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Opened 7 months ago
Closed 7 months ago
#17280 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-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.atomic._ribbons, chimerax.graphics._graphics, 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.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 124)
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{
"uptime" : 290000,
"procRole" : "Background",
"version" : 2,
"userID" : 504,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 5324,
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"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2025-04-02 18:26:48.5496 -0500",
"codeSigningMonitor" : 1,
"incident" : "875FD299-56D5-4B6B-BA45-A21B88551AF8",
"pid" : 3506,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-01 16:06:45.8113 -0500",
"procStartAbsTime" : 5725932445175,
"procExitAbsTime" : 7188211521229,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3501BEA6-E428-51C8-AAE1-7382D674882C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7EFF9947-246C-6A50-F14D-73A8885F4631",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 20505,
"sleepWakeUUID" : "D6833925-6423-4EA2-97AB-DA0F60C8F69D",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4299341824\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10042c000-100430000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":3506},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4299341824\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10042c000-100430000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
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 Mon Mar 31 16:21:28 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 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
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel medium violet red
> select clear
> show #!1 models
> color zone #1 near #3 distance 4.99
> select clear
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
——— End of log from Mon Mar 31 16:21:28 2025 ———
opened ChimeraX session
> hide #!1 models
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> color sel hot pink
> select clear
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/SLFN14_C1_Maps_color_scheme.cxs
> view p1
> show #!1 models
> color zone #1 near #3 distance 4.99
> hide #!3 models
> graphics silhouettes true
> ui tool show "Side View"
> view p1
> undo
> view p1
> save /Users/justinvanriper/Desktop/image10.png supersample 3
> save /Users/justinvanriper/Desktop/image11.png supersample 3
> show #!3 models
> hide #!1 models
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel cartoons
> nucleotides sel ladder
> hide sel cartoons
> show sel cartoons
> select clear
> cartoon style #3.1#!3 modeHelix tube sides 20
> save /Users/justinvanriper/Desktop/image12.png supersample 3
> lighting simple
> lighting soft
> view p1
> undo
> select clear
> view p1
> roll x 1 90
> show #!1 models
> hide #!3 models
> save /Users/justinvanriper/Desktop/image13.png supersample 3
> view p3
> view p5
> view p6
> view p7
Expected an objects specifier or a view name or a keyword
> view p11
Expected an objects specifier or a view name or a keyword
> view p22
Expected an objects specifier or a view name or a keyword
> view p1
> roll x 1 10
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> select #3/A,B:1-351
5258 atoms, 5358 bonds, 2 pseudobonds, 653 residues, 2 models selected
> show sel surfaces
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> color sel fromatoms target s
> select clear
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> transparcency #3 50
Unknown command: transparcency #3 50
> transparancy #3 50
Unknown command: transparancy #3 50
> transparency #3 50
> transparency #3 90
> transparency #3 80
> transparency #3 80select clear
Missing or invalid "percent" argument: Expected a number
> select #3/A,B:30,38,78,86,39,127,213,206,211,212
192 atoms, 180 bonds, 20 residues, 1 model selected
> show sel atoms
> color (#!3 & sel) byhetero
> color sel fromatoms target s
> select clear
> color sel fromatoms target s
> select #3/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> color sel cornflower blue
> select #3/B
