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Opened 14 months ago
Closed 14 months ago
#15867 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202312070253 (2023-12-07 02:53:36 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 0x00007ff84c37afc0 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1382 in
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1382 in get_tangents
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1189 in __init__
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 156 in _make_ribbon_graphics
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600 in compute_ribbons
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1891 in _update_graphics_if_needed
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX_Daily 2.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 2.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, 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, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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._minpack2, 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.__nnls, 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 (total: 118)
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{
"uptime" : 130000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 1525,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-09-02 23:34:13.8714 -0700",
"codeSigningMonitor" : 0,
"incident" : "E0C5DB92-C36C-4DBE-BB71-DD0A0772D094",
"pid" : 27961,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-02 22:19:43.7044 -0700",
"procStartAbsTime" : 132604664136581,
"procExitAbsTime" : 137074737319522,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily 2.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"D40440ED-A4F0-550B-8623-ACC5AA686B63","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4D6079BF-DD9B-0CD4-4F03-CBEA84B5C3BD",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 12077,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "C25A4DDB-0507-4117-8AEB-229C6D4BE6A7",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4554346327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f75d000-10f761000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily 2.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":27961},
"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\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" : "0xa9 is not in any region. Bytes before following region: 4554346327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f75d000-10f761000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily 2.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202312070253 (2023-12-07)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Dropbox (Scripps Research)/CRL4 processing good data
> set/model fitting/atomic model fit with Gabe.cxs"
Error opening map "/Users/zrizvi/Downloads/cryosparc_P341_J252_015_volume_map
(1).mrc": File cryosparc_P341_J252_015_volume_map (1).mrc, format mrc
[Errno 1] Operation not permitted:
'/Users/zrizvi/Downloads/cryosparc_P341_J252_015_volume_map (1).mrc'
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "/Users/zrizvi/Downloads/cryosparc_P341_J251_009_volume_map
(1).mrc": File cryosparc_P341_J251_009_volume_map (1).mrc, format mrc
[Errno 1] Operation not permitted:
'/Users/zrizvi/Downloads/cryosparc_P341_J251_009_volume_map (1).mrc'
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened volume maximum as #7, grid size 350,350,350, pixel 1.15, shown at level
0.21, step 1, values float32
Log from Fri Dec 8 11:01:25 2023UCSF ChimeraX version: 1.8.dev202312070253
(2023-12-07)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Desktop/NEW map fitting.cxs" format session
Opened cryosparc_P341_J252_015_volume_map (1).mrc as #1, grid size
350,350,350, pixel 1.15, shown at level 0.192, step 2, values float32
Opened cryosparc_P341_J251_009_volume_map (1).mrc as #2, grid size
350,350,350, pixel 1.15, shown at level 0.191, step 2, values float32
Opened volume maximum as #7, grid size 350,350,350, pixel 1.15, shown at level
0.263, step 1, values float32
Log from Thu Dec 7 10:40:16 2023UCSF ChimeraX version: 1.7rc202312020245
(2023-12-02)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs" format session
Opened cryosparc_P341_J252_015_volume_map (1).mrc as #1, grid size
350,350,350, pixel 1.15, shown at level 0.192, step 2, values float32
Opened cryosparc_P341_J251_009_volume_map (1).mrc as #2, grid size
350,350,350, pixel 1.15, shown at level 0.191, step 2, values float32
Opened volume maximum as #7, grid size 350,350,350, pixel 1.15, shown at level
0.192, step 1, values float32
Log from Tue Dec 5 16:02:00 2023UCSF ChimeraX version: 1.7rc202312020245
(2023-12-02)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Tue Dec 5 13:34:28 2023UCSF ChimeraX version: 1.7.dev202307220101
(2023-07-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zrizvi/Downloads/cryosparc_P341_J252_015_volume_map (1).mrc"
> format mrc
Opened cryosparc_P341_J252_015_volume_map (1).mrc as #1, grid size
350,350,350, pixel 1.15, shown at level 0.0357, step 2, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P341_J251_009_volume_map (1).mrc"
> format mrc
Opened cryosparc_P341_J251_009_volume_map (1).mrc as #2, grid size
350,350,350, pixel 1.15, shown at level 0.0367, step 2, values float32
> set bgColor white
> set bgColor #ffffff00
> volume #1 level 0.1586
> volume #2 level 0.1912
> volume #1 level 0.1916
> color #1 #2137bfff models
> color #1 #bf15b0ff models
> color #2 #1a2fffff models
> open 8D7Z format mmcif fromDatabase pdb
8d7z title:
Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 [more info...]
Chain information for 8d7z #3
---
Chain | Description | UniProt
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140
B | Protein cereblon | CRBN_HUMAN 1-442
C | DNA-binding protein Ikaros | IKZF1_HUMAN 112-196
Non-standard residues in 8d7z #3
---
QFC — Mezigdomide
ZN — zinc ion
> hide #!1 models
> ui mousemode right select
> select /B:263
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,14.637,0,1,0,61.712,0,0,1,71.707
> view matrix models #3,1,0,0,14.924,0,1,0,64.218,0,0,1,78.133
> view matrix models #3,1,0,0,51.043,0,1,0,41.402,0,0,1,77.968
> view matrix models #3,1,0,0,58.374,0,1,0,39.524,0,0,1,80.487
> view matrix models #3,1,0,0,59.919,0,1,0,58.24,0,0,1,79.998
> view matrix models #3,1,0,0,60.458,0,1,0,59.873,0,0,1,79.237
> fitmap #3 inMap #2
Fit molecule 8d7z (#3) to map cryosparc_P341_J251_009_volume_map (1).mrc (#2)
using 11228 atoms
average map value = 0.222, steps = 336
shifted from previous position = 8.82
rotated from previous position = 70.7 degrees
atoms outside contour = 4220, contour level = 0.19116
Position of 8d7z (#3) relative to cryosparc_P341_J251_009_volume_map (1).mrc
(#2) coordinates:
Matrix rotation and translation
0.34568495 -0.93027672 0.12282972 259.24476508
0.88463277 0.36674535 0.28796303 -8.88611186
-0.31293253 0.00911471 0.94973162 121.13298155
Axis -0.14775733 0.23090355 0.96169191
Axis point 158.33859819 179.39931931 0.00000000
Rotation angle (degrees) 70.66560143
Shift along axis 76.13545989
> select up
149 atoms, 150 bonds, 17 residues, 1 model selected
> select up
2944 atoms, 3013 bonds, 381 residues, 1 model selected
> select down
149 atoms, 150 bonds, 17 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> lighting soft
> transparency #2.1 50
> material transparentCastShadows true
> show #!1 models
> hide #!2 models
> hide #!3 models
> open 1ldk
1ldk title:
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex [more
info...]
Chain information for 1ldk #4
---
Chain | Description | UniProt
A | CULLIN HOMOLOG | CUL1_HUMAN 15-410
B | CULLIN HOMOLOG | CUL1_HUMAN 411-776
C | ring-box protein 1 | RBX1_HUMAN 1019-1108
D | CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 | SKP1_HUMAN 2002-2140
E | SKP2-like protein type gamma | SKP2_HUMAN 3109-3149
Non-standard residues in 1ldk #4
---
ZN — zinc ion
1ldk mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> view #4 clip false
> hide #!4 atoms
> show #!4 cartoons
> select #4/A,B,D,E
7188 atoms, 7306 bonds, 4 pseudobonds, 883 residues, 2 models selected
> ~ribbon sel
> undo
> ~ribbon sel
> select up
7922 atoms, 8059 bonds, 4 pseudobonds, 974 residues, 2 models selected
> select up
19150 atoms, 19507 bonds, 4 pseudobonds, 2516 residues, 7 models selected
> select up
19150 atoms, 19507 bonds, 4 pseudobonds, 2516 residues, 7 models selected
> color #4 #69fd3dff
> view #1 clip false
> select subtract #1
19150 atoms, 19507 bonds, 4 pseudobonds, 2516 residues, 5 models selected
> ui mousemode right select
> select #4/C:1056
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/C:1056
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,116.64,0,1,0,279.64,0,0,1,0.59234
> view matrix models #4,1,0,0,116.46,0,1,0,281.69,0,0,1,3.1105
> view matrix models #4,1,0,0,117.06,0,1,0,281.53,0,0,1,1.8002
> open 1ldk
1ldk title:
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex [more
info...]
