![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Last modified 8 months ago
#17280 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-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,
"osVersion" : {
"train" : "macOS 14.5",
"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
> select #3/A:555-912
2637 atoms, 2695 bonds, 3 pseudobonds, 329 residues, 2 models selected
> color sel sienna
> select clear
> select #3/B:352-554
1328 atoms, 1356 bonds, 1 pseudobond, 166 residues, 2 models selected
> color sel sandy brown
> color sel khaki
> select #3/B:555-912
2637 atoms, 2695 bonds, 3 pseudobonds, 329 residues, 2 models selected
> color sel sandy brown
> select clear
> cartoon style #3.1,3-4#!3 modeHelix tube sides 20
> select clear
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb
Chain information for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb #4
---
Chain | Description
A B | No description available
G | No description available
Computing secondary structure
> color sel light grey
> color #4l light grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #4 light grey
> select clear
> cartoon style #4#3.1,3-4#!3 modeHelix tube sides 20
> select clear
> nucleotides ladder
> view p1
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> undo
> color #4 #929292ff
> color #4 darkgrey
> color #4 silver
> color #4 darkgrey
> color #4 whitesmoke
> color #4 #cbccccff
> color #4 darkgrey
> color #4 silver
> select clear
> save /Users/justinvanriper/Desktop/image15.png supersample 3
> select #4/A,B
14582 atoms, 14894 bonds, 1824 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> roll y 1 90
> roll x 1 50
> select ~sel & ##selected
16334 atoms, 16851 bonds, 1 pseudobond, 1906 residues, 2 models selected
> select ~sel & ##selected
4 atoms, 4 residues, 1 model selected
> select ~sel & ##selected
16334 atoms, 16851 bonds, 1 pseudobond, 1906 residues, 2 models selected
> roll y -1 90
> roll x 1 90
> roll y -1 90
> select clear
> save /Users/justinvanriper/Desktop/image16.png supersample 3
> select #4/G
1752 atoms, 1957 bonds, 82 residues, 1 model selected
> select #4/G:1-7,75-82
322 atoms, 358 bonds, 15 residues, 1 model selected
> color sel forest green
> view name p01
> select #4/G:10-25
347 atoms, 388 bonds, 16 residues, 1 model selected
> color sel dodger blue
> select clear
> select #4/G:27-43
361 atoms, 403 bonds, 17 residues, 1 model selected
> color sel dark orchid
> selct clear
Unknown command: selct clear
> select #4/G:45-55
232 atoms, 257 bonds, 11 residues, 1 model selected
> color sel crimson
> select #4/G:58-74
361 atoms, 402 bonds, 17 residues, 1 model selected
> color sel gold
> select clear
> select #4/G:8,9,26,44,56,57
129 atoms, 140 bonds, 6 residues, 1 model selected
> color sel oldlace linen
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel old lace
> select clear
> save /Users/justinvanriper/Desktop/image17.png supersample 3
> select #4/G:26-57
679 atoms, 757 bonds, 32 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select ~sel & ##selected
15659 atoms, 16094 bonds, 1 pseudobond, 1878 residues, 2 models selected
> select up
15661 atoms, 16094 bonds, 1 pseudobond, 1880 residues, 2 models selected
> select #4/G:10-57
1026 atoms, 1146 bonds, 48 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/G:8-57
1069 atoms, 1194 bonds, 50 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/G:10-82
1557 atoms, 1739 bonds, 73 residues, 1 model selected
> select #4/G:1-57
1221 atoms, 1364 bonds, 57 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #4/G:1-57,77-82
1348 atoms, 1505 bonds, 63 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
> view p01
> view name p02
> save /Users/justinvanriper/Desktop/image18.png supersample 3
> roll y -1 90
> view name p03
> save /Users/justinvanriper/Desktop/image19.png supersample 3
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/SLFN14_session_alignment_RNA.cxs
> show cartoons
> view p01
> select #4/G:
Expected an objects specifier or a keyword
> select #4/G
1752 atoms, 1957 bonds, 82 residues, 1 model selected
> show sel atoms
> select clear
> view p1
> roll x 1 90
> select #3/A,B:352-912
7930 atoms, 8104 bonds, 8 pseudobonds, 990 residues, 2 models selected
> hide sel cartoons
> select #3,4/A,B:352-912
16848 atoms, 17224 bonds, 8 pseudobonds, 2112 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> select #4/G
1752 atoms, 1957 bonds, 82 residues, 1 model selected
> color sel old lace
> select #4/A,B
14582 atoms, 14894 bonds, 1824 residues, 1 model selected
> color sel old lace
> select clear
> select #3,4/A,B:218,219,220,223
144 atoms, 136 bonds, 16 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 144 atom styles
> select ::name="MG"
5 atoms, 5 residues, 2 models selected
> show sel atoms
> select clear
> select #3,4/A,B:206,211,213
108 atoms, 96 bonds, 12 residues, 2 models selected
> show sel atoms
> color sel byhetero target a
> select clear
> select #3/A,B:206,211,213
54 atoms, 48 bonds, 6 residues, 1 model selected
> select #3/A,B:218,219,220,223
72 atoms, 68 bonds, 8 residues, 1 model selected
> color sel white
> color sel old lace
> select #4/A,B:218,219,220,223
72 atoms, 68 bonds, 8 residues, 1 model selected
> color sel cyan
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting soft
> view name p11
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> color sel old lace
> select #4/A
7291 atoms, 7447 bonds, 912 residues, 1 model selected
> color sel cornflower blue target c
> color sel light blue target c
> select #4/B
7291 atoms, 7447 bonds, 912 residues, 1 model selected
> color sel cornflower blue target c
> select clear
> save /Users/justinvanriper/Desktop/image20.png supersample 3
> select #4 Mg
Expected a keyword
> select ::name="MG"
5 atoms, 5 residues, 2 models selected
> color sel byhetero
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> select #3/A,B
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> color sel old lace
> select clear
> save /Users/justinvanriper/Desktop/image21.png supersample 3
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/SLFN14_session_DiseaseMut_alignment_RNA.cxs
> select #4
16338 atoms, 16851 bonds, 1 pseudobond, 1910 residues, 2 models selected
> hide #!4 models
> coulombic #!3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb_A SES surface #3.3: minimum, -18.85, mean
0.28, maximum 15.66
Coulombic values for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb_B SES surface #3.4: minimum, -21.91, mean
0.09, maximum 16.30
Coulombic values for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb_C SES surface #3.5: minimum, -17.13, mean
-7.14, maximum 0.91
Coulombic values for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb_D SES surface #3.6: minimum, -17.77, mean
-8.59, maximum -1.01
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> hide sel surfaces
> select clear
> hide #!3 surfaces
> select ~sel & ##selected
Nothing selected
> 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
13193 atoms, 13462 bonds, 20 pseudobonds, 1648 residues, 3 models selected
> hide sel atoms
> select clear
> view name p21
> view p21
> show #!4 models
> hide #!4 models
> select ~sel & ##selected
Nothing selected
> view name p21
> save /Users/justinvanriper/Desktop/image22.png supersample 3
> hide #!3 models
> show #!4 models
> coulombic #!4
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_A SES surface #4.2:
minimum, -20.28, mean 0.14, maximum 20.52
Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_B SES surface #4.3:
minimum, -22.66, mean 0.14, maximum 17.42
Coulombic values for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb_G SES surface #4.4:
minimum, -49.29, mean -22.91, maximum -5.91
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!4 surfaces
> select #4/A,B:1-351
5664 atoms, 5772 bonds, 702 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> select clear
> save /Users/justinvanriper/Desktop/image23.png supersample 3
Unsupported scale factor (0.000000) detected on Display0
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_4/tRNA_ElectrostaticMap_SLFN14_Fig4.cxs
