![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18103 closed defect (duplicate)
Crash in python_instances_of_class saving session
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403290055 (2024-03-29 00:55:10 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001ea2f9e00 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2636 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 256 in include_state
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 260 in discovery
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 917 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 38 in _file_save
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/providers.py", line 56 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 165 in callback
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
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{
"uptime" : 1900000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,6",
"coalitionID" : 2275,
"osVersion" : {
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"build" : "22F66",
"releaseType" : "User"
},
"captureTime" : "2025-06-30 16:21:01.6265 -0400",
"incident" : "76E92FF9-9324-42FF-907B-D45328B1E7CA",
"pid" : 63865,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-20 10:58:31.2700 -0400",
"procStartAbsTime" : 36915959660409,
"procExitAbsTime" : 45628519314431,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"97F86206-D27D-5E6E-828E-24510B8A1510","thirdParty":true},
"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "374891C2-7817-A0E6-D242-CF314EBC6C71",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 23214,
"sleepWakeUUID" : "5E05977F-820F-4B52-B3E6-EB51AAF0C8DC",
"sip" : "enabled",
"vmRegionInfo" : "0x7232e3c is not in any region. Bytes before following region: 4213281220\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10244c000-102450000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000007232e3c","rawCodes":[1,119746108],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000007232e3c"},
"vmregioninfo" : "0x7232e3c is not in any region. Bytes before following region: 4213281220\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10244c000-102450000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/map_color.cxs
Opened J2561_3p28.mrc as #1, grid size 310,310,310, pixel 0.826, shown at
level 0.0891, step 1, values float32
Opened J2561_3p28.mrc gaussian as #7, grid size 310,310,310, pixel 0.826,
shown at level 0.0522, step 1, values float32
Log from Fri Jun 20 01:38:30 2025UCSF ChimeraX version: 1.8.dev202403290055
(2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/J2561_3p28.mrc
Opened J2561_3p28.mrc as #1, grid size 310,310,310, pixel 0.826, shown at
level 0.0231, step 2, values float32
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/NRAS_168_BRIL_real_space_refined-
> coot-10.pdb
Chain information for NRAS_168_BRIL_real_space_refined-coot-10.pdb #2
---
Chain | Description
A | No description available
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/Mb24_fit.pdb
Chain information for Mb24_fit.pdb #3
---
Chain | Description
A | No description available
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/Mb24.pdb
Chain information for Mb24.pdb #4
---
Chain | Description
A | No description available
> close #4
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/antiBRIL_Fab.pdb
Chain information for antiBRIL_Fab.pdb #4
---
Chain | Description
H | No description available
L | No description available
38 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> volume #1 step 1
> volume #1 level 0.1551
Drag select of 17 residues
Drag select of 133 atoms, 440 residues, 99 bonds
> hide sel atoms
> select clear
[Repeated 1 time(s)]Drag select of 235 residues
> select ~sel & ##selected
1832 atoms, 1575 bonds, 499 residues, 1 model selected
> hide sel cartoons
Drag select of 234 residues
Drag select of 2 residues
> hide sel cartoons
Drag select of 227 residues
Drag select of 233 residues
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.72367,0.067817,0.68681,-51.873,0.6146,0.3894,-0.68603,84.378,-0.31397,0.91857,0.24011,-2.2078
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.72367,0.067817,0.68681,-51.573,0.6146,0.3894,-0.68603,71.213,-0.31397,0.91857,0.24011,14.46
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.83828,0.27743,0.46938,-70.192,0.3652,0.35355,-0.86118,126.55,-0.40486,0.89333,0.19506,34.197
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.83828,0.27743,0.46938,-70.192,0.3652,0.35355,-0.86118,125.17,-0.40486,0.89333,0.19506,36.166
> ui tool show "Fit in Map"
> fitmap sel inMap #1
Fit molecule antiBRIL_Fab.pdb (#4) to map J2561_3p28.mrc (#1) using 1795 atoms
average map value = 0.1363, steps = 104
shifted from previous position = 3.91
rotated from previous position = 22.7 degrees
atoms outside contour = 1092, contour level = 0.1551
Position of antiBRIL_Fab.pdb (#4) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
0.95497069 -0.05061038 0.29235180 -15.12068713
0.29372381 0.30048009 -0.90743487 147.02545847
-0.04192027 0.95244438 0.30181515 -28.58758504
Axis 0.96828601 0.17402795 0.17926647
Axis point 0.00000000 95.24231938 87.48684543
Rotation angle (degrees) 73.82136721
Shift along axis 5.82059427
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.98851,-0.12196,-0.089277,277.66,0.023499,-0.70749,0.70633,138.32,-0.14931,0.69612,0.70223,-24.905
> fitmap sel inMap #1
Fit molecule antiBRIL_Fab.pdb (#4) to map J2561_3p28.mrc (#1) using 1795 atoms
average map value = 0.07125, steps = 172
shifted from previous position = 5.26
rotated from previous position = 19.6 degrees
atoms outside contour = 1414, contour level = 0.1551