6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
> color sel lightblue pale blue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/B
6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
> color sel light blue
> select clear
> transparency #3 80
> select #3/A,B:30,38,78,86,39,127,213,206,211,212
192 atoms, 180 bonds, 20 residues, 1 model selected
> color sel byhetero target a
> select clear
> select ::name="MG"
3 atoms, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero target a
> select clear
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> hide sel atoms
> select clear
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> select #3/A,B:30,38,78,82,86,39,127,213,206,211,212
206 atoms, 192 bonds, 22 residues, 1 model selected
> show sel atoms
> select clear
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> hide sel atoms
> select clear
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> view name p3
> view p2
> view p3
> select clear
> save /Users/justinvanriper/Desktop/image14.png supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> save /Users/justinvanriper/Desktop/image15.png supersample 3
> select #3/A,B:30,38,78,82,86,39,127,213,206,211,212,
Expected an objects specifier or a keyword
> select #3/A,B:30,38,78,82,86,39,127,213,206,211,212
206 atoms, 192 bonds, 22 residues, 1 model selected
> ui mousemode right select
> select clear
> hide surfaces
> view p3
> select #3/A,B:1-351
5258 atoms, 5358 bonds, 2 pseudobonds, 653 residues, 2 models selected
> show sel surfaces
> select clear
> select #3/A,B:214,39,137,79
72 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero target a
> select clear
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> select clear
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> hide sel cartoons
> select clear
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> hide sel atoms
> select clear
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image14.png supersample 3
> hide surfaces
> select /A:82@CB
1 atom, 1 residue, 1 model selected
> select clear
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure3C_session.cxs
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> hide sel atoms
> select ~sel & ##selected
Nothing selected
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> view p1
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> show sel cartoons
> select clear
> select#3/A:352-554
Unknown command: select#3/A:352-554
> select #3/A:352-554
1328 atoms, 1356 bonds, 1 pseudobond, 166 residues, 2 models selected
> color sel gold
[deleted to fit within ticket limits]
> volume zone #2 nearAtoms sel range 2.3
> volume zone #2 nearAtoms sel range 2.4
> volume #2 level 0.165
> volume zone #2 nearAtoms sel range 2.5
> volume zone #2 nearAtoms sel range 2.2
> volume zone #2 nearAtoms sel range 2.5
> volume zone #2 nearAtoms sel range 2.5view p2
Invalid "range" argument: Expected a number
> view p2
> ;ect c;ear
Incomplete command: sequence
> select clear
> volume #2 level 0.1502
> view p2
> hide #!2 models
> align #3 toAtoms #1.1
Unequal number of atoms to pair, 13446 and 13483
> matchmaker #3 to #1.1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker all_aligned_SLFN.cif, chain A (#1.1) with
real_space_refined_036_edited-coot-15_real_space_refined_015.pdb, chain A
(#3), sequence alignment score = 3964.3
RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
0.728)
> show #!1.2 models
> hide #!1.2 models
> hide #!1.1 models
> view p2
> view p3
Expected an objects specifier or a view name or a keyword
> view name p3
> view p2
> view p3
> select clear
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> show #!1.1 models
> show #!3#!1.1 atoms
> show #!3#!1.1 cartoons
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> undo
[Repeated 4 time(s)]
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> hide sel cartoons
> select clear
> hide #!1.1 models
> show #!1.2 models
> select #1.2
10301 atoms, 10474 bonds, 16 pseudobonds, 1306 residues, 2 models selected
> hide sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> hide #!1.2 models
> show #!1.3 models
> select #1.3
14346 atoms, 14642 bonds, 8 pseudobonds, 1774 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image3.png supersample 3
