![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17241 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f49acc00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.segment._segment (total: 119)
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"procRole" : "Foreground",
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"procLaunch" : "2025-03-29 12:21:56.3314 -0500",
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"procExitAbsTime" : 2967397421991,
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"codeSigningTeamID" : "LWV8X224YF",
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4365926400\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1043ac000-1043b0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at
level 0.0284, step 1, values float32
Opened
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at
level 0.00701, step 1, values float32
Log from Thu Mar 27 16:53:46 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at
level 0.0284, step 1, values float32
Opened
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at
level 0.00701, step 1, values float32
Log from Wed Mar 26 18:37:57 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM
> Maps/State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
> sharpened-highres.mrc" format mrc
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at
level 0.0049, step 2, values float32
> open
> "/Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/CryoEM
> Maps/State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
> sharpened-highres.mrc"
Opened
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at
level 0.00701, step 2, values float32
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc in map
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc using 33671 points
correlation = 0.8245, correlation about mean = 0.7206, overlap = 2069
steps = 60, shift = 0.77, angle = 1.48 degrees
Position of
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) relative to
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99987526 -0.01361448 -0.00800679 3.25328190
0.01377534 0.99969720 0.02038996 -4.19338540
0.00772676 -0.02049771 0.99976004 1.06230708
Axis -0.79135884 -0.30451436 0.53011526
Axis point 0.00000000 68.27155938 217.64147059
Rotation angle (degrees) 1.48033436
Shift along axis -0.73442213
> volume #1 level 0.0284
> volume #1 step 1
> volume #2 step 1
> surface dust #1 size 8.32
> surface dust #2 size 8.32
> lighting full
> open /Users/justinvanriper/Desktop/2024-05-03_apply_ncs_56-coot-0_RNA-
> WC_edited_modified_real_space_refined_061.pdb
Chain information for 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb #3
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) to map
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) using 13483 atoms
average map value = 0.03961, steps = 260
shifted from previous position = 3.36
rotated from previous position = 5.77 degrees
atoms outside contour = 11091, contour level = 0.0284
Position of 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) relative to
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) coordinates:
Matrix rotation and translation
0.99480463 -0.01991648 0.09983530 -7.78571490
0.01969956 0.99980096 0.00315823 -0.40546740
-0.09987833 -0.00117511 0.99499896 14.46516488
Axis -0.02127829 0.98066594 0.19452903
Axis point 135.56859660 0.00000000 84.49020469
Rotation angle (degrees) 5.84430165
Shift along axis 2.58193308
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) to map
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) using 13483 atoms
average map value = 0.03961, steps = 104
shifted from previous position = 0.00371
rotated from previous position = 0.00381 degrees
atoms outside contour = 11092, contour level = 0.0284
Position of 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) relative to
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) coordinates:
Matrix rotation and translation
0.99480232 -0.01990549 0.09986046 -7.78976604
0.01969464 0.99980125 0.00309692 -0.40019875
-0.09990226 -0.00111410 0.99499663 14.46298663
Axis -0.02067332 0.98070242 0.19441036
Axis point 135.51676875 0.00000000 84.52589260
Rotation angle (degrees) 5.84552505
Shift along axis 2.58031882
> ui mousemode right "rotate selected models"
> select clear
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> select #3
13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
> view matrix models
> #3,0.97334,0.090641,0.2107,-32.528,-0.11231,0.98929,0.09323,6.0511,-0.19999,-0.11441,0.9731,43.281
> view matrix models
> #3,0.96579,0.078425,0.24719,-34.703,-0.093033,0.99451,0.047964,8.7521,-0.24207,-0.06932,0.96778,43.581
> view matrix models
> #3,0.49419,-0.86308,0.10426,159.83,0.86885,0.48624,-0.093138,-29.911,0.029689,0.13662,0.99018,-18.884
> view matrix models
> #3,0.43314,-0.90103,0.022914,182.53,0.89896,0.43003,-0.083304,-27.905,0.065206,0.056681,0.99626,-14.115
> select clear
> select #2
2 models selected
> hide surfaces
> hide cartoons
> hide atoms
> select clear
> select #3
13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
> show sel cartoons
> view clip false
[Repeated 1 time(s)]
> show target m
> hide #!2 models
> select clear
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) to map
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) using 13483 atoms
average map value = 0.3207, steps = 104
shifted from previous position = 3.68
rotated from previous position = 7.08 degrees
atoms outside contour = 1877, contour level = 0.0284
Position of 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) relative to