Position of antiBRIL_Fab.pdb (#4) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
-0.93111352 -0.34246574 -0.12547836 308.85572785
0.22946865 -0.81745967 0.52830278 150.53150225
-0.28349910 0.46311651 0.83973290 6.28554317
Axis -0.10920202 0.26472116 0.95812193
Axis point 143.04576233 99.11712240 0.00000000
Rotation angle (degrees) 162.63448580
Shift along axis 12.14352214
> view matrix models
> #4,0.87743,0.35739,0.32,-60.554,0.2749,0.17207,-0.94595,173.98,-0.39313,0.91797,0.052733,45.422
> fitmap sel inMap #1
Fit molecule antiBRIL_Fab.pdb (#4) to map J2561_3p28.mrc (#1) using 1795 atoms
average map value = 0.1363, steps = 224
shifted from previous position = 6.99
rotated from previous position = 25.1 degrees
atoms outside contour = 1092, contour level = 0.1551
Position of antiBRIL_Fab.pdb (#4) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
0.95494909 -0.05023261 0.29248745 -15.18188686
0.29373295 0.30061571 -0.90738699 146.99612438
-0.04234590 0.95242159 0.30182767 -28.53109323
Axis 0.96826773 0.17432349 0.17907797
Axis point -0.00000000 95.19704944 87.50735163
Rotation angle (degrees) 73.81759259
Shift along axis 5.81545662
> view matrix models
> #4,-0.80223,0.088233,-0.59045,281.81,-0.48682,-0.66918,0.56143,212.37,-0.34559,0.73784,0.5798,7.332
> fitmap sel inMap #1
Fit molecule antiBRIL_Fab.pdb (#4) to map J2561_3p28.mrc (#1) using 1795 atoms
average map value = 0.07131, steps = 132
shifted from previous position = 4.69
rotated from previous position = 22.5 degrees
atoms outside contour = 1422, contour level = 0.1551
Position of antiBRIL_Fab.pdb (#4) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
-0.86595015 0.37398360 -0.33206415 223.62870337
-0.50006520 -0.65816281 0.56281125 211.58426148
-0.00807009 0.65342021 0.75695237 -40.61324622
Axis 0.09674663 -0.34594075 -0.93325510
Axis point 137.26208096 83.35700737 0.00000000
Rotation angle (degrees) 152.07731525
Shift along axis -13.65777589
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.86595,0.37398,-0.33206,225.97,-0.50007,-0.65816,0.56281,216.14,-0.0080701,0.65342,0.75695,-41.161
> fitmap sel inMap #1
Fit molecule antiBRIL_Fab.pdb (#4) to map J2561_3p28.mrc (#1) using 1795 atoms
average map value = 0.2177, steps = 96
shifted from previous position = 2.13
rotated from previous position = 17.2 degrees
atoms outside contour = 698, contour level = 0.1551
Position of antiBRIL_Fab.pdb (#4) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
-0.96283633 0.12810412 -0.23777201 263.88576204
-0.26243819 -0.65176097 0.71157138 168.32627461
-0.06381529 0.74752724 0.66115855 -37.99968510
Axis 0.08380497 -0.40545380 -0.91026586
Axis point 139.94872629 76.83794433 0.00000000
Rotation angle (degrees) 167.61257227
Shift along axis -11.54377228
> select clear
Drag select of 92 residues
> select add #3
727 atoms, 750 bonds, 94 residues, 1 model selected
> view matrix models #3,1,0,0,16.098,0,1,0,86.208,0,0,1,23.28
> volume #1 level 0.08909
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.82676,-0.37364,-0.42055,122.48,-0.14038,0.5869,-0.79739,242.2,0.54476,0.71829,0.43278,-22.46
> view matrix models
> #3,-0.80929,0.39848,0.43157,138.47,-0.41059,-0.90917,0.069512,278.18,0.42007,-0.12094,0.8994,-2.796
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.80929,0.39848,0.43157,141.34,-0.41059,-0.90917,0.069512,287.48,0.42007,-0.12094,0.8994,-21.817
> fitmap sel inMap #1
Fit molecule Mb24_fit.pdb (#3) to map J2561_3p28.mrc (#1) using 727 atoms
average map value = 0.06159, steps = 160
shifted from previous position = 2.46
rotated from previous position = 21.2 degrees
atoms outside contour = 576, contour level = 0.089093
Position of Mb24_fit.pdb (#3) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
-0.88527169 0.26390225 0.38294862 167.61668077
-0.14611961 -0.93954543 0.30968281 227.01971834
0.44152361 0.21819712 0.87031426 -45.17485962
Axis -0.21568261 -0.13809383 -0.96664942
Axis point 101.26089462 107.72226085 0.00000000
Rotation angle (degrees) 167.75548856
Shift along axis -23.83377362
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.81686,-0.22894,0.52946,179.59,-0.18236,-0.7683,-0.61356,340.73,0.54725,-0.59775,0.58584,45.86
> fitmap sel inMap #1
Fit molecule Mb24_fit.pdb (#3) to map J2561_3p28.mrc (#1) using 727 atoms
average map value = 0.06547, steps = 192
shifted from previous position = 1.56
rotated from previous position = 57.6 degrees
atoms outside contour = 556, contour level = 0.089093
Position of Mb24_fit.pdb (#3) relative to J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
-0.98498216 0.08493300 0.15032142 223.44489045
-0.05648414 -0.98124563 0.18430019 236.43569832
0.16315540 0.17304162 0.97130681 -23.77819242
Axis -0.07903858 -0.09009850 -0.99279160
Axis point 116.88993114 115.30608422 0.00000000
Rotation angle (degrees) 175.91582391
Shift along axis -15.35647832
> select clear
> save
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/anti_BRIL_Fab_fitted.pdb
> models #4 relModel #1
> close #2
> select H
Nothing selected
> save
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/Mb24_fitted.pdb
> models #3 relModel #1
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/Mb24_fitted-
> coot-0.pdb
Chain information for Mb24_fitted-coot-0.pdb #2
---
Chain | Description
A | No description available
> close #3
> volume #1 color #b2b2b295
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/NRAS_168_BRIL_real_space_refined-
> coot-10.pdb
Chain information for NRAS_168_BRIL_real_space_refined-coot-10.pdb #3
---
Chain | Description
A | No description available
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/NRAS_168_BRIL_real_space_refined-
> coot-5.pdb
Chain information for NRAS_168_BRIL_real_space_refined-coot-5.pdb #5
