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Opened 6 weeks ago
Closed 6 weeks ago
#18995 closed defect (duplicate)
Crash moving window between screens
| 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
The following bug report has been submitted:
Platform: macOS-26.0-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 0x00000001ee3f0800 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, psutil._psutil_osx, psutil._psutil_posix, 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 (total: 121)
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"procRole" : "Foreground",
"version" : 2,
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"codeSigningMonitor" : 2,
"incident" : "78C69E8C-84C8-4F2D-AF24-89AF708EDB6A",
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"cpuType" : "ARM-64",
"roots_installed" : 0,
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"procLaunch" : "2025-09-24 16:30:39.2544 +0100",
"procStartAbsTime" : 534112587936,
"procExitAbsTime" : 4586392031254,
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"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
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"wakeTime" : 16461,
"sleepWakeUUID" : "EAAE041A-F03A-4A18-8121-359CAEC1DE93",
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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/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/Paper
> work/Revision_Figures/Apo_density_Turret.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened Apo_Emready.mrc resampled as #6, grid size 440,440,440, pixel 0.65,
shown at level 2.12, step 1, values float32
restore_snapshot for "ZoneMask" returned None
opened ChimeraX session
> show #!6 models
> select add #6
3 models selected
> ui tool show Toolbar
> show #!2 surfaces
> hide #!2 surfaces
> show #!2 surfaces
> coulombic #!2
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
TRP 45
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ARG 52
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
TRP 53
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ARG 54
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLU 86
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ASP 88
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
LYS 164
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ARG 166
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ASP 182
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
LYS 184
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ARG 212
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLU 213
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ASN 214
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
LYS 216
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ASN 261
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLU 280
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
THR 304
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
ARG 305
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLU 310
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLN 312
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
LYS 314
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
GLU 316
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/A
LYS 320
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
TRP 45
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ARG 52
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
TRP 53
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ARG 54
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLU 86
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ASP 88
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
LYS 164
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ARG 166
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ASP 182
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
LYS 184
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ARG 212
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLU 213
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ASN 214
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
LYS 216
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ASN 261
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLU 280
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
THR 304
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
ARG 305
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLU 310
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLN 312
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
LYS 314
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
GLU 316
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/B
LYS 320
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
TRP 45
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ARG 52
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
TRP 53
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ARG 54
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLU 86
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ASP 88
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
LYS 164
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ARG 166
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ASP 182
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
LYS 184
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ARG 212
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLU 213
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ASN 214
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
LYS 216
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ASN 261
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLU 280
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
THR 304
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
ARG 305
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLU 310
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLN 312
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
LYS 314
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
GLU 316
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/C
LYS 320
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
TRP 45
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ARG 52
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
TRP 53
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ARG 54
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLU 86
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ASP 88
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
LYS 164
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ARG 166
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ASP 182
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
LYS 184
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ARG 212
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLU 213
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ASN 214
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
LYS 216
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ASN 261
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLU 280
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
THR 304
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
ARG 305
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLU 310
