![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 weeks ago
Closed 7 weeks ago
#18855 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fa46a0c0 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.morph._morph, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.segment._segment (total: 124)
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"version" : 2,
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"codeSigningMonitor" : 2,
"incident" : "DE499D8C-BEBD-43DF-B5D1-D1919BCF8ADD",
"pid" : 43202,
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"procLaunch" : "2025-09-03 08:50:03.9853 -0700",
"procStartAbsTime" : 2558126224602,
"procExitAbsTime" : 7777896735857,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","siriAssetIsNotReady","notOptedIn"]},
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "D28D0399-10ED-4854-BA5E-3DD6EA560079",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4341022359\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102bec000-102bf0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":43202},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4341022359\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102bec000-102bf0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/victor/Downloads/cryosparc_P89_J262_012_volume_map.mrc
Opened cryosparc_P89_J262_012_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.65, shown at level 0.00333, step 2, values float32
> lighting soft
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> surface dust #1 size 6.5
> volume #1 step 1
> volume #1 level 0.03932
> volume #1 level 0.02796
> open /Users/victor/Downloads/cryosparc_P89_J260_013_volume_map.mrc
Opened cryosparc_P89_J260_013_volume_map.mrc as #2, grid size 500,500,500,
pixel 0.65, shown at level 0.00345, step 2, values float32
> open /Users/victor/Downloads/cryosparc_P89_J256_014_volume_map.mrc
Opened cryosparc_P89_J256_014_volume_map.mrc as #3, grid size 500,500,500,
pixel 0.65, shown at level 0.00364, step 2, values float32
> surface dust #1 size 6.5
> surface dust #2 size 6.5
> surface dust #3 size 6.5
> volume #2 step 1
> volume #3 step 1
> volume #2 level 0.02558
> volume #3 level 0.0283
> lighting soft
> lighting full
> lighting soft
> volume #3 level 0.0286
> volume #1 level 0.02406
> volume #3 level 0.06214
> volume #2 level 0.06215
> volume #1 level 0.06208
> open /Users/victor/Downloads/cryosparc_P1_J291_012_volume_map.mrc
Opened cryosparc_P1_J291_012_volume_map.mrc as #4, grid size 360,360,360,
pixel 0.758, shown at level 0.00584, step 2, values float32
> volume #4 step 1
> volume #4 level 0.03788
> fitmap #2 inMap #3
Fit map cryosparc_P89_J260_013_volume_map.mrc in map
cryosparc_P89_J256_014_volume_map.mrc using 142707 points
correlation = 0.9963, correlation about mean = 0.9742, overlap = 2191
steps = 48, shift = 0.597, angle = 0.809 degrees
Position of cryosparc_P89_J260_013_volume_map.mrc (#2) relative to
cryosparc_P89_J256_014_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99990128 -0.00936024 -0.01047913 3.59565514
0.00937424 0.99995523 0.00128745 -1.25778897
0.01046661 -0.00138556 0.99994426 -1.65124142
Axis -0.09469187 -0.74200603 0.66367199
Axis point 127.66015473 0.00000000 337.37689146
Rotation angle (degrees) 0.80871455
Shift along axis -0.50307498
> volume #2 level 0.02751
> volume #3 level 0.02761
> close #1-4
> open /Users/victor/Downloads/cryosparc_P89_J256_014_volume_map.mrc
Opened cryosparc_P89_J256_014_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.65, shown at level 0.00364, step 2, values float32
> surface dust #1 size 6.5
> volume #1 step 1
> volume #1 level 0.01705
> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 249,249,249 imageMode orthoplanes
> volume #1 orthoplanes xyz positionPlanes 249,249,196
> volume #1 orthoplanes xyz positionPlanes 249,273,196
> volume #1 orthoplanes xyz positionPlanes 249,279,196
> volume #1 orthoplanes xyz positionPlanes 256,279,196
> volume #1 style surface
> open /Users/victor/Downloads/cryosparc_P89_J266_012_volume_map.mrc
Opened cryosparc_P89_J266_012_volume_map.mrc as #2, grid size 500,500,500,
pixel 0.65, shown at level 0.00363, step 2, values float32
> volume #2 step 1
> surface dust #2 size 6.5
> volume #2 level 0.01087
> volume #2 level 0.02051
> volume #2 level 0.03177
> volume #2 level 0.01649
> open /Users/victor/Downloads/cryosparc_P89_J247_011_volume_map(1).mrc
Opened cryosparc_P89_J247_011_volume_map(1).mrc as #3, grid size 360,360,360,
pixel 0.758, shown at level 0.00532, step 2, values float32
> volume #3 step 1
> volume #3 level 0.0149
> volume #3 level 0.03193
> volume #3 level 0.01916
> volume #3 level 0.03726
> open /Users/victor/Downloads/cryosparc_P89_J248_012_volume_map(1).mrc
Opened cryosparc_P89_J248_012_volume_map(1).mrc as #4, grid size 360,360,360,
pixel 0.758, shown at level 0.00685, step 2, values float32
> volume #4 step 1
> volume #4 level 0.03646
> fitmap #3 inMap #4
Fit map cryosparc_P89_J247_011_volume_map(1).mrc in map
cryosparc_P89_J248_012_volume_map(1).mrc using 157415 points
correlation = 0.9546, correlation about mean = 0.8395, overlap = 1727
steps = 68, shift = 0.339, angle = 0.471 degrees
Position of cryosparc_P89_J247_011_volume_map(1).mrc (#3) relative to
cryosparc_P89_J248_012_volume_map(1).mrc (#4) coordinates:
Matrix rotation and translation
0.99998543 0.00224522 0.00490976 -0.76100245
-0.00227559 0.99997826 0.00618938 -0.63980276
-0.00489576 -0.00620046 0.99996879 1.73815189
Axis -0.75389025 0.59664117 -0.27507963
Axis point 0.00000000 267.24532324 76.72574938
Rotation angle (degrees) 0.47081993
Shift along axis -0.28615052
> volume #4 level 0.04667
> surface dust #4 size 7.58
> volume #4 level 0.06606
> volume #3 level 0.06067
> volume #3 level 0.02342
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00208_volume_series/J272_class_01_00208_volume.mrc
Opened J272_class_01_00208_volume.mrc as #5, grid size 144,144,144, pixel 1.9,
shown at level 0.0408, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00208_volume_series/J272_class_00_00208_volume.mrc
Opened J272_class_00_00208_volume.mrc as #6, grid size 144,144,144, pixel 1.9,
shown at level 0.0403, step 1, values float32
> surface dust #3 size 7.58
> surface dust #5 size 19
> surface dust #6 size 19
> volume #5 level 0.1146
> volume #5 level 0.1817
> volume #5 region 0,0,0,143,143,143
> volume #6 level 0.2402
> volume #5 level 0.09786
> volume #6 level 0.2085
> volume #5 level 0.1213
> open
> /Users/victor/Downloads/cryosparc_P89_J271_00116_volume_series/J271_class_01_00116_volume.mrc
Opened J271_class_01_00116_volume.mrc as #7, grid size 192,192,192, pixel
1.42, shown at level 0.0201, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J271_00116_volume_series/J271_class_00_00116_volume.mrc
Opened J271_class_00_00116_volume.mrc as #8, grid size 192,192,192, pixel
1.42, shown at level 0.02, step 1, values float32
> close #5-6
> surface dust #7 size 14.2
> surface dust #8 size 14.2
> volume #7 level 0.1028
> volume #7 level 0.09879
> volume #8 level 0.07869
> volume #8 level 0.04582
> volume #8 level 0.003554
> volume #8 level 0.0106
> volume #8 level 0.005902
> volume #8 level 0.1538
> volume #8 level 0.1656
> fitmap #7 inMap #8
Fit map J271_class_01_00116_volume.mrc in map J271_class_00_00116_volume.mrc
using 20654 points
correlation = 0.9837, correlation about mean = 0.9351, overlap = 1439
steps = 44, shift = 0.0186, angle = 0.02 degrees
Position of J271_class_01_00116_volume.mrc (#7) relative to
J271_class_00_00116_volume.mrc (#8) coordinates:
Matrix rotation and translation
0.99999995 -0.00031146 -0.00007060 0.04725912
0.00031145 0.99999994 -0.00014075 -0.03876356
0.00007064 0.00014072 0.99999999 -0.03650375
Axis 0.40325697 -0.20234725 0.89243454
Axis point 128.17803637 159.06074756 0.00000000
Rotation angle (degrees) 0.01999608
Shift along axis -0.00567593
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_39_00013_volume.mrc
Opened J272_class_39_00013_volume.mrc as #5, grid size 144,144,144, pixel 1.9,
shown at level 0.116, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_38_00013_volume.mrc
Opened J272_class_38_00013_volume.mrc as #6, grid size 144,144,144, pixel 1.9,
shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_37_00013_volume.mrc
Opened J272_class_37_00013_volume.mrc as #9, grid size 144,144,144, pixel 1.9,
shown at level 0.106, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_36_00013_volume.mrc
Opened J272_class_36_00013_volume.mrc as #10, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_35_00013_volume.mrc
Opened J272_class_35_00013_volume.mrc as #11, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_34_00013_volume.mrc
Opened J272_class_34_00013_volume.mrc as #12, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_33_00013_volume.mrc
Opened J272_class_33_00013_volume.mrc as #13, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_32_00013_volume.mrc
Opened J272_class_32_00013_volume.mrc as #14, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_31_00013_volume.mrc
Opened J272_class_31_00013_volume.mrc as #15, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_30_00013_volume.mrc
Opened J272_class_30_00013_volume.mrc as #16, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_29_00013_volume.mrc
Opened J272_class_29_00013_volume.mrc as #17, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_28_00013_volume.mrc
Opened J272_class_28_00013_volume.mrc as #18, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_27_00013_volume.mrc
Opened J272_class_27_00013_volume.mrc as #19, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_26_00013_volume.mrc
Opened J272_class_26_00013_volume.mrc as #20, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_25_00013_volume.mrc
Opened J272_class_25_00013_volume.mrc as #21, grid size 144,144,144, pixel
1.9, shown at level 0.106, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_24_00013_volume.mrc
Opened J272_class_24_00013_volume.mrc as #22, grid size 144,144,144, pixel
1.9, shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_23_00013_volume.mrc
Opened J272_class_23_00013_volume.mrc as #23, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_22_00013_volume.mrc
Opened J272_class_22_00013_volume.mrc as #24, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_21_00013_volume.mrc
Opened J272_class_21_00013_volume.mrc as #25, grid size 144,144,144, pixel
1.9, shown at level 0.104, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_20_00013_volume.mrc
Opened J272_class_20_00013_volume.mrc as #26, grid size 144,144,144, pixel
1.9, shown at level 0.113, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_19_00013_volume.mrc
Opened J272_class_19_00013_volume.mrc as #27, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_18_00013_volume.mrc
Opened J272_class_18_00013_volume.mrc as #28, grid size 144,144,144, pixel
1.9, shown at level 0.121, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_17_00013_volume.mrc