---
Chain | Description
A | No description available
> dssp
> hide #!3 models
> hide #2 models
Drag select of 65 atoms, 158 residues, 2 pseudobonds, 58 bonds
Drag select of 5 residues
Drag select of 2 residues
> hide sel cartoons
> hide sel atoms
> select #5/A:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> dssp #5
> show #!3 models
> select clear
> hide #!5 models
Drag select of 108 residues
Drag select of 2 residues
> hide sel cartoons
> show #!5 models
> hide #!5 models
> select add #3
2127 atoms, 2157 bonds, 2 pseudobonds, 269 residues, 2 models selected
> show sel cartoons
> select clear
> undo
[Repeated 9 time(s)]
> hide #!3 models
> show #!3 models
> close #5
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/NRAS_168_BRIL_real_space_refined-
> coot-10.pdb
Chain information for NRAS_168_BRIL_real_space_refined-coot-10.pdb #5
---
Chain | Description
A | No description available
> hide #!3 models
> dssp #5
Drag select of 65 atoms, 166 residues, 2 pseudobonds, 58 bonds
> select add #5/A:105
1338 atoms, 65 bonds, 2 pseudobonds, 168 residues, 2 models selected
> select subtract #5/A:217
1329 atoms, 65 bonds, 2 pseudobonds, 167 residues, 2 models selected
> select subtract #5/A:218
1321 atoms, 65 bonds, 2 pseudobonds, 166 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!3 models
> hide #!5 models
> hide #4 models
> hide #!3 models
> show #!5 models
> show #!3 models
> hide #!5 models
Drag select of 106 residues
> select subtract #3/A:169
822 atoms, 105 residues, 1 model selected
> select subtract #3/A:170
814 atoms, 104 residues, 1 model selected
> select subtract #3/A:171
806 atoms, 103 residues, 1 model selected
> hide sel cartoons
> show #!5 models
> select #3/A:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
Drag select of 65 atoms, 162 residues, 2 pseudobonds, 58 bonds
> select subtract #3/A:168
1292 atoms, 58 bonds, 2 pseudobonds, 162 residues, 2 models selected
> select add #3/A:168
1300 atoms, 65 bonds, 2 pseudobonds, 163 residues, 2 models selected
> color (#!3 & sel) dark gray
> set bgColor white
> lighting soft
> select clear
Drag select of 108 residues
> select subtract #3/A:167
835 atoms, 107 residues, 2 models selected
> select subtract #3/A:168
827 atoms, 106 residues, 2 models selected
> color sel #aa7942ff
> select clear
> show #4 models
> select add #3
2127 atoms, 2157 bonds, 2 pseudobonds, 269 residues, 2 models selected
> select subtract #3
Nothing selected
> show #2 models
> show #!1 models
> hide #!1 models
> select #4/L:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 7 residues, 1 model selected
> select up
1636 atoms, 1671 bonds, 213 residues, 1 model selected
> select up
1778 atoms, 1678 bonds, 348 residues, 1 model selected
> select up
3642 atoms, 3431 bonds, 734 residues, 1 model selected
> select down
1778 atoms, 1678 bonds, 348 residues, 1 model selected
> color sel #87ceebff
> select #4/H:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
55 atoms, 54 bonds, 8 residues, 1 model selected
> select up
1698 atoms, 1746 bonds, 227 residues, 1 model selected
> select up
1864 atoms, 1753 bonds, 386 residues, 1 model selected
> select up
3642 atoms, 3431 bonds, 734 residues, 1 model selected
> select down
1864 atoms, 1753 bonds, 386 residues, 1 model selected
> color sel blue
> select clear
> select #2/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2
727 atoms, 750 bonds, 94 residues, 1 model selected
> color sel orange
> select clear
> volume #1 color #65b4ff
> volume #1 color #65b4ff46
> volume #1 color #65b4ff32
> volume #1 color #65b4ff20
> vop gaussian #1 sdev 2
Opened J2561_3p28.mrc gaussian as #6, grid size 310,310,310, pixel 0.826,
shown at step 1, values float32
> volume #6 level 0.0507
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> color #6 #a6b5beff models
> ui tool show "Color Zone"
> color zone #6 near sel distance 4.96
> volume #6 level 0.05712
> volume #6 level 0.05569
> color zone #6 near sel distance 5.18
> color zone #6 near sel distance 6.56
> select clear
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> select add #2
4649 atoms, 808 bonds, 2 pseudobonds, 596 residues, 5 models selected
> select clear
> select add #2
727 atoms, 750 bonds, 94 residues, 1 model selected
> color sel lime
> select clear
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> color zone #6 near sel distance 6.56
> select clear
> vop gaussian #1 sdev 1.5
Opened J2561_3p28.mrc gaussian as #7, grid size 310,310,310, pixel 0.826,
shown at step 1, values float32
> volume #7 level 0.04243
> volume #7 level 0.0548
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> color zone #7 near sel distance 4.96
> close #6
> volume #7 level 0.06472
> select clear
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> volume #7 color #b2b2b2
> color zone #7 near sel distance 4.96
> select clear
> hide #2 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> select clear
> volume #7 level 0.05219
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/map_color.png
> width 2000 height 1517 supersample 3 transparentBackground true
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/map_color.cxs
> includeMaps true
——— End of log from Fri Jun 20 01:38:30 2025 ———
opened ChimeraX session
> hide #!1 models
> show #2 models
> show #!3 models
> show #4 models
> show #!5 models
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> volume #1 color #b3c7d6
> volume #1 color #b3c7d6cf
> volume #1 color #b2b2b289
> ui tool show "Color Zone"
> color zone #1 near sel distance 4.96
> transparency #1 30
> select clear
> transparency #1 40
> graphics silhouettes true
> select clear
> volume #1 level 0.1061