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLN 312
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
LYS 314
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
GLU 316
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb #2/D
LYS 320
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb_A SES
surface #2.2: minimum, -16.50, mean -2.32, maximum 9.88
Coulombic values for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb_B SES
surface #2.3: minimum, -16.21, mean -2.32, maximum 12.65
Coulombic values for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb_C SES
surface #2.4: minimum, -16.61, mean -2.32, maximum 9.97
Coulombic values for
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb_D SES
surface #2.5: minimum, -16.27, mean -2.30, maximum 12.76
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> ui tool show "Surface Zone"
No atoms selected for zoning
> hide #!6 models
> show #!6 models
> select subtract #6
Nothing selected
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> select add #6
2 models selected
> select subtract #6
Nothing selected
> hide #!2 surfaces
> select add #6
2 models selected
No atoms selected for zoning
> select #2/A:103@CD1
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
15 atoms, 13 bonds, 2 residues, 2 models selected
> select up
172 atoms, 176 bonds, 23 residues, 2 models selected
> surface zone #6 nearAtoms sel distance 1.9
> color #6 #d6d6d6ff models
> color #6 #d6d6d690 models
> surface zone #6 nearAtoms sel distance 1.79
> surface zone #6 nearAtoms sel distance 97.66
> surface zone #6 nearAtoms sel distance 99.22
> surface zone #6 nearAtoms sel distance 650
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PhD/FinalDepositedMapsAndModels/Apo/cryosparc_P256_J1166_008_volume_map_sharp.mrc
Opened cryosparc_P256_J1166_008_volume_map_sharp.mrc as #1, grid size
440,440,440, pixel 0.65, shown at level 0.0436, step 2, values float32
> hide #!6 models
> volume #1 step 1
> surface zone #1 nearAtoms sel distance 3.9
> surface zone #1 nearAtoms sel distance 3.95
> surface zone #1 nearAtoms sel distance 8.74
> surface dust #1 size 6.5
> volume #1 level 0.01492
> volume #1 level 0.05508
> volume #1 level 0.04361
> volume #1 level 0.03213
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) using 8726 atoms
average map value = 0.3494, steps = 28
shifted from previous position = 0.007
rotated from previous position = 0.00719 degrees
atoms outside contour = 602, contour level = 0.032133
Position of
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997564 0.00697978 -0.00001845 -0.99840838
-0.00697979 0.99997564 -0.00002782 1.00188621
0.00001826 0.00002794 1.00000000 0.80724699
Axis 0.00399439 -0.00262977 -0.99998856
Axis point 142.73514930 143.07524068 0.00000000
Rotation angle (degrees) 0.39992005
Shift along axis -0.81386053
> volume #1 color #b2b2b272
> color #2 orchid
> color #2 #d783ffff
> fitmap #2 inMap #1
Fit molecule
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) using 8726 atoms
average map value = 0.3494, steps = 48
shifted from previous position = 0.0115
rotated from previous position = 0.0108 degrees
atoms outside contour = 600, contour level = 0.032133
Position of
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997476 0.00710414 0.00010001 -1.02002933
-0.00710413 0.99997476 -0.00010483 1.02681815
-0.00010076 0.00010412 0.99999999 0.81343209
Axis 0.01470358 0.01412768 -0.99979208
Axis point 145.65058441 142.41568691 0.00000000
Rotation angle (degrees) 0.40712478
Shift along axis -0.81375449
> surface zone #1 nearAtoms sel distance 8.74
> surface zone #1 nearAtoms sel distance 8.89
> surface zone #1 nearAtoms sel distance 18.13
> surface dust #1 size 6.5
> undo
> fitmap #2 inMap #1
Fit molecule
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
to map cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) using 8726 atoms
average map value = 0.3494, steps = 44
shifted from previous position = 0.0138
rotated from previous position = 0.00953 degrees
atoms outside contour = 604, contour level = 0.032133
Position of
apo_post_isolde_real_space_refined_014-coot-0_real_space_refined_015.pdb (#2)
relative to cryosparc_P256_J1166_008_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99997483 0.00709559 0.00000961 -1.01429097
-0.00709559 0.99997483 0.00003457 1.01714317
-0.00000936 -0.00003463 1.00000000 0.81282688
Axis -0.00487639 0.00133669 -0.99998722
Axis point 142.98958227 144.00819148 0.00000000
Rotation angle (degrees) 0.40655613
Shift along axis -0.80651080
> surface zone #1 nearAtoms sel distance 2.51
> surface zone #1 nearAtoms sel distance 2.47
> surface zone #1 nearAtoms sel distance 20.15
> surface zone #1 nearAtoms sel distance 20.3
> surface zone #1 nearAtoms sel distance 108.55
> surface dust #1 size 6.5
> volume #1 level 0.005804
> surface zone #1 nearAtoms sel distance 1.46
> surface zone #1 nearAtoms sel distance 1.47
> surface zone #1 nearAtoms sel distance 6.92
> surface zone #1 nearAtoms sel distance 7.03
> surface zone #1 nearAtoms sel distance 4.54
> surface unzone #1
> view orient
> volume #1 level 0.3481
> volume #1 level 0.03966
> surface zone #1 nearAtoms sel distance 4.54
> surface zone #1 nearAtoms sel distance 4.69
> surface zone #1 nearAtoms sel distance 13.54
> color #2 orchid
> open /Users/omallen/Library/CloudStorage/OneDrive-
> TheFrancisCrickInstitute/PP/Cul2_VHL/Spray_dimer_mask.mrc
Opened Spray_dimer_mask.mrc as #4, grid size 120,120,120, pixel 3.8, shown at
level 0.456, step 1, values float32
> hide #!2 models
> view orient
> volume #4 level 1.756
> volume #4 level 1.492
> hide #!4 models
> select ~sel & ##selected
8554 atoms, 8780 bonds, 8 pseudobonds, 1135 residues, 2 models selected
> open 3jyc
Summary of feedback from opening 3jyc fetched from pdb
---
note | Fetching compressed mmCIF 3jyc from http://files.rcsb.org/download/3jyc.cif
3jyc title:
Crystal structure of the eukaryotic strong inward-rectifier K+ channel Kir2.2
at 3.1 Angstrom resolution [more info...]
Chain information for 3jyc #5
---
Chain | Description
A | Inward-rectifier K+ channel Kir2.2
Non-standard residues in 3jyc #5
---
K — potassium ion
3jyc mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 3jyc assembly 1
'assembly' has no suffix
> open 3jyc assembly
'assembly' has no suffix
> open 3jyc assembly
'assembly' has no suffix
> open /Users/omallen/Downloads/3JYC.pdb1
3JYC.pdb1 title:
Crystal structure of the eukaryotic strong inward-rectifier K+ channel KIR2.2
At 3.1 angstrom resolution [more info...]
Chain information for 3JYC.pdb1
---
Chain | Description
7.1/A | No description available
7.2/A 7.3/A 7.4/A | No description available
> hide #!5 models
> hide #!7.1.2 models
> hide #7.1.1 models
> show #7.1.1 models
> hide #7.2.1 models
> hide #7.3.1 models
> hide #7.4.1 models
> combine #7.1 #7.2 #7.3 #7.4
Remapping chain ID 'A' in 3JYC.pdb1 #7.2 to 'B'
Remapping chain ID 'A' in 3JYC.pdb1 #7.3 to 'C'
Remapping chain ID 'A' in 3JYC.pdb1 #7.4 to 'D'
> hide #!8.2 models
Cell requested for row 6 is out of bounds for table with 15 rows! Resizing
table model.
> close #7
> close #5
> open /Users/omallen/Downloads/3SPI.pdb1
3SPI.pdb1 title:
Inward rectifier potassium channel KIR2.2 In complex with PIP2 [more info...]