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) coordinates:
Matrix rotation and translation
0.53358153 -0.84510500 -0.03298910 167.85814131
0.84235537 0.53452686 -0.06869114 -38.99484238
0.07568479 0.00886377 0.99709240 -8.19795878
Axis 0.04581637 -0.06420023 0.99688474
Axis point 119.41582054 132.60810071 0.00000000
Rotation angle (degrees) 57.81867815
Shift along axis 2.02170861
> hide #!1 models
> select #3:A/1-214
Nothing selected
> select #3
13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
> A/1-214
Unknown command: A/1-214
> select #3/A:1-214
1578 atoms, 1602 bonds, 1 pseudobond, 196 residues, 2 models selected
> select #3/A:1-351
2662 atoms, 2712 bonds, 1 pseudobond, 331 residues, 2 models selected
> color sel cornflower blue
> select #3/A:352-555
1322 atoms, 1350 bonds, 1 pseudobond, 165 residues, 2 models selected
> color sel gold
> select #3/A:556-912 khaki
Expected a keyword
> select #3/A:556-912
2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected
> color sel khaki
> color sel sienna
> select #3/B:1-351
2662 atoms, 2712 bonds, 1 pseudobond, 331 residues, 2 models selected
> color sel light blue
> select #3/B:352-555
1322 atoms, 1350 bonds, 1 pseudobond, 165 residues, 2 models selected
> color sel khaki
> view matrix models
> #3,0.17845,-0.98352,-0.029143,229.48,0.9838,0.17784,0.022506,-23.61,-0.016952,-0.032688,0.99932,7.7168
> select #3/B:556-912
2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/B:556-912
2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/B:556-912
2648 atoms, 2706 bonds, 3 pseudobonds, 330 residues, 2 models selected
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel blue
> color sel lightbrown
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel sandybrown
> select clear
> select #3/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> color sel light pink
> select #3/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> color sel pale violet red
> clear
Unknown command: clear
> select clear
> hide #3.2 models
> hide #3.1 models
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
> show #!1 models
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) to map
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) using 13483 atoms
average map value = 0.3207, steps = 172
shifted from previous position = 0.102
rotated from previous position = 21.7 degrees
atoms outside contour = 1875, contour level = 0.0284
Position of 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb (#3) relative to
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#1) coordinates:
Matrix rotation and translation
0.53357587 -0.84510873 -0.03298530 167.85658488
0.84235732 0.53452072 -0.06871500 -38.99499833
0.07570297 0.00887926 0.99709088 -8.19992537
Axis 0.04583939 -0.06420840 0.99688316
Axis point 119.41491024 132.60520438 0.00000000
Rotation angle (degrees) 57.81912908
Shift along axis 2.02388178
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
> color zone #1 near #3 distance 4.99
> ui tool show "Volume Viewer"
> ui tool show "Show Volume Menu"
> morph map #1 #1
Missing or invalid "structures" argument: invalid structures specifier
> morph map #1-2
Missing or invalid "structures" argument: invalid structures specifier
> morph map #1 #2
Missing or invalid "structures" argument: invalid structures specifier
> color #2 #929292ff models
> color #2 darkgrey models
> color #2 #919191ff models
> color #2 #929292ff models
> transparency #2 80
> transparency #2 20
> transparency #2 30
> set bgColor white
> lighting simple
> view name p2
> view p2
> rotate 90 x
Unknown command: rotate 90 x
> rotate x 90
Unknown command: rotate x 90
> roll x 90
> stop
> roll x 1 90
[Repeated 1 time(s)]
> view name p2
[Repeated 1 time(s)]
> roll y 1 90
[Repeated 2 time(s)]
> roll y 1 10
[Repeated 4 time(s)]
> hide #!2 models
> hide #!1 models
> show #!1 models
> view name p1
> roll y 1 90
> view name p2
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
> roll y 1 90
> view name p3
> roll y 1 90
> view name p4
> roll y 1 90
> roll x 1 90
> view name p5
> roll x 2 90
> view name p6
> roll x 1 90
> lighting full
> lighting soft
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
——— End of log from Wed Mar 26 18:37:57 2025 ———
opened ChimeraX session
> close #3
> show #!2 models
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
> coot-15_real_space_refined_015.pdb
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> hide #!1 target m
> hide #!2 target m
> select #3/A:1-351
2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
> color sel cornflower blue
> select #3/A:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel gold
> select #3/A:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel khaki
> color sel sienna
> select #3/B:1-351
2642 atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected
> color sel light blue
> select #3/B:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel khaki
> select #3/B:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/B:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel lightblue brown
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/B:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel blue
> color sel sandybrown
> select clear
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> color sel light pink
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel pale violet red
> select clear
> show #!1 target m
> color zone #1 near #3 distance 4.99
> transparency #1 50
> view p1
> transparency #1 100
> transparency #1 0
> hide #3.2 target m