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> color zone #1 near sel distance 4.96
> select clear
> transparency #1 40
> select clear
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select clear
> volume #1 level 0.08909
Drag select of 595 residues, 65 atoms, 2 pseudobonds, 58 bonds
> color zone #1 near sel distance 4.96
> transparency #1 40
> select clear
> ui tool show "Hide Dust"
> surface dust #1 size 4.96
> select clear
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/map_color.png
> width 2000 height 1517 supersample 3 transparentBackground true
> open /Users/apple/Downloads/cryosparc_P32_J2198_mask.mrc
Opened cryosparc_P32_J2198_mask.mrc as #6, grid size 150,150,150, pixel 1.65,
shown at level 0.321, step 1, values float32
> volume #6 level 0.8022
> volume #6 color #b2b2b29d
> open /Users/apple/Downloads/cryosparc_P32_J2643_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2643_002_volume_map_sharp.mrc as #8, grid size
310,310,310, pixel 0.826, shown at level 0.0215, step 2, values float32
> volume #8 step 1
> volume #8 level 0.06126
> volume #8 level 0.09152
> volume #8 color #ffffb2a9
> volume #8 color #ffffb2b7
> volume #8 level 0.08207
> volume #8 level 0.1048
> volume #8 level 0.1426
> volume #8 level 0.0745
> volume #8 level 0.09341
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/session.cxs
opened ChimeraX session
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:31
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:31-41
166 atoms, 168 bonds, 11 residues, 1 model selected
> select #1/A:31
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:31-40
145 atoms, 146 bonds, 10 residues, 1 model selected
> color sel magenta
> select #1/A:31-32
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #1/A:31-41
166 atoms, 168 bonds, 11 residues, 1 model selected
> color sel magenta
> select #1/A:71
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:61-71
166 atoms, 166 bonds, 11 residues, 1 model selected
> color sel lime
> select clear
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/lollipop.png
> width 2000 height 1517 supersample 3 transparentBackground true
> open /Users/apple/Downloads/cryosparc_P32_J2643_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2643_002_volume_map_sharp.mrc as #3, grid size
310,310,310, pixel 0.826, shown at level 0.0215, step 2, values float32
> volume #3 step 1
> volume #3 level 0.084
> hide #1 models
> hide #2 models
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/NRAS_168_BRIL_real_space_refined-
> coot-10.pdb
Chain information for NRAS_168_BRIL_real_space_refined-coot-10.pdb #4
---
Chain | Description
A | No description available
> close #1-2
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/J2561_3p28.mrc
Opened J2561_3p28.mrc as #1, grid size 310,310,310, pixel 0.826, shown at
level 0.0231, step 2, values float32
> volume #1 step 1
> volume #1 level 0.07919
> volume #1 level 0.09899
> volume #3 level 0.09502
> volume #1 level 0.1221
> open /Users/apple/Downloads/cryosparc_P32_J2642_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2642_002_volume_map_sharp.mrc as #2, grid size
310,310,310, pixel 0.826, shown at level 0.0217, step 2, values float32
> volume #2 step 1
> volume #2 level 0.1046
> volume #2 level 0.09493
> open /Users/apple/Downloads/cryosparc_P32_J2644_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2644_002_volume_map_sharp.mrc as #5, grid size
310,310,310, pixel 0.826, shown at level 0.0244, step 2, values float32
> volume #5 step 1
> volume #5 level 0.08438
> volume #3 level 0.08935
> volume #5 level 0.09822
> open /Users/apple/Downloads/cryosparc_P32_J2645_002_volume_mask_refine.mrc
Opened cryosparc_P32_J2645_002_volume_mask_refine.mrc as #6, grid size
310,310,310, pixel 0.826, shown at level 0.609, step 2, values float32
> volume #6 step 1
> volume #6 level 1
> volume #6 color #ffb2ffa7
> volume #6 level 0.9778
> volume #6 level 0.9871
> volume #6 level 0.9778
> volume #6 level 0.9926
> open /Users/apple/EM_temp/J2571_mask_Mb24.mrc
Opened J2571_mask_Mb24.mrc as #7, grid size 310,310,310, pixel 0.826, shown at
level 2.58e-06, step 2, values float32
> volume #7 step 1
> volume #7 level 0.003562
> volume #7 level 0.003384
> ui tool show "Map Eraser"
> volume erase #7 center 131.88,133.31,126.63 radius 26.246
Opened J2571_mask_Mb24.mrc copy as #9, grid size 310,310,310, pixel 0.826,
shown at step 1, values float32
> volume #7 color #ffb2b2af
> volume #9 color #ffb2b2a4
Can only have one displayed volume when erasing
> volume erase #9 center 136.45,141.16,119.07 radius 26.246
> volume #9 level 0.00196
> save /Users/apple/EM_temp/J2571_mask_Mb24_2_0p00196.mrc models #9
> open /Users/apple/Downloads/cryosparc_P32_J2651_003_volume_map_sharp.mrc
Opened cryosparc_P32_J2651_003_volume_map_sharp.mrc as #10, grid size
310,310,310, pixel 0.826, shown at level 0.0168, step 2, values float32
> volume #10 step 1
> volume #10 level 0.06456
> volume #10 level 0.0721
> volume #10 level 0.06959
> volume #3 level 0.09502
> close #10
> open /Users/apple/Downloads/cryosparc_P32_J2653_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2653_002_volume_map_sharp.mrc as #8, grid size
310,310,310, pixel 0.826, shown at level 0.0197, step 2, values float32
> volume #8 step 1
> volume #8 level 0.06165
> volume #8 color #99bfe5c1
> volume #8 level 0.1106
> open /Users/apple/EM_temp/J2091_Mask_subtract_0p0705.mrc
Opened J2091_Mask_subtract_0p0705.mrc as #10, grid size 150,150,150, pixel
1.65, shown at level 0.0903, step 1, values float32
> close #10
> open /Users/apple/EM_temp/J2091_mask_BRIL_0p203.mrc
Opened J2091_mask_BRIL_0p203.mrc as #10, grid size 150,150,150, pixel 1.65,
shown at level 0.0174, step 1, values float32