Opened J272_class_17_00013_volume.mrc as #29, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_16_00013_volume.mrc
Opened J272_class_16_00013_volume.mrc as #30, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_15_00013_volume.mrc
Opened J272_class_15_00013_volume.mrc as #31, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_14_00013_volume.mrc
Opened J272_class_14_00013_volume.mrc as #32, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_13_00013_volume.mrc
Opened J272_class_13_00013_volume.mrc as #33, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_12_00013_volume.mrc
Opened J272_class_12_00013_volume.mrc as #34, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_11_00013_volume.mrc
Opened J272_class_11_00013_volume.mrc as #35, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_10_00013_volume.mrc
Opened J272_class_10_00013_volume.mrc as #36, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_09_00013_volume.mrc
Opened J272_class_09_00013_volume.mrc as #37, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_08_00013_volume.mrc
Opened J272_class_08_00013_volume.mrc as #38, grid size 144,144,144, pixel
1.9, shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_07_00013_volume.mrc
Opened J272_class_07_00013_volume.mrc as #39, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_06_00013_volume.mrc
Opened J272_class_06_00013_volume.mrc as #40, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_05_00013_volume.mrc
Opened J272_class_05_00013_volume.mrc as #41, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_04_00013_volume.mrc
Opened J272_class_04_00013_volume.mrc as #42, grid size 144,144,144, pixel
1.9, shown at level 0.102, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_03_00013_volume.mrc
Opened J272_class_03_00013_volume.mrc as #43, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_02_00013_volume.mrc
Opened J272_class_02_00013_volume.mrc as #44, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_01_00013_volume.mrc
Opened J272_class_01_00013_volume.mrc as #45, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_00_00013_volume.mrc
Opened J272_class_00_00013_volume.mrc as #46, grid size 144,144,144, pixel
1.9, shown at level 0.104, step 1, values float32
> surface dust #7 size 14.2
> surface dust #8 size 14.2
> surface dust #5 size 19
> surface dust #6 size 19
> surface dust #9 size 19
> surface dust #10 size 19
> surface dust #11 size 19
> surface dust #12 size 19
> surface dust #13 size 19
> surface dust #14 size 19
> surface dust #15 size 19
> surface dust #16 size 19
> surface dust #17 size 19
> surface dust #18 size 19
> surface dust #19 size 19
> surface dust #20 size 19
> surface dust #21 size 19
> surface dust #22 size 19
> surface dust #23 size 19
> surface dust #24 size 19
> surface dust #25 size 19
> surface dust #26 size 19
> surface dust #27 size 19
> surface dust #28 size 19
> surface dust #29 size 19
> surface dust #30 size 19
> surface dust #31 size 19
> surface dust #32 size 19
> surface dust #33 size 19
> surface dust #34 size 19
> surface dust #35 size 19
> surface dust #36 size 19
> surface dust #37 size 19
> surface dust #38 size 19
> surface dust #39 size 19
> surface dust #40 size 19
> surface dust #41 size 19
> surface dust #42 size 19
> surface dust #43 size 19
> surface dust #44 size 19
> surface dust #45 size 19
> surface dust #46 size 19
> volume #5 level 0.231
> volume #6 level 0.2425
> volume #9 level 0.1945
> open /Users/victor/Downloads/cryosparc_P1_J291_012_volume_map(1).mrc
Opened cryosparc_P1_J291_012_volume_map(1).mrc as #47, grid size 360,360,360,
pixel 0.758, shown at level 0.00584, step 2, values float32
> hide #!9 models
> volume #47 step 1
> volume #47 level 0.03422
> volume #47 level 0.00767
> surface dust #47 size 7.58
> volume #47 level 0.03239
> show #!1 models
> show #!46 models
> show #!45 models
> close #1-46
> close #47
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix45_In_UnArm/HigherResMap_Input/CootINProgress/J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb
Chain information for
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #1
---
Chain | Description
C | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix45_In_DosArms/HigherResMap_Input/CootINProgress/J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
Chain information for
J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb #2
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix4_Up/HigherResMap_Input/CootINProgress/J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb
Chain information for J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb #3
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix4_Out/HigherResMap_Input/CootINProgress/J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb
Chain information for J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb
#4
---
Chain | Description
C D | No description available
E H | No description available
F | No description available
J | No description available
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 24354 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
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
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
~worm
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 tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui mousemode right select
Drag select of 260 atoms, 3510 residues, 8 pseudobonds, 264 bonds
> select add #1
27252 atoms, 7430 bonds, 12 pseudobonds, 3440 residues, 9 models selected
> select subtract #1
20164 atoms, 198 bonds, 6 pseudobonds, 2540 residues, 6 models selected
> select add #1
27252 atoms, 7430 bonds, 12 pseudobonds, 3440 residues, 9 models selected
> select add #2
28469 atoms, 15172 bonds, 16 pseudobonds, 3600 residues, 10 models selected
> select subtract #2
20818 atoms, 7364 bonds, 10 pseudobonds, 2630 residues, 7 models selected
> select add #2
28469 atoms, 15172 bonds, 16 pseudobonds, 3600 residues, 10 models selected
> select add #3
29686 atoms, 22972 bonds, 20 pseudobonds, 3760 residues, 11 models selected
> select subtract #3
21975 atoms, 15106 bonds, 14 pseudobonds, 2783 residues, 8 models selected
> select add #3
29686 atoms, 22972 bonds, 20 pseudobonds, 3760 residues, 11 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> select subtract #4
22450 atoms, 22906 bonds, 18 pseudobonds, 2847 residues, 9 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1542.4
RMSD between 254 pruned atom pairs is 0.611 angstroms; (across all 320 pairs:
5.074)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1526.7
RMSD between 249 pruned atom pairs is 0.664 angstroms; (across all 319 pairs:
5.701)
> select subtract #1
24549 atoms, 25040 bonds, 18 pseudobonds, 3119 residues, 9 models selected
> select subtract #2
16898 atoms, 17232 bonds, 12 pseudobonds, 2149 residues, 6 models selected
> select subtract #3
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> color sel bychain
> select subtract #1
Nothing selected
> show #!2 models
> hide #!1 models
> color #!2 bychain
> show #!3 models
> hide #!2 models
> color #!3 bychain
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> color #!4 bychain
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.97804,0.20775,-0.016797,242.17,0.20231,0.92687,-0.31619,28.187,-0.05012,-0.31265,-0.94855,324.97
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,16.295,0.13269,0.98868,0.070047,-18.151,-0.050667,-0.063813,0.99667,52.875
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,24.322,0.13269,0.98868,0.070047,-26.664,-0.050667,-0.063813,0.99667,19.531
> select subtract #3
Nothing selected
> show #!4 models
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.93258,-0.12141,-0.33992,72.752,0.11189,0.99258,-0.047568,-4.7571,0.34318,0.0063286,0.93925,-27.232
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.93258,-0.12141,-0.33992,75.003,0.11189,0.99258,-0.047568,-7.3297,0.34318,0.0063286,0.93925,-36.572
> select subtract #4
Nothing selected
> ui mousemode right select
Drag select of 260 atoms, 4331 residues, 8 pseudobonds, 264 bonds
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1542.4
RMSD between 254 pruned atom pairs is 0.611 angstroms; (across all 320 pairs:
5.074)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1526.7
RMSD between 249 pruned atom pairs is 0.664 angstroms; (across all 319 pairs:
5.701)
> undo
Drag select of 8 residues
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,24.329,0.13269,0.98868,0.070047,-27.261,-0.050667,-0.063813,0.99667,19.013
> select subtract #3
Nothing selected
> show #!4 models
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99454,-0.0062532,-0.10415,16.677,0.010101,0.99928,0.036453,-3.2295,0.10385,-0.037306,0.99389,3.8274
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99454,-0.0062532,-0.10415,19.146,0.010101,0.99928,0.036453,-5.5331,0.10385,-0.037306,0.99389,-6.6059
> select subtract #4
Nothing selected
> ui mousemode right select
Drag select of 93 residues
> select up
1302 atoms, 1327 bonds, 159 residues, 4 models selected
> select up
4742 atoms, 4845 bonds, 610 residues, 4 models selected
> select up
4873 atoms, 4976 bonds, 629 residues, 4 models selected
> select up
10225 atoms, 10435 bonds, 1298 residues, 4 models selected
> select up
10349 atoms, 10567 bonds, 1302 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
10349 atoms, 10567 bonds, 1302 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain F
(#2), sequence alignment score = 1633.9
RMSD between 315 pruned atom pairs is 0.411 angstroms; (across all 319 pairs:
0.604)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1515.7
RMSD between 257 pruned atom pairs is 0.596 angstroms; (across all 321 pairs:
5.079)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1507.8
RMSD between 251 pruned atom pairs is 0.640 angstroms; (across all 318 pairs:
5.361)
> select add #1
14874 atoms, 15181 bonds, 6 pseudobonds, 1880 residues, 6 models selected
> select subtract #1
7786 atoms, 7949 bonds, 980 residues, 3 models selected
> select add #2
12891 atoms, 13156 bonds, 6 pseudobonds, 1630 residues, 5 models selected
> select subtract #2
5240 atoms, 5348 bonds, 660 residues, 2 models selected
> select add #3
10373 atoms, 10582 bonds, 6 pseudobonds, 1313 residues, 4 models selected
> select subtract #3
2662 atoms, 2716 bonds, 336 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select add #2
14739 atoms, 15040 bonds, 12 pseudobonds, 1870 residues, 6 models selected
> select add #3
22450 atoms, 22906 bonds, 18 pseudobonds, 2847 residues, 9 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> ui tool show "Color Actions"
> color sel orange
> color sel lime
> color sel light sea green
> color sel purple
> color sel gray
> color sel dark gray
> color sel gray
> color sel light gray
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel bychain
No target buttons for the coloring action are checked
> color sel bychain
> lighting full