Chain information for 3SPI.pdb1
---
Chain | Description
5.1/A | No description available
5.2/A 5.3/A 5.4/A | No description available
> combine #5.1 #5.2 #5.3 #5.4
Remapping chain ID 'A' in 3SPI.pdb1 #5.2 to 'B'
Remapping chain ID 'A' in 3SPI.pdb1 #5.3 to 'C'
Remapping chain ID 'A' in 3SPI.pdb1 #5.4 to 'D'
> close #5.2-4#5#5.1
> rename #7 Kir2.2_extended
> rename #8 Kir2.2_docked
> tile
2 models tiled
> hide #!7-8 atoms
> show #!7-8 atoms
> hide #!7-8 atoms
> show #!7-8 surfaces
> hide #!7-8 surfaces
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> cartoon style (#7#8.1,3-6#!8 & coil) xsection oval
> cartoon style #7#8.1,3-6#!8 xsection barbell modeHelix default
> cartoon style #7#8.1,3-6#!8 modeHelix tube sides 20
> cartoon style #7#8.1,3-6#!8 xsection rectangle modeHelix default
> cartoon style #7#8.1,3-6#!8 xsection oval modeHelix default
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 36 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
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> open 6XIS
6xis title:
Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2
(Kir3.2) in apo form [more info...]
Chain information for 6xis #5
---
Chain | Description | UniProt
A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380
> select up
8557 atoms, 8780 bonds, 8 pseudobonds, 1138 residues, 6 models selected
> tile
3 models tiled
> rename #5 Kir3.2_extended
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!5.1 models
> tile row 1
Expected a models specifier or a keyword
> tile columns 5
3 models tiled
> ui mousemode right "move picked models"
> view matrix models
> #5,0.57004,-0.79514,0.2069,-254.27,-0.82146,-0.54666,0.16235,380.89,-0.015987,-0.26251,-0.9648,265.02
> view matrix models
> #5,0.25356,-0.96507,-0.065996,-124.34,-0.96715,-0.25163,-0.03622,389.86,0.018348,0.073012,-0.99716,208.56
> tile columns 5
3 models tiled
> open 6XIT
Summary of feedback from opening 6XIT fetched from pdb
---
note | Fetching compressed mmCIF 6xit from http://files.rcsb.org/download/6xit.cif
6xit title:
Cryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK2
(Kir3.2) in complex with PIP2 [more info...]
Chain information for 6xit #9
---
Chain | Description | UniProt
A B C D | G protein-activated inward rectifier potassium channel 2 | A0A338P6L0_MOUSE 52-380
Non-standard residues in 6xit #9
---
K — potassium ion
PIO —
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate (dioctanoyl l-alpha-
phosphatidyl-d-myo-inositol 4,5-diphosphate)
> tile columns 5
4 models tiled
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!5,7-9 atoms
> open 8TI1
Summary of feedback from opening 8TI1 fetched from pdb
---
notes | Fetching compressed mmCIF 8ti1 from http://files.rcsb.org/download/8ti1.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD P5S from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/P5S/P5S.cif
Fetching CCD PEF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/PEF/PEF.cif
Fetching CCD PT5 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/PT5/PT5.cif
8ti1 title:
Cryo-EM structure of a SUR1/Kir6.2-Q52R ATP-sensitive potassium channel in the
presence of PIP2 in the open conformation [more info...]
Chain information for 8ti1 #10
---
Chain | Description | UniProt
A B C D | ATP-sensitive inward rectifier potassium channel 11 | KCJ11_RAT 1-390
E F G H | SUR1 | A0A1S4NYG1_MESAU 1-1582
Non-standard residues in 8ti1 #10
---
K — potassium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
PT5 —
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
(Phosphatidylinositol 4,5-bisphosphate; PtdIns(4,5)P2)
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #10/E#10/F#10/G#10/H
34600 atoms, 35336 bonds, 20 pseudobonds, 4584 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 43856 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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide sel cartoons
> open 8TI2
Summary of feedback from opening 8TI2 fetched from pdb
---
note | Fetching compressed mmCIF 8ti2 from http://files.rcsb.org/download/8ti2.cif
8ti2 title:
Cryo-EM structure of a SUR1/Kir6.2-Q52R ATP-sensitive potassium channel in the
presence of PIP2 in the open conformation [more info...]
Chain information for 8ti2 #11
---
Chain | Description | UniProt
A B C D | ATP-sensitive inward rectifier potassium channel 11 | KCJ11_RAT 1-390
E F G H | SUR1 | A0A1S4NYG1_MESAU 1-1582
Non-standard residues in 8ti2 #11
---
K — potassium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
PT5 —
[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-
cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate
(Phosphatidylinositol 4,5-bisphosphate; PtdIns(4,5)P2)
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #10/E#10/F#10/G#10/H#11/E#11/F#11/G#11/H
74376 atoms, 75848 bonds, 40 pseudobonds, 10216 residues, 4 models selected
> hide sel cartoons
> hide sel atoms
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 49032 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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide sel cartoons
> open 7S5x
Summary of feedback from opening 7S5x fetched from pdb
---
notes | Fetching compressed mmCIF 7s5x from http://files.rcsb.org/download/7s5x.cif
Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif
7s5x title:
Human KATP channel in open conformation, focused on Kir and one SUR, position
1 [more info...]