> hide #!4 models
> show #!1 models
> close
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs
Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.15,
step 1, values float32
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
> 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
> show sel cartoons
> show sel atoms
> 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
> select #4/U:77,78,76,75,78
40 atoms, 43 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> 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
> 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
> hide sel atoms
> select clear
> 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
> 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
> 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
> select #3/A:383
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> show #!3 atoms
> hide #!3 atoms
> undo
> select clear
> 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
> lighting full
> 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
> 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
> view p1
> view p0402
> save /Users/justinvanriper/Desktop/image25.png supersample 3
> view p0401
Expected an objects specifier or a view name or a keyword
> view name p0401
> select #3/B:133,206,211,213,249,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel light blue
> color sel byhetero
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> show sel atoms
> color sel hot pink
> color sel byhetero
> select #3/C, #3/B:133
Expected an objects specifier or a keyword
> select #3/C #3/B:133
122 atoms, 134 bonds, 6 residues, 1 model selected
> select #3/C #3/B:133-250
911 atoms, 936 bonds, 1 pseudobond, 103 residues, 2 models selected
> show sel cartoons
> select#3/B:133-250
Unknown command: select#3/B:133-250
> select #3/B:133-250
800 atoms, 812 bonds, 1 pseudobond, 98 residues, 2 models selected
> volume zone #5 nearAtoms sel range 8
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> volume zone #5 nearAtoms sel range 8
> select #3/B:133-250
800 atoms, 812 bonds, 1 pseudobond, 98 residues, 2 models selected
> color sel light blue
> color sel byhetero
> select clear
> select #3/B:133-250 #3/C
911 atoms, 936 bonds, 1 pseudobond, 103 residues, 2 models selected
> volume zone #5 nearAtoms sel range 8
> select #3/B
6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
> color sel light blue
> color sel byhetero
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
Drag select of 5
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc
> select clear
Drag select of 1 atoms, 5
State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc
> select #5
4 models selected
> select #5
4 models selected
> select clear
> save /Users/justinvanriper/Desktop/image26.png supersample 3
> view name p0404
> view p0404
> view p0401
> close
> 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 #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select #1/A
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> select ~sel & ##selected
6862 atoms, 7024 bonds, 10 pseudobonds, 837 residues, 3 models selected
> select ~sel & ##selected
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> select ~sel & ##selected
6862 atoms, 7024 bonds, 10 pseudobonds, 837 residues, 3 models selected
> select ~sel & ##selected
6584 atoms, 6718 bonds, 10 pseudobonds, 823 residues, 3 models selected
> select #1/A:1-351
2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
> color sel cornflower blue
> select #1/B:1-351
2642 atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected
> color sel light blue
> select #1/B:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel khaki
> select #1/A:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel gold
> select #1/A:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel sienna
> select #1/B:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel sandy brown
> select clear
> split #1
Split real_space_refined_036_edited-coot-15_real_space_refined_015.pdb (#1)
into 4 models
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb D #1.4
---
Chain | Description
D | No description available
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> align #1.1 toAtoms #1.2
Unequal number of atoms to pair, 6584 and 6609
> align #1.1 #1.2
Missing required "to_atoms" argument
> matchmaker #1.1 #1.2
Missing required "to" argument
> matchmaker #1.1 to #1.2
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 B,
chain B (#1.2) with real_space_refined_036_edited-
coot-15_real_space_refined_015.pdb A, chain A (#1.1), sequence alignment score
= 4058.4
RMSD between 795 pruned atom pairs is 0.752 angstroms; (across all 820 pairs:
0.884)
> select clear
> color byhetero target a
> select clear
> select #1.2/B:1002@MG
1 atom, 1 residue, 1 model selected
> hide #1.3 models
> hide #1.4 models
> show #1.3 models
> hide #1.3 models
> show #1.4 models
> hide #1.4 models
> select clear
> hide #!1.1-2 atoms
> select ::name="MG"::name="ZN"
5 atoms, 5 residues, 2 models selected
> show sel atoms
> select clear
> select #1/A,B: 133,206,211,213,248,249
108 atoms, 98 bonds, 12 residues, 2 models selected
> show sel atoms
> select clear
> select #1/A,B: 284,282,318,219
62 atoms, 56 bonds, 8 residues, 2 models selected
> show sel atoms
> select clear
> select cleartransparency #1.2 50
Expected an objects specifier or a keyword
> transparency #1.2 50
> transparency #1.2 50 target c
> transparency #1.2 50 target c,a
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> transparency #1.2 50 target c a
Expected a keyword
> transparency #1.2 50 target a
> select #1.2
6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
> color sel old lace
> select clear
> hide #!1 models
> 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"
> "/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 State1_cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc as #2.1, grid size 300,300,300, pixel 0.832, shown at
level 0.0049, step 2, values float32
Opened
State2_cryosparc_P99_J209_008_volume_map_sharpClass2C1-flip_deepEMhancer-
sharpened-highres.mrc as #2.2, grid size 300,300,300, pixel 0.832, shown at
level 0.00701, step 2, values float32
> select clear
> volume #2.1 step 1
> volume #2.2 step 1
> volume #2.1 level 0.0284
> volume #2.2 level 0.03203
> surface dust #2.1 size 8.32
> surface dust #2.2 size 8.32
> surface dust #2.1 size 8.32
> surface dust #2.2 size 8.32
> surface dust #2.1 size 8.32
> surface dust #2.2 size 8.32
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> close #1
> 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 #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> color #2.2 darkgrey models
> hide #!2 models
> hide #!2.1-2 target m
> show #!2.2 target m
> hide #!1 target m
> show #!2.1 target m
> hide #!2.2 target m
> show #!1 target m
> hide #!2.1 target m
> show #!2.2 target m
> hide #!1 target m
> show #!1 target m
> hide #!2.2 target m
> show #!2.1 target m
> hide #!1 target m
> show #!2.2 target m
> hide #!2.1 target m
> show #!1 target m
> hide #!2.2 target m
> select #1/A:1-351
2616 atoms, 2666 bonds, 1 pseudobond, 325 residues, 2 models selected
> color sel cornflower blue
> select #1/B:1-351
2642 atoms, 2692 bonds, 1 pseudobond, 328 residues, 2 models selected
> color sel light blue
> select #1/B:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel khaki
> select #1/A:352-555
1334 atoms, 1362 bonds, 1 pseudobond, 167 residues, 2 models selected
> color sel gold
> select #1/A:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel sienna
> select #1/B:556-912
2631 atoms, 2689 bonds, 3 pseudobonds, 328 residues, 2 models selected
> color sel sandy brown
> select clear
> show #!2.1 models
> color zone #2.1 near #1 distance 4.99
> select clear
> hide #!2 models
> show #!2 models
> select #1/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> color sel hot pink
> select #1/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel medium violet red
> color zone #2.1 near sel & #1 distance 4.99
> hide #!2 models