> show #!1.4 models
> hide #!1.3 models
> select #1.4
13334 atoms, 13618 bonds, 6 pseudobonds, 1658 residues, 2 models selected
> hide sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image4.png supersample 3
> show #!1.3 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.4 models
> show #!1.5 models
> select #11.5
Nothing selected
> select #1.5
5162 atoms, 4961 bonds, 5 pseudobonds, 906 residues, 2 models selected
> hide sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image5.png supersample 3
> hide #!1.5 models
> select #3/A:1-351
2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
> show sel cartoons
> select clear
> select add #3/A:133@CB
1 atom, 1 bond, 1 residue, 1 model selected
> select add #3/A:190
12 atoms, 12 bonds, 2 residues, 1 model selected
> select add #3/A:189
21 atoms, 20 bonds, 3 residues, 1 model selected
> select add #3/A:206@CB
22 atoms, 20 bonds, 4 residues, 1 model selected
> select subtract #3/A:189
13 atoms, 12 bonds, 3 residues, 1 model selected
> select subtract #3/A:190
2 atoms, 1 bond, 2 residues, 1 model selected
> select add #3/A:192
11 atoms, 9 bonds, 3 residues, 1 model selected
> select add #3/A:211@CB
12 atoms, 9 bonds, 4 residues, 1 model selected
> select subtract #3/A:192
3 atoms, 1 bond, 3 residues, 1 model selected
> select add #3/D:7@OP1
4 atoms, 2 bonds, 4 residues, 1 model selected
> select add #3/A:202
12 atoms, 9 bonds, 5 residues, 1 model selected
> select subtract #3/A:202
4 atoms, 1 bond, 4 residues, 1 model selected
> select add #3/A:202
12 atoms, 8 bonds, 5 residues, 1 model selected
> select #3/A:202
8 atoms, 7 bonds, 1 residue, 1 model selected
> view p1
> select clear
> select #3/A:133,206,211,213,249,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> hide sel atoms
> show sel atoms
> select clear
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 142 atom styles
> nucleotides sel ladder
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select clear
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> view p22
> select #3/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> hide sel cartoons
> hide (#!3 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!3 & sel-residues)
> show (#!3 & sel-residues & backbone) target ab
> hide sel atoms
> select up
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> select up
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 6 models selected
> undo
[Repeated 5 time(s)]
> select backbone
34746 atoms, 34691 bonds, 57 pseudobonds, 8643 residues, 12 models selected
> hide sel & #!3 atoms
> select clear
> view p22
> view p2
> view p22
> view p2
> select #3/D:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #3/D:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Drag select of 4 atoms, 3 bonds, 2 shapes
> select clear
> select add #3/D:7@C5'
1 atom, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3/D:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
Drag select of 3 atoms, 2 bonds, 2 shapes
> hide sel atoms
> undo
> view p22
> view p2
> view p22
> select clear
> nucleotides sel ladder
[Repeated 3 time(s)]
> nucleotides sel atoms
> style nucleic & sel stick
Changed 20 atom styles
> select clear
[Repeated 1 time(s)]
> select #3/D:7@N1
1 atom, 1 residue, 1 model selected
> select #3/D:7@C1'
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 15 atoms, 16 bonds
> hide sel atoms
> view p22
> view p2
> view p1
> view p2
> view p22
> view p3
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> open /Users/justinvanriper/Downloads/9ere.pdb
9ere.pdb title:
SLFN11 dimer bound to TRNA-leu-taa [more info...]
Chain information for 9ere.pdb #4
---
Chain | Description | UniProt
A B | schlafen family member 11 | SLN11_HUMAN 1-901
T | RNA (76-mer) |
U | RNA (5'-R(P*CP*CP*up*GP*GP*up*ap*CP*CP*A)-3') |
Non-standard residues in 9ere.pdb #4
---
MG — magnesium ion
MN — manganese (II) ion
ZN — zinc ion
> matchmaker #4 #2
Missing required "to" argument
> matchmaker #4 #3
Missing required "to" argument
> matchmaker #4 to #3
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
chain A (#3) with 9ere.pdb, chain B (#4), sequence alignment score = 2189.5
RMSD between 442 pruned atom pairs is 1.346 angstroms; (across all 799 pairs:
3.355)