> lighting soft
> select subtract #1
24549 atoms, 25040 bonds, 18 pseudobonds, 3119 residues, 9 models selected
> select subtract #2
16898 atoms, 17232 bonds, 12 pseudobonds, 2149 residues, 6 models selected
> select subtract #3
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
Drag select of 5 atoms, 74 residues, 3 bonds
> select add #4
9621 atoms, 9369 bonds, 6 pseudobonds, 1230 residues, 6 models selected
> select subtract #4
434 atoms, 3 bonds, 58 residues, 3 models selected
> select add #3
8003 atoms, 7868 bonds, 6 pseudobonds, 1016 residues, 5 models selected
> select subtract #3
292 atoms, 2 bonds, 39 residues, 2 models selected
> select add #2
7791 atoms, 7809 bonds, 6 pseudobonds, 989 residues, 4 models selected
> select subtract #2
140 atoms, 1 bond, 19 residues, 1 model selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right translate
> Select #1,2,3,4/J
Unknown command: Select #1,2,3,4/J
> Select #1/J
Unknown command: Select #1/J
> Select #1/J
Unknown command: Select #1/J
> Select #2/J
Unknown command: Select #2/J
> Select #3/J
Unknown command: Select #3/J
> Select #3
Unknown command: Select #3
> select #1/J
2554 atoms, 2609 bonds, 1 pseudobond, 321 residues, 2 models selected
> select #1,2/J
5108 atoms, 5218 bonds, 2 pseudobonds, 642 residues, 4 models selected
> select #1,2,3,4/J
10276 atoms, 10494 bonds, 4 pseudobonds, 1291 residues, 8 models selected
> color (#!1-4 & sel) #009051ff
> color (#!1-4 & sel) #00f900ff
> color (#!1-4 & sel) #a730f9ff
> color (#!1-4 & sel) #4b4af9ff
> color (#!1-4 & sel) #b6aef9ff
> color (#!1-4 & sel) #f2e1f9ff
> color (#!1-4 & sel) #f2e2f9ff
> color (#!1-4 & sel) #f3f998ff
> color (#!1-4 & sel) #f9f777ff
> color (#!1-4 & sel) #f9623eff
> select add #4
16877 atoms, 17220 bonds, 9 pseudobonds, 2138 residues, 9 models selected
> select subtract #4
7690 atoms, 7854 bonds, 3 pseudobonds, 966 residues, 6 models selected
> select add #3
12819 atoms, 13084 bonds, 8 pseudobonds, 1619 residues, 7 models selected
> select subtract #3
5108 atoms, 5218 bonds, 2 pseudobonds, 642 residues, 4 models selected
> select add #2
10205 atoms, 10417 bonds, 7 pseudobonds, 1291 residues, 5 models selected
> select subtract #2
2554 atoms, 2609 bonds, 1 pseudobond, 321 residues, 2 models selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> show #!2 models
> show #!3 models
> show #!4 models
> show sel atoms
> color sel byhetero
> select add #1
7148 atoms, 7292 bonds, 6 pseudobonds, 906 residues, 6 models selected
> select subtract #1
60 atoms, 60 bonds, 6 residues, 3 models selected
> select add #2
7691 atoms, 7848 bonds, 6 pseudobonds, 974 residues, 5 models selected
> select subtract #2
40 atoms, 40 bonds, 4 residues, 2 models selected
> select add #3
7731 atoms, 7886 bonds, 6 pseudobonds, 979 residues, 4 models selected
> select subtract #3
20 atoms, 20 bonds, 2 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> open /Users/victor/Desktop/GiGet345_FL_Gold/GETProteins_PDBs/7spy_dimer.pdb
Chain information for 7spy_dimer.pdb #5
---
Chain | Description
A B | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open /Users/victor/Desktop/GiGet345_FL_Gold/GETProteins_PDBs/7SQ0.pdb
7SQ0.pdb title:
GET3 bound to adp and the transmembrane domain of the tail-anchored protein
BOS1 [more info...]
Chain information for 7SQ0.pdb #6
---
Chain | Description | UniProt
A B | atpase ASNA1 homolog | ASNA_GIAIC 1-94 125-354
C | TMD of the tail-anchored protein BOS1 |
Non-standard residues in 7SQ0.pdb #6
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select add #5
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #6
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,149.59,0,1,0,149.06,0,0,1,146.8
> select add #6
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> select #5,6/J,F:170
Nothing selected
> select #5,6/A
7265 atoms, 7188 bonds, 8 pseudobonds, 814 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7spy_dimer.pdb, chain A (#5) with 7SQ0.pdb, chain A (#6), sequence
alignment score = 1384.1
RMSD between 221 pruned atom pairs is 0.992 angstroms; (across all 282 pairs:
6.273)
> select add #5
10021 atoms, 9818 bonds, 9 pseudobonds, 1319 residues, 5 models selected
> select subtract #5
4509 atoms, 4558 bonds, 7 pseudobonds, 309 residues, 3 models selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select add #5
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> select add #6
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.16235,0.43993,-0.88323,127,0.86755,-0.49009,-0.084646,194.98,-0.4701,-0.75251,-0.46123,155.87,#6,0.24439,-0.95657,-0.15887,216.32,0.43078,0.25389,-0.86601,178.46,0.86874,0.1432,0.47412,-29.378
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.16235,0.43993,-0.88323,166.91,0.86755,-0.49009,-0.084646,193.11,-0.4701,-0.75251,-0.46123,145.41,#6,0.24439,-0.95657,-0.15887,256.23,0.43078,0.25389,-0.86601,176.59,0.86874,0.1432,0.47412,-39.843
> view matrix models
> #5,0.16235,0.43993,-0.88323,165.84,0.86755,-0.49009,-0.084646,186.04,-0.4701,-0.75251,-0.46123,126.5,#6,0.24439,-0.95657,-0.15887,255.16,0.43078,0.25389,-0.86601,169.52,0.86874,0.1432,0.47412,-58.755
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.21001,0.56347,-0.799,166.27,0.89186,-0.44526,-0.079595,187.04,-0.40061,-0.69588,-0.59604,132.68,#6,0.09606,-0.97356,-0.20724,283.49,0.39365,0.22838,-0.89044,181.05,0.91423,0.0039569,0.40518,-37
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.21001,0.56347,-0.799,165.06,0.89186,-0.44526,-0.079595,188.05,-0.40061,-0.69588,-0.59604,132.77,#6,0.09606,-0.97356,-0.20724,282.29,0.39365,0.22838,-0.89044,182.07,0.91423,0.0039569,0.40518,-36.908
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
~worm
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 tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select add #5
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> ui mousemode right select
Drag select of 254 residues, 1 atoms
> select up
4907 atoms, 4974 bonds, 538 residues, 6 models selected
> select up
17077 atoms, 17390 bonds, 1897 residues, 6 models selected
> select up
17082 atoms, 17394 bonds, 1898 residues, 6 models selected
> select up
17172 atoms, 17484 bonds, 1916 residues, 6 models selected
> select up
17541 atoms, 17682 bonds, 2105 residues, 6 models selected
> select up
46309 atoms, 46790 bonds, 5664 residues, 6 models selected
> select down
17541 atoms, 17682 bonds, 2105 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!2-6 & sel to #1 & sel
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain J (#3),
sequence alignment score = 1537.2
RMSD between 252 pruned atom pairs is 0.587 angstroms; (across all 320 pairs:
5.106)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain J
(#4), sequence alignment score = 1512
RMSD between 240 pruned atom pairs is 0.576 angstroms; (across all 319 pairs:
5.430)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with 7spy_dimer.pdb, chain A (#5), sequence alignment score = 1646.9
RMSD between 314 pruned atom pairs is 0.649 angstroms; (across all 319 pairs:
0.736)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with 7SQ0.pdb, chain A (#6), sequence alignment score = 1388.4
RMSD between 222 pruned atom pairs is 0.966 angstroms; (across all 290 pairs:
6.124)
> select add #1
22075 atoms, 22305 bonds, 6 pseudobonds, 2684 residues, 8 models selected
> select subtract #1
14987 atoms, 15073 bonds, 1784 residues, 5 models selected
> select add #2
20084 atoms, 20272 bonds, 6 pseudobonds, 2433 residues, 7 models selected
> select subtract #2
12433 atoms, 12464 bonds, 1463 residues, 4 models selected
> select add #3
17562 atoms, 17694 bonds, 6 pseudobonds, 2116 residues, 6 models selected
> select subtract #3
9851 atoms, 9828 bonds, 1139 residues, 3 models selected
> select add #4
16452 atoms, 16554 bonds, 6 pseudobonds, 1986 residues, 5 models selected
> select subtract #4
7265 atoms, 7188 bonds, 814 residues, 2 models selected
> select add #5
10021 atoms, 9818 bonds, 2 pseudobonds, 1319 residues, 3 models selected
> select subtract #5
4509 atoms, 4558 bonds, 309 residues, 1 model selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> hide #6.2.1 models
> ui mousemode right translate
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> ui mousemode right select
> select #6/C:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
123 atoms, 122 bonds, 19 residues, 1 model selected
> select up
138 atoms, 137 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!4 models
> select #5,6/A,F:170
27 atoms, 27 bonds, 2 residues, 2 models selected
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show sel atoms
> select #5,6/AF:170
Nothing selected
> select #5,6/A:170
27 atoms, 27 bonds, 2 residues, 2 models selected
> select #5,6/F:170
Nothing selected
> select #5,6/A,B:170
54 atoms, 54 bonds, 4 residues, 2 models selected
> show sel atoms
> hide H
> select clear
> ui mousemode right translate
> hide #!5 models
> hide #!6 models
> show #!2 models
> show #!3 models
> show #!4 models
> ui mousemode right select
> show #!1 models
Drag select of 1036 residues
> select up
7204 atoms, 7336 bonds, 936 residues, 4 models selected
> select up
7872 atoms, 8020 bonds, 1016 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
7872 atoms, 8020 bonds, 1016 residues, 4 models selected
> hide sel cartoons
Drag select of 179 residues
> select up
9226 atoms, 9397 bonds, 1193 residues, 4 models selected
> select up
9840 atoms, 10025 bonds, 1270 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
9840 atoms, 10025 bonds, 1270 residues, 4 models selected
> hide sel cartoons
Drag select of 146 residues
> select up
11000 atoms, 11211 bonds, 1414 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
11000 atoms, 11211 bonds, 1414 residues, 4 models selected
> hide sel cartoons
> select add #1
16120 atoms, 16438 bonds, 6 pseudobonds, 2060 residues, 6 models selected
> select subtract #1
9032 atoms, 9206 bonds, 1160 residues, 3 models selected
> select add #2
14135 atoms, 14416 bonds, 6 pseudobonds, 1804 residues, 5 models selected
> select subtract #2
6484 atoms, 6608 bonds, 834 residues, 2 models selected
> select add #3
11647 atoms, 11876 bonds, 6 pseudobonds, 1485 residues, 4 models selected
> select subtract #3
3936 atoms, 4010 bonds, 508 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> show sel & #!1 atoms
> select add #2
7711 atoms, 7868 bonds, 6 pseudobonds, 976 residues, 6 models selected
> select subtract #2
60 atoms, 60 bonds, 6 residues, 3 models selected
[deleted to fit within ticket limits]
> select #47.11
1 model selected
Ungrouped to 2 regions
> select #47.14
1 model selected
Ungrouped to 2 regions
> select #47.21
1 model selected
> select add #47
41 models selected
> select subtract #47
Nothing selected
Drag select of 233, 226, 217, 198, 184, 216, 206, 234, 210, 240, 155, 221,
176, 212, 193, 199, 55, 177, 147, 98, 200, 185, 38, 65, 42, 116, 203, 189,
142, 149, 151, 205, 194, 160, 91, 190
Saving 36 regions to mrc file...