> hide #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.1 models
> select clear
> color zone #2.1 near #1 distance 4.99
> select clear
> hide #!2.1 models
> show #!2.1 models
> show #!2.2 models
> hide #!1 models
> color #2.2 #ebebebff models
> color #2.2 white models
> color #2.2 #ebebebff models
> color #2.2 white models
> volume #2.1 level 0.04701
> hide #!2.2 models
> volume #2.1 level 0.05631
> show #!2.2 models
> volume #2.2 level 0.06777
> ui tool show "Side View"
> view name p1
> roll y 1 90
> roll y -1 90
> roll y -1 45
> roll y 1 45
> save /Users/justinvanriper/Desktop/image27.png supersample 3
> roll x 1 90
> save /Users/justinvanriper/Desktop/image28.png supersample 3
> view name p2
> roll x 1 180
> save /Users/justinvanriper/Desktop/image29.png supersample 3
> roll x 1 90
> roll y -1 90
> save /Users/justinvanriper/Desktop/image30.png supersample 3
> roll y 1 135
> save /Users/justinvanriper/Desktop/image31.png supersample 3
> hide #!2 models
> show #!1 models
> hide atoms
> hide cartoons
> select #1/A:284,282,318,319
28 atoms, 26 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel pink
> color sel light pink
> color sel magenta
> ui tool show "Color Actions"
> color sel orchid
> color sel pale violet red
> color sel hot pink
> color sel thistle
> color sel violet
> color sel plum
> color sel violet
> color sel light pink
> color sel violet
> color sel byhetero
> select clear
Drag select of 28 atoms, 26 bonds
> color sel #d6b8ddff
> color sel #f4b8fbff
> color sel #ecb1f1ff
> select clear
> color #1 byhetero
> select clear
> select ::name="ZN"
2 atoms, 2 residues, 1 model selected
> show sel atoms
> select backbone
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> hide sel atoms
> undo
> select clear
> select /A:318@N
1 atom, 1 residue, 1 model selected
> select add /A:319@O
2 atoms, 5 bonds, 2 residues, 1 model selected
> select add /A:318@O
3 atoms, 5 bonds, 2 residues, 1 model selected
> select subtract /A:318@O
2 atoms, 5 bonds, 2 residues, 1 model selected
> hide sel atoms
> select /A:319@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /A:318@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /A:318@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /A:319@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide atoms
> undo
> select /A:284@O
1 atom, 1 residue, 1 model selected
> select add /A:284@C
2 atoms, 1 residue, 1 model selected
> select add /A:284@CA
3 atoms, 1 residue, 1 model selected
> select subtract /A:284@CA
2 atoms, 1 residue, 1 model selected
> select add /A:284@CA
3 atoms, 1 bond, 1 residue, 1 model selected
> select subtract /A:284@CA
2 atoms, 1 residue, 1 model selected
> select add /A:284@N
3 atoms, 1 residue, 1 model selected
> hide sel atoms
> select /A:282@O
1 atom, 1 residue, 1 model selected
> select add /A:282@C
2 atoms, 1 residue, 1 model selected
> select add /A:282@N
3 atoms, 1 residue, 1 model selected
> select add /A:282@CA
4 atoms, 1 residue, 1 model selected
> hide sel atoms
> undo
> select subtract /A:282@CA
3 atoms, 1 residue, 1 model selected
> hide sel atoms
> color #1.1 black models
> color #1.1 #212121ff models
> color #1.1 #424242ff models
> select clear
Drag select of 3 atoms, 2 bonds, 1 pseudobonds
> ~hbonds
> select clear
> hide cartoons
> hide atoms
> undo
> select clear
> select main
13188 atoms, 13462 bonds, 13 pseudobonds, 1643 residues, 3 models selected
> select clear
> delete sel
> hide pseudobonds
> select /A:1001@ZN
1 atom, 1 residue, 1 model selected
> show pseudobonds sel
Expected ',' or a keyword
> show sel pseudobonds
> metalBonds
Unknown command: metalBonds
> metalBonds #1
Unknown command: metalBonds #1
> hbonds sel reveal true
0 hydrogen bonds found
> ~hbonds
> hide sel pbonds
> select clear
> save /Users/justinvanriper/Desktop/image32.png supersample 3
> open
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/PDB_for_Figures/Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb
Chain information for Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb #3
---
Chain | Description
A B | No description available
G | No description available
Computing secondary structure
> matchmaker #3 to #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 real_space_refined_036_edited-coot-15_real_space_refined_015.pdb,
chain A (#1) with Aligned_AlphaFold_SLFN14-tRNA_Ser.pdb, chain A (#3),
sequence alignment score = 3942.6
RMSD between 766 pruned atom pairs is 1.001 angstroms; (across all 820 pairs:
1.544)
> select clear
> hide #!1 models
> select #3/C:1@ZN
1 atom, 1 residue, 1 model selected
> show pbonds
> select clear
===== Log before crash end =====
Log:
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_/Figures/Figure_5/Figure_5_aligned_session_v4.cxs
Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.397,
step 1, values float32
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 0.149, step 1, values float32
Log from Wed Apr 2 14:23:23 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_/Figures/Figure_5/Figure_5_aligned_session_v2.cxs
Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.15,
step 1, values float32
Log from Sun Mar 30 16:27:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/justinvanriper/Library/CloudStorage/OneDrive-
> BaylorCollegeofMedicine/Pillon
> Lab/SLFN14/SLFN14_Figure5_Drafts/Figure5_draft_images/SLFN_Family_Alignments_Figures.cxs"
> format session
Log from Thu Aug 1 13:17:53 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/justinvanriper/Desktop/all_aligned_SLFN.cif
Summary of feedback from opening
/Users/justinvanriper/Desktop/all_aligned_SLFN.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 13552
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "GLY" on line 13558
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 23886
Unknown polymer entity '2' on line 28036
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 51632
Missing or incomplete sequence information. Inferred polymer connectivity.
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
107 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for all_aligned_SLFN.cif
---
Chain | Description
1.1/A 1.1/B | No description available
1.2/A | No description available
1.3/A 1.3/C | No description available
1.4/A 1.4/B | No description available
1.5/A | No description available
1.6/A | No description available
1.2/B | No description available
1.3/B 1.3/D | No description available
1.5/B | No description available
1.1/C | No description available
1.2/C | No description available
1.1/D | No description available
1.2/D | No description available
> hide #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #1.6 models
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show cartoons
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> show sel cartoons
> nucleotides sel ladder
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> color sel light pink
> select #1.1/B,D
6740 atoms, 6886 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> show sel cartoons
> nucleotides sel ladder
> set bgColor white
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> save /Users/justinvanriper/Desktop/SLFFN14_alignments_all.cxs
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #1.1/A:180-316
1126 atoms, 1150 bonds, 137 residues, 1 model selected
> show sel cartoons
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show sel cartoons, show sel atoms, nucleotides sel ladder
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> show sel cartoons
> show sel atoms
> nucleotides sel ladder
> hide atoms
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> show sel cartoons
> select #1.1/C,D
215 atoms, 238 bonds, 10 residues, 1 model selected
> show sel cartoons
> show sel atoms
> nucloetides ladder
Unknown command: nucloetides ladder
> nucloetides sel ladder
Unknown command: nucloetides sel ladder
> nucleotides sel ladder
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel blue violet
> color sel byhetero
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel blue violet
> color sel byhetero
> ui tool show "Color Actions"
> color sel cornflower blue target c