> hide #4.1 models
> hide #!4.2 models
> select #4
14541 atoms, 14958 bonds, 32 pseudobonds, 1719 residues, 4 models selected
> hide sel cartoons
> hide sel atoms
> select #4/A
6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected
> show sel cartoons
> select ::name="MN"
5 atoms, 5 residues, 2 models selected
> show sel & #!4 cartoons
> show sel & #!4 atoms
> select clear
> select #4/A:1002@MN
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #4/A
6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected
> hide sel cartoons
> select #4/B:135,214,216,209,252,251
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> view p3
> select clear
> select backbone
42034 atoms, 42022 bonds, 66 pseudobonds, 10353 residues, 14 models selected
> select subtract #3/D:7@P
42033 atoms, 42018 bonds, 66 pseudobonds, 10353 residues, 14 models selected
> select subtract #3/D:7@O5'
42032 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected
> select subtract #3/D:7@OP2
42031 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected
> select subtract #3/D:7@OP1
42030 atoms, 42017 bonds, 66 pseudobonds, 10353 residues, 14 models selected
> hide sel & #!3-4 atoms
> select clear
> view p3
> show #!1.2 models
> hide #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> select add #4
14541 atoms, 14958 bonds, 32 pseudobonds, 1719 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.50735,0.86168,0.0098541,-105.53,-0.86116,0.5074,-0.030957,188.4,-0.031675,0.0072203,0.99947,-48.483
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.51937,0.8476,0.10874,-118.71,-0.85399,0.5194,0.030262,176.55,-0.030827,-0.10858,0.99361,-26.909
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.51937,0.8476,0.10874,-119.41,-0.85399,0.5194,0.030262,176.13,-0.030827,-0.10858,0.99361,-26.965
> view matrix models
> #4,0.51937,0.8476,0.10874,-119.38,-0.85399,0.5194,0.030262,176.16,-0.030827,-0.10858,0.99361,-26.984
> view p3
> select clear
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> color #4 #bbbbbbff
> color #3.1#!1,3-4 byhetero
> undo
> ui mousemode right select
> select #4/B:1003@MN
1 atom, 1 residue, 1 model selected
> select add #4/B:1002@MN
2 atoms, 2 residues, 1 model selected
> select clear
[Repeated 1 time(s)]Drag select of 68 atoms, 51 bonds
> color sel byhetero
> select clear
> select #4/B:1003@MN
1 atom, 1 residue, 1 model selected
> select add #4/B:1002@MN
2 atoms, 2 residues, 1 model selected
> color sel #c3c3c3ff
> select clear
> view p3
> select #4/C
Nothing selected
> select #4/D
Nothing selected
> select #4/A
6667 atoms, 6809 bonds, 11 pseudobonds, 829 residues, 3 models selected
> select #4/B
6668 atoms, 6809 bonds, 14 pseudobonds, 830 residues, 3 models selected
> select #4/C
Nothing selected
> select #4/D
Nothing selected
> select #4/E
Nothing selected
> select #4/F
Nothing selected
> select ::name="A"::name="C"::name="G"::name="U"
1670 atoms, 1858 bonds, 3 pseudobonds, 78 residues, 4 models selected
> show sel & #!3-4 cartoons
> select #4/U:77
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/U:76,77
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/U:76
Nothing selected
> nucleotides #!3-4 atoms
> style nucleic & #!3-4 stick
Changed 1455 atom styles
Drag select of 13 atoms, 13 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select add #4/U:77@C4'
1 atom, 1 bond, 1 residue, 1 model selected
> select add #4/U:77@C5'
2 atoms, 1 bond, 1 residue, 1 model selected
> select subtract #4/U:77@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
[Repeated 2 time(s)]
> select add #4/U:77@C5'
2 atoms, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/U:77@P
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 20 atoms, 13 bonds
> select subtract #4/B:1002@MN
19 atoms, 13 bonds, 7 residues, 2 models selected
> select clear
Drag select of 11 atoms, 8 bonds
> color sel byhetero
> select #4/U:77@P
1 atom, 1 residue, 1 model selected
> color sel #cacacaff
> select clear
> view p3
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session.cxs
> save /Users/justinvanriper/Desktop/image3.png supersample 3
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs
——— End of log from Sun Mar 30 16:27:42 2025 ———
opened ChimeraX session
> show #!2 models
> view p21