Opened J252_Core.mrc as #48, grid size 101,94,75, pixel 0.758, shown at step
1, values float32
Wrote J252_Core.mrc
> select add #47
41 models selected
> select subtract #47
Nothing selected
> hide #!47 models
> volume #48 level 0.005393
> volume #48 color #cccc9982
> show #!43 models
> volume #43 level 0.06723
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!47 models
> hide #!48 models
> select #47.18
1 model selected
Ungrouped to 2 regions
> select #47.15
1 model selected
Ungrouped to 2 regions
> select #47.18
1 model selected
Ungrouped to 0 regions
> select #47.14
1 model selected
Ungrouped to 0 regions
> select #47.14
1 model selected
> select add #47.18
2 models selected
> select add #47
43 models selected
> select subtract #47
Nothing selected
Drag select of 233, 25801 of 27604 triangles, 226, 198, 16395 of 17028
triangles, 216, 17287 of 17308 triangles, 206, 234, 210, 240, 155, 221, 176,
212, 193, 199, 55, 177, 147, 98, 200, 185, 38, 65, 42, 116, 203, 189, 142,
149, 151, 205, 194, 160, 91, 190, 18364 of 19164 triangles, 43, 137
Saving 36 regions to mrc file...
Opened J252_core.mrc as #49, grid size 101,88,75, pixel 0.758, shown at step
1, values float32
Wrote J252_core.mrc
> select add #47
43 models selected
> select subtract #47
Nothing selected
> hide #!47 models
> show #!48 models
> hide #!48 models
> volume #49 level 0.004863
> volume resample #49 onGrid #43
Opened J252_core.mrc resampled as #50, grid size 360,360,360, pixel 0.758,
shown at step 1, values float32
> volume #48 color #cccc9987
> volume #50 color #ffffb280
> show #!43 models
> hide #!50 models
> show #!50 models
> save /Users/victor/Desktop/J252_Core.mrc models #50
> hide #!50 models
> open /Users/victor/Downloads/cryosparc_P1_J324_mask.mrc
Opened cryosparc_P1_J324_mask.mrc as #51, grid size 360,360,360, pixel 0.758,
shown at level 0.708, step 2, values float32
> volume #51 step 1
> volume #51 level 0.003795
> volume #51 color #b2ffff83
> volume #51 level 0.8098
> volume #51 level 0.3007
> volume #43 level 0.02851
> volume #51 level 0.8363
> open /Users/victor/Downloads/cryosparc_P1_J324_mask(1).mrc
Opened cryosparc_P1_J324_mask(1).mrc as #52, grid size 360,360,360, pixel
0.758, shown at level 0.279, step 2, values float32
> volume #52 step 1
> volume #52 color #b2b2ff7e
> volume #52 color #b2b2ff7d
> volume #52 level 0.7633
> volume #52 level 0.01246
> volume #52 level 0.4413
> open /Users/victor/Downloads/cryosparc_P1_J324_mask(2).mrc
Opened cryosparc_P1_J324_mask(2).mrc as #53, grid size 360,360,360, pixel
0.758, shown at level 0.0697, step 2, values float32
> volume #53 step 1
> volume #53 color #ffb2ff7e
> volume #53 color #ffb2ff7d
> volume #53 level 0.02873
> volume #52 color #b2b2ff
> open /Users/victor/Downloads/cryosparc_P1_J283_005_volume_map_sharp.mrc
Opened cryosparc_P1_J283_005_volume_map_sharp.mrc as #54, grid size
360,360,360, pixel 0.758, shown at level 0.0555, step 2, values float32
> hide #!43 models
> hide #!52 models
> hide #!53 models
> surface dust #54 size 7.58
> volume #54 step 1
> volume #54 level 0.2603
> show #!53 models
> show #!52 models
> show #!51 models
> show #!50 models
> show #!49 models
> show #!48 models
> show #!47 models
> show #!46 models
> show #!45 models
> show #!44 models
> show #!43 models
> show #!42 models
> show #!41 models
> show #!40 models
> show #!39 models
> show #!38 models
> show #!37 models
> show #!36 models
> show #!35 models
> show #!34 models
> show #!33 models
> show #!32 models
> show #!31 models
> show #!30 models
> show #!29 models
> show #!28 models
> show #!27 models
> show #!26 models
> show #!25 models
> show #!24 models
> close #11-54
> show #!1 models
> show #!2 models
> open
> /Users/victor/Downloads/cryosparc_P1_J318_00613_volume_series/J318_class_03_00613_volume.mrc
Opened J318_class_03_00613_volume.mrc as #11, grid size 84,84,84, pixel 3.25,
shown at level 0.0773, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P1_J318_00613_volume_series/J318_class_02_00613_volume.mrc
Opened J318_class_02_00613_volume.mrc as #12, grid size 84,84,84, pixel 3.25,
shown at level 0.0612, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P1_J318_00613_volume_series/J318_class_01_00613_volume.mrc
Opened J318_class_01_00613_volume.mrc as #13, grid size 84,84,84, pixel 3.25,
shown at level 0.0692, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P1_J318_00613_volume_series/J318_class_00_00613_volume.mrc
Opened J318_class_00_00613_volume.mrc as #14, grid size 84,84,84, pixel 3.25,
shown at level 0.0701, step 1, values float32
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
Drag select of 11 J318_class_03_00613_volume.mrc
> select subtract #11
Nothing selected
> select add #11
2 models selected
> select subtract #11
Nothing selected
> ui mousemode right translate
> show #!12 models
> hide #!11 models
> show #!11 models
> show #!13 models
> hide #!13 models
> close #13
> show #!14 models
> hide #!14 models
> hide #!12 models
> volume #11 level 0.2626
> show #!12 models
> hide #!11 models
> volume #12 level 0.1015
> volume #12 level 0.2285
> volume #12 level 0.1304
> volume #12 level 0.1477
> ui tool show "Side View"
> volume #12 level 0.06116
> show #!14 models
> hide #!12 models
> volume #14 level 0.1121
> volume #14 level 0.1851
> volume #14 level 0.005517
> view
> show #!12 models
> hide #!14 models
> volume #12 level 0.006359
> volume #11 level 0.2341
> show #!12 models
> volume #12 level 0.2342
> hide #!12 models
> show #!12 models
> hide #!11 models
> hide #!12 models
> show #!11 models
> volume #11 level 0.05168
> volume #11 level 0.1885
> show #!12 models
> show #!14 models
> volume #14 level 0.2328
> volume #11 level 0.4594
> volume #12 level 0.4592
> hide #!11 models
> show #!14 models
> volume #14 level 0.4545
> hide #!14 models
> close #14
> close #11
> volume #12 level 0.2349
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/victor/Desktop/Get3_Morph.cxs
Log from Wed Sep 10 10:31:54 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/victor/Downloads/cryosparc_P89_J262_012_volume_map.mrc
Opened cryosparc_P89_J262_012_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.65, shown at level 0.00333, step 2, values float32
> lighting soft
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 1 maps.