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel blue violet target a
> color sel byhetero
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> hide sel catoons; hide sel atoms
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel catoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel cartoons
> hide sel atoms
> ui mousemode right select
Drag select of 455 residues
> hide sel cartoons
Drag select of 40 residues
> hide sel cartoons
> ui tool show "Side View"
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> size stickRadius 0.4
Changed 58414 bond radii
> size stickRadius 0.3
Changed 58414 bond radii
> size stickRadius 0.35
Changed 58414 bond radii
> select clear
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> show sel & #!1.1 atoms
> color (#!1.1 & sel) byelement
> select clear
> select #1.1/B:1002@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> view name p1
> show #!1.2 models
> select #1.2/A
2595 atoms, 2639 bonds, 3 pseudobonds, 329 residues, 2 models selected
> select #1.2/A:134,205,210,212,247,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> select ~sel & ##selected
10247 atoms, 10425 bonds, 16 pseudobonds, 1300 residues, 2 models selected
> hide cartoons
Drag select of 40 atoms, 39 bonds, 10 shapes
> hide atoms
> select #1.2/A:134,205,210,212,247,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> select #1.2/A:134,205,210,212,247,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
Drag select of 12 atoms, 11 bonds
> color #1.2 #ffcc99ff
> color #1.2 #ccccccff
> select #1.2/A:134,205,210,212,247,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel light grey
> select #1.2/A:134,205,210,212,247,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel light grey
> color sel byhetero
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> show sel & #!1.1 atoms
> size stickRadius 0.2
Changed 58414 bond radii
> show #!1.3 models
> select #1.3/A
4151 atoms, 4221 bonds, 2 pseudobonds, 513 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #1.3/A:129,200,205,207
38 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1.3/A:129,200,205,207
38 atoms, 34 bonds, 4 residues, 1 model selected
> color sel light grey
> color sel byhetero
> select #1.4/A:135,209,214,216,251,252
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel light grey
> color sel byhetero
> select #1.4/A:135,209,214,216,251,252
54 atoms, 49 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel light grey
> color sel byhetero
> show #!1.4 models
> show #!1.5 models
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> show sel atoms
Drag select of 4 atoms
> hide sel atoms
> select #1.5/A:120,191,196,233
37 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel light grey
> color sel byhetero
> select #1.5/B:120,191,196,233
37 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel light grey
> color sel byhetero
Drag select of 37 atoms, 33 bonds
> hide sel atoms
> show #1.6 models
> close #1.6
> hide #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.5 models
> hide #!1.2 models
> view name p2
> hide #!1.4 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.5 models
> show #!1.5 models
Drag select of 239 atoms, 214 bonds
> hide sel target a
> show (sel-residues & sidechain) target ab
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> show sel atoms
> select clear
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 1 pseudobond, 6 residues, 2 models selected
> color sel blue violoet
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 1 pseudobond, 6 residues, 2 models selected
> color sel blue violet
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> view p1
> select #1.1/A
6634 atoms, 6769 bonds, 7 pseudobonds, 828 residues, 3 models selected
> show sel cartoons
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> show sel cartoons
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> show sel cartoons
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show sel cartoons
> select #1.1/C
109 atoms, 121 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show atoms
> show sel atoms
Drag select of 205 residues
> hide sel cartoons
> hide sel atoms
> select clear
[Repeated 1 time(s)]Drag select of 273 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
Drag select of 6 residues
> hide sel cartoons
Drag select of 4 residues
> hide sel cartoons
> view p1
> cartoon style sel modeHelix tube sides 20
Drag select of 38 atoms, 356 residues, 30 bonds, 10 shapes
> select clear
> show #!1.2 models
> hide #!1.2 models
> view p1
> show #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> hide #!1.2 models
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light gray target c
> select clear
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel blue violoet
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cornflower blue target a
> select clear
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel blue
> ui tool show "Color Actions"
> color sel blue target a
> select ~sel & ##selected
13429 atoms, 13727 bonds, 12 pseudobonds, 1660 residues, 2 models selected
> select down
13429 atoms, 13727 bonds, 12 pseudobonds, 1660 residues, 2 models selected
> select clear
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> color sel cornflower blue
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> color sel light pink
> select #1.1/A:1002@MG
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #1.1/A:133,206,211,213,248,249
54 atoms, 49 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orange target a
> color sel orange red target a
> color sel magenta target a
> color sel deep pink target a
[Repeated 1 time(s)]
> size stickRadius 0.4
Changed 57471 bond radii
> size stickRadius 0.3
Changed 57471 bond radii
> size stickRadius 0.34
Changed 57471 bond radii
> ui tool show "Color Actions"
> color sel dark violet target a
> color sel medium violet red target a
> color sel violet target a
> color sel medium violet red target a
> color sel rebecca purple target a
> color sel deep pink target a
> color sel magenta target a
> color sel deep pink target a
[Repeated 1 time(s)]
> color sel medium violet red target a
[Repeated 2 time(s)]
> color sel dark violet target a
> color sel orange red target a
> color sel red target a
> color sel orange red target a
> color sel crimson target a
[Repeated 1 time(s)]
> color sel orange red target a
> color sel crimson target a
> color sel red target a
> color sel crimson target a
> color sel byhetero target a
> color sel dark orange target a
> color sel byhetero target a
> color sel green target a
> color sel forest green target a
[Repeated 1 time(s)]
> color sel dark orange target a
> color sel byhetero target a
> select clear
> view name p1
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> select #1.1/B:1002@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> save /Users/justinvanriper/Desktop/image3.png supersample 3
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> select up
6634 atoms, 6769 bonds, 828 residues, 1 model selected
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> hide sel cartoons
> undo
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> save /Users/justinvanriper/Desktop/image4.png supersample 3
> select #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> hide sel cartoons
Drag select of 40 atoms, 39 bonds, 10 shapes
> hide sel atoms
> view p2
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> size stickRadius 0.2
Changed 57471 bond radii
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.5 models
> select pbonds
50 pseudobonds, 8 models selected
> hide pbonds
> select clear
> select #1.4/B:1002@MG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> show #!1.3 models
> hide #!1.4 models
> show #!1.2 models
> show #!1.4 models
> show #!1.5 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.5 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> show cartoons
> hide #!1.2 models
> show #!1.3 models
> select #1.3/A:242
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1.3/A:243
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel light grey