> hide #!3 target m
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
——— End of log from Thu Mar 27 16:53:46 2025 ———
opened ChimeraX session
> show #!3 models
> hide #!1 models
> show atoms
> show #!1 models
> color zone #1 near #3 distance 4.99
> volume #1 level 0.1174
> hide #!3 models
> show #!3 models
> hide #!1 models
> ui mousemode right select
> select /B:1002@MG
1 atom, 1 residue, 1 model selected
> color sel light blue
> select /A:1002@MG
1 atom, 1 residue, 1 model selected
> select /A:1003@MG
1 atom, 1 residue, 1 model selected
> select /A:1002@MG
1 atom, 1 residue, 1 model selected
> select add /A:1003@MG
2 atoms, 2 residues, 1 model selected
> color sel cornflower blue
> show #!1 models
> volume #1 level 0.05688
> volume #1 level 0.028
> open /Users/justinvanriper/Desktop/2024-05-03_apply_ncs_56-coot-0_RNA-
> WC_edited_modified_real_space_refined_061.pdb
Chain information for 2024-05-03_apply_ncs_56-coot-0_RNA-
WC_edited_modified_real_space_refined_061.pdb #4
---
Chain | Description
A B | No description available
C | No description available
D | No description available
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> select #4/A:668
6 atoms, 5 bonds, 1 residue, 1 model selected
Drag select of 1
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc , 5 residues
> select #1
2 models selected
> select #4/A:667
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #4/A:668
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #4
13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
> select subtract #4/A:668
13477 atoms, 13769 bonds, 20 pseudobonds, 1665 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> view p1
> hide #!4 models
> show #!4 models
> close #4
> hide #!3 models
> view p1
> ui tool show "Side View"
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> view p5
> show #!3 models
> color zone #1 near #3 distance 4.99
> hide #!3 models
> save /Users/justinvanriper/Desktop/image3.png supersample 3
> view p1
> show #!3 models
> hide #!1 models
> hide atoms
> undo
> show #!3 models
> undo
> hide #!3 models
> show #!3 models
> hide #!1 models
> undo
> hide #!1 models
> select #1/A,B
Nothing selected
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel atoms
> view p1
> select clear
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 253 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 253 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 253 atom styles
> show sel cartoons
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> select clear
> cartoon style (#3.1#!3 & coil) xsection oval
> cartoon style #3.1#!3 xsection barbell modeHelix default
> cartoon style #3.1#!3 modeHelix tube sides 20
> view p1
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select ::name="MG"::name="ZN"
5 atoms, 5 residues, 1 model selected
> show sel atoms
> color sel byelement
> select clear
> view p1
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> view p1
> roll y 1 1
> roll y 1 1 1
Expected a keyword
> roll y 1 -1
Missing or invalid "frames" argument: Expected 'forever' or an integer >= 1
> roll y -1 -
Expected 'forever' or an integer >= 1 or a keyword
> roll y -1 1
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> view p6
> viewp5
Unknown command: viewp5
> view p5
> piew p1
Unknown command: piew p1
> view p1
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sele cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sele cartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel cartoons
> select clear
Drag select of 2 atoms
> select down
2 atoms, 2 residues, 1 model selected
> select up
13193 atoms, 13462 bonds, 1648 residues, 1 model selected
> select ~sel & ##selected
253 atoms, 280 bonds, 12 residues, 1 model selected
> select down
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> show sel cartoons
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 4.99
> undo
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> volume zone #1 nearAtoms sel & #3 range 4.99
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> volume zone #1 nearAtoms sel & #3 range 4.99
> select clear
> volume #1 level 0.1561
> color zone #1 near #3 distance 4.99
Drag select of 1
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc , 4 residues
> volume #1 level 0.06359
> volume #1 level 0.028
> select clear
> volume zone #1 nearAtoms #3 range 4.99
> help help:user/tools/toolbar.html
No help found for 'help:user/tools/zone.html'
> volume #!1 style image
> volume #!1 style surface
> volume show
> hide #!2 models
Drag select of 1
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc , 11 residues, 1 shapes
> select clear
> close
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #1, grid size 300,300,300, pixel 0.832, shown at
level 0.0284, step 1, values float32
Opened
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at
level 0.00701, step 1, values float32
opened ChimeraX session
> show #!3 models
> hide #!3 models
> ui tool show "Map Eraser"
> ui tool show "Map Filter"
> ui tool show "Segment Map"
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Showing 43 region surfaces
2810 watershed regions, grouped to 43 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 43 regions, 43 surfaces
> hide #!1 models
> close #4
> show #!1 models
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Showing 43 region surfaces
2810 watershed regions, grouped to 43 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 43 regions, 43 surfaces
> hide #!1 models
> show #!1 models
> close #4
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 586 regions.