> surface dust #1 size 6.5
> volume #1 step 1
> volume #1 level 0.03932
> volume #1 level 0.02796
> open /Users/victor/Downloads/cryosparc_P89_J260_013_volume_map.mrc
Opened cryosparc_P89_J260_013_volume_map.mrc as #2, grid size 500,500,500,
pixel 0.65, shown at level 0.00345, step 2, values float32
> open /Users/victor/Downloads/cryosparc_P89_J256_014_volume_map.mrc
Opened cryosparc_P89_J256_014_volume_map.mrc as #3, grid size 500,500,500,
pixel 0.65, shown at level 0.00364, step 2, values float32
> surface dust #1 size 6.5
> surface dust #2 size 6.5
> surface dust #3 size 6.5
> volume #2 step 1
> volume #3 step 1
> volume #2 level 0.02558
> volume #3 level 0.0283
> lighting soft
> lighting full
> lighting soft
> volume #3 level 0.0286
> volume #1 level 0.02406
> volume #3 level 0.06214
> volume #2 level 0.06215
> volume #1 level 0.06208
> open /Users/victor/Downloads/cryosparc_P1_J291_012_volume_map.mrc
Opened cryosparc_P1_J291_012_volume_map.mrc as #4, grid size 360,360,360,
pixel 0.758, shown at level 0.00584, step 2, values float32
> volume #4 step 1
> volume #4 level 0.03788
> fitmap #2 inMap #3
Fit map cryosparc_P89_J260_013_volume_map.mrc in map
cryosparc_P89_J256_014_volume_map.mrc using 142707 points
correlation = 0.9963, correlation about mean = 0.9742, overlap = 2191
steps = 48, shift = 0.597, angle = 0.809 degrees
Position of cryosparc_P89_J260_013_volume_map.mrc (#2) relative to
cryosparc_P89_J256_014_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99990128 -0.00936024 -0.01047913 3.59565514
0.00937424 0.99995523 0.00128745 -1.25778897
0.01046661 -0.00138556 0.99994426 -1.65124142
Axis -0.09469187 -0.74200603 0.66367199
Axis point 127.66015473 0.00000000 337.37689146
Rotation angle (degrees) 0.80871455
Shift along axis -0.50307498
> volume #2 level 0.02751
> volume #3 level 0.02761
> close #1-4
> open /Users/victor/Downloads/cryosparc_P89_J256_014_volume_map.mrc
Opened cryosparc_P89_J256_014_volume_map.mrc as #1, grid size 500,500,500,
pixel 0.65, shown at level 0.00364, step 2, values float32
> surface dust #1 size 6.5
> volume #1 step 1
> volume #1 level 0.01705
> volume #1 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 249,249,249 imageMode orthoplanes
> volume #1 orthoplanes xyz positionPlanes 249,249,196
> volume #1 orthoplanes xyz positionPlanes 249,273,196
[Repeated 1 time(s)]
> volume #1 orthoplanes xyz positionPlanes 249,279,196
> volume #1 orthoplanes xyz positionPlanes 256,279,196
> volume #1 style surface
> open /Users/victor/Downloads/cryosparc_P89_J266_012_volume_map.mrc
Opened cryosparc_P89_J266_012_volume_map.mrc as #2, grid size 500,500,500,
pixel 0.65, shown at level 0.00363, step 2, values float32
> volume #2 step 1
> surface dust #2 size 6.5
> volume #2 level 0.01087
> volume #2 level 0.02051
> volume #2 level 0.03177
> volume #2 level 0.01649
> open /Users/victor/Downloads/cryosparc_P89_J247_011_volume_map(1).mrc
Opened cryosparc_P89_J247_011_volume_map(1).mrc as #3, grid size 360,360,360,
pixel 0.758, shown at level 0.00532, step 2, values float32
> volume #3 step 1
> volume #3 level 0.0149
> volume #3 level 0.03193
> volume #3 level 0.01916
> volume #3 level 0.03726
> open /Users/victor/Downloads/cryosparc_P89_J248_012_volume_map(1).mrc
Opened cryosparc_P89_J248_012_volume_map(1).mrc as #4, grid size 360,360,360,
pixel 0.758, shown at level 0.00685, step 2, values float32
> volume #4 step 1
> volume #4 level 0.03646
> fitmap #3 inMap #4
Fit map cryosparc_P89_J247_011_volume_map(1).mrc in map
cryosparc_P89_J248_012_volume_map(1).mrc using 157415 points
correlation = 0.9546, correlation about mean = 0.8395, overlap = 1727
steps = 68, shift = 0.339, angle = 0.471 degrees
Position of cryosparc_P89_J247_011_volume_map(1).mrc (#3) relative to
cryosparc_P89_J248_012_volume_map(1).mrc (#4) coordinates:
Matrix rotation and translation
0.99998543 0.00224522 0.00490976 -0.76100245
-0.00227559 0.99997826 0.00618938 -0.63980276
-0.00489576 -0.00620046 0.99996879 1.73815189
Axis -0.75389025 0.59664117 -0.27507963
Axis point 0.00000000 267.24532324 76.72574938
Rotation angle (degrees) 0.47081993
Shift along axis -0.28615052
> volume #4 level 0.04667
> surface dust #4 size 7.58
> volume #4 level 0.06606
> volume #3 level 0.06067
> volume #3 level 0.02342
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00208_volume_series/J272_class_01_00208_volume.mrc
Opened J272_class_01_00208_volume.mrc as #5, grid size 144,144,144, pixel 1.9,
shown at level 0.0408, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00208_volume_series/J272_class_00_00208_volume.mrc
Opened J272_class_00_00208_volume.mrc as #6, grid size 144,144,144, pixel 1.9,
shown at level 0.0403, step 1, values float32
> surface dust #3 size 7.58
> surface dust #5 size 19
> surface dust #6 size 19
> volume #5 level 0.1146
> volume #5 level 0.1817
> volume #5 region 0,0,0,143,143,143
> volume #6 level 0.2402
> volume #5 level 0.09786
> volume #6 level 0.2085
> volume #5 level 0.1213
> open
> /Users/victor/Downloads/cryosparc_P89_J271_00116_volume_series/J271_class_01_00116_volume.mrc
Opened J271_class_01_00116_volume.mrc as #7, grid size 192,192,192, pixel
1.42, shown at level 0.0201, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J271_00116_volume_series/J271_class_00_00116_volume.mrc
Opened J271_class_00_00116_volume.mrc as #8, grid size 192,192,192, pixel
1.42, shown at level 0.02, step 1, values float32
> close #5-6
> surface dust #7 size 14.2
> surface dust #8 size 14.2
> volume #7 level 0.1028
> volume #7 level 0.09879
> volume #8 level 0.07869
> volume #8 level 0.04582
> volume #8 level 0.003554
> volume #8 level 0.0106
> volume #8 level 0.005902
> volume #8 level 0.1538
> volume #8 level 0.1656
> fitmap #7 inMap #8
Fit map J271_class_01_00116_volume.mrc in map J271_class_00_00116_volume.mrc
using 20654 points
correlation = 0.9837, correlation about mean = 0.9351, overlap = 1439
steps = 44, shift = 0.0186, angle = 0.02 degrees
Position of J271_class_01_00116_volume.mrc (#7) relative to
J271_class_00_00116_volume.mrc (#8) coordinates:
Matrix rotation and translation
0.99999995 -0.00031146 -0.00007060 0.04725912
0.00031145 0.99999994 -0.00014075 -0.03876356
0.00007064 0.00014072 0.99999999 -0.03650375
Axis 0.40325697 -0.20234725 0.89243454
Axis point 128.17803637 159.06074756 0.00000000
Rotation angle (degrees) 0.01999608
Shift along axis -0.00567593
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_39_00013_volume.mrc
Opened J272_class_39_00013_volume.mrc as #5, grid size 144,144,144, pixel 1.9,
shown at level 0.116, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_38_00013_volume.mrc
Opened J272_class_38_00013_volume.mrc as #6, grid size 144,144,144, pixel 1.9,
shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_37_00013_volume.mrc
Opened J272_class_37_00013_volume.mrc as #9, grid size 144,144,144, pixel 1.9,
shown at level 0.106, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_36_00013_volume.mrc
Opened J272_class_36_00013_volume.mrc as #10, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_35_00013_volume.mrc
Opened J272_class_35_00013_volume.mrc as #11, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_34_00013_volume.mrc
Opened J272_class_34_00013_volume.mrc as #12, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_33_00013_volume.mrc
Opened J272_class_33_00013_volume.mrc as #13, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_32_00013_volume.mrc
Opened J272_class_32_00013_volume.mrc as #14, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_31_00013_volume.mrc
Opened J272_class_31_00013_volume.mrc as #15, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_30_00013_volume.mrc
Opened J272_class_30_00013_volume.mrc as #16, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_29_00013_volume.mrc
Opened J272_class_29_00013_volume.mrc as #17, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_28_00013_volume.mrc
Opened J272_class_28_00013_volume.mrc as #18, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_27_00013_volume.mrc
Opened J272_class_27_00013_volume.mrc as #19, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_26_00013_volume.mrc
Opened J272_class_26_00013_volume.mrc as #20, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_25_00013_volume.mrc
Opened J272_class_25_00013_volume.mrc as #21, grid size 144,144,144, pixel
1.9, shown at level 0.106, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_24_00013_volume.mrc
Opened J272_class_24_00013_volume.mrc as #22, grid size 144,144,144, pixel
1.9, shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_23_00013_volume.mrc
Opened J272_class_23_00013_volume.mrc as #23, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_22_00013_volume.mrc
Opened J272_class_22_00013_volume.mrc as #24, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_21_00013_volume.mrc
Opened J272_class_21_00013_volume.mrc as #25, grid size 144,144,144, pixel
1.9, shown at level 0.104, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_20_00013_volume.mrc
Opened J272_class_20_00013_volume.mrc as #26, grid size 144,144,144, pixel
1.9, shown at level 0.113, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_19_00013_volume.mrc
Opened J272_class_19_00013_volume.mrc as #27, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_18_00013_volume.mrc
Opened J272_class_18_00013_volume.mrc as #28, grid size 144,144,144, pixel
1.9, shown at level 0.121, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_17_00013_volume.mrc
Opened J272_class_17_00013_volume.mrc as #29, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_16_00013_volume.mrc
Opened J272_class_16_00013_volume.mrc as #30, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_15_00013_volume.mrc
Opened J272_class_15_00013_volume.mrc as #31, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_14_00013_volume.mrc
Opened J272_class_14_00013_volume.mrc as #32, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_13_00013_volume.mrc