> color sel byhetero
> hide cartoons
> hide pbonds
> hide sel target a
> show (sel-residues & sidechain) target ab
> hide pbonds
> view name final
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> show cartoons
> select #1.5/B:198
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #1.5/B:232
17 atoms, 16 bonds, 2 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> color sel light grey
> color sel byhetero
> hide cartoons
> hide pbonds
> hide #!1.5 models
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> show #!1.2 models
> save /Users/justinvanriper/Desktop/image2.png supersample 3
> hide #!1.2 models
> show #!1.3 models
> save /Users/justinvanriper/Desktop/image3.png supersample 3
> hide #!1.3 models
> show #!1.4 models
> save /Users/justinvanriper/Desktop/image4.png supersample 3
> hide #!1.4 models
> show #!1.5 models
> save /Users/justinvanriper/Desktop/image5.png supersample 3
> hide #!1.5 models
> show cartoons
> view p1
> view p2
> view p3
Expected an objects specifier or a view name or a keyword
> view p1
> select #1.1/B,C
6743 atoms, 6890 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
Drag select of 180 residues
Drag select of 389 residues
> hide sel cartoons
Drag select of 90 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 8 residues
> hide sel cartoons
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> show sel atoms
> select clear
> save /Users/justinvanriper/Desktop/image6.png supersample 3
> show #1.1.1 models
> select #1.1/A
6634 atoms, 6769 bonds, 6 pseudobonds, 828 residues, 2 models selected
> show cartoons
> select #1.1/B,C
6743 atoms, 6890 bonds, 6 pseudobonds, 833 residues, 2 models selected
> hide sel cartoons
> hide #1.1.1 models
> show #1.1.1 models
> select #1.1/A:349
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A #1.1/B
Alignment identifier is 1
> select #1.1/A-B:381-383
48 atoms, 46 bonds, 6 residues, 1 model selected
> select #1.1/A-B:381-402
378 atoms, 386 bonds, 44 residues, 1 model selected
> select #1.1/A-B:334-335
28 atoms, 26 bonds, 4 residues, 1 model selected
> select #1.1/A-B:334-405
694 atoms, 706 bonds, 2 pseudobonds, 82 residues, 2 models selected
> select #1.1/A-B:334-337
56 atoms, 54 bonds, 8 residues, 1 model selected
> select #1.1/A-B:334-384
326 atoms, 328 bonds, 2 pseudobonds, 40 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> select #1.1/A:349
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A-B:381-384
68 atoms, 68 bonds, 8 residues, 1 model selected
> select #1.1/A-B:381-403
396 atoms, 404 bonds, 46 residues, 1 model selected
Drag select of 145 residues
> hide sel cartoons
Drag select of 178 residues
> hide sel cartoons
> view p1
Drag select of 173 residues
> hide sel cartoons
Drag select of 49 residues
> hide sel cartoons
> view p1
> save /Users/justinvanriper/Desktop/image7.png supersample 3
> size stickRadius 0.3
Changed 57471 bond radii
> size stickRadius 0.35
Changed 57471 bond radii
> size stickRadius 0.34
Changed 57471 bond radii
> size stickRadius 0.4
Changed 57471 bond radii
> size stickRadius 0.3
Changed 57471 bond radii
> size stickRadius 0.35
Changed 57471 bond radii
> save /Users/justinvanriper/Desktop/image8.png supersample 3
> view final
> hide cartoons
> hide pbonds
> select #1.1/D
106 atoms, 117 bonds, 5 residues, 1 model selected
> hide sel atoms
> size stickRadius 0.2
Changed 57471 bond radii
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.5 models
> save /Users/justinvanriper/Desktop/image9.png supersample 3
> select #1.1/A:211@CD
1 atom, 1 residue, 1 model selected
> view ginal
Expected an objects specifier or a view name or a keyword
> view final
> color sel byhetero
> select add #1.5/B:198@CA
1 atom, 3 bonds, 1 residue, 1 model selected
> select add #1.5/B:198@CG2
2 atoms, 3 bonds, 1 residue, 1 model selected
> select add #1.5/B:198@CG1
3 atoms, 3 bonds, 1 residue, 1 model selected
> color sel byhetero
> view final
> select clear
> show #!1.4 models
> hide #!1.5 models
> select #1.4/A:1002@MG
1 atom, 1 residue, 1 model selected
> color sel light grey
> select clear
[Repeated 1 time(s)]
> view final
> save /Users/justinvanriper/Desktop/image1.png supersample 3
> hide #!1.4 models
> show #!1.2 models
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> show sel & #!1.1 atoms
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> select ::name="MG"
6 atoms, 6 residues, 3 models selected
> hide sel atoms
> show sel atoms
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #1.1.1 models
> show #!1.1 models
> show #1.1.1 models
> select #1.4/A
6667 atoms, 6809 bonds, 4 pseudobonds, 829 residues, 3 models selected
> select #1.4/A:1002
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.5 models
> show #!1.4 models
> show #!1.5 models
> show #!1.3 models
> show #!1.2 models
> view final
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> select add #1.4
13334 atoms, 13618 bonds, 7 pseudobonds, 1658 residues, 3 models selected
> select subtract #1.4
Nothing selected
> select clear
> select #1.1/A:1002@MG
1 atom, 1 residue, 1 model selected
> show #1.1/A cartoons
Drag select of 477 residues
> hide sel cartoons
Drag select of 64 residues
> hide sel cartoons
Drag select of 4 residues
Drag select of 1 residues
> hide sel cartoons
> save /Users/justinvanriper/Desktop/SLFN_Family_Alignments_Figures.cxs
——— End of log from Thu Aug 1 13:17:53 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> view matrix models #1.1,1,0,0,0.028681,0,1,0,-1.0855,0,0,1,0.26887
> view matrix models #1.1,1,0,0,5.6932,0,1,0,-8.7173,0,0,1,5.9219
> undo
[Repeated 6 time(s)]
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> ui mousemode right select
> select #1.1/B:1002@MG
1 atom, 1 residue, 1 model selected
> select #1.4/B:1002@MG
1 atom, 1 residue, 1 model selected
> select add #1.1/B:1002@MG
2 atoms, 2 residues, 2 models selected
Drag select of 2 atoms
> hide sel atoms
> open
> /Users/justinvanriper/Downloads/cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
> sharpened-highres.mrc
Opened cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc as #2, grid size 300,300,300, pixel 0.832, shown at level 0.0049,
step 2, values float32
> volume #2 step 1
> surface dust #2 size 8.32
> lighting full
> lighting soft
> lighting simple
> lighting soft
> hide #!1.3 models
> select add #1.3
14348 atoms, 14642 bonds, 9 pseudobonds, 1776 residues, 5 models selected
> select add #1.4
27681 atoms, 28260 bonds, 16 pseudobonds, 3433 residues, 7 models selected
> select subtract #1.4
14347 atoms, 14642 bonds, 9 pseudobonds, 1775 residues, 4 models selected
> select subtract #1.3
1 atom, 1 residue, 1 model selected
> select add #1.1
13483 atoms, 13776 bonds, 12 pseudobonds, 1666 residues, 2 models selected
> select subtract #1.1
Nothing selected
> select add #1
56626 atoms, 57471 bonds, 51 pseudobonds, 7310 residues, 15 models selected
> show #!1.3 models
> hide #!2 models
> show #!2 models
> fitmap #1 to #2
Expected a keyword
> fitmap #1 #2
Missing required "in_map" argument
> fitmap #1 inMap #2
Fit molecules all_aligned_SLFN.cif (#1.1), all_aligned_SLFN.cif (#1.2),
all_aligned_SLFN.cif (#1.3), all_aligned_SLFN.cif (#1.4), all_aligned_SLFN.cif
(#1.5) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 56626 atoms
average map value = 0.03678, steps = 108
shifted from previous position = 1.51
rotated from previous position = 2.3 degrees
atoms outside contour = 43242, contour level = 0.0049001
Position of all_aligned_SLFN.cif (#1.1) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99978234 0.01984455 -0.00643950 -2.55579678
-0.01961186 0.99921634 0.03438151 -2.62383682
0.00711674 -0.03424774 0.99938803 3.12635629
Axis -0.85449739 -0.16878777 -0.49126867
Axis point 0.00000000 105.62417749 73.36727950
Rotation angle (degrees) 2.30148392
Shift along axis 1.09091235
Position of all_aligned_SLFN.cif (#1.2) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99978234 0.01984455 -0.00643950 -2.55579678
-0.01961186 0.99921634 0.03438151 -2.62383682
0.00711674 -0.03424774 0.99938803 3.12635629
Axis -0.85449739 -0.16878777 -0.49126867