> volume #10 color #b2b2b2b5
> volume #10 level 0.07637
Drag select of 65 atoms, 268 residues, 2 pseudobonds, 58 bonds
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Model_building/NRAS_168_BRIL_Fab_Mb24/Mb24_fitted-
> coot-0.pdb
Chain information for Mb24_fitted-coot-0.pdb #11
---
Chain | Description
A | No description available
Drag select of 65 atoms, 362 residues, 2 pseudobonds, 58 bonds
> color (#11#!4 & sel) orange red
> ui tool show "Color Zone"
> color zone #2 near sel distance 4.96
> color zone #2 near sel distance 5.25
> color zone #2 near sel distance 4.37
> volume splitbyzone #2
Opened cryosparc_P32_J2642_002_volume_map_sharp.mrc 0 as #12.1, grid size
310,310,310, pixel 0.826, shown at level 0.0949, step 1, values float32
Opened cryosparc_P32_J2642_002_volume_map_sharp.mrc 1 as #12.2, grid size
310,310,310, pixel 0.826, shown at level 0.0949, step 1, values float32
> close #12.1
> vop gaussian #12.2 sdev 3
Opened cryosparc_P32_J2642_002_volume_map_sharp.mrc 1 gaussian as #13, grid
size 310,310,310, pixel 0.826, shown at step 1, values float32
> volume #13 level 0.01345
> ui tool show "Map Eraser"
> volume #13 color #b2b2ff74
> volume erase #13 center 125.44,122.73,138.29 radius 12.931
> volume erase #13 center 126.67,130.01,139.24 radius 12.931
> volume erase #13 center 126.05,111.7,131.17 radius 12.931
> volume erase #13 center 137.48,125.24,140.48 radius 12.931
> save /Users/apple/EM_temp/J2642_Mask_NRAS_BRIL_0p0135.mrc models #13
> open /Users/apple/Downloads/cryosparc_P32_J2679_002_volume_map_sharp.mrc
Opened cryosparc_P32_J2679_002_volume_map_sharp.mrc as #14, grid size
300,300,300, pixel 0.825, shown at level 0.0605, step 2, values float32
> volume #14 step 1
> volume #14 level 0.2275
> ui tool show "Fit in Map"
> fitmap sel inMap #14
Fit molecules NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4), Mb24_fitted-
coot-0.pdb (#11) to map cryosparc_P32_J2679_002_volume_map_sharp.mrc (#14)
using 2854 atoms
average map value = 0.2033, steps = 72
shifted from previous position = 4.79
rotated from previous position = 3.61 degrees
atoms outside contour = 1671, contour level = 0.22749
Position of NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4) relative to
cryosparc_P32_J2679_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.99915596 -0.00442766 -0.04083819 4.18126413
0.00637243 0.99884543 0.04761502 -7.91640678
0.04058022 -0.04783507 0.99803059 -1.45800202
Axis -0.75801040 -0.64657873 0.08576817
Axis point 0.00000000 -39.53610858 140.53008620
Rotation angle (degrees) 3.60978362
Shift along axis 1.82408838
Position of Mb24_fitted-coot-0.pdb (#11) relative to
cryosparc_P32_J2679_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.99915596 -0.00442766 -0.04083819 4.18126413
0.00637243 0.99884543 0.04761502 -7.91640678
0.04058022 -0.04783507 0.99803059 -1.45800202
Axis -0.75801040 -0.64657873 0.08576817
Axis point 0.00000000 -39.53610858 140.53008620
Rotation angle (degrees) 3.60978362
Shift along axis 1.82408838
> select clear
> hide #11 models
> hide #!12 models
> hide #!4 models
> show #!4 models
> show #11 models
> hide #11 models
> show #11 models
> volume #14 color #ffb2ffb5
> lighting simple
> hide #11 models
Drag select of 65 atoms, 268 residues, 2 pseudobonds, 58 bonds
> fitmap sel inMap #14
Fit molecule NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4) to map
cryosparc_P32_J2679_002_volume_map_sharp.mrc (#14) using 2127 atoms
average map value = 0.2166, steps = 64
shifted from previous position = 0.595
rotated from previous position = 3.15 degrees
atoms outside contour = 1163, contour level = 0.22749
Position of NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4) relative to
cryosparc_P32_J2679_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.99986583 -0.00894723 0.01372130 -3.88497248
0.00820837 0.99856134 0.05298944 -8.87695673
-0.01417567 -0.05286970 0.99850080 5.51056709
Axis -0.95532675 0.25175647 0.15482083
Axis point 0.00000000 92.27164585 181.09704697
Rotation angle (degrees) 3.17608053
Shift along axis 2.32973741
> select clear
> volume #14 level 0.331
> open /Users/apple/Downloads/cryosparc_P32_J2675_004_volume_map_sharp.mrc
Opened cryosparc_P32_J2675_004_volume_map_sharp.mrc as #15, grid size
300,300,300, pixel 0.825, shown at level 0.0659, step 2, values float32
> volume #15 step 1
> volume #15 level 0.2614
> volume #15 color #ffb2b292
> volume #15 level 0.2614
> open /Users/apple/Downloads/cryosparc_P32_J2678_004_volume_map_sharp.mrc
Opened cryosparc_P32_J2678_004_volume_map_sharp.mrc as #16, grid size
300,300,300, pixel 0.825, shown at level 0.0646, step 2, values float32
> volume #16 step 1
> volume #16 color #b2ffb2bf
> volume #16 level 0.2412
Drag select of 65 atoms, 268 residues, 2 pseudobonds, 58 bonds
> fitmap sel inMap #1
Fit molecule NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4) to map
J2561_3p28.mrc (#1) using 2127 atoms
average map value = 0.1398, steps = 92
shifted from previous position = 5.16
rotated from previous position = 3.15 degrees
atoms outside contour = 1030, contour level = 0.1221
Position of NRAS_168_BRIL_real_space_refined-coot-10.pdb (#4) relative to
J2561_3p28.mrc (#1) coordinates:
Matrix rotation and translation
0.99999060 -0.00079573 -0.00426324 0.77399830
0.00080247 0.99999843 0.00157988 -0.35880631
0.00426197 -0.00158329 0.99998966 -0.30208034
Axis -0.34261257 -0.92339096 0.17310620
Axis point 71.88295671 0.00000000 182.50581602
Rotation angle (degrees) 0.26449275
Shift along axis 0.01384497
> volume #1 level 0.09491
> show #11 models
> open /Users/apple/Downloads/1xd2.pdb
1xd2.pdb title:
Crystal structure of A ternary ras:sos:ras*GDP complex [more info...]