Expected an objects specifier or a view name or a keyword
> view name p1
> select clear
> hide #!2 models
> select #4/U:77@P
1 atom, 1 residue, 1 model selected
Drag select of 6 atoms, 5 bonds
> select clear
Drag select of 8 atoms, 6 bonds
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select #3/D:7
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #4/U:77
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #!2 models
> hide #!4 models
> select clear
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc , 52 atoms, 45 bonds
> volume zone #1 nearAtoms sel range 5 minimalBounds false
> volume zone #2 nearAtoms sel range 5 minimalBounds false
> volume zone #2 nearAtoms sel range 2minimalBounds false
Invalid "range" argument: Expected a number
> volume zone #2 nearAtoms sel range 2 minimalBounds false
> volume zone #2 nearAtoms sel range 20 minimalBounds false
> volume #2 level 0.06773
> volume #2 style mesh
> volume #2 level 0.3939
> volume #2 style surface
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> select #4/B:1002@MN
1 atom, 1 residue, 1 model selected
> select add #4/B:1003@MN
2 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #4/U:66,65
Nothing selected
> select #4/U:77,78
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/U:77,78,76
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select #4/U:77,78,76
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
> select #4/U:77,78,76,75
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #4/U:77,78,76,75,78
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
[Repeated 1 time(s)]
> hide sel cartoons
> select clear
> select #4/U
83 atoms, 91 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/T
1123 atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected
> show sel atoms
> hide sel atoms
> select #4/T:76
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/U:77
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4/U:78-90
63 atoms, 69 bonds, 3 residues, 1 model selected
> hide sel atoms
> show #!3 models
> select clear
> select #4/T:76
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> select clear
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc , 104 atoms, 90 bonds
> volume zone #2 nearAtoms sel range 20 minimalBounds false
> volume zone #2 nearAtoms sel range 200 minimalBounds false
> volume #2 level 0.0284
> volume #2 level 0.1858
> hide #!4 models
> volume #2 level 0.1334
> select #3/C:7-5
Nothing selected
> select #3/D:7-5
Nothing selected
> select #3/D:5-7
60 atoms, 65 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero target a
> color sel orange
> color sel byhetero
> select clear
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc
> select #2
4 models selected
> select #2
4 models selected
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc
> select #2
4 models selected
> select #2
4 models selected
> select clear
> select #2
4 models selected
> select #2
4 models selected
> select #2
4 models selected
> select #2
4 models selected
> select #2
4 models selected
> select #2
4 models selected
> select clear
> volume #2 level 0.2908
> volume #2 level 0.1184
> volume #2 level 0.3695
> 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"
Opened State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #5, 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_/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
> hide #!5 models
> align #6 #3
Missing required "to_atoms" argument
> matchMaker #6 #3
Unknown command: matchMaker #6 #3
> matchMaker #6 to #3
Unknown command: matchMaker #6 to #3
> matchmaker #6 to #3
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
chain B (#3) with real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb, chain B (#6), sequence alignment score =
4287.2
RMSD between 823 pruned atom pairs is 0.000 angstroms; (across all 823 pairs:
0.000)
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> fitMap #5 #2
Unknown command: fitMap #5 #2
> fitMap #5 to #2
Unknown command: fitMap #5 to #2
> fitMap #5 inMap #2
Unknown command: fitMap #5 inMap #2
> fitmap #5 inMap #2
Fit map State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc in map
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc using 33671 points