Showing 200 of 586 region surfaces
2810 watershed regions, grouped to 586 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 586 regions, 200 surfaces
> hide #!1 models
> ui mousemode right select
> select #4.24
1 model selected
> select #4.123
1 model selected
> select add #4.24
2 models selected
> select add #4.107
3 models selected
Drag select of 4941, 5971 of 12956 triangles, 4979, 6 of 9804 triangles, 5008,
1625 of 8428 triangles, 5026, 2061 of 8244 triangles, 4805, 3602 of 7044
triangles, 5009, 675 of 7244 triangles
Drag select of 4931, 13906 of 14284 triangles, 4981, 4933, 8150 of 12936
triangles, 4943, 3041 of 12152 triangles, 4973, 3073 of 13940 triangles, 4941,
289 of 12956 triangles, 4997, 4932, 9543 of 11212 triangles, 4951, 12360 of
12952 triangles, 4963, 4992, 4098 of 12168 triangles, 5014, 4960, 9574 of
11024 triangles, 4993, 4358 of 11144 triangles, 5015, 11661 of 12484
triangles, 4974, 9517 of 10752 triangles, 4946, 8427 of 10256 triangles, 4961,
8737 of 11192 triangles, 5029, 7244 of 11724 triangles, 5012, 4980, 2886 of
9640 triangles, 5022, 4930, 4972, 7645 of 9732 triangles, 4979, 1295 of 9804
triangles, 4994, 4942, 5384 of 9016 triangles, 5004, 4982, 4958, 5023, 8831 of
8872 triangles, 5028, 7339 of 8628 triangles, 5008, 381 of 8428 triangles,
5017, 5027, 6848 of 9700 triangles, 5003, 5026, 3101 of 8244 triangles, 4984,
4950, 7094 of 7232 triangles, 4971, 618 of 7168 triangles, 4970, 63 of 6888
triangles, 4959, 5011, 5088 of 7268 triangles, 4983, 4996, 7014 of 7304
triangles, 4805, 1575 of 7044 triangles, 5009, 4685 of 7244 triangles, 4964,
5002, 5931 of 6604 triangles, 5005, 5019, 232 of 6968 triangles, 4995, 2320 of
5680 triangles, 4845, 5021, 5010, 4901, 210 of 4552 triangles, 4914, 742 of
3908 triangles, 4915, 402 of 3672 triangles, 4540, 4616, 369 of 2760
triangles, 4679, 3935, 4345, 209 of 2100 triangles, 3425, 3433, 1116 of 1564
triangles, 4179, 4379, 1368 of 1380 triangles, 4334, 3765, 502 of 1228
triangles, 3127, 3352, 1777, 561 of 880 triangles, 3575, 4332, 1911, 1761,
4311, 2626, 2272, 4381, 2336, 2614, 2803, 3819, 1709, 519 of 668 triangles,
3743, 2320, 589 of 664 triangles, 1803, 2797, 354 of 624 triangles, 2593, 3746
Grouped 91 regions
> select clear
Drag select of 4921, 1009 of 13124 triangles, 4934, 37 of 12676 triangles,
4998, 5973 of 11336 triangles, 4927, 754 of 11760 triangles, 4936, 3189 of
11252 triangles, 4988, 11707 of 12064 triangles, 4957, 10520 of 11756
triangles, 4948, 2509 of 12344 triangles, 4949, 6047 of 11080 triangles, 4937,
1932 of 10884 triangles, 4990, 9539 of 9624 triangles, 4940, 7591 of 9652
triangles, 4938, 1130 of 11176 triangles, 4939, 7839 of 8620 triangles, 5030,
8329 of 10184 triangles, 4922, 743 of 8868 triangles, 4954, 5016, 8009 of 9852
triangles, 4955, 594 of 8812 triangles, 4969, 7585 of 7896 triangles, 4967,
1620 of 8492 triangles, 4956, 7597 of 9032 triangles, 4968, 8883 of 8952
triangles, 4987, 1778 of 7432 triangles, 4989, 5018, 1459 of 8492 triangles,
4953, 7121 of 7152 triangles, 4977, 4235 of 7280 triangles, 5020, 4595 of 7752
triangles, 4991, 5007, 7038 of 7440 triangles, 4978, 6236 of 6788 triangles,
4999, 6180 of 6528 triangles, 4834, 5353 of 6384 triangles, 4966, 2177 of 6344
triangles, 4986, 796 of 5944 triangles, 4779, 2056 of 4576 triangles, 5025,