Chain information for 1ldk #5
---
Chain | Description | UniProt
A | CULLIN HOMOLOG | CUL1_HUMAN 15-410
B | CULLIN HOMOLOG | CUL1_HUMAN 411-776
C | ring-box protein 1 | RBX1_HUMAN 1019-1108
D | CYCLIN A/CDK2-ASSOCIATED PROTEIN P19 | SKP1_HUMAN 2002-2140
E | SKP2-like protein type gamma | SKP2_HUMAN 3109-3149
Non-standard residues in 1ldk #5
---
ZN — zinc ion
1ldk mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> hide #!4 models
> hide #!1 models
> view #5 clip false
> hide #!5 atoms
> show #!5 cartoons
> set bgColor black
> set bgColor transparent
> hide #!5 models
> show #!4 models
> show #!1 models
> set bgColor white
> set bgColor #ffffff00
> view #4 clip false
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,106.81,0,1,0,260.53,0,0,1,-0.062957
> view matrix models
> #4,0.26016,0.96347,-0.06355,183.55,-0.86672,0.20401,-0.45517,404.34,-0.42558,0.1735,0.88813,54.745
> view matrix models
> #4,0.26016,0.96347,-0.06355,187.4,-0.86672,0.20401,-0.45517,414.02,-0.42558,0.1735,0.88813,61.186
> view matrix models
> #4,-0.068083,0.99107,-0.11466,224.11,-0.85676,-0.11697,-0.50227,419.64,-0.5112,0.06404,0.85707,73.216
> view matrix models
> #4,-0.068083,0.99107,-0.11466,224.17,-0.85676,-0.11697,-0.50227,419.57,-0.5112,0.06404,0.85707,72.573
> view matrix models
> #4,-0.068083,0.99107,-0.11466,227.83,-0.85676,-0.11697,-0.50227,404.19,-0.5112,0.06404,0.85707,70.881
> view matrix models
> #4,-0.068083,0.99107,-0.11466,236.07,-0.85676,-0.11697,-0.50227,398.4,-0.5112,0.06404,0.85707,68.939
> view matrix models
> #4,-0.068083,0.99107,-0.11466,242.9,-0.85676,-0.11697,-0.50227,406.85,-0.5112,0.06404,0.85707,64.157
> fitmap #4 inMap #1
Fit molecule 1ldk (#4) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 7922 atoms
average map value = 0.06574, steps = 2000
shifted from previous position = 21.9
rotated from previous position = 22.5 degrees
atoms outside contour = 6937, contour level = 0.19164
Position of 1ldk (#4) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.08130969 0.93359263 -0.34898930 270.54534968
-0.68814663 -0.20071142 -0.69725830 416.21903381
-0.72100135 0.29684967 0.62612884 118.35415509
Axis 0.51289840 0.19193527 -0.83671744
Axis point 354.23259493 124.50593002 0.00000000
Rotation angle (degrees) 104.27856314
Shift along axis 119.62040690
> view matrix models
> #4,0.08131,0.93359,-0.34899,260.39,-0.68815,-0.20071,-0.69726,418.43,-0.721,0.29685,0.62613,117.94
> view matrix models
> #4,0.08131,0.93359,-0.34899,263.5,-0.68815,-0.20071,-0.69726,426.05,-0.721,0.29685,0.62613,119.67
> fitmap #4 inMap #1
Fit molecule 1ldk (#4) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 7922 atoms
average map value = 0.06574, steps = 1380
shifted from previous position = 12.2
rotated from previous position = 0.085 degrees
atoms outside contour = 6936, contour level = 0.19164
Position of 1ldk (#4) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.08099250 0.93382790 -0.34843317 270.46914404
-0.68907898 -0.20011836 -0.69650758 416.17560695
-0.72014608 0.29650986 0.62727309 118.13586016
Axis 0.51224038 0.19174524 -0.83716399
Axis point 354.10840794 124.37421516 0.00000000
Rotation angle (degrees) 104.23658701
Shift along axis 119.44582111
> fitmap #4 inMap #1
Fit molecule 1ldk (#4) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 7922 atoms
average map value = 0.06573, steps = 380
shifted from previous position = 0.0345
rotated from previous position = 0.0392 degrees
atoms outside contour = 6940, contour level = 0.19164
Position of 1ldk (#4) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.08117672 0.93374346 -0.34861653 270.47248331
-0.68953217 -0.19994859 -0.69610771 416.14803943
-0.71969141 0.29689005 0.62761498 118.04243328
Axis 0.51218363 0.19139870 -0.83727801
Axis point 354.13053876 124.27257166 0.00000000
Rotation angle (degrees) 104.21602055
Shift along axis 119.34743627
> open /Users/zrizvi/Downloads/AF-Q5BI50-F1-model_v4.pdb
AF-Q5BI50-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for cullin 4, isoform A (Q5BI50) [more
info...]
Chain information for AF-Q5BI50-F1-model_v4.pdb #6
---
Chain | Description | UniProt
A | cullin 4, isoform A | Q5BI50_DROME 1-821
> view #6 clip false
> color #6 #63d9dbff
> view #1 clip false
> hide #!4 models
> ui mousemode right select
> select #6/A:556
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,94.334,0,1,0,285.57,0,0,1,96.154
> view matrix models #6,1,0,0,102.54,0,1,0,321.48,0,0,1,113.42
> view matrix models
> #6,-0.028823,0.58505,0.81048,80.825,0.49527,-0.69594,0.51998,327.18,0.86826,0.41639,-0.2697,134.8
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models
> #6,-0.028823,0.58505,0.81048,82.054,0.49527,-0.69594,0.51998,321.3,0.86826,0.41639,-0.2697,128.35
> view matrix models
> #6,-0.028823,0.58505,0.81048,117.6,0.49527,-0.69594,0.51998,219.5,0.86826,0.41639,-0.2697,143.52
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models
> #6,-0.028823,0.58505,0.81048,141.53,0.49527,-0.69594,0.51998,198.15,0.86826,0.41639,-0.2697,188.15
> view matrix models
> #6,-0.028823,0.58505,0.81048,149.72,0.49527,-0.69594,0.51998,191.45,0.86826,0.41639,-0.2697,194.67
> view matrix models
> #6,-0.028823,0.58505,0.81048,206.02,0.49527,-0.69594,0.51998,232.55,0.86826,0.41639,-0.2697,211.11
> view matrix models
> #6,-0.028823,0.58505,0.81048,185.13,0.49527,-0.69594,0.51998,264.83,0.86826,0.41639,-0.2697,206.33
> view matrix models
> #6,-0.028823,0.58505,0.81048,186.15,0.49527,-0.69594,0.51998,259.95,0.86826,0.41639,-0.2697,205.3
> fitmap #6 inMap #1
Fit molecule AF-Q5BI50-F1-model_v4.pdb (#6) to map
cryosparc_P341_J252_015_volume_map (1).mrc (#1) using 6629 atoms
average map value = 0.1033, steps = 480
shifted from previous position = 16.5
rotated from previous position = 29.7 degrees
atoms outside contour = 5066, contour level = 0.19164
Position of AF-Q5BI50-F1-model_v4.pdb (#6) relative to
cryosparc_P341_J252_015_volume_map (1).mrc (#1) coordinates:
Matrix rotation and translation
-0.08318899 0.85023909 0.51978176 197.23110747
0.73455839 -0.30015644 0.60854753 260.14227065
0.67342674 0.43243450 -0.59958055 195.18666244
Axis -0.67533976 -0.58918166 -0.44360025
Axis point 0.00000000 45.47638956 30.86147336
Rotation angle (degrees) 172.50795945
Shift along axis -373.05391525
> lighting soft
> transparency #1.1 50
> material transparentCastShadows true
> show #!4 models
> show #!2 models
> show #!3 models
> color #3 #e1b94dff
> color #3 #e1801aff
> save "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs"
——— End of log from Tue Dec 5 13:34:28 2023 ———
opened ChimeraX session
> hide #6 models
> hide #!3 models
> hide #!4 models
> vop max #1 #2
Opened volume maximum as #7, grid size 350,350,350, pixel 1.15, shown at step
1, values float32
> show #!3 models
> show #!4 models
> show #6 models
> lighting soft
> transparency #7.1 50
> material transparentCastShadows true
> open 1R4N
Summary of feedback from opening 1R4N fetched from pdb
---
note | Fetching compressed mmCIF 1r4n from
http://files.rcsb.org/download/1r4n.cif
1r4n title:
APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP [more
info...]
Chain information for 1r4n #8
---
Chain | Description | UniProt
A C E G | amyloid beta precursor protein-binding protein 1 | ULA1_HUMAN 1-534
B D F H | ubiquitin-activating enzyme E1C | UBA3_HUMAN 12-918
I J K L | Ubiquitin-like protein NEDD8 | NEDD8_HUMAN 101-176
Non-standard residues in 1r4n #8
---
ATP — adenosine-5'-triphosphate
ZN — zinc ion
1r4n mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> hide #!3 models
> hide #!4 models
> close #5
> hide #6 models
> hide #!7 models
> view #8 clip false
> hide #!8 atoms
> hide #!8 cartoons
> show #!8 cartoons
> sequence chain #8/I#8/J#8/K#8/L
Alignment identifier is 1
> select #8/A,C,E,G,B,D,F,H
29343 atoms, 29956 bonds, 24 pseudobonds, 3743 residues, 3 models selected
> ~ribbon sel
> select #8/J,K,L
1801 atoms, 1815 bonds, 229 residues, 1 model selected
> ~ribbon sel
> color #8 #d67671ff
> color #8 #d66c5bff
> save "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs"
> close #8
> open 4P5O
Summary of feedback from opening 4P5O fetched from pdb
---
notes | Fetching compressed mmCIF 4p5o from
http://files.rcsb.org/download/4p5o.cif
Fetching CCD AME from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif
4p5o title:
Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-
like protein-substrate intermediate trapped in action [more info...]