Chain information for 7s5x #12
---
Chain | Description | UniProt
A B C D | ATP-sensitive inward rectifier potassium channel 11 | B2RC52_HUMAN 1-390
E | ATP-binding cassette sub-family C member 8 | ABCC8_HUMAN 3-1582
Non-standard residues in 7s5x #12
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> close #10-11
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 21153 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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #12/E
11137 atoms, 11376 bonds, 16 pseudobonds, 1416 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> open 7TYS
Summary of feedback from opening 7TYS fetched from pdb
---
notes | Fetching compressed mmCIF 7tys from http://files.rcsb.org/download/7tys.cif
Fetching CCD 65I from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/65I/65I.cif
Fetching CCD BJX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/BJX/BJX.cif
Fetching CCD POV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/POV/POV.cif
7tys title:
Cryo-EM structure of the pancreatic ATP-sensitive potassium channel bound to
ATP and repaglinide with Kir6.2-CTD in the up conformation [more info...]
Chain information for 7tys #10
---
Chain | Description | UniProt
A B C D | ATP-sensitive inward rectifier potassium channel 11 | KCJ11_RAT 1-390
E | ATP-binding cassette sub-family C member 8 | ABCC8_CRICR 1-1582
Non-standard residues in 7tys #10
---
65I —
(9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl
undecanoate
ATP — adenosine-5'-triphosphate
BJX — Repaglinide
(2-ethoxy-4-[2-({(1S)-3-methyl-1-[2-(piperidin-1-yl)phenyl]butyl}amino)-2-oxoethyl]benzoic
acid)
K — potassium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
P5S —
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
(phosphatidyl serine)
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 20372 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 default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #10/E#12/E
21638 atoms, 22090 bonds, 20 pseudobonds, 2857 residues, 5 models selected
> hide sel cartoons
> hide sel atoms
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 88, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 154, in status
r.draw_background()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> open "/Users/omallen/Downloads/cryosparc_P313_J702_002_volume_map (1).mrc"
Opened cryosparc_P313_J702_002_volume_map (1).mrc as #11, grid size
256,256,256, pixel 1.58, shown at level 0.208, step 1, values float32
> hide #!12 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> color #11 silver models
> color #11 darkgrey models
> open "/Users/omallen/Downloads/cryosparc_P313_J702_002_volume_map (1).mrc"
Opened cryosparc_P313_J702_002_volume_map (1).mrc as #13, grid size
256,256,256, pixel 1.58, shown at level 0.208, step 1, values float32
> close #13
> volume #11 level 0.5247
> volume #11 level 0.5932
> view orient
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Class3D/job279/run_it035_class001.mrc
Opened run_it035_class001.mrc as #13, grid size 180,180,180, pixel 1.9, shown
at level 0.0216, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Class3D/job279/run_it035_class003.mrc
Opened run_it035_class003.mrc as #14, grid size 180,180,180, pixel 1.9, shown
at level 0.0109, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Class3D/job279/run_it035_class002.mrc
Opened run_it035_class002.mrc as #15, grid size 180,180,180, pixel 1.9, shown
at level 0.015, step 1, values float32
> tile
3 models tiled
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Refine3D/job281/run_class001.mrc
Opened run_class001.mrc as #16, grid size 180,180,180, pixel 1.9, shown at
level 0.0108, step 1, values float32
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Refine3D/job271/run_class001.mrc
Opened run_class001.mrc as #17, grid size 180,180,180, pixel 1.9, shown at
level 0.0111, step 1, values float32
> tile
2 models tiled
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Refine3D/job198/run_class001.mrc
Opened run_class001.mrc as #18, grid size 320,320,320, pixel 0.95, shown at
level 0.00545, step 2, values float32
> open /Volumes/lab-
> enchevr/home/users/enchevr/cluster_processing/gJC067_VHL_20msE2/Refine3D/job195/run_class001.mrc
Opened run_class001.mrc as #19, grid size 320,320,320, pixel 0.95, shown at
level 0.00673, step 2, values float32
> open /Users/omallen/Downloads/cryosparc_P313_J750_map_sharp.mrc
Opened cryosparc_P313_J750_map_sharp.mrc as #20, grid size 256,256,256, pixel
1.58, shown at level 0.112, step 1, values float32
> volume #20 level 0.7741
> volume #20 level 1.222
> view orient
> open 6SJ7
6sj7 title:
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and
Indisulam [more info...]