5000, 3343 of 4680 triangles, 5024, 3593 of 5056 triangles, 4497, 1704 of 3980
triangles, 4752, 529 of 3996 triangles, 5001, 4888, 5034, 342 of 2680
triangles, 4559, 4677, 1201 of 2184 triangles, 4070, 3309, 3303, 585 of 1328
triangles, 3811, 3171, 3810, 3785, 1169, 1774, 842, 277 of 656 triangles,
5035, 180519 of 441496 triangles
> select clear
Drag select of 4998, 287 of 11336 triangles, 4988, 6728 of 12064 triangles,
4957, 1224 of 11756 triangles, 4949, 10 of 11080 triangles, 4990, 3398 of 9624
triangles, 4940, 1074 of 9652 triangles, 4939, 1973 of 8620 triangles, 5030,
4954, 2590 of 9916 triangles, 5016, 936 of 9852 triangles, 4969, 2254 of 7896
triangles, 4956, 1052 of 9032 triangles, 4968, 954 of 8952 triangles, 4989,
3004 of 8036 triangles, 4953, 1841 of 7152 triangles, 4977, 215 of 7280
triangles, 5020, 4294 of 7752 triangles, 4991, 6328 of 6492 triangles, 5007,
4978, 2396 of 6788 triangles, 4999, 2566 of 6528 triangles, 4834, 1856 of 6384
triangles, 4966, 205 of 6344 triangles, 5025, 1877 of 4916 triangles, 5000,
418 of 4680 triangles, 5001, 3108 of 4428 triangles, 4888, 3283 of 3520
triangles, 4559, 4070, 3811, 3171, 3768, 3810, 3785, 1169, 229 of 660
triangles, 1774, 5035, 438539 of 441496 triangles
Grouped 37 regions
Drag select of 4921, 4925 of 13124 triangles, 4924, 12326 of 12972 triangles,
4934, 11512 of 12676 triangles, 4936, 2111 of 11252 triangles, 4944, 11517 of
11904 triangles, 4926, 43 of 10188 triangles, 4928, 4945, 5370 of 9852
triangles, 4935, 506 of 9332 triangles, 4938, 4922, 100 of 8868 triangles,
5013, 218 of 8844 triangles, 4955, 2254 of 8812 triangles, 5018, 7742 of 8492
triangles, 4986, 5024, 4752, 777 of 3996 triangles, 4853, 1202 of 3528
triangles, 3309, 121, 35 of 1176 triangles, 343, 3726, 478, 25, 513 of 772
triangles, 302, 679, 470 of 676 triangles, 4336, 176 of 940 triangles, 842,
5036, 320747 of 620392 triangles
Grouped 29 regions
> undo
Ungrouped to 29 regions
> transparency #4 50
> show #!3 models
> select #4.33
1 model selected
> select add #4.16
2 models selected
> select add #4.4
3 models selected
> select add #4.17
4 models selected
> select add #4.26
5 models selected
> select add #4.14
6 models selected
> select add #4.35
7 models selected
> select subtract #4.35
6 models selected
> select add #4.5
7 models selected
> select add #4.10
8 models selected
> select add #4.8
9 models selected
> select add #4.46
10 models selected
Grouped 10 regions
> select add #4.29
2 models selected
Grouped 2 regions
> select add #4.24
2 models selected
Grouped 2 regions
> select add #4.131
2 models selected
> select add #4.12
3 models selected
> select add #4.34
4 models selected
> select add #4.21
5 models selected
Grouped 5 regions
> select add #4.93
2 models selected
> select add #4.20
3 models selected
Grouped 3 regions
> select add #4.97
2 models selected
> select add #4.200
3 models selected
> select add #4.134
4 models selected
Grouped 4 regions
> select #4.183
1 model selected
> select add #4.2
2 models selected
> select add #4.72
3 models selected
Grouped 3 regions
> select clear
> select add #4.107
1 model selected
> select add #4.35
2 models selected
> select add #4.129
3 models selected
> select add #4.136
4 models selected
> select subtract #4.35
3 models selected
> select add #4.35
4 models selected
> select add #4.22
5 models selected