Chain information for 4p5o #5
---
Chain | Description | UniProt
A C | Cullin-1 | CUL1_HUMAN 411-776
B D | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 3-108
E F | DCN1-like protein 1 | DCNL1_HUMAN 62-259
G I | NEDD8-conjugating enzyme Ubc12 | UBC12_HUMAN 2-183
H K | NEDD8 | NEDD8_HUMAN 1-76
Non-standard residues in 4p5o #5
---
ZN — zinc ion
4p5o mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> show #!5 target m
> view #5 clip false
> hide #!5 atoms
> show #!5 cartoons
> select #5/A,C,D,E,F,G,I,H
12364 atoms, 12598 bonds, 22 pseudobonds, 1536 residues, 3 models selected
> ~ribbon sel
> color #5 #e97c7cff
> color #5 #e96a61ff
> undo
[Repeated 1 time(s)]
> show #!1 models
> view #5 clip false
> view #1 clip false
> ui mousemode right select
> select #5/K:48
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,18.013,0,1,0,228.62,0,0,1,-4.003
> view matrix models #5,1,0,0,18.011,0,1,0,262.98,0,0,1,-0.45074
> view matrix models #5,1,0,0,37.323,0,1,0,316.24,0,0,1,-1.3664
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models #5,1,0,0,42.283,0,1,0,326.19,0,0,1,-3.2345
> view matrix models
> #5,0.26553,-0.36212,-0.89351,70.619,-0.62293,-0.77179,0.12767,317.11,-0.73583,0.52269,-0.43051,45.171
> view matrix models
> #5,0.2878,0.34684,-0.89267,73.55,-0.68089,-0.58138,-0.44541,335.51,-0.67347,0.736,0.068839,30.72
> view matrix models
> #5,0.2878,0.34684,-0.89267,68.708,-0.68089,-0.58138,-0.44541,318.99,-0.67347,0.736,0.068839,29.566
> view matrix models
> #5,0.2878,0.34684,-0.89267,61.038,-0.68089,-0.58138,-0.44541,299.26,-0.67347,0.736,0.068839,32.86
> view matrix models
> #5,0.2878,0.34684,-0.89267,55.055,-0.68089,-0.58138,-0.44541,265.04,-0.67347,0.736,0.068839,38.542
> view matrix models
> #5,0.2878,0.34684,-0.89267,70.007,-0.68089,-0.58138,-0.44541,197.55,-0.67347,0.736,0.068839,50.193
> view matrix models
> #5,0.2878,0.34684,-0.89267,84.127,-0.68089,-0.58138,-0.44541,154.89,-0.67347,0.736,0.068839,69.012
> view matrix models
> #5,0.2878,0.34684,-0.89267,102.44,-0.68089,-0.58138,-0.44541,126.32,-0.67347,0.736,0.068839,81.219
> view matrix models
> #5,0.2878,0.34684,-0.89267,133.9,-0.68089,-0.58138,-0.44541,95.37,-0.67347,0.736,0.068839,101.64
> view matrix models
> #5,0.2878,0.34684,-0.89267,183.31,-0.68089,-0.58138,-0.44541,73.575,-0.67347,0.736,0.068839,152.21
> view matrix models
> #5,0.2878,0.34684,-0.89267,232.87,-0.68089,-0.58138,-0.44541,72.967,-0.67347,0.736,0.068839,186.74
> view matrix models
> #5,0.2878,0.34684,-0.89267,316.89,-0.68089,-0.58138,-0.44541,115.83,-0.67347,0.736,0.068839,200.22
> view matrix models
> #5,0.2878,0.34684,-0.89267,357.28,-0.68089,-0.58138,-0.44541,159.52,-0.67347,0.736,0.068839,201.19
> view matrix models
> #5,0.2878,0.34684,-0.89267,370.43,-0.68089,-0.58138,-0.44541,232.19,-0.67347,0.736,0.068839,210.08
> view matrix models
> #5,0.2878,0.34684,-0.89267,371.79,-0.68089,-0.58138,-0.44541,267.99,-0.67347,0.736,0.068839,189.6
> view matrix models
> #5,0.2878,0.34684,-0.89267,344.97,-0.68089,-0.58138,-0.44541,314.39,-0.67347,0.736,0.068839,192.11
> view matrix models
> #5,0.2878,0.34684,-0.89267,287.4,-0.68089,-0.58138,-0.44541,341.02,-0.67347,0.736,0.068839,184.35
> view matrix models
> #5,0.2878,0.34684,-0.89267,236.95,-0.68089,-0.58138,-0.44541,334.68,-0.67347,0.736,0.068839,174.53
> view matrix models
> #5,0.2878,0.34684,-0.89267,206.17,-0.68089,-0.58138,-0.44541,287.34,-0.67347,0.736,0.068839,163.68
> view matrix models
> #5,0.2878,0.34684,-0.89267,239.68,-0.68089,-0.58138,-0.44541,261.26,-0.67347,0.736,0.068839,140.04
> view matrix models
> #5,0.2878,0.34684,-0.89267,241.1,-0.68089,-0.58138,-0.44541,265.12,-0.67347,0.736,0.068839,139.34
> view matrix models
> #5,0.2878,0.34684,-0.89267,250.25,-0.68089,-0.58138,-0.44541,262.99,-0.67347,0.736,0.068839,150.61
> fitmap #5 inMap #1
Fit molecule 4p5o (#5) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 13577 atoms
average map value = 0.0952, steps = 428
shifted from previous position = 37.7
rotated from previous position = 58.8 degrees
atoms outside contour = 10994, contour level = 0.19164
Position of 4p5o (#5) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.00644276 0.96416191 -0.26523633 221.13676153
-0.28149644 -0.25626430 -0.92470988 275.86467716
-0.95954064 0.06870540 0.27305919 180.35127462
Axis 0.57158975 0.39948774 -0.71672498
Axis point 276.96975710 123.39516699 0.00000000
Rotation angle (degrees) 119.65814090
Shift along axis 107.34180099
> view matrix models
> #5,-0.0064428,0.96416,-0.26524,261.72,-0.2815,-0.25626,-0.92471,283.8,-0.95954,0.068705,0.27306,147.34
> view matrix models
> #5,-0.0064428,0.96416,-0.26524,257.33,-0.2815,-0.25626,-0.92471,286.39,-0.95954,0.068705,0.27306,151.06
> fitmap #5 inMap #1
Fit molecule 4p5o (#5) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 13577 atoms
average map value = 0.09506, steps = 296
shifted from previous position = 44.9
rotated from previous position = 3.24 degrees
atoms outside contour = 11097, contour level = 0.19164
Position of 4p5o (#5) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
-0.04205567 0.95920398 -0.27956938 223.11519322
-0.32028248 -0.27799300 -0.90561528 277.37957471
-0.94638811 0.05145491 0.31890741 174.29082733
Axis 0.55277518 0.38513460 -0.73899320
Axis point 269.77669300 118.88726501 0.00000000
Rotation angle (degrees) 120.03775994
Shift along axis 101.36127655
> view matrix models
> #5,-0.042056,0.9592,-0.27957,260.25,-0.32028,-0.27799,-0.90562,290.72,-0.94639,0.051455,0.31891,147.16
> view matrix models
> #5,-0.042056,0.9592,-0.27957,249.98,-0.32028,-0.27799,-0.90562,262.91,-0.94639,0.051455,0.31891,154.14
> view matrix models
> #5,0.82946,-0.45179,-0.32846,242.05,-0.53098,-0.45525,-0.71471,257.17,0.17337,0.76722,-0.61751,181.27
> view matrix models
> #5,0.82946,-0.45179,-0.32846,244.93,-0.53098,-0.45525,-0.71471,282.36,0.17337,0.76722,-0.61751,180.46
> fitmap #5 inMap #1
Fit molecule 4p5o (#5) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 13577 atoms
average map value = 0.09448, steps = 408
shifted from previous position = 47
rotated from previous position = 63.3 degrees
atoms outside contour = 11218, contour level = 0.19164
Position of 4p5o (#5) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.85862717 -0.38905943 -0.33375461 210.47937913
-0.11195437 0.49304973 -0.86276775 267.10875531
0.50022555 0.77816112 0.37978899 147.06050762
Axis 0.88153749 -0.44802965 0.14886599
Axis point 0.00000000 75.51777607 310.79787197
Rotation angle (degrees) 68.54730347
Shift along axis 87.76513174
> view matrix models
> #5,0.85863,-0.38906,-0.33375,225.85,-0.11195,0.49305,-0.86277,280.12,0.50023,0.77816,0.37979,126.38
> view matrix models
> #5,0.85863,-0.38906,-0.33375,232.79,-0.11195,0.49305,-0.86277,289.33,0.50023,0.77816,0.37979,125.45
> fitmap #5 inMap #1
Fit molecule 4p5o (#5) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 13577 atoms
average map value = 0.09448, steps = 196
shifted from previous position = 38.2
rotated from previous position = 0.00948 degrees
atoms outside contour = 11219, contour level = 0.19164
Position of 4p5o (#5) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.85858119 -0.38904199 -0.33389320 210.48070280
-0.11203096 0.49316050 -0.86269449 267.11763076
0.50028732 0.77809964 0.37983358 147.07121735
Axis 0.88148547 -0.44814763 0.14881891
Axis point 0.00000000 75.50754609 310.83597322
Rotation angle (degrees) 68.54393657
Shift along axis 87.71452614
> view matrix models
> #5,0.85858,-0.38904,-0.33389,237.26,-0.11203,0.49316,-0.86269,285.41,0.50029,0.7781,0.37983,133.64
> view matrix models
> #5,0.85858,-0.38904,-0.33389,235.29,-0.11203,0.49316,-0.86269,287.29,0.50029,0.7781,0.37983,134.49
> view matrix models
> #5,0.63148,0.34285,-0.69547,250.26,-0.55707,-0.4233,-0.71449,280.58,-0.53935,0.83861,-0.076313,152.56
> fitmap #5 inMap #1
Fit molecule 4p5o (#5) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 13577 atoms
average map value = 0.0815, steps = 316
shifted from previous position = 49.1
rotated from previous position = 33.3 degrees
atoms outside contour = 11304, contour level = 0.19164
Position of 4p5o (#5) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.70754317 0.56423880 -0.42546120 219.74962405
-0.57275851 0.10523263 -0.81294144 279.63250796
-0.41392070 0.81887769 0.39762921 170.77483538
Axis 0.82046246 -0.00580245 -0.57167096
Axis point 0.00000000 -6.44939812 351.65323768
Rotation angle (degrees) 83.96116610
Shift along axis 81.04674874
> view matrix models