Chain information for 6sj7 #21
---
Chain | Description | UniProt
A | DDB1- and CUL4-associated factor 15 | DCA15_HUMAN 1-600
B | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140
C | RNA binding protein 39 | Q7Z3L0_HUMAN 248-328
D | DET1- and DDB1-associated protein 1 | DDA1_HUMAN 2-102
Non-standard residues in 6sj7 #21
---
EF6 — N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide (Indisulam)
> ui tool show "Fit in Map"
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = 0.001165, steps = 440
shifted from previous position = 30
rotated from previous position = 12.3 degrees
atoms outside contour = 10007, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
0.99911018 -0.04201545 -0.00368153 -9.57277990
-0.00271901 0.02294302 -0.99973308 379.08199012
0.04208870 0.99885350 0.02280837 -41.79740202
Axis 0.99954478 -0.02289088 0.01965317
Axis point 0.00000000 210.62226146 172.90172249
Rotation angle (degrees) 88.71470285
Shift along axis -19.06739281
> view matrix models
> #21,0.98799,0.15104,-0.032567,7.4899,-0.15142,0.98843,-0.0094108,51.73,0.030769,0.014229,0.99943,-19.417
> view matrix models
> #21,-0.81773,0.46288,0.34214,206.23,0.27058,-0.21553,0.93826,94.821,0.50805,0.85982,0.050997,-50.62
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = -0.01554, steps = 216
shifted from previous position = 40.2
rotated from previous position = 36.8 degrees
atoms outside contour = 10007, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
-0.64791377 -0.54769937 -0.52937052 535.28287342
0.58915207 -0.80084106 0.10748692 216.48444310
-0.48281216 -0.24223749 0.84155417 195.57083374
Axis -0.29380245 -0.03911354 0.95506557
Axis point 260.18116945 205.78938973 0.00000000
Rotation angle (degrees) 143.47529719
Shift along axis 21.04807925
> select down
30192 atoms, 30870 bonds, 20 pseudobonds, 3992 residues, 6 models selected
> hide #!21.1 models
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = -0.01554, steps = 64
shifted from previous position = 0.0156
rotated from previous position = 0.0175 degrees
atoms outside contour = 10007, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
-0.64797007 -0.54785633 -0.52913914 535.27546672
0.58928062 -0.80075042 0.10745753 216.45623784
-0.48257968 -0.24218217 0.84170342 195.53185352
Axis -0.29367015 -0.03910632 0.95510656
Axis point 260.15310683 205.79439919 0.00000000
Rotation angle (degrees) 143.46646085
Shift along axis 21.09452180
> ~tile
> view matrix models
> #21,0.57043,0.70674,-0.41848,64.238,-0.17829,0.6039,0.77686,12.737,0.80176,-0.36854,0.47049,17.487
> view matrix models
> #21,0.57043,0.70674,-0.41848,102.26,-0.17829,0.6039,0.77686,49.836,0.80176,-0.36854,0.47049,68.374
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = 0.7699, steps = 212
shifted from previous position = 25.4
rotated from previous position = 41.9 degrees
atoms outside contour = 7360, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
0.97109054 -0.10949394 -0.21211844 130.56673143
-0.05113050 0.77256671 -0.63287151 192.33263025
0.23317124 0.62542126 0.74463375 3.68812477
Axis 0.94181114 -0.33329190 0.04368405
Axis point 0.00000000 117.73105851 292.68188141
Rotation angle (degrees) 41.91424374
Shift along axis 59.02740697
> view matrix models
> #21,0.2159,0.95341,-0.2107,81.175,0.04162,0.20661,0.97754,54.398,0.97553,-0.21982,0.0049265,118.54
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = 0.8511, steps = 128
shifted from previous position = 5.25
rotated from previous position = 18.9 degrees
atoms outside contour = 7289, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
0.83956341 0.13930712 -0.52509695 156.23673709
0.11052644 0.90254816 0.41616190 26.67362035
0.53189960 -0.40743140 0.74234929 111.14747062
Axis -0.61448911 -0.78863301 -0.02147348
Axis point -111.24894374 -0.00000000 191.76994685
Rotation angle (degrees) 42.07823782
Shift along axis -119.42819402
> view matrix models
> #21,-0.94897,-0.16919,-0.26612,360.52,-0.15483,-0.4852,0.86059,178.25,-0.27473,0.85788,0.43425,88.162
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = 0.8207, steps = 80
shifted from previous position = 5.11
rotated from previous position = 13.1 degrees
atoms outside contour = 7581, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
-0.69146797 0.70650762 0.15072831 178.50897711
-0.62734864 -0.69072019 0.35963774 310.20590985
0.35819789 0.15411877 0.92083748 43.70393609
Axis -0.15051370 -0.15194225 -0.97686190
Axis point 144.94247830 119.20699434 0.00000000
Rotation angle (degrees) 136.94304001
Shift along axis -116.69414258
> view matrix models
> #21,0.10352,-0.90617,-0.41004,350.21,0.6644,-0.24379,0.7065,71.394,-0.74017,-0.34557,0.57683,270.45
> fitmap #21 inMap #20
Fit molecule 6sj7 (#21) to map cryosparc_P313_J750_map_sharp.mrc (#20) using
10007 atoms
average map value = 1.117, steps = 100
shifted from previous position = 5.97
rotated from previous position = 21.9 degrees
atoms outside contour = 5834, contour level = 1.2222
Position of 6sj7 (#21) relative to cryosparc_P313_J750_map_sharp.mrc (#20)