> select add #4.118
6 models selected
> select subtract #4.118
5 models selected
Grouped 5 regions
> select #4.79
1 model selected
> select add #4.1
2 models selected
> select add #4.2
3 models selected
> select add #4.117
4 models selected
Grouped 4 regions
> select #4.3
1 model selected
> select #4.4
1 model selected
> select #4.3
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> select clear
> select #4.4
1 model selected
> select #4.18
1 model selected
> select #4.130
1 model selected
> select add #4.6
2 models selected
> select #4.7
1 model selected
> select add #4.1
2 models selected
> select subtract #4.1
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> select #4.19
1 model selected
> select add #4.18
2 models selected
> select add #4.1
3 models selected
> select #4.23
1 model selected
> select add #4.19
2 models selected
> select add #4.1
3 models selected
Grouped 3 regions
Grouped 1 regions
Showing 43 grouped regions
> select clear
> select #4.89
1 model selected
> select add #4.70
2 models selected
> select add #4.1
3 models selected
Grouped 3 regions
> select #4.108
1 model selected
> select add #4.69
2 models selected
> select add #4.1
3 models selected
Grouped 3 regions
> select clear
> select #4.144
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> select add #4.111
2 models selected
> select subtract #4.1
1 model selected
Grouped 1 regions
> select add #4.1
2 models selected
> select subtract #4.2
1 model selected
Grouped 1 regions
> select subtract #4.1
Nothing selected
> select #4.1
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select #4.30
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> select clear
Drag select of 4967, 87 of 8492 triangles, 5006, 45 of 6456 triangles, 3593,
12 of 1160 triangles, 3721, 183 of 696 triangles, 5058, 2221 of 825204
triangles, 6 residues
> select clear
> select #4.18
1 model selected
> select #4.6
1 model selected
> select add #4.4
2 models selected
Grouped 2 regions
> select clear
> select #4.13
1 model selected
> select clear
Drag select of 4752, 815 of 3996 triangles, 4336, 335 of 940 triangles, 4922,
591 of 8868 triangles, 5058, 53286 of 825204 triangles, 131 residues
Grouped 4 regions
> select clear
Drag select of 4967, 494 of 8492 triangles, 5006, 273 of 6456 triangles, 3593,
964 of 1160 triangles, 3721, 127 of 696 triangles, 5060, 146635 of 830732
triangles, 286 residues
Grouped 5 regions
> select clear
Drag select of 4911, 243 of 4000 triangles, 5059, 1839 of 32708 triangles,
5061, 42369 of 839400 triangles, 1 atoms, 89 residues
Grouped 3 regions
Ungrouped to 3 regions
> select clear
> select #4.32
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select clear
> select #4.18
1 model selected
> select clear
> select #4.4
1 model selected
> select #4.18
1 model selected
> select #4.130
1 model selected
> select add #4.18
2 models selected
> select add #4.1
3 models selected
> select clear
> transparency #4 50
Drag select of 5018, 32 of 8492 triangles, 4911, 37 of 4000 triangles, 5063,
304 of 845928 triangles, 3 residues
> select clear
> select #4.124
1 model selected
> select add #4.1
2 models selected
Grouped 2 regions
> select clear
> select #4.18
1 model selected
> select add #4.130
2 models selected
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 586 regions.