correlation = 0.2174, correlation about mean = 0.04112, overlap = 237.1
steps = 80, shift = 0.594, angle = 1.18 degrees
Position of
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#5) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.49093697 -0.86901817 -0.06154935 180.57446509
0.85839817 0.49458163 -0.13616756 -28.14054668
0.14877326 0.01401584 0.98877201 -18.53097395
Axis 0.08598408 -0.12041542 0.98899285
Axis point 115.25822066 140.21594117 0.00000000
Rotation angle (degrees) 60.84687762
Shift along axis 0.58808435
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> select add #5
3 models selected
> view matrix models
> #5,0.86956,0.28743,0.40156,-77.867,-0.36997,0.91778,0.14421,37.739,-0.32709,-0.27397,0.90441,92.416
> view matrix models
> #5,0.93675,0.31834,-0.14547,-14.538,-0.31142,0.94778,0.068705,36.682,0.15974,-0.019057,0.98697,-15.975
> view matrix models
> #5,0.9119,0.36696,0.18378,-63.838,-0.39413,0.90789,0.14284,42.361,-0.11444,-0.20269,0.97253,46.091
> view matrix models
> #5,0.83191,0.18763,0.52222,-76.207,-0.3153,0.93425,0.16662,25.403,-0.45662,-0.30327,0.83638,122.4
> view matrix models
> #5,0.80642,0.251,0.53543,-83.467,-0.30673,0.95167,0.015837,42.909,-0.50558,-0.177,0.84443,110.24
> view matrix models
> #5,0.58595,0.6547,0.47753,-102.55,-0.73093,0.68143,-0.037369,141.33,-0.34987,-0.32714,0.87782,106.29
> view matrix models
> #5,0.55983,0.70952,0.42799,-99.825,-0.77263,0.63361,-0.039764,153.52,-0.29939,-0.30842,0.90291,93.808
> view matrix models
> #5,0.56832,0.70324,0.42716,-99.932,-0.7727,0.63456,-0.016629,150.18,-0.28275,-0.32061,0.90402,93.202
> volume #5 level 0.07792
> volume #5 step 1
> transparency #6 50
> transparency #5 50
> hide #!2 models
> select add #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 6 models selected
> show sel cartoons
> view matrix models
> #3,0.72097,0.44589,-0.53046,47.646,-0.54116,0.84042,-0.029076,86.505,0.43284,0.30802,0.84721,-86.27,#5,0.59849,0.71718,0.35702,-96.718,-0.76798,0.64047,0.00080783,146.6,-0.22808,-0.27467,0.9341,76.454
> view matrix models
> #3,0.71289,0.45635,-0.53247,47.56,-0.54968,0.83513,-0.020195,86.962,0.43547,0.30709,0.84621,-86.325,#5,0.58873,0.72613,0.35515,-96.319,-0.77632,0.63033,-0.0018491,149.32,-0.2252,-0.27462,0.93481,75.977
> view matrix models
> #3,0.71287,0.45638,-0.53248,47.56,-0.5497,0.83512,-0.020173,86.963,0.43548,0.30709,0.8462,-86.325,#5,0.58871,0.72615,0.35514,-96.318,-0.77634,0.63031,-0.0018557,149.33,-0.2252,-0.27462,0.93481,75.976
> select subtract #3
3 models selected
> view matrix models
> #5,0.64532,0.75454,-0.11929,-46.01,-0.73531,0.65587,0.17073,118.84,0.20706,-0.022467,0.97807,-15.117
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.64532,0.75454,-0.11929,-33.098,-0.73531,0.65587,0.17073,117.84,0.20706,-0.022467,0.97807,-17.108
> view matrix models
> #5,0.64532,0.75454,-0.11929,-31.521,-0.73531,0.65587,0.17073,112.2,0.20706,-0.022467,0.97807,-17.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.6506,0.75522,-0.079794,-37.34,-0.75574,0.65419,0.029836,133.07,0.074734,0.040893,0.99636,-11.503
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.6506,0.75522,-0.079794,-37.908,-0.75574,0.65419,0.029836,135.06,0.074734,0.040893,0.99636,-14.225
> fitmap #3 inMap #5
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#5) using 13446 atoms
average map value = 0.3504, steps = 116
shifted from previous position = 2.36
rotated from previous position = 9.54 degrees
atoms outside contour = 2689, contour level = 0.077924
Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) relative to
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#5) coordinates:
Matrix rotation and translation
0.85608006 -0.45325355 -0.24837099 110.20658380
0.30092060 0.82781164 -0.47347089 41.63304292
0.42020676 0.33058905 0.84506637 -85.76061070
Axis 0.62364205 -0.51855984 0.58494982
Axis point 0.00000000 250.94986784 -6.64552907
Rotation angle (degrees) 40.13933325
Shift along axis -3.02541784
> select clear
> ui mousemode right zoom
> transparency #5 90
> hide #!3 cartoons
> volume #5 level 0.5427
> volume #5 level 0.2616
> volume #5 level 0.1192
> select #3/D:
Expected an objects specifier or a keyword
> select #3/D:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> matchmaker #2 #3