coordinates:
Matrix rotation and translation
-0.84219635 -0.52326896 -0.12998041 384.55835250
0.53010425 -0.84763691 -0.02238629 242.28499715
-0.09846214 -0.08775682 0.99126381 116.70939486
Axis -0.06191152 -0.02985051 0.99763516
Axis point 160.87003598 178.66708153 0.00000000
Rotation angle (degrees) 148.13395729
Shift along axis 85.39247172
> select #21/C
619 atoms, 630 bonds, 79 residues, 1 model selected
> color sel red
> volume #20 level 0.8889
> volume #20 level 1.274
> volume #20 level 1.17
> volume #20 level 0.389
> open /Users/omallen/Downloads/cryosparc_P313_J746_003_volume_map.mrc
Opened cryosparc_P313_J746_003_volume_map.mrc as #22, grid size 256,256,256,
pixel 1.58, shown at level 0.02, step 1, values float32
> volume #22 level 1.229
> view matrix models
> #21,-0.13765,-0.98497,0.10433,312.43,0.97337,-0.11503,0.19832,87.015,-0.18334,0.12885,0.97457,85.264
> fitmap #21 inMap #22
Fit molecule 6sj7 (#21) to map cryosparc_P313_J746_003_volume_map.mrc (#22)
using 10007 atoms
average map value = 1.165, steps = 200
shifted from previous position = 23.7
rotated from previous position = 55.1 degrees
atoms outside contour = 5492, contour level = 1.2287
Position of 6sj7 (#21) relative to cryosparc_P313_J746_003_volume_map.mrc
(#22) coordinates:
Matrix rotation and translation
-0.86423121 -0.48560544 -0.13149814 382.28587131
0.48784295 -0.87276926 0.01682457 245.22452439
-0.12293764 -0.04961012 0.99117363 110.96786604
Axis -0.06808575 -0.00877325 0.99764090
Axis point 162.82022095 173.74230344 0.00000000
Rotation angle (degrees) 150.79898369
Shift along axis 82.52644448
> volume #22 level 0.9537
> volume #22 level 1.193
> volume #22 color #b2ffff7f
> volume #22 level 0.8596
> open /Users/omallen/Downloads/cryosparc_P313_J741_002_volume_map.mrc
Opened cryosparc_P313_J741_002_volume_map.mrc as #23, grid size 128,128,128,
pixel 3.16, shown at level 0.22, step 1, values float32
> view matrix models
> #23,0.9021,0.43126,0.015057,-82.108,0.21831,-0.42601,-0.87798,437.03,-0.37222,0.79532,-0.47846,204.3
> view matrix models
> #23,0.96779,-0.19088,0.16417,8.4047,0.019125,-0.59446,-0.8039,500.58,0.25104,0.78114,-0.57166,102.37
> fitmap #23 inMap #22
Fit map cryosparc_P313_J741_002_volume_map.mrc in map
cryosparc_P313_J746_003_volume_map.mrc using 20969 points
correlation = 0.6533, correlation about mean = 0.2228, overlap = 1.41e+04
steps = 632, shift = 31.1, angle = 94.6 degrees
Position of cryosparc_P313_J741_002_volume_map.mrc (#23) relative to
cryosparc_P313_J746_003_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
-0.05944164 0.60873406 0.79114445 -92.73196204
0.98701291 0.15432894 -0.04458808 -23.25626831
-0.14923876 0.77821940 -0.61000194 190.53322334
Axis 0.63024433 0.72030360 0.28974956
Axis point 14.42332459 0.00000000 120.60379817
Rotation angle (degrees) 139.24932742
Shift along axis -19.98845001
> volume #23 level 0.4862
> volume #23 color #b2b2ff5e
> view matrix models
> #23,-0.31325,-0.86167,-0.39924,493.6,-0.86389,0.083939,0.49664,267.7,-0.39443,0.50047,-0.77068,320.75
> view matrix models
> #23,0.37798,-0.78944,-0.48365,389.72,-0.91782,-0.38801,-0.083965,462.74,-0.12138,0.47565,-0.87122,285.1
> view matrix models
> #23,0.081624,-0.6725,-0.73558,480.24,-0.99562,-0.021309,-0.090998,433.04,0.045522,0.73979,-0.6713,173.37
> fitmap #23 inMap #22
Fit map cryosparc_P313_J741_002_volume_map.mrc in map
cryosparc_P313_J746_003_volume_map.mrc using 17381 points
correlation = 0.6678, correlation about mean = 0.1317, overlap = 1.38e+04
steps = 1296, shift = 37.9, angle = 180 degrees
Position of cryosparc_P313_J741_002_volume_map.mrc (#23) relative to
cryosparc_P313_J746_003_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
-0.07506867 0.60503488 0.79265218 -89.14326730
0.98529999 0.16733139 -0.03441128 -27.75658585
-0.15345561 0.77841698 -0.60870221 190.92879737
Axis 0.62333542 0.72554379 0.29161475
Axis point 17.63642401 0.00000000 120.63301200
Rotation angle (degrees) 139.30750469
Shift along axis -20.02712087
> fitmap #23 inMap #22
Fit map cryosparc_P313_J741_002_volume_map.mrc in map
cryosparc_P313_J746_003_volume_map.mrc using 17381 points
correlation = 0.6678, correlation about mean = 0.1316, overlap = 1.38e+04
steps = 104, shift = 0.0222, angle = 0.0468 degrees
Position of cryosparc_P313_J741_002_volume_map.mrc (#23) relative to
cryosparc_P313_J746_003_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
-0.07583869 0.60487198 0.79270321 -88.96126548
0.98527277 0.16764438 -0.03365900 -27.98532627
-0.15325162 0.77847624 -0.60867782 190.86821295
Axis 0.62304443 0.72570659 0.29183144
Axis point 17.76670553 0.00000000 120.59106151
Rotation angle (degrees) 139.32651798
Shift along axis -20.03461093
> volume #23 color #b2b2ff93
> view matrix models
> #23,0.37909,0.45405,0.8063,-151.68,0.82172,-0.56586,-0.067681,174.62,0.42553,0.68821,-0.58762,85.168
> view matrix models
> #23,0.6712,0.063155,0.73858,-134.94,0.52586,-0.74281,-0.41437,294.2,0.52246,0.66652,-0.53178,85.6