> #5,0.70754,0.56424,-0.42546,257.48,-0.57276,0.10523,-0.81294,294.54,-0.41392,0.81888,0.39763,148.29
> view matrix models
> #5,0.70754,0.56424,-0.42546,252.09,-0.57276,0.10523,-0.81294,277.86,-0.41392,0.81888,0.39763,140.44
> view matrix models
> #5,0.70754,0.56424,-0.42546,249.1,-0.57276,0.10523,-0.81294,285.57,-0.41392,0.81888,0.39763,144.44
> view matrix models
> #5,0.70754,0.56424,-0.42546,252.59,-0.57276,0.10523,-0.81294,286.76,-0.41392,0.81888,0.39763,139.5
> transparency #1.1 0
> transparency #1.1 50
> lighting soft
> material transparentCastShadows true
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #6 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> view matrix models
> #5,0.70754,0.56424,-0.42546,251.8,-0.57276,0.10523,-0.81294,281.4,-0.41392,0.81888,0.39763,139.87
> hide #!5 models
> view matrix models
> #5,0.70754,0.56424,-0.42546,246.4,-0.57276,0.10523,-0.81294,273.84,-0.41392,0.81888,0.39763,146.44
> view matrix models
> #5,0.70754,0.56424,-0.42546,243.13,-0.57276,0.10523,-0.81294,271.6,-0.41392,0.81888,0.39763,150.73
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.70754,0.56424,-0.42546,237.04,-0.57276,0.10523,-0.81294,263.87,-0.41392,0.81888,0.39763,158.25
> view matrix models
> #5,0.70754,0.56424,-0.42546,214.96,-0.57276,0.10523,-0.81294,247.51,-0.41392,0.81888,0.39763,187.11
> view matrix models
> #5,0.70754,0.56424,-0.42546,214.94,-0.57276,0.10523,-0.81294,247.52,-0.41392,0.81888,0.39763,187.13
> ui mousemode right select
> select #6/A:309
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.083189,0.85024,0.51978,196.29,0.73456,-0.30016,0.60855,258.3,0.67343,0.43243,-0.59958,196.26
> fitmap #6 inMap #1
Fit molecule AF-Q5BI50-F1-model_v4.pdb (#6) to map
cryosparc_P341_J252_015_volume_map (1).mrc (#1) using 6629 atoms
average map value = 0.1033, steps = 68
shifted from previous position = 2.34
rotated from previous position = 0.0229 degrees
atoms outside contour = 5065, contour level = 0.19164
Position of AF-Q5BI50-F1-model_v4.pdb (#6) relative to
cryosparc_P341_J252_015_volume_map (1).mrc (#1) coordinates:
Matrix rotation and translation
-0.08346241 0.85034578 0.51956335 197.24268693
0.73463593 -0.29977604 0.60864142 260.14713638
0.67330831 0.43248858 -0.59967453 195.19511208
Axis -0.67523679 -0.58934193 -0.44354410
Axis point 0.00000000 45.43890262 30.86254679
Rotation angle (degrees) 172.50510647
Shift along axis -373.07877399
> hide #6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #6,-0.083462,0.85035,0.51956,219.19,0.73464,-0.29978,0.60864,287.38,0.67331,0.43249,-0.59967,168.02
> view matrix models
> #6,-0.083462,0.85035,0.51956,222.88,0.73464,-0.29978,0.60864,304.97,0.67331,0.43249,-0.59967,154.96
> ui mousemode right select
> select #5/K:13
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.70754,0.56424,-0.42546,235.61,-0.57276,0.10523,-0.81294,279.85,-0.41392,0.81888,0.39763,134.17
> view matrix models
> #5,0.70754,0.56424,-0.42546,235.93,-0.57276,0.10523,-0.81294,281.1,-0.41392,0.81888,0.39763,133.38
> show #6 models
> hide #6 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #6 models
> hide #!2 models
> hide #!3 models
> hide #!5 models
> ui mousemode right select
> select #6/A:365
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.083462,0.85035,0.51956,195.5,0.73464,-0.29978,0.60864,260.38,0.67331,0.43249,-0.59967,210.05
> fitmap #6 inMap #1
Fit molecule AF-Q5BI50-F1-model_v4.pdb (#6) to map
cryosparc_P341_J252_015_volume_map (1).mrc (#1) using 6629 atoms
average map value = 0.1044, steps = 428
shifted from previous position = 13.5
rotated from previous position = 14 degrees
atoms outside contour = 5066, contour level = 0.19164
Position of AF-Q5BI50-F1-model_v4.pdb (#6) relative to
cryosparc_P341_J252_015_volume_map (1).mrc (#1) coordinates:
Matrix rotation and translation
-0.25284933 0.90084702 0.35290488 195.32210035
0.70444568 -0.07861191 0.70539099 259.70041982
0.66319190 0.42695996 -0.61472083 196.81075461
Axis -0.60417892 -0.67330454 -0.42617933
Axis point -22.00166890 0.00000000 13.41350797
Rotation angle (degrees) 166.67814060
Shift along axis -376.74364442
> show #!5 models
> show #!2 models
> show #!3 models
> show #!7 models
> hide #!1 models
> hide #!2 models
> hide #!7 models
> show #!7 models
> save "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs"
> open 2AWF
Summary of feedback from opening 2AWF fetched from pdb
---
note | Fetching compressed mmCIF 2awf from
http://files.rcsb.org/download/2awf.cif
2awf title:
Structure of human Ubiquitin-conjugating enzyme E2 G1 [more info...]
Chain information for 2awf #8
---
Chain | Description | UniProt
A | Ubiquitin-conjugating enzyme E2 G1 | UB2G1_HUMAN 8-160
> hide #!7 models
> hide #6 models
> hide #!5 models
> hide #!3 models
> show #!1 models
> view #8 clip false
> color #8 #fa9e2dff
> color #8 #fa7927ff
> color #8 #fa9c10ff
> color #8 #fa10f6ff
> color #8 #2dfaf6ff
> color #8 #3cfa49ff
> color #8 #cbfa76ff
> color #8 #e5fab1ff
> color #8 #efc4faff
> color #8 #5d4c62ff
> ui mousemode right select
> select #8/A:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,33.034,0,1,0,229.98,0,0,1,114.03
> view matrix models #8,1,0,0,34.086,0,1,0,239.33,0,0,1,126.86
> view matrix models #8,1,0,0,42.602,0,1,0,259.64,0,0,1,121.45
> view matrix models #8,1,0,0,67.743,0,1,0,190.49,0,0,1,116.2
> view matrix models #8,1,0,0,135.18,0,1,0,139.58,0,0,1,109.45
> view matrix models #8,1,0,0,189.85,0,1,0,131.06,0,0,1,125.52
> view matrix models #8,1,0,0,215.26,0,1,0,139.17,0,0,1,131.53
> view matrix models #8,1,0,0,234.61,0,1,0,158.55,0,0,1,133.29
> view matrix models #8,1,0,0,247.35,0,1,0,180.84,0,0,1,130.25
> view matrix models #8,1,0,0,235.95,0,1,0,212.01,0,0,1,130.36
> view matrix models #8,1,0,0,218.16,0,1,0,196.05,0,0,1,131.56
> view matrix models #8,1,0,0,216.33,0,1,0,209.08,0,0,1,130.07
> view matrix models #8,1,0,0,207.74,0,1,0,213.72,0,0,1,126.7
> fitmap #8 inMap #1
Fit molecule 2awf (#8) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 1031 atoms
average map value = 0.1446, steps = 188
shifted from previous position = 7.34
rotated from previous position = 50.3 degrees
atoms outside contour = 731, contour level = 0.19164
Position of 2awf (#8) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.85011555 0.04752861 -0.52444693 217.02475173
-0.37062928 0.76148129 -0.53177080 228.95045664
0.37408219 0.64644201 0.66496258 114.09882740
Axis 0.76526753 -0.58360862 -0.27160005
Axis point 0.00000000 38.01985309 415.10929182
Rotation angle (degrees) 50.33633893
Shift along axis 1.47528694
> view matrix models
> #8,0.85012,0.047529,-0.52445,215.05,-0.37063,0.76148,-0.53177,222.31,0.37408,0.64644,0.66496,115.33
> view matrix models
> #8,0.85012,0.047529,-0.52445,214.98,-0.37063,0.76148,-0.53177,222.41,0.37408,0.64644,0.66496,115.43
> fitmap #8 inMap #1
Fit molecule 2awf (#8) to map cryosparc_P341_J252_015_volume_map (1).mrc (#1)
using 1031 atoms
average map value = 0.1446, steps = 76
shifted from previous position = 6.97
rotated from previous position = 0.177 degrees
atoms outside contour = 733, contour level = 0.19164
Position of 2awf (#8) relative to cryosparc_P341_J252_015_volume_map (1).mrc
(#1) coordinates:
Matrix rotation and translation
0.85005222 0.04778150 -0.52452659 217.03962838
-0.37199961 0.75947351 -0.53368182 229.00201489
0.37286393 0.64878110 0.66336684 114.07794994
Axis 0.76651801 -0.58172311 -0.27211828
Axis point -0.00000000 38.18931613 414.18268976
Rotation angle (degrees) 50.47266433
Shift along axis 2.10632428
> show #!2 models
> show #!3 models
> show #6 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> show #!4 models
> show #!7 models
> hide #!7 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #6 models
> hide #!5 models
> hide #!3 models
> hide #!4 models
> lighting soft
> transparency #1.1 0
> transparency #1.1 50
> material transparentCastShadows true
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!1 models
> hide #!2 models
> show #6 models
> hide #!7 models
> color #6 #e17976ff
> show #!7 models
> hide #!7 models
> save "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs"
> save "/Users/zrizvi/Desktop/atomic model fitting on cryo em map.png" width
> 799 height 624 supersample 3
> show #!7 models
> save "/Users/zrizvi/Desktop/atomic model fitting on cryo em map after
> volmax.png" width 799 height 624 supersample 3
> hide #!7 models
> show #!1 models
> show #!2 models
> save "/Users/zrizvi/Desktop/atomic model fitting on cryo em map on real