Missing required "to" argument
> matchmaker #2 to #3
No molecules/chains to match specified
> show #!2 models
> hide #!2 models
> show #!4 models
> matchmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
chain A (#3) with 9ere.pdb, chain B (#4), sequence alignment score = 2189.5
RMSD between 442 pruned atom pairs is 1.346 angstroms; (across all 799 pairs:
3.355)
> select clear
> hide #!4 models
> volume #5 level 0.1491
> show #!3 cartoons
> hide #!3 cartoons
> show #!3 cartoons
> hide #!3 cartoons
> ui mousemode right select
Drag select of 72 atoms, 67 bonds, 5
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc
> select clear
> show #!3 cartoons
> select backbone
48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
> show sel & #!3 atoms
> select clear
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel medium violet red
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> color sel byhetero
> select clear
> volume #5 level 0.1379
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select clear
> select #5
4 models selected
> select #3/C:1@C1'
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> ui mousemode right zoom
> volume #5 level 0.1267
> volume #5 level 0.1342
> volume #5 level 0.1491
> volume #5 level 0.1229
> volume #5 level 0.1941
> volume #5 level 0.2429
> volume #5 level 0.1267
> show #!4 models
> volume #5 level 0.09292
> volume #5 level 0.2541
> size stickRadius 0.3 sidechain
Expected a keyword
> stickRadius 0.3 sidechain
Unknown command: stickRadius 0.3 sidechain
> size stickRadius 0.2
Changed 99913 bond radii
> size stickRadius 0.1
Changed 99913 bond radii
> size stickRadius 0.15
Changed 99913 bond radii
> hide #!4 models
> select #3/A:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:251-252
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3/A:251-254
31 atoms, 30 bonds, 4 residues, 1 model selected
> select #3/A:251-255
38 atoms, 37 bonds, 5 residues, 1 model selected
> select #3/A:251-256
42 atoms, 41 bonds, 6 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> hide #!3 cartoons
> select backbone
48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
> hide sel & #!3 atoms
> select clear
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> select #3/D backbone
Expected a keyword
> select #3/D,
Expected an objects specifier or a keyword
> select backbone & sel
84 atoms, 90 bonds, 7 residues, 1 model selected
> select backbone & sel
84 atoms, 90 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> view name p11
> select clear
> volume #5 level 0.2316
> view p11
> select backbone
48750 atoms, 48734 bonds, 78 pseudobonds, 12008 residues, 16 models selected
> show sel & #!3 atoms
> show sel & #!3 cartoons
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select clear
> hide #!5 models
> show #!4 models
> show #!3-4 cartoons
> select #4/U
83 atoms, 91 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #4/T
1123 atoms, 1249 bonds, 6 pseudobonds, 56 residues, 3 models selected
> hide sel cartoons
> select #3/D:1-6
122 atoms, 134 bonds, 6 residues, 1 model selected
> hide sel atoms
> select clear
> select #3/C:1@C1'
1 atom, 1 residue, 1 model selected
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/B:254
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/B:251
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
> view p11
> select #4/B:136
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #4/B:134
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/B:135
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select clear
[Repeated 1 time(s)]
> hide #!3-4 cartoons
> view p1
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!5 models
> volume #5 level 0.2277
> view p11
> select clear
> ui mousemode right zoom
> select #3/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> show sel cartoons
> ;ect c;ear
Incomplete command: sequence
> select clear
> select #3/A:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:135140
Nothing selected
> select #3/A:135-140
41 atoms, 40 bonds, 6 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> volume #5 level 0.1143
> size stickRadius 0.1
Changed 99913 bond radii
> size stickRadius 0.15
Changed 99913 bond radii
> size stickRadius 0.2
Changed 99913 bond radii