> open /Users/omallen/Downloads/cryosparc_P313_J748_003_volume_map.mrc
Opened cryosparc_P313_J748_003_volume_map.mrc as #24, grid size 256,256,256,
pixel 1.58, shown at level 0.029, step 1, values float32
> fitmap #24 inMap #22
Fit map cryosparc_P313_J748_003_volume_map.mrc in map
cryosparc_P313_J746_003_volume_map.mrc using 167118 points
correlation = 0.8778, correlation about mean = 0.7373, overlap = 9.889e+04
steps = 180, shift = 7.06, angle = 13 degrees
Position of cryosparc_P313_J748_003_volume_map.mrc (#24) relative to
cryosparc_P313_J746_003_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
0.97595035 -0.21501341 -0.03591854 52.28791273
0.21666457 0.97490746 0.05110688 -48.87474002
0.02402859 -0.05766006 0.99804707 6.57931654
Axis -0.24214129 -0.13345670 0.96101868
Axis point 250.40847557 215.38349264 0.00000000
Rotation angle (degrees) 12.97900253
Shift along axis 0.18444459
> volume #24 level 0.6334
> volume #24 color #ffb2ff72
> fitmap #24 inMap #22
Fit map cryosparc_P313_J748_003_volume_map.mrc in map
cryosparc_P313_J746_003_volume_map.mrc using 70766 points
correlation = 0.9244, correlation about mean = 0.4284, overlap = 8.848e+04
steps = 44, shift = 0.169, angle = 0.173 degrees
Position of cryosparc_P313_J748_003_volume_map.mrc (#24) relative to
cryosparc_P313_J746_003_volume_map.mrc (#22) coordinates:
Matrix rotation and translation
0.97550466 -0.21661211 -0.03833879 53.31639067
0.21841882 0.97448209 0.05174809 -49.36990006
0.02615120 -0.05885442 0.99792398 6.45351023
Axis -0.24389742 -0.14221145 0.95931744
Axis point 251.36042649 217.94723486 0.00000000
Rotation angle (degrees) 13.10520706
Shift along axis 0.20819984
> volume #24 level 0.7132
> volume #24 level 0.8158
> volume #22 level 1.034
> volume #22 color #a9a9a97a
> open /Volumes/lab-enchevr/home/users/omallen/EMReady/J743_Emready.mrc
Opened J743_Emready.mrc as #25, grid size 403,403,403, pixel 1, shown at level
0.000534, step 2, values float32
> volume #25 step 1
> volume #25 level 1.001
> volume #25 level 2.54
> fitmap #21 inMap #25
Fit molecule 6sj7 (#21) to map J743_Emready.mrc (#25) using 10007 atoms
average map value = 3.129, steps = 68
shifted from previous position = 4.12
rotated from previous position = 3.78 degrees
atoms outside contour = 3559, contour level = 2.5403
Position of 6sj7 (#21) relative to J743_Emready.mrc (#25) coordinates:
Matrix rotation and translation
-0.84050302 -0.52789874 -0.12197368 384.06154918
0.53387596 -0.84531790 -0.02034952 241.24068666
-0.09236405 -0.08222265 0.99232470 115.20799698
Axis -0.05815209 -0.02782891 0.99791978
Axis point 160.22281304 178.38166474 0.00000000
Rotation angle (degrees) 147.85971848
Shift along axis 85.92089033
> volume #25 color #ffb2b280
> volume #25 level 2.925
> volume #25 color #92929274
> fitmap #21 inMap #25
Fit molecule 6sj7 (#21) to map J743_Emready.mrc (#25) using 10007 atoms
average map value = 3.129, steps = 44
shifted from previous position = 0.0193
rotated from previous position = 0.0151 degrees
atoms outside contour = 4125, contour level = 2.9251
Position of 6sj7 (#21) relative to J743_Emready.mrc (#25) coordinates:
Matrix rotation and translation
-0.84055608 -0.52782516 -0.12192651 384.04950031
0.53382152 -0.84534615 -0.02060222 241.30139512
-0.09219574 -0.08240431 0.99232528 115.21248675
Axis -0.05809235 -0.02794614 0.99791998
Axis point 160.20828519 178.40833275 0.00000000
Rotation angle (degrees) 147.86406592
Shift along axis 85.91906301
> select #21/D
424 atoms, 434 bonds, 1 pseudobond, 52 residues, 2 models selected
> open /Volumes/lab-enchevr/home/users/omallen/EMReady/J756_Emready.mrc
Opened J756_Emready.mrc as #26, grid size 403,403,403, pixel 1, shown at level
0.0205, step 2, values float32
> view matrix models
> #26,-0.97686,0.1782,0.11827,527.9,0.21237,0.87369,0.43769,-141.44,-0.025333,0.45268,-0.89131,177.72
> volume #26 step 1
> view orient
> volume #26 level 3.218
> view matrix models
> #21,-0.84056,-0.52783,-0.12193,587.05,0.53382,-0.84535,-0.020602,249.51,-0.092196,-0.082404,0.99233,-42.287
> view matrix models
> #21,0.85094,-0.52279,-0.051017,373.73,0.51261,0.8053,0.29785,9.556,-0.11463,-0.2796,0.95325,19.172
> fitmap #21 inMap #26
Fit molecule 6sj7 (#21) to map J756_Emready.mrc (#26) using 10007 atoms
average map value = 2.339, steps = 208
shifted from previous position = 7.72
rotated from previous position = 34 degrees
atoms outside contour = 5996, contour level = 3.2184
Position of 6sj7 (#21) relative to J756_Emready.mrc (#26) coordinates:
Matrix rotation and translation
-0.95909114 0.20305132 0.19726717 262.82575280
0.28128813 0.76216630 0.58307761 36.42774958
-0.03195571 0.61471349 -0.78810288 240.59698823
Axis 0.12951504 0.93842227 0.32029594
Axis point 135.23695061 0.00000000 106.11282230
Rotation angle (degrees) 172.98483434
Shift along axis 145.28673905
> view matrix models
> #21,-0.81099,0.1296,0.57052,409.27,-0.15,-0.98862,0.011349,337.37,0.5655,-0.076371,0.82121,-66.706
> fitmap #21 inMap #26
Fit molecule 6sj7 (#21) to map J756_Emready.mrc (#26) using 10007 atoms