Opened J272_class_13_00013_volume.mrc as #33, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_12_00013_volume.mrc
Opened J272_class_12_00013_volume.mrc as #34, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_11_00013_volume.mrc
Opened J272_class_11_00013_volume.mrc as #35, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_10_00013_volume.mrc
Opened J272_class_10_00013_volume.mrc as #36, grid size 144,144,144, pixel
1.9, shown at level 0.112, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_09_00013_volume.mrc
Opened J272_class_09_00013_volume.mrc as #37, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_08_00013_volume.mrc
Opened J272_class_08_00013_volume.mrc as #38, grid size 144,144,144, pixel
1.9, shown at level 0.111, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_07_00013_volume.mrc
Opened J272_class_07_00013_volume.mrc as #39, grid size 144,144,144, pixel
1.9, shown at level 0.109, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_06_00013_volume.mrc
Opened J272_class_06_00013_volume.mrc as #40, grid size 144,144,144, pixel
1.9, shown at level 0.11, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_05_00013_volume.mrc
Opened J272_class_05_00013_volume.mrc as #41, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_04_00013_volume.mrc
Opened J272_class_04_00013_volume.mrc as #42, grid size 144,144,144, pixel
1.9, shown at level 0.102, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_03_00013_volume.mrc
Opened J272_class_03_00013_volume.mrc as #43, grid size 144,144,144, pixel
1.9, shown at level 0.107, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_02_00013_volume.mrc
Opened J272_class_02_00013_volume.mrc as #44, grid size 144,144,144, pixel
1.9, shown at level 0.114, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_01_00013_volume.mrc
Opened J272_class_01_00013_volume.mrc as #45, grid size 144,144,144, pixel
1.9, shown at level 0.108, step 1, values float32
> open
> /Users/victor/Downloads/cryosparc_P89_J272_00013_volume_series/J272_class_00_00013_volume.mrc
Opened J272_class_00_00013_volume.mrc as #46, grid size 144,144,144, pixel
1.9, shown at level 0.104, step 1, values float32
> surface dust #7 size 14.2
> surface dust #8 size 14.2
> surface dust #5 size 19
> surface dust #6 size 19
> surface dust #9 size 19
> surface dust #10 size 19
> surface dust #11 size 19
> surface dust #12 size 19
> surface dust #13 size 19
> surface dust #14 size 19
> surface dust #15 size 19
> surface dust #16 size 19
> surface dust #17 size 19
> surface dust #18 size 19
> surface dust #19 size 19
> surface dust #20 size 19
> surface dust #21 size 19
> surface dust #22 size 19
> surface dust #23 size 19
> surface dust #24 size 19
> surface dust #25 size 19
> surface dust #26 size 19
> surface dust #27 size 19
> surface dust #28 size 19
> surface dust #29 size 19
> surface dust #30 size 19
> surface dust #31 size 19
> surface dust #32 size 19
> surface dust #33 size 19
> surface dust #34 size 19
> surface dust #35 size 19
> surface dust #36 size 19
> surface dust #37 size 19
> surface dust #38 size 19
> surface dust #39 size 19
> surface dust #40 size 19
> surface dust #41 size 19
> surface dust #42 size 19
> surface dust #43 size 19
> surface dust #44 size 19
> surface dust #45 size 19
> surface dust #46 size 19
> volume #5 level 0.231
> volume #6 level 0.2425
> volume #9 level 0.1945
> open /Users/victor/Downloads/cryosparc_P1_J291_012_volume_map(1).mrc
Opened cryosparc_P1_J291_012_volume_map(1).mrc as #47, grid size 360,360,360,
pixel 0.758, shown at level 0.00584, step 2, values float32
> hide #!9 models
> volume #47 step 1
> volume #47 level 0.03422
> volume #47 level 0.00767
[Repeated 1 time(s)]
> surface dust #47 size 7.58
> volume #47 level 0.03239
> show #!1 models
> show #!46 models
> show #!45 models
> close #1-46
> close #47
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix45_In_UnArm/HigherResMap_Input/CootINProgress/J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb
Chain information for
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #1
---
Chain | Description
C | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix45_In_DosArms/HigherResMap_Input/CootINProgress/J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
Chain information for
J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb #2
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix4_Up/HigherResMap_Input/CootINProgress/J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb
Chain information for J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb #3
---
Chain | Description
C | No description available
D | No description available
E | No description available
F | No description available
J | No description available
> open
> /Users/victor/Desktop/GiGet345_FL_Gold/GiG3_AlphHelix4_Out/HigherResMap_Input/CootINProgress/J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb
Chain information for J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb
#4
---
Chain | Description
C D | No description available
E H | No description available
F | No description available
J | No description available
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 24354 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
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
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
~worm
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 tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui mousemode right select
Drag select of 260 atoms, 3510 residues, 8 pseudobonds, 264 bonds
> select add #1
27252 atoms, 7430 bonds, 12 pseudobonds, 3440 residues, 9 models selected
> select subtract #1
20164 atoms, 198 bonds, 6 pseudobonds, 2540 residues, 6 models selected
> select add #1
27252 atoms, 7430 bonds, 12 pseudobonds, 3440 residues, 9 models selected
> select add #2
28469 atoms, 15172 bonds, 16 pseudobonds, 3600 residues, 10 models selected
> select subtract #2
20818 atoms, 7364 bonds, 10 pseudobonds, 2630 residues, 7 models selected
> select add #2
28469 atoms, 15172 bonds, 16 pseudobonds, 3600 residues, 10 models selected
> select add #3
29686 atoms, 22972 bonds, 20 pseudobonds, 3760 residues, 11 models selected
> select subtract #3
21975 atoms, 15106 bonds, 14 pseudobonds, 2783 residues, 8 models selected
> select add #3
29686 atoms, 22972 bonds, 20 pseudobonds, 3760 residues, 11 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> select subtract #4
22450 atoms, 22906 bonds, 18 pseudobonds, 2847 residues, 9 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1542.4
RMSD between 254 pruned atom pairs is 0.611 angstroms; (across all 320 pairs:
5.074)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1526.7
RMSD between 249 pruned atom pairs is 0.664 angstroms; (across all 319 pairs:
5.701)
> select subtract #1
24549 atoms, 25040 bonds, 18 pseudobonds, 3119 residues, 9 models selected
> select subtract #2
16898 atoms, 17232 bonds, 12 pseudobonds, 2149 residues, 6 models selected
> select subtract #3
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> color sel bychain
> select subtract #1
Nothing selected
> show #!2 models
> hide #!1 models
> color #!2 bychain
> show #!3 models
> hide #!2 models
> color #!3 bychain
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> color #!4 bychain
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.97804,0.20775,-0.016797,242.17,0.20231,0.92687,-0.31619,28.187,-0.05012,-0.31265,-0.94855,324.97
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,16.295,0.13269,0.98868,0.070047,-18.151,-0.050667,-0.063813,0.99667,52.875
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,24.322,0.13269,0.98868,0.070047,-26.664,-0.050667,-0.063813,0.99667,19.531
> select subtract #3
Nothing selected
> show #!4 models
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.93258,-0.12141,-0.33992,72.752,0.11189,0.99258,-0.047568,-4.7571,0.34318,0.0063286,0.93925,-27.232
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.93258,-0.12141,-0.33992,75.003,0.11189,0.99258,-0.047568,-7.3297,0.34318,0.0063286,0.93925,-36.572
> select subtract #4
Nothing selected
> ui mousemode right select
Drag select of 260 atoms, 4331 residues, 8 pseudobonds, 264 bonds
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1542.4
RMSD between 254 pruned atom pairs is 0.611 angstroms; (across all 320 pairs:
5.074)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1526.7
RMSD between 249 pruned atom pairs is 0.664 angstroms; (across all 319 pairs:
5.701)
> undo
[Repeated 7 time(s)]Drag select of 8 residues
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #3
7711 atoms, 7866 bonds, 6 pseudobonds, 977 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98986,-0.1358,0.041625,24.329,0.13269,0.98868,0.070047,-27.261,-0.050667,-0.063813,0.99667,19.013
> select subtract #3
Nothing selected
> show #!4 models
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99454,-0.0062532,-0.10415,16.677,0.010101,0.99928,0.036453,-3.2295,0.10385,-0.037306,0.99389,3.8274
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99454,-0.0062532,-0.10415,19.146,0.010101,0.99928,0.036453,-5.5331,0.10385,-0.037306,0.99389,-6.6059
> select subtract #4
Nothing selected
> ui mousemode right select
Drag select of 93 residues
> select up
1302 atoms, 1327 bonds, 159 residues, 4 models selected
> select up
4742 atoms, 4845 bonds, 610 residues, 4 models selected
> select up
4873 atoms, 4976 bonds, 629 residues, 4 models selected
> select up
10225 atoms, 10435 bonds, 1298 residues, 4 models selected
> select up
10349 atoms, 10567 bonds, 1302 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
10349 atoms, 10567 bonds, 1302 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2-4 & sel to #1 & sel
Computing secondary structure
[Repeated 3 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain F
(#2), sequence alignment score = 1633.9
RMSD between 315 pruned atom pairs is 0.411 angstroms; (across all 319 pairs:
0.604)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain F (#3),
sequence alignment score = 1515.7