Axis point 0.00000000 105.62417749 73.36727950
Rotation angle (degrees) 2.30148392
Shift along axis 1.09091235
Position of all_aligned_SLFN.cif (#1.3) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99978234 0.01984455 -0.00643950 -2.55579678
-0.01961186 0.99921634 0.03438151 -2.62383682
0.00711674 -0.03424774 0.99938803 3.12635629
Axis -0.85449739 -0.16878777 -0.49126867
Axis point 0.00000000 105.62417749 73.36727950
Rotation angle (degrees) 2.30148392
Shift along axis 1.09091235
Position of all_aligned_SLFN.cif (#1.4) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99978234 0.01984455 -0.00643950 -2.55579678
-0.01961186 0.99921634 0.03438151 -2.62383682
0.00711674 -0.03424774 0.99938803 3.12635629
Axis -0.85449739 -0.16878777 -0.49126867
Axis point 0.00000000 105.62417749 73.36727950
Rotation angle (degrees) 2.30148392
Shift along axis 1.09091235
Position of all_aligned_SLFN.cif (#1.5) relative to
cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-sharpened-
highres.mrc (#2) coordinates:
Matrix rotation and translation
0.99978234 0.01984455 -0.00643950 -2.55579678
-0.01961186 0.99921634 0.03438151 -2.62383682
0.00711674 -0.03424774 0.99938803 3.12635629
Axis -0.85449739 -0.16878777 -0.49126867
Axis point 0.00000000 105.62417749 73.36727950
Rotation angle (degrees) 2.30148392
Shift along axis 1.09091235
> hide #!2 models
> show #!1.3 models
> hide #!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
> matchmaker #3 #1
Missing required "to" argument
> matchmaker #3 to #1
Specify a single 'to' model only
> 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 #!2 models
> ui mousemode right rotate
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.99515,0.098138,0.0064363,-12.459,-0.09771,0.99402,-0.048809,19.329,-0.011188,0.047943,0.99879,-4.4154
> view matrix models
> #2,0.47802,0.46441,-0.74553,103.42,-0.7247,0.68812,-0.036009,134.97,0.49629,0.5575,0.6655,-89.337
> view matrix models
> #2,0.69209,0.72031,-0.04649,-45.074,-0.71049,0.69118,0.13222,111.25,0.12737,-0.058477,0.99013,-7.5108
> view matrix models
> #2,0.64049,0.73429,-0.22493,-17.447,-0.72548,0.67459,0.13642,114.67,0.25191,0.075804,0.96478,-36.733
> view matrix models
> #2,0.50071,0.84809,-0.1733,-20.624,-0.83512,0.52596,0.16105,143.9,0.22773,0.064085,0.97161,-33.096
> view matrix models
> #2,0.55426,0.83134,0.040907,-52.732,-0.83234,0.55369,0.025237,157.49,-0.0016697,-0.048037,0.99884,6.3529
> view matrix models
> #2,0.54925,0.83515,0.029066,-51.059,-0.83387,0.54548,0.084295,151.14,0.054544,-0.070537,0.99602,2.4296
> view matrix models
> #2,0.47841,0.8769,0.046701,-49.588,-0.87704,0.47447,0.075363,166.59,0.043927,-0.077012,0.99606,4.5714
> view matrix models
> #2,0.48897,0.86406,0.1196,-58.658,-0.8723,0.48419,0.068276,165.69,0.0010878,-0.13771,0.99047,18.267
> fitmap map #3 inMap #2
Missing or invalid "atomsOrMap" argument: invalid objects specifier
> fitmap #3 inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 76
shifted from previous position = 3.29
rotated from previous position = 3.6 degrees
atoms outside contour = 713, contour level = 0.0049001
Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00006645 -0.00003656 -0.00279354
-0.00006644 0.99999999 0.00017232 -0.01425049
0.00003658 -0.00017231 0.99999999 0.00900773
Axis -0.91526123 -0.19423949 -0.35294178
Axis point 0.00000000 56.66272325 80.28668892
Rotation angle (degrees) 0.01078700
Shift along axis 0.00214563
> volume #2 level 0.1498
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
> ui mousemode right translate
> volume #2 level 0.3454
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.2911
> volume #2 level 0.0284
> volume #2 style mesh
> ui mousemode right select
> select clear
> volume #2 level 0.1008
> volume #2 style surface
> volume #2 level 0.07544
> select clear
> hide #!2 models
> select #3/A:206,211,213
27 atoms, 24 bonds, 3 residues, 1 model selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> volume zone #2 nearAtoms sel range 5
> show #!2 models
> volume zone #2 nearAtoms sel range 1
> volume zone #2 nearAtoms sel range 2
> volume zone #2 nearAtoms sel range 3
> volume zone #2 nearAtoms sel range 2
> select sidechain #3/A:206,211,213
Expected a keyword
> select #3/A:206,211,213 sidechain
Expected a keyword
> select sidechain & #3/A:206,211,213
18 atoms, 15 bonds, 3 residues, 1 model selected
> select up
27 atoms, 24 bonds, 3 residues, 1 model selected
> select up
141 atoms, 144 bonds, 16 residues, 1 model selected
> select down
27 atoms, 24 bonds, 3 residues, 1 model selected
> select down
18 atoms, 15 bonds, 3 residues, 1 model selected
> select sidechain & #3/A:206,211,213
18 atoms, 15 bonds, 3 residues, 1 model selected
> volume zone #2 nearAtoms sel range 2
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> select up
27 atoms, 24 bonds, 3 residues, 1 model selected
> select down
18 atoms, 15 bonds, 3 residues, 1 model selected
> transparency #2 50
Drag select of 1 residues
> volume #2 level 0.1008
> surface dust #2 size 8.32
[Repeated 1 time(s)]
> volume zone #2 nearAtoms sel range 2
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select clear
> volume show
> volume hide
> volume show
[Repeated 1 time(s)]
> select down
Nothing selected
> select #2
2 models selected
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> volume zone #2 nearAtoms sel range 2
> select clear
> volume #2 level 0.01393
> volume #2 level 0.0284
> fitmap #3 inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 40
shifted from previous position = 0.0107
rotated from previous position = 0.0149 degrees
atoms outside contour = 1486, contour level = 0.0284
Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00004132 -0.00004587 -0.00356102
-0.00004132 1.00000000 -0.00008578 0.01324767
0.00004587 0.00008579 1.00000000 -0.01510254
Axis 0.81167482 -0.43401395 -0.39091671
Axis point 0.00000000 188.52719661 140.57808315
Rotation angle (degrees) 0.00605547
Shift along axis -0.00273622
> show #!1 models
> hide #!1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!2 models
> show #!2 models
> fitmap #3 inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 40
shifted from previous position = 0.0104
rotated from previous position = 0.0113 degrees
atoms outside contour = 1489, contour level = 0.0284
Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00006037 -0.00004170 -0.00151559
-0.00006036 1.00000000 0.00011091 -0.00511879
0.00004171 -0.00011091 1.00000000 0.00183937
Axis -0.83401456 -0.31360939 -0.45394809
Axis point 0.00000000 24.90828027 40.40123494
Rotation angle (degrees) 0.00761946
Shift along axis 0.00203434
> hide #!2 models
> show #!1 models
> show #!1.1 models
> align #1.1 #3
Missing required "to_atoms" argument
> matchmaker maker #1.1 #3
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchMaker #1.1 #3
Unknown command: matchMaker #1.1 #3
> matchMaker #1.1 to #3
Unknown command: matchMaker #1.1 to #3
> matchmaker #1.1 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 A (#3) with all_aligned_SLFN.cif, chain A (#1.1), sequence alignment
score = 3964.3
RMSD between 811 pruned atom pairs is 0.653 angstroms; (across all 816 pairs:
0.728)
> hide #!3 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!2 models
> hide #!2 models
> undo
[Repeated 9 time(s)]
> redo
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> hide #!2 models
> select #3/A,B:351-912
7930 atoms, 8104 bonds, 8 pseudobonds, 990 residues, 2 models selected
> hide sel cartoons
> select clear
> select #3/B
6609 atoms, 6744 bonds, 10 pseudobonds, 825 residues, 3 models selected
> hide sel cartoons
> select clear
[Repeated 13 time(s)]
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right select
> select clear
[Repeated 2 time(s)]
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
> select clear
[Repeated 1 time(s)]
> select add #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
Drag select of 19 atoms, 19 bonds
Drag select of 29 atoms, 4 pseudobonds, 26 bonds
Drag select of 15 atoms, 10 bonds
Drag select of 24 atoms, 21 bonds
Drag select of 1 atoms, 1 bonds
Drag select of 2 atoms, 3 bonds