> size stickRadius 0.17
Changed 99913 bond radii
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v3.cxs
> ui tool show "Side View"
> volume #5 level 0.1964
> volume #5 level 0.1377
> volume #5 level 0.1416
> volume #5 level 0.1534
> select #3/D:5-7
60 atoms, 65 bonds, 3 residues, 1 model selected
> show sel atoms
> select ~sel & ##selected
13386 atoms, 13677 bonds, 20 pseudobonds, 1657 residues, 3 models selected
> select ~sel & ##selected
60 atoms, 65 bonds, 3 residues, 1 model selected
> select #3/D:4-7
82 atoms, 90 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> volume #5 level 0.1456
> volume #5 level 0.1495
> volume #5 level 0.1143
> hide #!5 models
> ui mousemode right select
> select clear
[Repeated 3 time(s)]
> select #3/A:383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> show #!3 atoms
> hide #!3 atoms
> undo
[Repeated 1 time(s)]
> select clear
[Repeated 2 time(s)]
> select #3/c
111 atoms, 124 bonds, 5 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select clear
> select #3/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> show sel cartoons
> select clear
> hide #!3 models
> show #!3 models
> hide #!3 atoms
> select #3/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> show #!6 models
> hide #!6 models
> show #!5 models
> select ::name="MG"
16 atoms, 16 residues, 6 models selected
> show sel & #!3 atoms
> select clear
> volume #5 level 0.1338
> volume #5 level 0.1808
> volume #5 level 0.1064
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select clearviewname p0402
Expected an objects specifier or a keyword
> viewname p0402
Unknown command: viewname p0402
> view name p0402
> volume #5 level 0.1338
> lighting flat
[Repeated 1 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> view p0402
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> color sel cornflower blue
> select #3/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> color sel cornflowerblue bloue
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel cornflower blue
> cor sel byHetero target a
Unknown command: cor sel byHetero target a
> color sel byhetero target a
> select clear
> volume #2 level 0.3969
> volume mask #1 atomSpec sel distance 5 softEdge 2 modelId #4
Expected a keyword
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> volume mask #5 atomSpec sel distance 5 softEdge 2 modelId #4
Expected a keyword
> volume mask #5 atomSpec sel distance 5 softEdge 2
Expected a keyword
> volume zone #5 nearAtoms sel range 6 minimalBounds false
> volume zone #5 nearAtoms sel range 2
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume zone #5 nearAtoms sel range 2
> select #3/D & select #3/A:206,211,213,
Expected a keyword
> select #3/D, #3/A:206,211,213,
Expected an objects specifier or a keyword
> select #3/D, #3/A:206,211,213
Expected an objects specifier or a keyword
> select #3/D #3/A:206,211,213
169 atoms, 180 bonds, 10 residues, 1 model selected
> volume zone #5 nearAtoms sel range 2
> select #3/D #3/A:206,211,213,133
180 atoms, 190 bonds, 11 residues, 1 model selected
> select #3/D #3/A:206,211,213,133.24,249
Expected a keyword
> select #3/D #3/A:206,211,213,133,248,249
196 atoms, 205 bonds, 13 residues, 1 model selected
> volume zone #5 nearAtoms sel range 2
> volume zone #5 nearAtoms sel range 4
> volume zone #5 nearAtoms sel range 6
> volume zone #5 nearAtoms sel range 8
> select #3/D #3/A:200-249
548 atoms, 571 bonds, 57 residues, 1 model selected
> volume zone #5 nearAtoms sel range 8
> select #3/D #3/A:140-249
855 atoms, 881 bonds, 1 pseudobond, 94 residues, 2 models selected
> volume zone #5 nearAtoms sel range 8
> select clear
> ui tool show "Side View"
> volume #5 level 0.1495
> save /Users/justinvanriper/Desktop/image24.png supersample 3
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v4.cxs
——— End of log from Wed Apr 2 14:23:23 2025 ———
opened ChimeraX session
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: 8 days, 5 hours, 18 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
Acer XF270H B:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
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 |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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