RMSD between 257 pruned atom pairs is 0.596 angstroms; (across all 321 pairs:
5.079)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain F
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain F
(#4), sequence alignment score = 1507.8
RMSD between 251 pruned atom pairs is 0.640 angstroms; (across all 318 pairs:
5.361)
> select add #1
14874 atoms, 15181 bonds, 6 pseudobonds, 1880 residues, 6 models selected
> select subtract #1
7786 atoms, 7949 bonds, 980 residues, 3 models selected
> select add #2
12891 atoms, 13156 bonds, 6 pseudobonds, 1630 residues, 5 models selected
> select subtract #2
5240 atoms, 5348 bonds, 660 residues, 2 models selected
> select add #3
10373 atoms, 10582 bonds, 6 pseudobonds, 1313 residues, 4 models selected
> select subtract #3
2662 atoms, 2716 bonds, 336 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select add #2
14739 atoms, 15040 bonds, 12 pseudobonds, 1870 residues, 6 models selected
> select add #3
22450 atoms, 22906 bonds, 18 pseudobonds, 2847 residues, 9 models selected
> select add #4
31637 atoms, 32272 bonds, 24 pseudobonds, 4019 residues, 12 models selected
> ui tool show "Color Actions"
> color sel orange
> color sel lime
> color sel light sea green
> color sel purple
> color sel gray
> color sel dark gray
> color sel gray
> color sel light gray
> color sel gray
> color sel dark gray
> color sel dim gray
> color sel bychain
[Repeated 2 time(s)]No target buttons for the coloring action are checked
[Repeated 3 time(s)]
> color sel bychain
> lighting full
> lighting soft
> select subtract #1
24549 atoms, 25040 bonds, 18 pseudobonds, 3119 residues, 9 models selected
> select subtract #2
16898 atoms, 17232 bonds, 12 pseudobonds, 2149 residues, 6 models selected
> select subtract #3
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
Drag select of 5 atoms, 74 residues, 3 bonds
> select add #4
9621 atoms, 9369 bonds, 6 pseudobonds, 1230 residues, 6 models selected
> select subtract #4
434 atoms, 3 bonds, 58 residues, 3 models selected
> select add #3
8003 atoms, 7868 bonds, 6 pseudobonds, 1016 residues, 5 models selected
> select subtract #3
292 atoms, 2 bonds, 39 residues, 2 models selected
> select add #2
7791 atoms, 7809 bonds, 6 pseudobonds, 989 residues, 4 models selected
> select subtract #2
140 atoms, 1 bond, 19 residues, 1 model selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right translate
> Select #1,2,3,4/J
Unknown command: Select #1,2,3,4/J
> Select #1/J
Unknown command: Select #1/J
> Select #1/J
Unknown command: Select #1/J
> Select #2/J
Unknown command: Select #2/J
> Select #3/J
Unknown command: Select #3/J
> Select #3
Unknown command: Select #3
> select #1/J
2554 atoms, 2609 bonds, 1 pseudobond, 321 residues, 2 models selected
> select #1,2/J
5108 atoms, 5218 bonds, 2 pseudobonds, 642 residues, 4 models selected
> select #1,2,3,4/J
10276 atoms, 10494 bonds, 4 pseudobonds, 1291 residues, 8 models selected
> color (#!1-4 & sel) #009051ff
> color (#!1-4 & sel) #00f900ff
> color (#!1-4 & sel) #a730f9ff
> color (#!1-4 & sel) #4b4af9ff
> color (#!1-4 & sel) #b6aef9ff
> color (#!1-4 & sel) #f2e1f9ff
> color (#!1-4 & sel) #f2e2f9ff
> color (#!1-4 & sel) #f3f998ff
> color (#!1-4 & sel) #f9f777ff
> color (#!1-4 & sel) #f9623eff
[Repeated 1 time(s)]
> select add #4
16877 atoms, 17220 bonds, 9 pseudobonds, 2138 residues, 9 models selected
> select subtract #4
7690 atoms, 7854 bonds, 3 pseudobonds, 966 residues, 6 models selected
> select add #3
12819 atoms, 13084 bonds, 8 pseudobonds, 1619 residues, 7 models selected
> select subtract #3
5108 atoms, 5218 bonds, 2 pseudobonds, 642 residues, 4 models selected
> select add #2
10205 atoms, 10417 bonds, 7 pseudobonds, 1291 residues, 5 models selected
> select subtract #2
2554 atoms, 2609 bonds, 1 pseudobond, 321 residues, 2 models selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> show #!2 models
> show #!3 models
> show #!4 models
> show sel atoms
> color sel byhetero
> select add #1
7148 atoms, 7292 bonds, 6 pseudobonds, 906 residues, 6 models selected
> select subtract #1
60 atoms, 60 bonds, 6 residues, 3 models selected
> select add #2
7691 atoms, 7848 bonds, 6 pseudobonds, 974 residues, 5 models selected
> select subtract #2
40 atoms, 40 bonds, 4 residues, 2 models selected
> select add #3
7731 atoms, 7886 bonds, 6 pseudobonds, 979 residues, 4 models selected
> select subtract #3
20 atoms, 20 bonds, 2 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> open /Users/victor/Desktop/GiGet345_FL_Gold/GETProteins_PDBs/7spy_dimer.pdb
Chain information for 7spy_dimer.pdb #5
---
Chain | Description
A B | No description available
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> open /Users/victor/Desktop/GiGet345_FL_Gold/GETProteins_PDBs/7SQ0.pdb
7SQ0.pdb title:
GET3 bound to adp and the transmembrane domain of the tail-anchored protein
BOS1 [more info...]
Chain information for 7SQ0.pdb #6
---
Chain | Description | UniProt
A B | atpase ASNA1 homolog | ASNA_GIAIC 1-94 125-354
C | TMD of the tail-anchored protein BOS1 |
Non-standard residues in 7SQ0.pdb #6
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select add #5
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #6
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,149.59,0,1,0,149.06,0,0,1,146.8
> select add #6
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> select #5,6/J,F:170
Nothing selected
> select #5,6/A
7265 atoms, 7188 bonds, 8 pseudobonds, 814 residues, 5 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5 & sel
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7spy_dimer.pdb, chain A (#5) with 7SQ0.pdb, chain A (#6), sequence
alignment score = 1384.1
RMSD between 221 pruned atom pairs is 0.992 angstroms; (across all 282 pairs:
6.273)
> select add #5
10021 atoms, 9818 bonds, 9 pseudobonds, 1319 residues, 5 models selected
> select subtract #5
4509 atoms, 4558 bonds, 7 pseudobonds, 309 residues, 3 models selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select add #5
5512 atoms, 5260 bonds, 2 pseudobonds, 1010 residues, 2 models selected
> select add #6
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.16235,0.43993,-0.88323,127,0.86755,-0.49009,-0.084646,194.98,-0.4701,-0.75251,-0.46123,155.87,#6,0.24439,-0.95657,-0.15887,216.32,0.43078,0.25389,-0.86601,178.46,0.86874,0.1432,0.47412,-29.378
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.16235,0.43993,-0.88323,166.91,0.86755,-0.49009,-0.084646,193.11,-0.4701,-0.75251,-0.46123,145.41,#6,0.24439,-0.95657,-0.15887,256.23,0.43078,0.25389,-0.86601,176.59,0.86874,0.1432,0.47412,-39.843
> view matrix models
> #5,0.16235,0.43993,-0.88323,165.84,0.86755,-0.49009,-0.084646,186.04,-0.4701,-0.75251,-0.46123,126.5,#6,0.24439,-0.95657,-0.15887,255.16,0.43078,0.25389,-0.86601,169.52,0.86874,0.1432,0.47412,-58.755
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.21001,0.56347,-0.799,166.27,0.89186,-0.44526,-0.079595,187.04,-0.40061,-0.69588,-0.59604,132.68,#6,0.09606,-0.97356,-0.20724,283.49,0.39365,0.22838,-0.89044,181.05,0.91423,0.0039569,0.40518,-37
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.21001,0.56347,-0.799,165.06,0.89186,-0.44526,-0.079595,188.05,-0.40061,-0.69588,-0.59604,132.77,#6,0.09606,-0.97356,-0.20724,282.29,0.39365,0.22838,-0.89044,182.07,0.91423,0.0039569,0.40518,-36.908
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
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
~worm
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 tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select add #5
14672 atoms, 14518 bonds, 16 pseudobonds, 1645 residues, 6 models selected
> select subtract #5
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> ui mousemode right select
Drag select of 254 residues, 1 atoms
> select up
4907 atoms, 4974 bonds, 538 residues, 6 models selected
> select up
17077 atoms, 17390 bonds, 1897 residues, 6 models selected
> select up
17082 atoms, 17394 bonds, 1898 residues, 6 models selected
> select up
17172 atoms, 17484 bonds, 1916 residues, 6 models selected
> select up
17541 atoms, 17682 bonds, 2105 residues, 6 models selected
> select up
46309 atoms, 46790 bonds, 5664 residues, 6 models selected
> select down
17541 atoms, 17682 bonds, 2105 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #!2-6 & sel to #1 & sel
Computing secondary structure
[Repeated 5 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb, chain J
(#2), sequence alignment score = 1666.5
RMSD between 317 pruned atom pairs is 0.398 angstroms; (across all 320 pairs:
0.453)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J250_Map_OUT_BothUP_real_space_refined_003-coot-0.pdb, chain J (#3),
sequence alignment score = 1537.2
RMSD between 252 pruned atom pairs is 0.587 angstroms; (across all 320 pairs:
5.106)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with J247_Get3_OUT_1DownOut_real_space_refined_007-coot-0.pdb, chain J
(#4), sequence alignment score = 1512
RMSD between 240 pruned atom pairs is 0.576 angstroms; (across all 319 pairs:
5.430)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with 7spy_dimer.pdb, chain A (#5), sequence alignment score = 1646.9
RMSD between 314 pruned atom pairs is 0.649 angstroms; (across all 319 pairs:
0.736)
Matchmaker J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb, chain J
(#1) with 7SQ0.pdb, chain A (#6), sequence alignment score = 1388.4
RMSD between 222 pruned atom pairs is 0.966 angstroms; (across all 290 pairs:
6.124)
> select add #1
22075 atoms, 22305 bonds, 6 pseudobonds, 2684 residues, 8 models selected
> select subtract #1
14987 atoms, 15073 bonds, 1784 residues, 5 models selected
> select add #2
20084 atoms, 20272 bonds, 6 pseudobonds, 2433 residues, 7 models selected
> select subtract #2
12433 atoms, 12464 bonds, 1463 residues, 4 models selected
> select add #3
17562 atoms, 17694 bonds, 6 pseudobonds, 2116 residues, 6 models selected
> select subtract #3
9851 atoms, 9828 bonds, 1139 residues, 3 models selected
> select add #4
16452 atoms, 16554 bonds, 6 pseudobonds, 1986 residues, 5 models selected