> ones.png" width 799 height 624 supersample 3
> hide #!1 models
> hide #!2 models
> show #!7 models
> save "/Users/zrizvi/Desktop/atomic model fitting on cryo em map after volmax
> substrate missing view.png" width 799 height 624 supersample 3
> save "/Users/zrizvi/Desktop/cullin c term messed up view.png" width 799
> height 624 supersample 3
> hide #!3 models
> hide #!5 models
> hide #6 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> volume #!7 style image
[Repeated 1 time(s)]
> hide #!7 models
> show #!7 models
> undo
[Repeated 5 time(s)]
> hide #6 models
> hide #!7 models
> hide #!8 models
> color #7 #acacacff models
> color #7 #afafafff models
> show #!7 models
> volume #!7 style surface
> volume #!7 style mesh
> volume #!7 showOutlineBox true
> volume #!7 style surface
> show #!8 models
> show #6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!3 models
> transparency #7.1 50
> hide #!3 models
> hide #!5 models
> hide #6 models
> hide #!8 models
> volume #!7 style surface
[Repeated 1 time(s)]
> transparency #7.1 0
> save "/Users/zrizvi/Desktop/volmax map.png" width 799 height 624 supersample
> 3
> show #!8 models
> show #6 models
> show #!5 models
> show #!3 models
> volume #!7 showOutlineBox false
> movie record
> turn y 1 360
> movie record
Already recording a movie
> stop
> movie record
Already recording a movie
> movie record
Already recording a movie
> movie record
Already recording a movie
> save "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs"
——— End of log from Tue Dec 5 16:02:00 2023 ———
opened ChimeraX session
> hide #!7 models
> save "/Users/zrizvi/Desktop/atomic fit .png" width 864 height 624
> supersample 3
> open "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs" format session
No such file/path: /Users/zrizvi/Desktop/crl4 atomic fitting.cxs
> open "/Users/zrizvi/Desktop/crl4 atomic fitting.cxs" format session
No such file/path: /Users/zrizvi/Desktop/crl4 atomic fitting.cxs
> show #!7 models
> transparency #7.1 50
> hide #!7 models
> hide #!8 models
> hide #!5 models
> hide #!3 models
> select add #6
6638 atoms, 6747 bonds, 822 residues, 2 models selected
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!7 models
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.78633,-0.4087,0.4633,206.07,0.0048413,0.75397,0.65689,252.41,-0.61779,-0.51429,0.59485,180.58,#8,-0.65939,0.71436,-0.23428,164.14,0.59245,0.30192,-0.74689,266.17,-0.46282,-0.63129,-0.62231,260.02
> view matrix models
> #6,0.61111,-0.5303,0.58765,204.56,0.1231,0.79705,0.59124,253.42,-0.78192,-0.28897,0.55236,179.19,#8,-0.759,0.53481,-0.37135,183.2,0.61897,0.41576,-0.66634,254.49,-0.20197,-0.73561,-0.64659,267.52
> view matrix models
> #6,-0.11464,-0.85111,-0.51232,227.05,0.29037,-0.5219,0.80206,261.2,-0.95002,-0.056811,0.30697,181.55,#8,-0.68763,-0.40964,0.59947,228.92,-0.7184,0.26424,-0.64349,273.92,0.1052,-0.87314,-0.47598,271.51
> view matrix models
> #6,-0.38439,0.44197,-0.8105,221,-0.33994,-0.88402,-0.32085,284.6,-0.8583,0.15219,0.49005,176.41,#8,0.66534,-0.37596,0.64496,216.74,-0.70397,-0.60352,0.37442,312.44,0.24848,-0.70315,-0.66621,262.81
> view matrix models
> #6,-0.21179,0.92277,-0.32194,207.86,-0.60518,-0.38248,-0.69819,286.96,-0.7674,0.046964,0.63945,174.64,#8,0.99085,-0.01114,0.13447,201.04,-0.092162,-0.78379,0.61415,315.94,0.098558,-0.62093,-0.77765,260.5
> view matrix models
> #6,-0.30204,0.69718,-0.65016,215.88,-0.49179,-0.69821,-0.52024,286.52,-0.81665,0.16261,0.55375,175.18,#8,0.85923,-0.20637,0.46813,207.36,-0.45357,-0.73054,0.51047,316.98,0.23664,-0.65094,-0.7213,260.37
> view matrix models
> #6,-0.30204,0.69718,-0.65016,195.5,-0.49179,-0.69821,-0.52024,254.24,-0.81665,0.16261,0.55375,179.53,#8,0.85923,-0.20637,0.46813,186.99,-0.45357,-0.73054,0.51047,284.7,0.23664,-0.65094,-0.7213,264.73
> view matrix models
> #6,-0.30204,0.69718,-0.65016,198.09,-0.49179,-0.69821,-0.52024,258.17,-0.81665,0.16261,0.55375,178.61,#8,0.85923,-0.20637,0.46813,189.58,-0.45357,-0.73054,0.51047,288.63,0.23664,-0.65094,-0.7213,263.81
> view matrix models
> #6,-0.31625,0.65402,-0.6872,199.14,-0.4433,-0.74231,-0.50246,258.29,-0.83874,0.14573,0.52468,179.28,#8,0.8284,-0.23685,0.5076,191,-0.51021,-0.69306,0.50927,286.01,0.23118,-0.68086,-0.69497,265.44
> view matrix models
> #6,-0.31625,0.65402,-0.6872,199.85,-0.4433,-0.74231,-0.50246,258.59,-0.83874,0.14573,0.52468,180.76,#8,0.8284,-0.23685,0.5076,191.72,-0.51021,-0.69306,0.50927,286.32,0.23118,-0.68086,-0.69497,266.92
> fitmap #6 inMap #7
Fit molecule AF-Q5BI50-F1-model_v4.pdb (#6) to map volume maximum (#7) using
6629 atoms
average map value = 0.1771, steps = 216
shifted from previous position = 5.26
rotated from previous position = 29.1 degrees
atoms outside contour = 3876, contour level = 0.19164
Position of AF-Q5BI50-F1-model_v4.pdb (#6) relative to volume maximum (#7)
coordinates:
Matrix rotation and translation
0.01270629 0.91101470 -0.41217807 200.27021041
-0.55931010 -0.33521814 -0.75815632 256.24864835
-0.82886113 0.24016871 0.50528034 183.88299848
Axis 0.54690365 0.22826782 -0.80547514
Axis point 263.80055245 78.00810165 0.00000000
Rotation angle (degrees) 114.11790851
Shift along axis 19.90864596
> volume #7 change image level -0.003992,0 level 0.05719,0.8 level 1.816,1
> volume #7 level 0.104
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #7 level 0.3293
> view matrix models
> #6,0.012706,0.91101,-0.41218,195.62,-0.55931,-0.33522,-0.75816,265.52,-0.82886,0.24017,0.50528,192.73,#8,0.8284,-0.23685,0.5076,187.06,-0.51021,-0.69306,0.50927,295.58,0.23118,-0.68086,-0.69497,275.77
> undo
> select clear
> show #!5 models
> show #!8 models
> select add #8
1031 atoms, 1006 bonds, 1 pseudobond, 175 residues, 2 models selected
> view matrix models
> #8,0.8284,-0.23685,0.5076,202.03,-0.51021,-0.69306,0.50927,271.66,0.23118,-0.68086,-0.69497,225.7
> view matrix models
> #8,0.8284,-0.23685,0.5076,219.12,-0.51021,-0.69306,0.50927,245.48,0.23118,-0.68086,-0.69497,155.97
> volume #7 level 0.225
> volume #7 level 0.1833
> open 6ttu
Summary of feedback from opening 6ttu fetched from pdb
---
note | Fetching compressed mmCIF 6ttu from
http://files.rcsb.org/download/6ttu.cif
6ttu title:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]
Chain information for 6ttu #9
---
Chain | Description | UniProt
C | Cullin-1 | CUL1_HUMAN 1-776
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |
N | NEDD8 | NEDD8_HUMAN 1-76
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108
S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605
U | Polyubiquitin-C | UBC_HUMAN 1-76
Non-standard residues in 6ttu #9
---
ZN — zinc ion
> view #9 clip false
> hide sel atoms
[Repeated 1 time(s)]
> select subtract #8
Nothing selected
> hide #6#!4-5,8-9 atoms
> show #6#!4-5,8-9 cartoons
> hide #!4 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> matchmaker #9 to #6
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 AF-Q5BI50-F1-model_v4.pdb, chain A (#6) with 6ttu, chain C (#9),
sequence alignment score = 1298.3
RMSD between 187 pruned atom pairs is 1.126 angstroms; (across all 668 pairs:
16.441)
> hide #!8 models
> hide #6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> show #!4 models
> matchmaker #4 to #6
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 AF-Q5BI50-F1-model_v4.pdb, chain A (#6) with 1ldk, chain B (#4),
sequence alignment score = 617.8
RMSD between 189 pruned atom pairs is 1.192 angstroms; (across all 355 pairs:
4.748)
> hide #!4 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #6 models
> delete #4/D
> delete #4/E
> delete #4/A
> delete #4/B
> combine #6/A:545-1000
> hide #10 models
> show #10 models
> hide #6 models
> hide #10 models
> show #10 models
> show #6 models
> hide #6 models
> delete #6/A:545-1000
> hide #10 models
> show #6 models
> show #!5 models
> hide #!5 models
> show #10 models
> delete #10/A:1-544
> hide #6 models
> show #6 models
> hide #10 models
> show #10 models
> select add #6
4363 atoms, 4430 bonds, 544 residues, 1 model selected
> select add #4
5097 atoms, 5183 bonds, 13 pseudobonds, 635 residues, 3 models selected
> select subtract #6
734 atoms, 753 bonds, 13 pseudobonds, 91 residues, 2 models selected
> select add #10
3000 atoms, 3061 bonds, 13 pseudobonds, 368 residues, 3 models selected
> select #10/A:1-732
1510 atoms, 1542 bonds, 188 residues, 1 model selected
> select #10/A:1-732 #4
2244 atoms, 2295 bonds, 13 pseudobonds, 279 residues, 3 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.