Drag select of 12 atoms, 12 bonds
> hide sel atoms
Drag select of 34 atoms, 20 bonds
> hide sel atoms
Drag select of 2 atoms
> hide sel atoms
> select #3/A:78@CB
1 atom, 1 residue, 1 model selected
> hide #!1.1 models
Drag select of 10 atoms, 29 residues, 8 bonds
> hide sel atoms
> select clear
Drag select of 6 atoms, 9 residues, 4 bonds
> hide sel atoms
Drag select of 17 atoms, 25 residues, 4 pseudobonds, 13 bonds
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> show #!1.1 models
> hide #!1 models
> show #!1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> select #1.1/A:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:214
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:136@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:136@CG2
1 atom, 1 residue, 1 model selected
> select #3/A:136
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/A:133
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:212
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #3.1 models
> hide #3.2 models
> cartoon style sel modeHelix tube sides 20
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> color sel cornflower blue
> select clear
> select #3/A:133,2016,211,213,249,248
45 atoms, 41 bonds, 5 residues, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> color sel backbone cornflower blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color red backbone & /A:133,206,211,213,248,249
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red backbone & #3/A:133,206,211,213,248,249
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3/A:133,206,211,213,248,249 & color backbone red
Expected a keyword
> select #3/A:133,206,211,213,248,249 & color red backbone
Expected a keyword
> select #3/A:133,2016,211,213,249,248
45 atoms, 41 bonds, 5 residues, 1 model selected
> select #3/A:133,206,211,213,249,248
54 atoms, 49 bonds, 6 residues, 1 model selected
> color sel orange
> color sel byhetero
> ui tool show "Color Actions"
> color sel cornflower blue target cspf
> select clear
> view p1
> view p2
> view p1
> hide #!1.1 models
> select #3/A:1003@MG
1 atom, 1 residue, 1 model selected
> select add #3/A:1002@MG
2 atoms, 2 residues, 1 model selected
> color sel byelement
> select clear
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #3/C,D
253 atoms, 280 bonds, 12 residues, 1 model selected
> show sel cartoons
> select clear
> select #3/C:2
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/C:1
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3/C:2
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #3/C:3
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #3/C:4
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #3/C:5
111 atoms, 120 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #3/C
111 atoms, 124 bonds, 5 residues, 1 model selected
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> color sel pale violet red
> select clear
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> show sel atoms
> nucleotides sel ladder
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> color #3.2 black models
> hide #3.2 models
> show #3.2 models
> color #3.1 #6495ed00 models
> color #3.1 cornflowerblue models
> view name p11
> vire p2
Unknown command: vire p2
> view p2
> show #!1.1 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!1.1 models
> hide cartoons
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> hide sel atoms
Drag select of 239 atoms, 201 bonds, 5 pseudobonds
> select backbone
34746 atoms, 34691 bonds, 62 pseudobonds, 8643 residues, 17 models selected
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models
> #1.1,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.2,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.3,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.4,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#1.5,1,0,0,-0.11227,0,1,0,-0.18066,0,0,1,0.45681,#3,0.48893,0.86408,0.11967,-58.776,-0.87232,0.48413,0.068366,165.51,0.0011374,-0.13782,0.99046,18.726
> select add #1
63342 atoms, 64183 bonds, 59 pseudobonds, 8965 residues, 13 models selected
> select subtract #1.1
49859 atoms, 50407 bonds, 47 pseudobonds, 7299 residues, 11 models selected
> select add #1
63342 atoms, 64183 bonds, 59 pseudobonds, 8965 residues, 13 models selected
> select subtract #1
6716 atoms, 6712 bonds, 12 pseudobonds, 1655 residues, 2 models selected
> view matrix models
> #3,0.48893,0.86408,0.11967,-58.637,-0.87232,0.48413,0.068366,166.23,0.0011374,-0.13782,0.99046,16.797
> view matrix models
> #3,0.48893,0.86408,0.11967,-59.011,-0.87232,0.48413,0.068366,166.4,0.0011374,-0.13782,0.99046,16.755
> view matrix models
> #3,0.48893,0.86408,0.11967,-58.793,-0.87232,0.48413,0.068366,166.88,0.0011374,-0.13782,0.99046,16.902
> view matrix models
> #3,0.48893,0.86408,0.11967,-58.625,-0.87232,0.48413,0.068366,167.25,0.0011374,-0.13782,0.99046,17.017
> view matrix models
> #3,0.48893,0.86408,0.11967,-58.535,-0.87232,0.48413,0.068366,167.41,0.0011374,-0.13782,0.99046,17.156
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.49063,0.86171,0.12936,-59.282,-0.87134,0.48635,0.065052,167.29,-0.006858,-0.14463,0.98946,19.083
> view matrix models
> #3,0.47006,0.87172,0.13835,-59.22,-0.88263,0.46475,0.070539,171.05,-0.002808,-0.15527,0.98787,20.262
> view matrix models
> #3,0.46863,0.87844,0.093401,-55.878,-0.88303,0.46275,0.07824,170.67,0.025508,-0.11914,0.99255,11.659
> select #3,#1.1
Expected an objects specifier or a keyword
> select #3,1.1
13483 atoms, 13776 bonds, 20 pseudobonds, 1666 residues, 3 models selected
> show sel cartoons
> hide #!1.1 models
> show #!1.1 models
> select #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> show sel cartoons
> matchmaker maker #3 to #1.1
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> 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)
> select clear
> hide cartoons
> view p2
> hide #!1 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
> show #!1 models
> hide #!1 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
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #3.2 models
> hide #!2 models
> ui mousemode right select
Drag select of 32 atoms, 24 bonds
> select clear
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 cartoons
> save
> /Users/justinvanriper/Desktop/SLFN14_Figures_Round_2_Revision_Nat_Com_/ChimeraX_sessions/Figure5_alignedfiles_and_map.cxs
> surface dust #2 size 8.32
> ui mousemode right "translate selected models"
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!3 models
> show #3.1 models
> hide #!3 models
> show #!3 models
> select add #2
4 models selected
> view matrix models
> #2,0.48897,0.86406,0.1196,-57.839,-0.8723,0.48419,0.068276,166.16,0.0010878,-0.13771,0.99047,18.386
> view matrix models
> #2,0.48897,0.86406,0.1196,-58.089,-0.8723,0.48419,0.068276,166.55,0.0010878,-0.13771,0.99047,18.727
> view matrix models
> #2,0.48897,0.86406,0.1196,-58.642,-0.8723,0.48419,0.068276,166.16,0.0010878,-0.13771,0.99047,18.62
> view matrix models
> #2,0.48897,0.86406,0.1196,-59.549,-0.8723,0.48419,0.068276,165.88,0.0010878,-0.13771,0.99047,17.459
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.40736,0.90161,0.14548,-57.285,-0.91324,0.40081,0.073143,180.79,0.0076376,-0.16265,0.98665,20.234
> view matrix models
> #2,0.46634,0.86424,0.18872,-65.594,-0.88348,0.4658,0.050027,171.92,-0.044671,-0.19006,0.98076,30.986
> view matrix models
> #2,0.51985,0.7748,0.35978,-83.124,-0.83128,0.55583,0.0041312,160.02,-0.19678,-0.30123,0.93303,70.093
> view matrix models
> #2,0.52461,0.80745,0.26985,-76.253,-0.83481,0.55006,-0.022946,164.66,-0.16696,-0.21324,0.96263,51.58
> view matrix models
> #2,0.4793,0.85608,0.19337,-66.804,-0.86923,0.49349,-0.030249,176.97,-0.12132,-0.15358,0.98066,36.09
> view matrix models
> #2,0.46412,0.86465,0.1923,-65.825,-0.87821,0.47749,-0.027378,179.73,-0.11549,-0.15617,0.98095,35.643
> view matrix models
> #2,0.47314,0.8608,0.1875,-65.864,-0.87645,0.4815,0.0011274,175.35,-0.089308,-0.16486,0.98226,33.265
> view matrix models
> #2,0.56676,0.809,0.1559,-67.127,-0.82184,0.56846,0.037859,152.93,-0.057996,-0.14958,0.98705,26.809