Showing 200 of 586 region surfaces
2810 watershed regions, grouped to 586 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 586 regions, 200 surfaces
> select #4.107
1 model selected
> select add #4.24
2 models selected
> select add #4.6
3 models selected
> select #4.6
1 model selected
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 586 regions.
Showing 200 of 586 region surfaces
2810 watershed regions, grouped to 586 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 586 regions, 200 surfaces
> select #4.123
1 model selected
> select #4.6
1 model selected
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 586 regions.
Showing 200 of 586 region surfaces
2810 watershed regions, grouped to 586 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 586 regions, 200 surfaces
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 1796 regions.
Showing 200 of 1796 region surfaces
2810 watershed regions, grouped to 1796 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 1796 regions, 200 surfaces
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 1233 regions.
Showing 200 of 1233 region surfaces
2810 watershed regions, grouped to 1233 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 1233 regions, 200 surfaces
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 897 regions.
Showing 200 of 897 region surfaces
2810 watershed regions, grouped to 897 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 897 regions, 200 surfaces
Only showing 200 of 897 regions.
Showing 200 of 897 region surfaces
Only showing 200 of 897 regions.
Showing 200 of 897 region surfaces
Only showing 200 of 897 regions.
Showing 200 of 897 region surfaces
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 700 regions.
Showing 200 of 700 region surfaces
2810 watershed regions, grouped to 700 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 700 regions, 200 surfaces
> select clear
Segmenting State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc, density threshold 0.028400
Only showing 200 of 586 regions.
Showing 200 of 586 region surfaces
2810 watershed regions, grouped to 586 regions
Showing State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.seg - 586 regions, 200 surfaces
> select #4.24
1 model selected
> select #4.6
1 model selected
> select #4.107
1 model selected
> select #4.24
1 model selected
> select #4.129
1 model selected
> select #4.136
1 model selected
> select #4.79
1 model selected
> select #4.136
1 model selected
> select add #4.24
2 models selected
> select add #4.107
3 models selected
> select add #4.6
4 models selected
> select subtract #4.6
3 models selected
Grouped 3 regions
> select #4.123
1 model selected
> select clear
Only showing 200 of 584 regions.
Showing 200 of 584 region surfaces
> select #4.123
1 model selected
> select add #4.24
2 models selected
Grouped 2 regions
> select #4.35
1 model selected
Drag select of 4925, 524 of 10872 triangles, 4922, 733 of 8868 triangles,
4955, 1164 of 8812 triangles, 4965, 30 of 8528 triangles, 4947, 699 of 7780
triangles, 4752, 411 of 3996 triangles, 4916, 390 of 3732 triangles, 4696, 41
of 3024 triangles, 3090, 171 of 1128 triangles, 679, 239 of 676 triangles, 7
atoms, 15 residues, 4 bonds
> select clear
> close #4
> show #!1 models
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui mousemode right "map eraser"
> ui mousemode right translate
> ui mousemode right zone
> select ~sel & ##selected
Nothing selected
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> ui mousemode right zone
> select add #1
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 5 models selected
> ui mousemode right zone
> transparency #3 50
> transparency #1 50
> select clear
> hide #!1 models
> show #!1 models
> select #3
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select #3/A:206,30,78,38,39,127,133,213,211,212
98 atoms, 92 bonds, 10 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select backbone
6572 atoms, 6558 bonds, 12 pseudobonds, 1643 residues, 2 models selected
> hide sel atoms
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> view sel
No displayed objects specified.
> view
> view sel
No displayed objects specified.