> fitmap sel inMap #7
Fit molecules 1ldk (#4), copy of AF-Q5BI50-F1-model_v4.pdb (#10) to map volume
maximum (#7) using 2244 atoms
average map value = 0.1694, steps = 252
shifted from previous position = 7.74
rotated from previous position = 19.4 degrees
atoms outside contour = 1357, contour level = 0.18329
Position of 1ldk (#4) relative to volume maximum (#7) coordinates:
Matrix rotation and translation
0.00439861 -0.94871265 0.31610909 168.21113536
-0.83798279 0.16900043 0.51886771 252.79041527
-0.54567893 -0.26717627 -0.79426151 303.37554105
Axis -0.67087629 0.73552265 0.09450621
Axis point 264.01028708 0.00000000 83.42942322
Rotation angle (degrees) 144.13808607
Shift along axis 101.75508655
Position of copy of AF-Q5BI50-F1-model_v4.pdb (#10) relative to volume maximum
(#7) coordinates:
Matrix rotation and translation
0.29562230 0.86613133 -0.40301857 199.10297676
-0.66720207 -0.11473624 -0.73598709 256.30742903
-0.68370232 0.48646902 0.54396602 178.15559397
Axis 0.61709571 0.14168912 -0.77402653
Axis point 313.03344956 39.86153268 0.00000000
Rotation angle (degrees) 97.90748575
Shift along axis 21.28441186
> select subtract #4
1510 atoms, 1542 bonds, 188 residues, 1 model selected
> fitmap sel inMap #7
Fit molecule copy of AF-Q5BI50-F1-model_v4.pdb (#10) to map volume maximum
(#7) using 1510 atoms
average map value = 0.1808, steps = 124
shifted from previous position = 1.38
rotated from previous position = 10.8 degrees
atoms outside contour = 827, contour level = 0.18329
Position of copy of AF-Q5BI50-F1-model_v4.pdb (#10) relative to volume maximum
(#7) coordinates:
Matrix rotation and translation
0.27731171 0.81064561 -0.51570525 196.97811122
-0.59816509 -0.27437043 -0.75294049 255.73648764
-0.75186218 0.51727610 0.40881377 174.48301504
Axis 0.66450066 0.12354305 -0.73700474
Axis point 303.18559714 55.08159617 0.00000000
Rotation angle (degrees) 107.10492430
Shift along axis 33.89174284
> select add #10
2266 atoms, 2308 bonds, 277 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #4
734 atoms, 753 bonds, 13 pseudobonds, 91 residues, 2 models selected
> view matrix models
> #4,0.0043986,-0.94871,0.31611,182.08,-0.83798,0.169,0.51887,261.04,-0.54568,-0.26718,-0.79426,307.07
> view matrix models
> #4,0.0043986,-0.94871,0.31611,182.98,-0.83798,0.169,0.51887,256.58,-0.54568,-0.26718,-0.79426,304.75
> view matrix models
> #4,-0.0032882,-0.95549,0.29501,186.85,-0.86391,0.15129,0.48038,264.67,-0.50363,-0.25329,-0.82596,305.89
> view matrix models
> #4,-0.064794,-0.57271,-0.8172,362.04,-0.58438,-0.64203,0.49628,236.03,-0.80889,0.50971,-0.29308,253.35
> view matrix models
> #4,-0.20571,-0.22722,-0.95187,395.61,-0.70831,-0.63659,0.30504,276,-0.67527,0.73696,-0.029986,202.08
> view matrix models
> #4,-0.80072,-0.33947,-0.49356,378.11,-0.28055,-0.51547,0.80968,161.93,-0.52928,0.7868,0.31752,136.53
> view matrix models
> #4,-0.80072,-0.33947,-0.49356,369.14,-0.28055,-0.51547,0.80968,161.88,-0.52928,0.7868,0.31752,147.66
> view matrix models
> #4,-0.70451,-0.56061,-0.43518,351.35,-0.11544,-0.51451,0.84968,141.28,-0.70024,0.64884,0.29776,165.43
> view matrix models
> #4,-0.70451,-0.56061,-0.43518,358.01,-0.11544,-0.51451,0.84968,138.25,-0.70024,0.64884,0.29776,163.26
> view matrix models
> #4,-0.70451,-0.56061,-0.43518,356.3,-0.11544,-0.51451,0.84968,142.35,-0.70024,0.64884,0.29776,165.74
> view matrix models
> #4,-0.70451,-0.56061,-0.43518,357.56,-0.11544,-0.51451,0.84968,140.03,-0.70024,0.64884,0.29776,164.32
> view matrix models
> #4,-0.71292,-0.5552,-0.42836,357.28,-0.092422,-0.53114,0.84223,139.1,-0.69512,0.64003,0.32735,159.35
> view matrix models
> #4,-0.71292,-0.5552,-0.42836,358.15,-0.092422,-0.53114,0.84223,137.98,-0.69512,0.64003,0.32735,158.65
> show #!9 models
> hide #!4 models
> hide #6 models
> show #6 models
> hide #6 models
> matchmaker #9 to #10
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 copy of AF-Q5BI50-F1-model_v4.pdb, chain A (#10) with 6ttu, chain C
(#9), sequence alignment score = 740.4
RMSD between 122 pruned atom pairs is 1.376 angstroms; (across all 248 pairs:
14.020)
> matchmaker #4 to #9
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 6ttu, chain R (#9) with 1ldk, chain C (#4), sequence alignment
score = 372.9
RMSD between 18 pruned atom pairs is 1.044 angstroms; (across all 79 pairs:
11.369)
> show #!4 models
> hide #!9 models
> show #!9 models
> matchmaker #4 to #9/R
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 6ttu, chain R (#9) with 1ldk, chain C (#4), sequence alignment
score = 372.9
RMSD between 18 pruned atom pairs is 1.044 angstroms; (across all 79 pairs:
11.369)
> hide #!4 models
> hide #!9 models
> show #!9 models
> matchmaker #4 to #9/C
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 6ttu, chain C (#9) with 1ldk, chain C (#4), sequence alignment
score = 16.2
RMSD between 4 pruned atom pairs is 1.100 angstroms; (across all 63 pairs:
23.019)
> delete #9/C
> fitmap #7/R
Missing required "in_map" argument
> fitmap #9/R
Missing required "in_map" argument
> fitmap #9/R inMap #7
Fit molecule 6ttu (#9) to map volume maximum (#7) using 669 atoms
average map value = 0.1693, steps = 176
shifted from previous position = 6.32
rotated from previous position = 21.9 degrees
atoms outside contour = 422, contour level = 0.18329
Position of 6ttu (#9) relative to volume maximum (#7) coordinates:
Matrix rotation and translation
-0.34309411 0.71257609 -0.61198181 224.16534564
-0.85065663 -0.51201294 -0.11927298 492.28853921
-0.39833368 0.47966453 0.78182621 12.78412980
Axis 0.35490026 -0.12659714 -0.92629313
Axis point 260.65387243 179.39279465 0.00000000
Rotation angle (degrees) 122.45522933
Shift along axis 5.39216553
> undo
> show #!9 models
> show #6 models
> delete #9/T
> delete #9/S
> volume #7 level 0.2626
> save "/Users/zrizvi/Desktop/NEW map fitting.cxs"
——— End of log from Thu Dec 7 10:40:16 2023 ———
opened ChimeraX session
> show #!3 models
> select subtract #4
Nothing selected
> show #!4 models
> hide #!4 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #!9 models
> show #!9 models
> open /Users/zrizvi/Downloads/AF-Q13619-F1-model_v4.pdb
AF-Q13619-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for cullin-4A (Q13619) [more info...]
