id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18995 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ 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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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 }}} " defect closed normal Window Toolkit duplicate all ChimeraX