Chain information for 1xd2.pdb #17
---
Chain | Description | UniProt
A | C-H-RAS | RASH_HUMAN 1-166
B | C-H-RAS | RASH_HUMAN 1-166
C | SOS-1 | SOS1_HUMAN 566-1049
Non-standard residues in 1xd2.pdb #17
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
PO4 — phosphate ion
> ui tool show Matchmaker
> matchmaker #!17 to #4
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 NRAS_168_BRIL_real_space_refined-coot-10.pdb, chain A (#4) with
1xd2.pdb, chain B (#17), sequence alignment score = 622.2
RMSD between 130 pruned atom pairs is 0.936 angstroms; (across all 160 pairs:
3.489)
Drag select of 119 atoms, 193 residues, 4 pseudobonds, 103 bonds
> ui tool show Matchmaker
> matchmaker #!17 & sel to #4
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 NRAS_168_BRIL_real_space_refined-coot-10.pdb, chain A (#4) with
1xd2.pdb, chain A (#17), sequence alignment score = 592.5
RMSD between 140 pruned atom pairs is 0.990 angstroms; (across all 160 pairs:
1.490)
> close #17
> open /Users/apple/Downloads/6vjj.pdb
6vjj.pdb title:
Crystal structure of wild-type KRAS4B (gmppnp-bound) In complex with ras-
binding domain (RBD) of RAF1/craf [more info...]
Chain information for 6vjj.pdb #17
---
Chain | Description | UniProt
A | gtpase kras | RASK_HUMAN 1-169
B | raf proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-131
Non-standard residues in 6vjj.pdb #17
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
108 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!17 & sel to #4
No molecules/chains to match specified
> ui tool show Matchmaker
> matchmaker #!17 to #4
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 NRAS_168_BRIL_real_space_refined-coot-10.pdb, chain A (#4) with
6vjj.pdb, chain A (#17), sequence alignment score = 611.4
RMSD between 133 pruned atom pairs is 1.022 angstroms; (across all 161 pairs:
1.746)
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/dimer_session.cxs
Opened dimer_map_J2075.mrc as #2, grid size 150,150,150, pixel 1.65, shown at
level 0.446, step 1, values float32
opened ChimeraX session
> hide #4 models
> hide #5 models
> open /Users/apple/Downloads/6vjj.pdb
6vjj.pdb title:
Crystal structure of wild-type KRAS4B (gmppnp-bound) In complex with ras-
binding domain (RBD) of RAF1/craf [more info...]
Chain information for 6vjj.pdb #6
---
Chain | Description | UniProt
A | gtpase kras | RASK_HUMAN 1-169
B | raf proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-131
Non-standard residues in 6vjj.pdb #6
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GNP — phosphoaminophosphonic acid-guanylate ester
MG — magnesium ion
MPD — (4S)-2-methyl-2,4-pentanediol
108 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!6 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 NRAS_168_BRIL.pdb, chain A (#3) with 6vjj.pdb, chain A (#6),
sequence alignment score = 802.9
RMSD between 154 pruned atom pairs is 0.713 angstroms; (across all 167 pairs:
1.166)
> matchmaker #!6 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 NRAS_168_BRIL.pdb, chain A (#3) with 6vjj.pdb, chain A (#6),
sequence alignment score = 802.9
RMSD between 154 pruned atom pairs is 0.713 angstroms; (across all 167 pairs:
1.166)
> select clear
> hide #3 models
> show #4 models
> show #5 models
> hide #1 models
> ui tool show Matchmaker
> matchmaker #!6 to #5
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 Mb24.pdb, chain A (#5) with 6vjj.pdb, chain A (#6), sequence
alignment score = 16.5
RMSD between 7 pruned atom pairs is 0.722 angstroms; (across all 26 pairs:
16.707)
> matchmaker #!6 to #4
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 NRAS_168_BRIL.pdb, chain A (#4) with 6vjj.pdb, chain A (#6),
sequence alignment score = 802.9
RMSD between 154 pruned atom pairs is 0.713 angstroms; (across all 167 pairs:
1.166)
> matchmaker #!6 to #4
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 NRAS_168_BRIL.pdb, chain A (#4) with 6vjj.pdb, chain A (#6),
sequence alignment score = 802.9
RMSD between 154 pruned atom pairs is 0.713 angstroms; (across all 167 pairs:
1.166)
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #5 models
> hide #!6 models
> show #3 models
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/dimer_map_J2075.mrc
Opened dimer_map_J2075.mrc as #7, grid size 150,150,150, pixel 1.65, shown at
level 0.27, step 1, values float32
> select #7
2 models selected
> ui mousemode right "translate selected models"
> show #!2 models
> view matrix models #7,1,0,0,30.463,0,1,0,-20.857,0,0,1,20.609
> ui mousemode right "rotate selected models"
> volume #7 level 0.5228
> view matrix models
> #7,0.32076,-0.86178,-0.393,268.53,0.5777,0.50681,-0.63984,31.618,0.75058,-0.021802,0.66042,-39.916
> view matrix models
> #7,-0.1511,0.66121,-0.73482,212.87,-0.85355,0.28768,0.43438,121.72,0.49862,0.69285,0.52091,-64.362
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.1511,0.66121,-0.73482,228.4,-0.85355,0.28768,0.43438,109.15,0.49862,0.69285,0.52091,-49.14
> view matrix models
> #7,-0.1511,0.66121,-0.73482,223.4,-0.85355,0.28768,0.43438,100.09,0.49862,0.69285,0.52091,-45.441
> view matrix models
> #7,-0.1511,0.66121,-0.73482,222.75,-0.85355,0.28768,0.43438,102.67,0.49862,0.69285,0.52091,-52.791
> ui tool show "Fit in Map"
> fitmap #7 inMap #2
Fit map dimer_map_J2075.mrc in map dimer_map_J2075.mrc using 13641 points
correlation = 0.4493, correlation about mean = 0.1976, overlap = 1126
steps = 132, shift = 5.82, angle = 18.1 degrees
Position of dimer_map_J2075.mrc (#7) relative to dimer_map_J2075.mrc (#2)
coordinates:
Matrix rotation and translation
-0.12790175 0.44196666 -0.88786633 261.10033095
-0.78656193 0.50009616 0.36224876 82.59346473
0.60412041 0.74469410 0.28367097 -36.97615245
Axis 0.19411790 -0.75728818 -0.62356464
Axis point 157.78115535 0.00000000 91.19130802
Rotation angle (degrees) 99.90803875
Shift along axis 11.19421495
> select clear
> volume #7 color #e5bf9994
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/dimer_map_J2075.mrc
Opened dimer_map_J2075.mrc as #8, grid size 150,150,150, pixel 1.65, shown at
level 0.27, step 1, values float32
> select #8
2 models selected
> view matrix models #8,1,0,0,-7.1104,0,1,0,-52.976,0,0,1,41.704
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.74242,-0.65036,-0.16078,323.22,-0.12441,-0.10198,0.98698,-45.396,-0.65829,0.75275,-0.0052023,181.64
> view matrix models