Chain information for AF-Q13619-F1-model_v4.pdb #11
---
Chain | Description | UniProt
A | cullin-4A | CUL4A_HUMAN 1-759
> hide #6 models
> close #6
> color #11 #a5866bff
> color #11 #a57768ff
> view #11 clip false
> ui mousemode right select
> select #11/A:244
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,18.067,0,1,0,241.82,0,0,1,152.61
> view matrix models #11,1,0,0,30.181,0,1,0,294.94,0,0,1,156.71
> view matrix models #11,1,0,0,43.565,0,1,0,314.61,0,0,1,126.1
> view matrix models
> #11,0.85164,-0.013206,0.52397,50.779,-0.51976,-0.15019,0.84101,350.15,0.067589,-0.98857,-0.13477,132.06
> view matrix models
> #11,0.58928,-0.70311,0.39798,64.247,-0.50113,0.068293,0.86267,345.92,-0.63373,-0.7078,-0.31211,126.97
> view matrix models
> #11,-0.45893,-0.86058,0.22087,69.392,-0.2259,0.35345,0.90777,339.61,-0.85927,0.36671,-0.35661,105.56
> view matrix models
> #11,-0.45893,-0.86058,0.22087,53.627,-0.2259,0.35345,0.90777,335.63,-0.85927,0.36671,-0.35661,158.91
> view matrix models
> #11,-0.83111,-0.55542,0.02761,46.559,-0.50451,0.73217,-0.4576,312.47,0.23395,-0.39425,-0.88873,163.57
> view matrix models
> #11,-0.75869,-0.28682,0.58492,47.606,-0.63757,0.51129,-0.57627,316.02,-0.13378,-0.81013,-0.57077,177.3
> view matrix models
> #11,-0.39502,-0.87858,-0.26845,47.796,-0.78967,0.47405,-0.38949,319.64,0.46946,0.058134,-0.88104,153.58
> view matrix models
> #11,-0.39502,-0.87858,-0.26845,47.726,-0.78967,0.47405,-0.38949,298.67,0.46946,0.058134,-0.88104,134.95
> hide #!9 models
> hide #10 models
> view matrix models
> #11,-0.39502,-0.87858,-0.26845,50.763,-0.78967,0.47405,-0.38949,289.98,0.46946,0.058134,-0.88104,130.75
> view matrix models
> #11,-0.39502,-0.87858,-0.26845,59.675,-0.78967,0.47405,-0.38949,256.6,0.46946,0.058134,-0.88104,126.34
> view matrix models
> #11,0.34852,0.030145,0.93682,53.002,0.40142,-0.90798,-0.12012,283.19,0.84699,0.41792,-0.32855,124.29
> view matrix models
> #11,0.34852,0.030145,0.93682,63.981,0.40142,-0.90798,-0.12012,219.9,0.84699,0.41792,-0.32855,141.18
> view matrix models
> #11,0.34852,0.030145,0.93682,63.631,0.40142,-0.90798,-0.12012,222.84,0.84699,0.41792,-0.32855,139.72
> hide #!7 models
> hide #!3 models
> show #!7 models
> view matrix models
> #11,0.34852,0.030145,0.93682,63.092,0.40142,-0.90798,-0.12012,222.25,0.84699,0.41792,-0.32855,142.62
> view matrix models
> #11,0.34852,0.030145,0.93682,113.24,0.40142,-0.90798,-0.12012,178.11,0.84699,0.41792,-0.32855,169.37
> view matrix models
> #11,0.34852,0.030145,0.93682,95.249,0.40142,-0.90798,-0.12012,232.96,0.84699,0.41792,-0.32855,170.58
> view matrix models
> #11,0.34852,0.030145,0.93682,102.71,0.40142,-0.90798,-0.12012,263.44,0.84699,0.41792,-0.32855,158.96
> view matrix models
> #11,0.36331,0.52986,0.76633,90.457,0.57907,-0.77278,0.25979,264.62,0.72986,0.34937,-0.58758,157.66
> view matrix models
> #11,0.36331,0.52986,0.76633,119.51,0.57907,-0.77278,0.25979,214.24,0.72986,0.34937,-0.58758,164.53
> view matrix models
> #11,0.36331,0.52986,0.76633,181.14,0.57907,-0.77278,0.25979,211.69,0.72986,0.34937,-0.58758,181.53
> view matrix models
> #11,0.36331,0.52986,0.76633,168.79,0.57907,-0.77278,0.25979,240.17,0.72986,0.34937,-0.58758,167.48
> view matrix models
> #11,0.36331,0.52986,0.76633,189.73,0.57907,-0.77278,0.25979,264.57,0.72986,0.34937,-0.58758,161.46
> view matrix models
> #11,0.36331,0.52986,0.76633,190.02,0.57907,-0.77278,0.25979,254.25,0.72986,0.34937,-0.58758,166.67
> fitmap #11 inMap #7
Fit molecule AF-Q13619-F1-model_v4.pdb (#11) to map volume maximum (#7) using
6161 atoms
average map value = 0.1897, steps = 192
shifted from previous position = 19.1
rotated from previous position = 18.3 degrees
atoms outside contour = 4705, contour level = 0.26258
Position of AF-Q13619-F1-model_v4.pdb (#11) relative to volume maximum (#7)
coordinates:
Matrix rotation and translation
0.32423324 0.64604553 0.69101234 200.51253108
0.39930083 -0.75567714 0.51914448 256.74075990
0.85757317 0.10759790 -0.50298214 183.32397273
Axis -0.81023775 -0.32791882 -0.48578188
Axis point 0.00000000 89.40744523 19.86913792
Rotation angle (degrees) 165.28764296
Shift along axis -335.70841430
> select up
181 atoms, 182 bonds, 22 residues, 1 model selected
> select up
6161 atoms, 6274 bonds, 759 residues, 1 model selected
> select up
38039 atoms, 38725 bonds, 4923 residues, 13 models selected
> select down
6161 atoms, 6274 bonds, 759 residues, 1 model selected
> select down
181 atoms, 182 bonds, 22 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> combine #11/A:545-1000
[Repeated 1 time(s)]
> hide #12 models
> show #12 models
> hide #11 models
> hide #12 models
> show #11 models
> hide #11 models
> show #12 models
> hide #6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color #3 #dc93d3ff
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> color #12 #2eaea0ff
> hide #!9 models
> show #!9 models
> open 6ttu
6ttu title:
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]
Chain information for 6ttu #13
---
Chain | Description | UniProt
C | Cullin-1 | CUL1_HUMAN 1-776
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |
N | NEDD8 | NEDD8_HUMAN 1-76
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108
S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605
U | Polyubiquitin-C | UBC_HUMAN 1-76
Non-standard residues in 6ttu #13
---
ZN — zinc ion
> select #13/D:2-147
1135 atoms, 1171 bonds, 146 residues, 1 model selected
> sequence chain #13/N
Alignment identifier is 13/N
> select #13/N:0-76
605 atoms, 610 bonds, 77 residues, 1 model selected
> select #13/R:19-104
666 atoms, 685 bonds, 1 pseudobond, 79 residues, 2 models selected
> select #13/U:1-75
575 atoms, 581 bonds, 75 residues, 1 model selected
> select #13/T:179-583
3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected
> select #13/D:2-147
1135 atoms, 1171 bonds, 146 residues, 1 model selected
> select #13/I:20-33
58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected
> select #13/I:20-33
58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected
> select #13/I:20-33
58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected
> hide #!13 models
> select add #13
12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected
> select subtract #13
Nothing selected
> set bgColor black
> hide #!9 models
> show #!9 models
> delete #9/I
> delete #9/U
> view #7 clip false
> volume #7 level 0.2099
> set bgColor white
> hide #!9 models
> hide #!3 models
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #12/A:701
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.32423,0.64605,0.69101,203.36,0.3993,-0.75568,0.51914,258.42,0.85757,0.1076,-0.50298,180.44
> fitmap #12 inMap #7
Fit molecule copy of AF-Q13619-F1-model_v4.pdb (#12) to map volume maximum
(#7) using 6161 atoms
average map value = 0.1897, steps = 80
shifted from previous position = 4.39
rotated from previous position = 0.0049 degrees
atoms outside contour = 3735, contour level = 0.20989
Position of copy of AF-Q13619-F1-model_v4.pdb (#12) relative to volume maximum
(#7) coordinates:
Matrix rotation and translation
0.32424934 0.64605591 0.69099508 200.51126430
0.39923430 -0.75567920 0.51919264 256.73901318
0.85759805 0.10752106 -0.50295614 183.32435295
Axis -0.81024064 -0.32790338 -0.48578748
Axis point 0.00000000 89.40940580 19.86527274
Rotation angle (degrees) 165.28312725
Shift along axis -335.70464085
> show #12/I687 as cartoon
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui mousemode right select
> select #12/A:688
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #12/A:687
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show #12/I687
Alignment identifier is 12/A
> select #12/A:700
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:700-705
51 atoms, 50 bonds, 6 residues, 1 model selected
> undo
[Repeated 9 time(s)]
> select #12/A:700
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:700-705
51 atoms, 50 bonds, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> color sel blue
> color sel byelement
> select clear
> undo
[Repeated 5 time(s)]Alignment identifier is 12/A
> select #12/A:700
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #12/A:700-705
51 atoms, 50 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> show #!3 models
> show #!9 models
> hide #!3 models
> hide #12 models
> select #9/D:140
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> fitmap #9 inMap #7
Fit molecule 6ttu (#9) to map volume maximum (#7) using 2409 atoms
average map value = 0.1513, steps = 220
shifted from previous position = 30.2
rotated from previous position = 17.3 degrees
atoms outside contour = 1846, contour level = 0.20989
Position of 6ttu (#9) relative to volume maximum (#7) coordinates:
Matrix rotation and translation
-0.33169654 0.84376958 -0.42193636 192.71969307
-0.80499516 -0.48635680 -0.33976442 530.76236045
-0.49189450 0.22695804 0.84055330 75.10029806
Axis 0.32479766 0.04009412 -0.94493330
Axis point 273.68539648 208.51608660 0.00000000
Rotation angle (degrees) 119.25845741
Shift along axis 12.91058388
> undo
[Repeated 3 time(s)]
> redo
[Repeated 3 time(s)]
> hide #!3 models
> hide #12 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.3317,0.84377,-0.42194,187.88,-0.805,-0.48636,-0.33976,509.85,-0.49189,0.22696,0.84055,60.669
> show #12 models
> view matrix models
> #9,-0.3317,0.84377,-0.42194,184.47,-0.805,-0.48636,-0.33976,509.18,-0.49189,0.22696,0.84055,66.438
> show #!3 models
> save "/Users/zrizvi/Desktop/atomic model fit with Gabe.png" width 864 height
> 624 supersample 3
> save "/Users/zrizvi/Desktop/atomic model fit with Gabe.cxs"
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> hide #!9 models
> show #!9 models
> delete #9/D
> show #!8 models
> save "/Users/zrizvi/Desktop/Nedd8 fit eith alphafold cul4A.png" width 864