> transparency #1 0
> lighting flat
> lighting simple
> lighting soft
> ui tool show "Map Eraser"
> ui mousemode right "map eraser"
> volume erase #1 center 126.16,127.52,75.004 radius 9.8503
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc copy as #5, grid size 300,300,300, pixel 0.832, shown at
step 1, values float32
> surface dust #5 size 8.32
> color zone #5 near sel & #3 distance 4.99
> ui tool show "Side View"
> volume erase #5 center 128.63,124.53,84.079 radius 9.7344
> volume erase #5 center 132.39,124.33,79.777 radius 9.7344
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "map eraser"
> volume erase #5 center 127.03,128.33,81.913 radius 9.7344
> volume erase #5 center 121.21,128.07,80.526 radius 9.7344
> volume erase #5 center 120.51,123.8,91.733 radius 3.4944
> volume erase #5 center 133.38,129.59,91.359 radius 3.4944
> volume erase #5 center 135.27,126.82,91.657 radius 3.4944
> volume erase #5 center 132.35,125.7,92.357 radius 3.4944
> volume erase #5 center 129.36,129.27,92.047 radius 3.4944
> volume erase #5 center 131.03,133.1,90.028 radius 3.4944
> volume erase #5 center 111.11,128.5,76.024 radius 3.4944
> ui mousemode right "clip rotate"
> ui mousemode right clip
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show sel cartoons
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/real_space_refined_036_edited-
> coot-15_real_space_refined_015.pdb
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> ui mousemode right "map eraser"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right "map eraser"
> volume erase #5 center 129.86,135.02,86.514 radius 3.4944
> volume erase #5 center 127.05,135.67,85.958 radius 3.4944
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "map eraser"
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> color sel pink
> show sel cartoons
> style sel stick
Changed 253 atom styles
> nucleotides sel ladder
> show #!5 models
> ui mousemode right "map eraser"
> volume erase #5 center 119.18,130.82,93.577 radius 3.4944
> ui mousemode right clip
> ui mousemode right "map eraser"
> volume erase #5 center 116.79,130.48,91.244 radius 3.4944
> volume erase #5 center 118.94,133.17,88.8 radius 3.4944
> volume erase #5 center 116.46,132.91,86.596 radius 3.4944
> volume erase #5 center 116.13,134.32,85.34 radius 3.4944
> volume erase #5 center 114.79,134.88,84.489 radius 3.4944
> volume erase #5 center 112.27,134.3,78.833 radius 3.4944
> volume erase #5 center 116.78,134.23,90.159 radius 3.4944
> ui mousemode right clip
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right "map eraser"
> volume erase #5 center 134.63,121.08,91.48 radius 3.4944
> volume erase #5 center 111.98,134.4,85.753 radius 3.4944
> volume erase #5 center 115.57,134.24,86.552 radius 3.4944
> volume erase #5 center 115.34,134.57,86.557 radius 3.4944
> volume erase #5 center 115.03,135.09,86.684 radius 3.4944
> volume erase #5 center 115.43,135.36,86.979 radius 3.4944
> hide #4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> select #3/A:206,30,78,38,39,127,133,213,211,212
98 atoms, 92 bonds, 10 residues, 1 model selected
> select up
576 atoms, 581 bonds, 70 residues, 1 model selected
> select down
98 atoms, 92 bonds, 10 residues, 1 model selected
> select #3/A:206,30,78,38,39,127,133,213,211,212
98 atoms, 92 bonds, 10 residues, 1 model selected
> color sel cornflower blue
> select clear
> show #!3 atoms
> ui mousemode right select
> select #3/B:1002@MG
1 atom, 1 residue, 1 model selected
> select add #3/A:1002@MG
2 atoms, 2 residues, 1 model selected
> select add #3/A:1003@MG
3 atoms, 3 residues, 1 model selected
> select up
13193 atoms, 13462 bonds, 1648 residues, 1 model selected
> select down
3 atoms, 3 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #3/B:1002@MG
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> color sel light blue
> select clear
> show #!5 models
> color zone #5 near #3 distance 4.99
> show #!6 models
> select #6/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> delete sel
> hide #!5 models
> hide #!3 models
> show #!3 models
> select #6/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> color sel light pink
> select #6/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel pale violet red
> select clear
> select #3
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select clear
> select ::name="MG"::name="ZN"
5 atoms, 5 residues, 1 model selected
> show sel atoms
> color sel byelement
> select clear
> show #4 models
> hide #4 models
> close #4
> show #!5 models
> close #4
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/RNA_Den_deleted_maps.cxs
> hide cartoons
> show cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> select #3
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel cartoons
> select #3/A:206,211,212,213
38 atoms, 37 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> transparency #5 50
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD92LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.121.1
OS Loader Version: 10151.121.1
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 days, 7 hours, 35 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
OMEN 27qs:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 120.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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