average map value = 2.313, steps = 176
shifted from previous position = 6.13
rotated from previous position = 26.6 degrees
atoms outside contour = 6037, contour level = 3.2184
Position of 6sj7 (#21) relative to J756_Emready.mrc (#26) coordinates:
Matrix rotation and translation
0.95289573 -0.10753763 -0.28359370 138.01271012
-0.02008537 -0.95535452 0.29477841 314.94315821
-0.30263229 -0.27519700 -0.91251318 394.87200576
Axis -0.98789491 0.03299815 0.15157433
Axis point 0.00000000 189.97703238 184.36971592
Rotation angle (degrees) 163.23303540
Shift along axis -66.09705391
> volume #26 level 2.023
> volume #26 level 4.494
> view matrix models #25,1,0,0,201.31,0,1,0,-30.677,0,0,1,-136.72
> view matrix models #25,1,0,0,251.18,0,1,0,42.032,0,0,1,-123.92
> fitmap #25 inMap #26
Fit map J743_Emready.mrc in map J756_Emready.mrc using 160613 points
correlation = -0.9741, correlation about mean = 0.006341, overlap = -1.292e+04
steps = 348, shift = 59, angle = 18.8 degrees
Position of J743_Emready.mrc (#25) relative to J756_Emready.mrc (#26)
coordinates:
Matrix rotation and translation
-0.85776873 0.49585223 -0.13551149 243.98911763
0.37718354 0.78624449 0.48944068 -6.64009249
0.34923542 0.36871421 -0.86144324 306.51709966
Axis -0.23512541 -0.94408720 -0.23111770
Axis point 103.57688310 0.00000000 168.95876521
Rotation angle (degrees) 165.12400872
Shift along axis -121.94074359
> view matrix models
> #25,0.94644,-0.30066,0.11771,260.34,0.30024,0.95362,0.021792,-80.433,-0.1188,0.014717,0.99281,-94.277
> fitmap #25 inMap #26
Fit map J743_Emready.mrc in map J756_Emready.mrc using 160613 points
correlation = 0.8273, correlation about mean = 0.008472, overlap = 1.78e+06
steps = 344, shift = 25.7, angle = 56 degrees
Position of J743_Emready.mrc (#25) relative to J756_Emready.mrc (#26)
coordinates:
Matrix rotation and translation
-0.07567291 0.98330848 -0.16546310 53.97668980
0.62748363 0.17592295 0.75849549 -95.43426191
0.77494381 -0.04642783 -0.63032258 198.05304948
Axis -0.62495289 -0.73014410 -0.27626703
Axis point 19.64217121 0.00000000 127.63716091
Rotation angle (degrees) 139.91021877
Shift along axis -18.76765146
> fitmap #24 inMap #25
Fit map cryosparc_P313_J748_003_volume_map.mrc in map J743_Emready.mrc using
55236 points
correlation = -0.3379, correlation about mean = -0.04026, overlap = -161.9
steps = 2000, shift = 67.1, angle = 63.7 degrees
Position of cryosparc_P313_J748_003_volume_map.mrc (#24) relative to
J743_Emready.mrc (#25) coordinates:
Matrix rotation and translation
0.12436525 0.60907837 -0.78329868 140.42313105
-0.09380184 0.79310886 0.60181355 175.96585262
0.98779274 -0.00136984 0.15576785 -9.24694873
Axis -0.30179413 -0.88614011 -0.35167600
Axis point 85.80918930 0.00000000 8.19414261
Rotation angle (degrees) 87.90130284
Shift along axis -195.05734686
> fitmap #21 inMap #25
Fit molecule 6sj7 (#21) to map J743_Emready.mrc (#25) using 10007 atoms
average map value = 3.129, steps = 252
shifted from previous position = 3.1
rotated from previous position = 46.9 degrees
atoms outside contour = 4120, contour level = 2.9251
Position of 6sj7 (#21) relative to J743_Emready.mrc (#25) coordinates:
Matrix rotation and translation
-0.84049807 -0.52790872 -0.12196465 384.06047063
0.53388592 -0.84531143 -0.02035678 241.24544998
-0.09235159 -0.08222504 0.99232566 115.20786725
Axis -0.05814644 -0.02783162 0.99792003
Axis point 160.22045610 178.38520027 0.00000000
Rotation angle (degrees) 147.85905153
Shift along axis 85.92223749
> volume #26 level 2.949
> volume #26 level 2.202
> close #25
> close #26
> close #24
> close #23
> close #22
> close #20
> close #19
> close #18
> close #17
> close #16
> close #15
> close #14
> close #13
> hide #!21 models
> select add #21
10007 atoms, 10195 bonds, 22 pseudobonds, 1261 residues, 3 models selected
> select subtract #21.1
10007 atoms, 10195 bonds, 1261 residues, 1 model selected
> select add #21
10007 atoms, 10195 bonds, 22 pseudobonds, 1261 residues, 3 models selected
> select subtract #21
Nothing selected
> show #!8 models
> show #!7 models
> show #!5 models
> show #!9 models
> view orient
> show #!10 models
> hide #!10 models
> view orient
> show #!10 models
> hide #!10 models
Cell requested for row 4 is out of bounds for table with 16 rows! Resizing
table model.
> rename #9 Kir3.1_docked
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 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: Mac14,9
Model Number: MPHE3B/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0 (25A354)
Kernel Version: Darwin 25.0.0
Time since boot: 5 days, 8 hours, 14 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
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
DELL U2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL U2419H:
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
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 6 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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