> height 624 supersample 3
> save "/Users/zrizvi/Desktop/E2 with Rbx1 fit.png" width 864 height 624
> supersample 3
> save "/Users/zrizvi/Desktop/with ube2G1.png" width 864 height 624
> supersample 3
> save "/Users/zrizvi/Desktop/missing substarte density.png" width 864 height
> 624 supersample 3
> save "/Users/zrizvi/Desktop/with ube2G1.png" width 864 height 624
> supersample 3
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> open /Users/zrizvi/Downloads/cryosparc_P341_J270_class_00_00122_volume.mrc
Opened cryosparc_P341_J270_class_00_00122_volume.mrc as #14, grid size
128,128,128, pixel 2.7, shown at level 0.359, step 1, values float32
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!3 models
> hide #12 models
> view #14 clip false
> volume #14 level 0.3752
> open /Users/zrizvi/Downloads/cryosparc_P341_J270_class_01_00122_volume.mrc
Opened cryosparc_P341_J270_class_01_00122_volume.mrc as #15, grid size
128,128,128, pixel 2.7, shown at level 0.246, step 1, values float32
> open /Users/zrizvi/Downloads/cryosparc_P341_J270_class_02_00122_volume.mrc
Opened cryosparc_P341_J270_class_02_00122_volume.mrc as #16, grid size
128,128,128, pixel 2.7, shown at level 0.179, step 1, values float32
> open /Users/zrizvi/Downloads/cryosparc_P341_J270_class_03_00122_volume.mrc
Opened cryosparc_P341_J270_class_03_00122_volume.mrc as #17, grid size
128,128,128, pixel 2.7, shown at level 0.181, step 1, values float32
> open /Users/zrizvi/Downloads/cryosparc_P341_J270_class_04_00122_volume.mrc
Opened cryosparc_P341_J270_class_04_00122_volume.mrc as #18, grid size
128,128,128, pixel 2.7, shown at level 0.182, step 1, values float32
> tile
5 models tiled
> open /Users/zrizvi/Downloads/cryosparc_P341_J272_class_00_00122_volume.mrc
Opened cryosparc_P341_J272_class_00_00122_volume.mrc as #19, grid size
128,128,128, pixel 2.7, shown at level 0.373, step 1, values float32
> hide #!14 models
> view #19 clip false
> volume #19 level 0.5099
> open /Users/zrizvi/Downloads/cryosparc_P341_J272_class_03_00122_volume.mrc
Opened cryosparc_P341_J272_class_03_00122_volume.mrc as #20, grid size
128,128,128, pixel 2.7, shown at level 0.287, step 1, values float32
> open /Users/zrizvi/Downloads/cryosparc_P341_J272_class_02_00122_volume.mrc
Opened cryosparc_P341_J272_class_02_00122_volume.mrc as #21, grid size
128,128,128, pixel 2.7, shown at level 0.311, step 1, values float32
> open /Users/zrizvi/Downloads/cryosparc_P341_J272_class_01_00122_volume.mrc
Opened cryosparc_P341_J272_class_01_00122_volume.mrc as #22, grid size
128,128,128, pixel 2.7, shown at level 0.22, step 1, values float32
> tile
8 models tiled
> hide #!15 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> view #19-22 clip false
> volume #22 level 0.3413
> volume #21 level 0.4754
> volume #20 level 0.3776
> color #19 #e3f7e1ff models
> color #19 #e9f7f0ff models
> color #19 #838b87ff models
> color #19 #929b96ff models
> color #19 #989b94ff models
> color #20 #d6d6d6ff models
> color #20 silver models
> color #21 #d6d6d6ff models
> color #22 white models
> color #22 #ebebebff models
> color #22 #d6d6d6ff models
> color #22 #919191ff models
> color #21 #929292ff models
> color #20 #929292ff models
> view #19 clip false
> save "/Users/zrizvi/Desktop/IMAGE 1.png" width 864 height 624 supersample 3
> view #20 clip false
> volume #20 level 0.6313
> save "/Users/zrizvi/Desktop/IMAGE 2.png" width 864 height 624 supersample 3
> view #21 clip false
> volume #21 level 0.574
> save "/Users/zrizvi/Desktop/IMAGE 3.png" width 864 height 624 supersample 3
> view #22 clip false
> volume #22 level 0.336
> volume #22 level 0.6801
> volume #22 level 0.4049
> save "/Users/zrizvi/Desktop/IMAGE 4.png" width 864 height 624 supersample 3
> open /Users/zrizvi/Downloads/cryosparc_P341_J271_003_volume_map.mrc
Opened cryosparc_P341_J271_003_volume_map.mrc as #23, grid size 300,300,300,
pixel 1.15, shown at level 0.106, step 2, values float32
> view #23 clip false
> volume #23 level 0.1374
> volume #23 level 0.1282
> open "/Users/zrizvi/Downloads/cryosparc_P351_J139_003_volume_map (1).mrc"
Opened cryosparc_P351_J139_003_volume_map (1).mrc as #24, grid size
250,250,250, pixel 0.91, shown at level 0.0705, step 1, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P351_J139_003_volume_map (1).mrc"
Opened cryosparc_P351_J139_003_volume_map (1).mrc as #25, grid size
250,250,250, pixel 0.91, shown at level 0.0705, step 1, values float32
> view #25 clip false
[Repeated 1 time(s)]
> hide #!23 models
> close #14-25
> save "/Users/zrizvi/Desktop/atomic model fit with Gabe.cxs"
——— End of log from Fri Dec 8 11:01:25 2023 ———
opened ChimeraX session
> show #!7 models
> view #7 clip false
> show #!3 models
> show #12 models
> show #10 models
> show #11 models
> show #!13 models
> hide #!13 models
> show #!9 models
> show #!8 models
> show #6 models
> hide #6 models
> show #!4 models
> hide #!4 models
> hide #10 models
> show #10 models
> hide #11 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-5
46 atoms, 47 bonds, 5 residues, 1 model selected
> select clear
Drag select of 7 residues
> select clear
> select #3/A:248
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:206-248
319 atoms, 327 bonds, 43 residues, 1 model selected
> select
> #3/A:4-10,18-21,30-34,38-44,49-56,61-67,76-81,85-94,97-107,121-124,130-134,139-144,155-158,164-166,177-184,187-194,210-211,218-221,229-232,237-240,245-248,258-263,270-275,279-284,289-290,295-296,302-307,311-316,321-326,331-336,347-353,359-365,374-379,386-392,396-402,409-413,424-428,433-437,444-445,459-463,467-471,476-480,489-490,498-503,507-512,515-520,528-533,538-542,557-560,566-569,576-580,588-595,600-606,611-613,627-629,637-639,649-652,657-661,666-668,678-682,690-694,699-704,710-716,720-727,732-743,749-751,764-765,785-795,801-806,811-819,828-835,846-854,857-866,874-876,879-884,887-893,899-903,913-914,920-924,929-935,942-949,954-961,964-969,973-978,993-999,1004-1009,1025-1032,1037-1042,1076-1077,1082-1083,1088-1090
3732 atoms, 3708 bonds, 511 residues, 1 model selected
> select #3/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1-5
46 atoms, 47 bonds, 5 residues, 1 model selected
> select clear
> select #3/A:1127-1128
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3/A:1127-1140
114 atoms, 114 bonds, 14 residues, 1 model selected
> select #3/A:1114
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:1114-1125
72 atoms, 72 bonds, 12 residues, 1 model selected
> select clear
> close session
> open 8d7z
Summary of feedback from opening 8d7z fetched from pdb
---
warnings | Unable to fetch template for 'ZN': will connect using distance
criteria
Unable to fetch template for 'QFC': will connect using distance criteria
8d7z title:
Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 [more info...]
Chain information for 8d7z #1
---
Chain | Description | UniProt
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140
B | Protein cereblon | CRBN_HUMAN 1-442
C | DNA-binding protein Ikaros | IKZF1_HUMAN 112-196
Non-standard residues in 8d7z #1
---
QFC — Mezigdomide
ZN — zinc ion
> color /A:1-710 light blue
> color /A:710-5000 steel blue
> color /A:392-709 cornflower blue
> color /B:1-190 navajowhite
> color /B:191-320 light salmon
> color /B:321-500 tomato
> color /C gold
> lighting soft
> show cartoons
> show surfaces
> hide surfaces
> show atoms
> hide atoms
> lighting flat
> lighting simple
> lighting flat
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> color bynucleotide
> show cartoons
> show atoms
> hide atoms
> color bynucleotide
> select :QFC
42 atoms, 47 bonds, 1 residue, 1 model selected
> select :ZN
2 atoms, 2 residues, 1 model selected
> select :QFC
42 atoms, 47 bonds, 1 residue, 1 model selected
> select QFC
Expected an objects specifier or a keyword
> select #QFC
Expected an objects specifier or a keyword
> select :QFC
42 atoms, 47 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /B 1-47
Expected a keyword
> sequence chain #1/B
Alignment identifier is 1/B
> select clear
> select /B:45-46
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /B:45-123
594 atoms, 606 bonds, 79 residues, 1 model selected
> select /B:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:48-77
223 atoms, 228 bonds, 30 residues, 1 model selected
> select /B:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:48-63
119 atoms, 122 bonds, 16 residues, 1 model selected
> select /B 48-63
Expected a keyword
> select /B :48-63
119 atoms, 122 bonds, 16 residues, 1 model selected
> color sel gold
> color sel dark goldenrod
> select clear
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting full
> cartoon style modeHelix tube sides 20
> undo
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.8.dev202312070253 (2023-12-07)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 3 days, 4 hours, 8 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.14
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.51.1
ChimeraX-AtomicLibrary: 12.1.3
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: 2.10.5
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: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
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.dev202312070253
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
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
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.14.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.4
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: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.46.0
funcparserlib: 2.0.0a0
glfw: 2.6.3
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.41
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 14 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Zeba,
--Eric