> #8,-0.82906,-0.55761,0.041704,299.75,-0.068885,0.17586,0.982,-81.654,-0.5549,0.81126,-0.18421,183.92
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.82906,-0.55761,0.041704,287.46,-0.068885,0.17586,0.982,-91.032,-0.5549,0.81126,-0.18421,187.23
> fitmap #8 inMap #7
Fit map dimer_map_J2075.mrc in map dimer_map_J2075.mrc using 33741 points
correlation = 0.4073, correlation about mean = 0.1846, overlap = 1602
steps = 168, shift = 10.2, angle = 3.44 degrees
Position of dimer_map_J2075.mrc (#8) relative to dimer_map_J2075.mrc (#7)
coordinates:
Matrix rotation and translation
-0.14558471 0.43806557 -0.88707590 263.58063541
-0.78781458 0.49104285 0.37178637 82.03291826
0.59845908 0.75297774 0.27362611 -35.54167131
Axis 0.19414952 -0.75661709 -0.62436892
Axis point 157.83962974 0.00000000 90.82484725
Rotation angle (degrees) 100.97950649
Shift along axis 11.29766129
> select clear
> volume #8 level 0.5163
> show #!6 models
> hide #3 models
> show #3 models
> hide #3 models
> show #5 models
> select #4/A:36
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #4/A:27
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #5/A:44
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #5/A:43
34 atoms, 34 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select #4/A:32
21 atoms, 21 bonds, 1 residue, 1 model selected
> select add #4/A:31
36 atoms, 35 bonds, 2 residues, 1 model selected
> select add #6/A:32
48 atoms, 47 bonds, 3 residues, 2 models selected
> show sel atoms
> select clear
> volume #2 level 0.5018
> open /Users/apple/Downloads/7tvj.cif
7tvj.cif title:
Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex [more
info...]
Chain information for 7tvj.cif #9
---
Chain | Description | UniProt
A D | Tyrosine-protein phosphatase non-receptor type 11 | PTN11_HUMAN 224-525
B E | Mb(SHP2PTP_13) |
Non-standard residues in 7tvj.cif #9
---
FLC — citrate anion
7tvj.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
60 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!6 models
> hide #5 models
> hide #4 models
> select #9/A:525
5 atoms, 4 bonds, 1 residue, 1 model selected
> open "/Users/apple/Downloads/AF-P08962-F1-model_v4 (2).pdb"
AF-P08962-F1-model_v4 (2).pdb title:
Alphafold monomer V2.0 prediction for CD63 antigen (P08962) [more info...]
Chain information for AF-P08962-F1-model_v4 (2).pdb #10
---
Chain | Description | UniProt
A | CD63 antigen | CD63_HUMAN 1-238
> hide #!9 models
> set bgColor white
> lighting soft
> lighting simple
> save /Users/apple/Downloads/CD63.png width 1152 height 874 supersample 3
> save /Users/apple/Downloads/CD63.png width 1152 height 874 supersample 3
> transparentBackground true
> hide #10 models
> show #!7 models
> hide #!7 models
> show #!2 models
> show #3 models
> show #4 models
> show #!6 models
> hide #!6 models
Drag select of 336 residues, 26 atoms, 25 bonds
> select ~sel & ##selected
3308 atoms, 3330 bonds, 212 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select clear
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer_1.pdb
> models #3 relModel #2
No model chosen to save relative to
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer_2.pdb
> models #4 relModel #2
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #11
---
Chain | Description
A B | No description available
> hide #11 models
> show #11 models
> hide #4 models
> hide #3 models
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #12
---
Chain | Description
A B | No description available
> hide #12 models
Drag select of 170 residues
> ui tool show Matchmaker
> matchmaker #11/B to #12/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#12) with ras_dimer.pdb, chain B (#11),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> show #12 models
> select clear
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #13
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #12/B to #11/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#11) with ras_dimer.pdb, chain B (#12),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> matchmaker #13/B to #12/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#12) with ras_dimer.pdb, chain B (#13),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #14
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #14/B to #13/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#13) with ras_dimer.pdb, chain B (#14),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #15
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #15/B to #14/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#14) with ras_dimer.pdb, chain B (#15),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #16
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #16/B to #15/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#15) with ras_dimer.pdb, chain B (#16),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/ras_dimer.pdb
Chain information for ras_dimer.pdb #17
---
Chain | Description
A B | No description available
> ui tool show Matchmaker
> matchmaker #17/B to #16/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#16) with ras_dimer.pdb, chain B (#17),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> matchmaker #17/B to #16/A pairing ss
Parameters
---
Chain pairing | ss
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 ras_dimer.pdb, chain A (#16) with ras_dimer.pdb, chain B (#17),
sequence alignment score = 1247
RMSD between 168 pruned atom pairs is 0.001 angstroms; (across all 168 pairs:
0.001)
> dssp
> open /Users/apple/Downloads/41594_2021_667_MOESM6_ESM.pdb
Summary of feedback from opening
/Users/apple/Downloads/41594_2021_667_MOESM6_ESM.pdb
---
warnings | Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
155926 messages similar to the above omitted
Chain information for 41594_2021_667_MOESM6_ESM.pdb #18
---
Chain | Description
A B E G P Q W Y | No description available
C D F H R S X Z | No description available
I J K N O T U V | No description available
c d f h r s x z | No description available
i j k n o t u v | No description available
> select add #18
255930 atoms, 254765 bonds, 8 pseudobonds, 12195 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select #18/B:7
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/P:131
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #18/A
1524 atoms, 1546 bonds, 1 pseudobond, 187 residues, 2 models selected
