0.33389,-0.9418,188.29,0.41225,0.86397,0.28915,-84.482
> fitmap #42 inMap #3
Fit map OPEN cryosparc_P341_J2526_map (3).mrc in map 6a. combination of 2526
and 2540 emready2 using 311826 points
correlation = 0.9154, correlation about mean = 0.7726, overlap = 5.891e+04
steps = 164, shift = 5.11, angle = 13 degrees
Position of OPEN cryosparc_P341_J2526_map (3).mrc (#42) relative to 6a.
combination of 2526 and 2540 emready2 (#3) coordinates:
Matrix rotation and translation
0.99999988 -0.00020781 -0.00043686 0.14986729
0.00020809 0.99999978 0.00063070 -0.27744247
0.00043673 -0.00063079 0.99999970 0.09652282
Axis -0.79348717 -0.54949254 0.26160285
Axis point 0.00000000 128.45846825 388.72679196
Rotation angle (degrees) 0.04554435
Shift along axis 0.05878544
> select clear
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> close #42-43
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2526_map (3).mrc"
Opened cryosparc_P341_J2526_map (3).mrc as #42, grid size 300,300,300, pixel
0.74, shown at level 0.0102, step 2, values float32
> select add #42
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,99.53,0.61004,-0.27092,-0.74462,189.76,0.6772,0.66618,0.31242,-94.907
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,88.89,0.61004,-0.27092,-0.74462,181.52,0.6772,0.66618,0.31242,-80.942
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #42,0.4114,-0.69485,0.58986,94.879,0.61004,-0.27092,-0.74462,190.11,0.6772,0.66618,0.31242,-70.537
> ui mousemode right translate
> fitmap #6 inMap #42
Fit molecule 6c. vvd+iberdo open.pdb (#6) to map cryosparc_P341_J2526_map
(3).mrc (#42) using 8572 atoms
average map value = 0.03997, steps = 100
shifted from previous position = 5.84
rotated from previous position = 6.69 degrees
atoms outside contour = 769, contour level = 0.010172
Position of 6c. vvd+iberdo open.pdb (#6) relative to cryosparc_P341_J2526_map
(3).mrc (#42) coordinates:
Matrix rotation and translation
0.99998883 0.00472722 0.00003282 -0.62446445
-0.00472717 0.99998796 -0.00131983 0.56931961
-0.00003906 0.00131966 0.99999913 -0.56430308
Axis 0.26889250 0.00732175 -0.96314237
Axis point 119.45514153 153.98357738 0.00000000
Rotation angle (degrees) 0.28121410
Shift along axis 0.37975882
> select clear
> open "/Users/zrizvi/Downloads/cryosparc_P341_J2527_map (3).mrc"
Opened INT1 cryosparc_P341_J2527_map (3).mrc as #43, grid size 300,300,300,
pixel 0.74, shown at level 0.00925, step 2, values float32
> hide #!6 models
> select add #43
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #43,0.20325,-0.63332,0.74673,97.599,0.52292,-0.57456,-0.62963,229.83,0.8278,0.51845,0.2144,-80.796
> ui mousemode right "translate selected models"
> view matrix models
> #43,0.20325,-0.63332,0.74673,90.103,0.52292,-0.57456,-0.62963,217.46,0.8278,0.51845,0.2144,-64.405
> ui mousemode right translate
> fitmap #43 inMap #42
Fit map INT1 cryosparc_P341_J2527_map (3).mrc in map cryosparc_P341_J2526_map
(3).mrc using 33711 points
correlation = 0.9633, correlation about mean = 0.8938, overlap = 38.63
steps = 208, shift = 16.4, angle = 21.5 degrees
Position of INT1 cryosparc_P341_J2527_map (3).mrc (#43) relative to
cryosparc_P341_J2526_map (3).mrc (#42) coordinates:
Matrix rotation and translation
0.99994614 0.00789387 -0.00673806 -0.33316626
-0.00767360 0.99945480 0.03211278 -2.42129604
0.00698788 -0.03205935 0.99946154 4.08392857
Axis -0.95147544 -0.20351341 -0.23081764
Axis point 0.00000000 125.11362206 78.36602072
Rotation angle (degrees) 1.93251941
Shift along axis -0.13287701
> select clear
> volume #42 step 1
> volume #43 step 1
> show #!6 models
> color zone #42 near #6 distance 8
> color zone #42 near #6 distance 15
> hide #!6 models
> show #!43 models
> color #43 #d6d6d6ff models
> color #43 #d6d6d682 models
[Repeated 1 time(s)]
> color #43 #d6d6d6ff models
> volume #43 level 0.004475
> color #43 #d6d6d680 models
> ui tool show "Side View"
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/openTOintVVDshift.png" width
> 1800 height 2071 supersample 4 transparentBackground true
> ui tool show "Side View"
> volume #43 level 0.002738
> volume #42 level 0.01417
> volume #42 level 0.009173
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig
> maps/openTOintVVDshiftFULLimage.png" width 1800 height 2071 supersample 4
> transparentBackground true
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/2025-VVD-CRBN-
> inhibitor/Figures/Fig 2b final EMready fig maps/0. figure 2 making .cxs"
> includeMaps true
[Repeated 1 time(s)]
——— End of log from Fri Feb 27 10:44:17 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 26 minutes, 8 seconds
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
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: Yes
Connection Type: Internal
DELL U3011:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
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: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503130118
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.7
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: 2.15
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.7
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-ProfileGrids: 1.0.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.44
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
coverage: 7.6.12
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.17.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
pluggy: 1.5.0
prompt_toolkit: 3.0.50
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: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pyzmq: 26.3.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.21
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.43.0
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash destroying OpenGL context on exit |
comment:2 by , 3 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
ChimeraX crashed when you quit while the Qt windows toolkit was trying to delete its OpenGL graphics context. This is a known problem with Qt that has probably been fixed in the newer Qt version in ChimeraX 1.10 and ChimeraX 1.11. If you get this crash on exit often you might want to update ChimeraX. But beware that newer versions of the Qt window toolkit have other crashing behavior on Mac especially with multiple displays. So if your current ChimeraX is working well you might stick with it.
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Reported by Zeba Rizvi