> select subtract #4
7265 atoms, 7188 bonds, 814 residues, 2 models selected
> select add #5
10021 atoms, 9818 bonds, 2 pseudobonds, 1319 residues, 3 models selected
> select subtract #5
4509 atoms, 4558 bonds, 309 residues, 1 model selected
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> hide #6.2.1 models
> ui mousemode right translate
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> ui mousemode right select
> select #6/C:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
123 atoms, 122 bonds, 19 residues, 1 model selected
> select up
138 atoms, 137 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select add #6
9160 atoms, 9258 bonds, 14 pseudobonds, 635 residues, 4 models selected
> select subtract #6
Nothing selected
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!4 models
> select #5,6/A,F:170
27 atoms, 27 bonds, 2 residues, 2 models selected
> show #!5 models
> show #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show sel atoms
> select #5,6/AF:170
Nothing selected
> select #5,6/A:170
27 atoms, 27 bonds, 2 residues, 2 models selected
> select #5,6/F:170
Nothing selected
> select #5,6/A,B:170
54 atoms, 54 bonds, 4 residues, 2 models selected
> show sel atoms
> hide H
> select clear
> ui mousemode right translate
> hide #!5 models
> hide #!6 models
> show #!2 models
> show #!3 models
> show #!4 models
> ui mousemode right select
> show #!1 models
Drag select of 1036 residues
> select up
7204 atoms, 7336 bonds, 936 residues, 4 models selected
> select up
7872 atoms, 8020 bonds, 1016 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
7872 atoms, 8020 bonds, 1016 residues, 4 models selected
> hide sel cartoons
Drag select of 179 residues
> select up
9226 atoms, 9397 bonds, 1193 residues, 4 models selected
> select up
9840 atoms, 10025 bonds, 1270 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
9840 atoms, 10025 bonds, 1270 residues, 4 models selected
> hide sel cartoons
Drag select of 146 residues
> select up
11000 atoms, 11211 bonds, 1414 residues, 4 models selected
> select up
31637 atoms, 32272 bonds, 4019 residues, 4 models selected
> select down
11000 atoms, 11211 bonds, 1414 residues, 4 models selected
> hide sel cartoons
> select add #1
16120 atoms, 16438 bonds, 6 pseudobonds, 2060 residues, 6 models selected
> select subtract #1
9032 atoms, 9206 bonds, 1160 residues, 3 models selected
> select add #2
14135 atoms, 14416 bonds, 6 pseudobonds, 1804 residues, 5 models selected
> select subtract #2
6484 atoms, 6608 bonds, 834 residues, 2 models selected
> select add #3
11647 atoms, 11876 bonds, 6 pseudobonds, 1485 residues, 4 models selected
> select subtract #3
3936 atoms, 4010 bonds, 508 residues, 1 model selected
> select add #4
9187 atoms, 9366 bonds, 6 pseudobonds, 1172 residues, 3 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> show sel & #!1 atoms
> select add #2
7711 atoms, 7868 bonds, 6 pseudobonds, 976 residues, 6 models selected
> select subtract #2
60 atoms, 60 bonds, 6 residues, 3 models selected
> select add #3
7751 atoms, 7906 bonds, 6 pseudobonds, 981 residues, 5 models selected
> select subtract #3
40 atoms, 40 bonds, 4 residues, 2 models selected
> select add #4
9207 atoms, 9386 bonds, 6 pseudobonds, 1174 residues, 4 models selected
> select subtract #4
20 atoms, 20 bonds, 2 residues, 1 model selected
> show #!5 models
> select clear
Drag select of 13 atoms, 47 residues, 11 bonds
> ui mousemode right translate
> select add #5
5703 atoms, 5267 bonds, 2 pseudobonds, 1035 residues, 3 models selected
> select subtract #5
191 atoms, 7 bonds, 25 residues, 1 model selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> ui mousemode right select
> select add #1/F:170@CG
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross ignoreHiddenModels true
134 contacts
> hide #7 models
> close #7
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!5 models
> show #!2 models
> show #!3 models
> show #!4 models
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> show sel atoms
> select add #4
9247 atoms, 9426 bonds, 6 pseudobonds, 1178 residues, 6 models selected
> select subtract #4
60 atoms, 60 bonds, 6 residues, 3 models selected
> select add #3
7751 atoms, 7906 bonds, 6 pseudobonds, 981 residues, 5 models selected
> select subtract #3
40 atoms, 40 bonds, 4 residues, 2 models selected
> select add #2
7671 atoms, 7828 bonds, 6 pseudobonds, 972 residues, 4 models selected
> select subtract #2
20 atoms, 20 bonds, 2 residues, 1 model selected
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!3 models
> select clear
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!1 models
> show #!4 models
> morph #1,2
models have different number of chains, 4 (Morph -
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #/C,Morph -
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #/E,Morph -
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #/F,Morph -
J252_GiGet3_IN_OneGet45_real_space_refined_003-coot-0.pdb #/J) and 5
(J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
#2/C,J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
#2/D,J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
#2/E,J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb
#2/F,J254_GiGet3_IN_TwoGet45_real_space_refined_002-coot-0.pdb #2/J)
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select add #2
7651 atoms, 7808 bonds, 6 pseudobonds, 970 residues, 3 models selected
> show sel cartoons
> select clear
Drag select of 173 residues
Drag select of 25 residues
> select up
1854 atoms, 1886 bonds, 240 residues, 1 model selected
> select up
2548 atoms, 2598 bonds, 326 residues, 1 model selected
> select up
7651 atoms, 7808 bonds, 970 residues, 1 model selected
> select down
2548 atoms, 2598 bonds, 326 residues, 1 model selected
> delete sel
> hide #!2 models
> show #!1 models
> select add #1
7088 atoms, 7232 bonds, 6 pseudobonds, 900 residues, 3 models selected
> show sel cartoons
> select clear
Drag select of 57 residues
Drag select of 148 residues
> select up
1065 atoms, 1083 bonds, 140 residues, 1 model selected
> select up
1968 atoms, 2005 bonds, 254 residues, 1 model selected
> delete sel
> view
> morph #1,2
Computed 51 frame morph #7
> coordset #7 1,51
> close #7
> show #!3 models
> show #!4 models
> show #!3-4 cartoons
Drag select of 327 residues
Drag select of 188 residues
> select up
4252 atoms, 4324 bonds, 555 residues, 2 models selected
> select up
6484 atoms, 6608 bonds, 834 residues, 2 models selected
> delete sel
> morph #1,2,3,4
Computed 151 frame morph #7
> coordset #7 1,151
> morph #1,2,4
Computed 101 frame morph #8
> coordset #8 1,101
> hide #!7 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
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
~worm
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
nucleotides tube/slab shape box
Drag select of 3 residues
> select clear
[Repeated 1 time(s)]
> select #8/F:169
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
94 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> select #8/J:169
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
94 atoms, 96 bonds, 12 residues, 1 model selected
> show sel atoms
> view
> select clear
> color #!8 byhetero
> hide #!8 models
> morph #1,4
Computed 51 frame morph #9
> coordset #9 1,51
> show #!9 atoms
> color #!9 byhetero
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> hide sel atoms
> select #1,2,3,4/J,F:170
80 atoms, 80 bonds, 8 residues, 4 models selected
> select add #4
5311 atoms, 5416 bonds, 6 pseudobonds, 670 residues, 6 models selected
> select add #3
10454 atoms, 10664 bonds, 12 pseudobonds, 1319 residues, 8 models selected
> select add #2
15537 atoms, 15854 bonds, 18 pseudobonds, 1961 residues, 10 models selected
> select add #1
20637 atoms, 21061 bonds, 24 pseudobonds, 2605 residues, 12 models selected
> select subtract #2
15534 atoms, 15851 bonds, 18 pseudobonds, 1961 residues, 9 models selected
> select subtract #1
10414 atoms, 10624 bonds, 12 pseudobonds, 1315 residues, 6 models selected
> select subtract #3
5251 atoms, 5356 bonds, 6 pseudobonds, 664 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> select #9/J,F:170,142
38 atoms, 36 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> select subtract #9
Nothing selected
> select add #9/F:173
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #9/F:141
19 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> select subtract #9
Nothing selected
> select #9/J,F:170,142, 141, 173
76 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> select add #9
4981 atoms, 5083 bonds, 4 pseudobonds, 633 residues, 2 models selected
> select subtract #9
Nothing selected
> ui mousemode right translate
> show #!8 models
> hide #!9 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!7 models
> show #!8 models
> hide #!7 models
> show #!9 models
> hide #!8 models
> show #!1 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> hide #!1 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!5 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> morph #5,1
Computed 51 frame morph #10
> coordset #10 1,51
> hide #!10 models
> show #!9 models
> close #10
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!7 models
> hide #!8 models
> select #7/J,F:170,142, 141, 173
76 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #7
4915 atoms, 5017 bonds, 4 pseudobonds, 624 residues, 2 models selected
> select subtract #7
Nothing selected
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!9 models
> save /Users/victor/Desktop/Get3_Morph.cxs includeMaps true
——— End of log from Wed Sep 10 10:31:54 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: MX2H3LL/A
Chip: Apple M4 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 33 days, 15 hours, 30 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
C27F398:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 7 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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