> select #18/A,B,P,Q
6102 atoms, 6190 bonds, 4 pseudobonds, 748 residues, 2 models selected
> select #18/A,B,P,Q,W,Y,E,G
12206 atoms, 12382 bonds, 8 pseudobonds, 1496 residues, 2 models selected
> select ~sel & ##selected
243724 atoms, 242383 bonds, 10699 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 1480 residues
> view matrix models #18,1,0,0,26.761,0,1,0,93.343,0,0,1,174.39
> view matrix models #18,1,0,0,73.234,0,1,0,118,0,0,1,202.6
> view matrix models #18,1,0,0,51.837,0,1,0,51.99,0,0,1,153.45
> select ~sel & ##selected
243988 atoms, 242655 bonds, 8 pseudobonds, 10715 residues, 2 models selected
> delete atoms (#!18 & sel)
> delete bonds (#!18 & sel)
Drag select of 1480 residues
> ui tool show Matchmaker
> matchmaker #!18 to #11/A pairing bs
Parameters
---
Chain pairing | bs
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 ras_dimer.pdb, chain A (#11) with 41594_2021_667_MOESM6_ESM.pdb,
chain E (#18), sequence alignment score = 778.3
RMSD between 146 pruned atom pairs is 1.021 angstroms; (across all 168 pairs:
2.185)
> show #5 models
> hide #!18 models
> show #1 models
> hide #5 models
> hide #1 models
> show #!18 models
> hide #!18 models
> show #!18 models
> view matrix models
> #18,-0.80718,0.4142,0.42059,134.26,0.45825,-0.009461,0.88878,28.852,0.37211,0.91014,-0.18217,114.53
> view matrix models
> #18,-0.80718,0.4142,0.42059,138.12,0.45825,-0.009461,0.88878,26.07,0.37211,0.91014,-0.18217,106.73
> open /Users/apple/Downloads/41594_2021_667_MOESM7_ESM.pdb
Chain information for 41594_2021_667_MOESM7_ESM.pdb #19
---
Chain | Description
A B | No description available
> hide #!18 models
Drag select of 27329 atoms, 370 residues, 2 pseudobonds, 26736 bonds
> select clear
Drag select of 27329 atoms, 370 residues, 2 pseudobonds, 26736 bonds
> hide sel atoms
> select clear
> hide #!19 models
> show #!18 models
> select clear
> select #15/A:150
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #15/A:149
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #15/A:88
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:128
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #17/A:129
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #15/B:129
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #13/A:88
39 atoms, 37 bonds, 2 residues, 2 models selected
> select #11/A:161
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #15/B:122
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #17/B:25
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #16/A:29
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #17/B:25
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #16/A:26
31 atoms, 29 bonds, 2 residues, 2 models selected
Drag select of 8 residues
Drag select of 5 residues
> show sel atoms
> select clear
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #!18 models
> hide #18.1 models
> save
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Mb24_NRAS/dimer_session.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403290055 (2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/session.cxs
Log from Fri Jun 20 00:53:33 2025UCSF ChimeraX version: 1.8.dev202403290055
(2024-03-29)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/HRAS_BRIL_3A.pdb
Chain information for HRAS_BRIL_3A.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/apple/Documents/NYU_Langone/Koide_Lab/Models_map/antiBril_Fab.pdb
Chain information for antiBril_Fab.pdb #2
---
Chain | Description
H | No description available
L | No description available
38 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> lighting soft
Drag select of 716 residues, 133 atoms, 99 bonds
> hide sel atoms
> select clear
> select #2/L:12
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:24
6 atoms, 5 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
55 atoms, 54 bonds, 8 residues, 1 model selected
> select up
1698 atoms, 1746 bonds, 227 residues, 1 model selected
> select up
1864 atoms, 1753 bonds, 386 residues, 1 model selected
> select up
3642 atoms, 3431 bonds, 734 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
1864 atoms, 1753 bonds, 386 residues, 1 model selected
> color sel blue
> select clear
> select #1/A:166
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1/A:167
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add #1/A:168
27 atoms, 26 bonds, 2 residues, 1 model selected
> select add #1/A:169
37 atoms, 35 bonds, 3 residues, 1 model selected
> color sel red
> select clear
> select #1/A:171
10 atoms, 9 bonds, 1 residue, 1 model selected
> hide #2 models
Drag select of 109 residues
> select subtract #1/A:168
1674 atoms, 108 residues, 1 model selected
> select subtract #1/A:169
1664 atoms, 107 residues, 1 model selected
> color sel #aa7942ff
> select add #1/A:169
1674 atoms, 9 bonds, 108 residues, 1 model selected
> select add #1/A:168
1684 atoms, 18 bonds, 109 residues, 1 model selected
> select add #1/A:167
1701 atoms, 35 bonds, 110 residues, 1 model selected
> select ~sel & ##selected
2616 atoms, 2635 bonds, 166 residues, 1 model selected
> color sel light gray
> show #2 models
> color sel dark gray
> select clear
> undo
> select clear
> undo
> color sel light gray
> color sel forest green
> color sel yellow
> color sel dark gray
> select clear
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/lollipop.png
> width 2000 height 1517 supersample 3 transparentBackground true
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/2D_image.png
> width 2000 height 1517 supersample 3 transparentBackground true
> save /Users/apple/Documents/NYU_Langone/Koide_Lab/For_poster/session.cxs
——— End of log from Fri Jun 20 00:53:33 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: MNWA3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 56 days, 19 hours, 34 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 38
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2413:
Resolution: 1200 x 1920
UI Looks like: 1200 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 90
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
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: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403290055
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class saving session |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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