> view matrix models
> #2,0.50028,0.84503,0.18877,-67.476,-0.86237,0.50583,0.021132,167.98,-0.077631,-0.17337,0.98179,32.916
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.50028,0.84503,0.18877,-65.329,-0.86237,0.50583,0.021132,165.99,-0.077631,-0.17337,0.98179,32.636
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.52798,0.82687,0.1937,-67.181,-0.84696,0.52943,0.048615,157.58,-0.062353,-0.18973,0.97985,33.003
> view matrix models
> #2,0.50792,0.84968,0.14163,-60.82,-0.86131,0.49859,0.097719,156.93,0.012414,-0.17162,0.98508,20.672
> view matrix models
> #2,0.48388,0.86251,0.14809,-60.224,-0.87513,0.47635,0.085094,163.06,0.0028543,-0.17077,0.98531,21.74
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.48388,0.86251,0.14809,-61.455,-0.87513,0.47635,0.085094,162.01,0.0028543,-0.17077,0.98531,23.993
> view matrix models
> #2,0.48388,0.86251,0.14809,-60.934,-0.87513,0.47635,0.085094,162.77,0.0028543,-0.17077,0.98531,22.016
> view matrix models
> #2,0.48388,0.86251,0.14809,-60.859,-0.87513,0.47635,0.085094,164.04,0.0028543,-0.17077,0.98531,20.478
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.48083,0.86314,0.15424,-61.343,-0.87561,0.48191,0.032763,170.12,-0.046053,-0.15081,0.98749,23.86
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.48083,0.86314,0.15424,-61.207,-0.87561,0.48191,0.032763,169.77,-0.046053,-0.15081,0.98749,25.375
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.47873,0.86361,0.15807,-61.493,-0.87457,0.4849,-0.00055203,173.54,-0.077125,-0.13798,0.98743,27.692
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.47873,0.86361,0.15807,-61.593,-0.87457,0.4849,-0.00055203,174.46,-0.077125,-0.13798,0.98743,27.789
> select subtract #2
Nothing selected
> fitmap #2 #3 moveModel false moveMap true
Expected a keyword
> fitmap #3 #2 moveWholeMolecules false
Missing required "in_map" argument
> fitmap #2 #3 moveWholeMolecules false
Missing required "in_map" argument
Must specify one map, got 0
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 80
shifted from previous position = 1.68
rotated from previous position = 5.74 degrees
atoms outside contour = 1486, contour level = 0.0284
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show cartoons
> hide #!1.1 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> hide #!2 models
> hide #!3 models
> show #!1.3 models
> show #!1.4 models
> show #!1.5 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #!1.5 models
> show #!1.1 models
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3504, steps = 28
shifted from previous position = 0.0115
rotated from previous position = 0.0206 degrees
atoms outside contour = 1483, contour level = 0.0284
> 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)
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> 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)
> fitmap #3 moveWholeMolecules false inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> 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)
> fitmap #3 inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
Position of real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) relative to cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) coordinates:
Matrix rotation and translation
0.97266502 -0.18741863 -0.13710221 45.36695106
0.15853109 0.96736060 -0.19769010 7.37317493
0.16967808 0.17055129 0.97062949 -43.56203686
Axis 0.62297837 -0.51900056 0.58526607
Axis point 0.00000000 250.60204610 -6.86010354
Rotation angle (degrees) 17.19046649
Shift along axis -1.05943510
> 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)
> fitmap #3 moveWholeMolecules false inMap #2
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> 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)
> align #2 toAtoms #3
Unequal number of atoms to pair, 0 and 13446
> fitmap #3 inMap #2 moveWholeMolecules false moveWholeMolecules false
Repeated keyword argument "moveWholeMolecules"
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> 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 #!1.1 models
> hide #!1.5 models
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> hide #!1.5 models
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!2 models
> show #!1.1 models
> 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)
> select add #2
2 models selected
> select subtract #2
Nothing selected
> 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)
> fitmap #3 inMap #2 moveWholeMolecules false
Fit molecule real_space_refined_036_edited-coot-15_real_space_refined_015.pdb
(#3) to map cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc (#2) using 13446 atoms
average map value = 0.3505, steps = 96
shifted from previous position = 1.92
rotated from previous position = 5.74 degrees
atoms outside contour = 1489, contour level = 0.0284
> hide #!1 models
> view p2
> show #!3 cartoons
> select add #3
13446 atoms, 13742 bonds, 20 pseudobonds, 1660 residues, 3 models selected
> hide sel cartoons
> hide #!2 models
> select clear
> ui mousemode right select
Drag select of 32 atoms, 24 bonds
> volume zone #2 nearAtoms sel range 4
> show #!2 models
> volume zone #2 nearAtoms sel range 3
> surface dust #2 size 8.32
> volume zone #2 nearAtoms sel range 2
> volume #2 level 0.04919
> volume #2 level 0.1858
> volume #2 level 0.2631
> volume zone #2 nearAtoms sel range 1
> volume #2 level 0.3284
> volume zone #2 nearAtoms sel range 5
> volume #2 level 0.8037
> volume zone #2 nearAtoms sel range 2
> volume #2 level 0.2571
> transparency #2 10
> transparency #2 90
> select clear
> volume #2 level 0.2363
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> show sel cartoons
> select clear
> select #3/D:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #3/D:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #3/D:2
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #3/D:3
60 atoms, 63 bonds, 3 residues, 1 model selected
> select add #3/D:4
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #3/D:5
102 atoms, 108 bonds, 5 residues, 1 model selected
> select add #3/D:7
122 atoms, 129 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #3/D:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> undo
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> select #3/D
142 atoms, 156 bonds, 7 residues, 1 model selected
> show sel atoms
> select #3/D:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
Drag select of 40 atoms, 39 bonds, 10 shapes
> hide sel atoms
> select #3/D:7@P
1 atom, 1 residue, 1 model selected
> select subtract #3/D:7@P
Nothing selected
> select #3/D:7@P
1 atom, 1 residue, 1 model selected
> view p2
> show sel atoms
> nucleotides sel ladder
[Repeated 2 time(s)]
> nucleotides sel fill
> style nucleic & sel stick
Changed 20 atom styles
> color sel byelement
> select clear
> view p2
Drag select of 15 atoms, 16 bonds, 2 shapes
> hide sel atoms
> select #3/D:7@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
> view p2
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc , 36 atoms, 27 bonds
> volume zone #2 nearAtoms sel range 2
> volume #2 level 0.2245
> select clear
> volume #2 level 0.2839
> view p2
> volume #2 level 0.1591
> volume zone #2 nearAtoms sel range 3
no atoms specified for zone
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc , 35 atoms, 27 bonds
> volume zone #2 nearAtoms sel range 3
> volume #2 level 0.1027
> volume zone #2 nearAtoms sel range 4
> volume #2 level 0.3076
> volume zone #2 nearAtoms sel range 1
> volume #2 level 0.5631
> volume zone #2 nearAtoms sel range 2
> volume #2 level 0.3403
> volume zone #2 nearAtoms sel range 2.5
> volume #2 level 0.2898
> volume zone #2 nearAtoms sel range 2
> view p2
> select clear
> volume #2 level 0.1413
> select clear
> view p2
> view p22
Expected an objects specifier or a view name or a keyword
> view name p22
> view p2
[Repeated 1 time(s)]
> view p22
Drag select of 2 cryosparc_P99_J208_009_volume_map_sharpClss1C1_deepEMhancer-
sharpened-highres.mrc , 36 atoms, 27 bonds
> 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
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