id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17340 Crash moving window between screens ruchi.sharma@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84a1b0f80 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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All rights reserved. How to cite UCSF ChimeraX > open /Users/ruchigautamsharma/Downloads/9gz1.cif 9gz1.cif title: Beta-cardiac myosin interacting heads motif complexed to mavacamten [more info...] Chain information for 9gz1.cif #1 --- Chain | Description | UniProt A B | Myosin-7 | MYH7_HUMAN 2-1138 C E | Myosin light chain 1/3, skeletal muscle isoform | MYL1_MOUSE 1-187 D F | Myosin regulatory light chain 11 | MYL11_MOUSE 1-168 Non-standard residues in 9gz1.cif #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion PO4 — phosphate ion XB2 — 6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione > open > /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J395_004_volume_map_sharp.mrc Opened cryosparc_P30_J395_004_volume_map_sharp.mrc as #2, grid size 300,300,300, pixel 0.83, shown at level 0.0692, step 2, values float32 > select add #1 19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-0.87037,0,1,0,-36.512,0,0,1,32.991 > view matrix models #1,1,0,0,-1.4608,0,1,0,-66.48,0,0,1,62.095 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.22929,0.90551,0.35704,-80.488,-0.95278,0.13376,0.27263,167.42,0.19911,-0.40268,0.89342,110.69 > view matrix models > #1,-0.41226,0.5412,0.7329,14.553,-0.87648,-0.45515,-0.15692,311.05,0.24865,-0.70707,0.66199,184.84 > view matrix models > #1,-0.71467,-0.017305,0.69925,150.47,-0.54439,-0.61395,-0.57159,348.27,0.43919,-0.78916,0.42935,204.02 > view matrix models > #1,-0.44098,0.53067,-0.72382,237.56,-0.35154,-0.84416,-0.40473,330.42,-0.8258,0.075977,0.55882,238.21 > view matrix models > #1,0.25981,-0.28602,-0.92233,289.58,-0.39672,-0.90242,0.1681,260.71,-0.88041,0.32223,-0.34793,343.44 > view matrix models > #1,0.88601,-0.41122,-0.21422,110.78,-0.38472,-0.90986,0.15541,261.97,-0.25882,-0.055284,-0.96434,401.68 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.88601,-0.41122,-0.21422,107.68,-0.38472,-0.90986,0.15541,291.22,-0.25882,-0.055284,-0.96434,313.09 > view matrix models > #1,0.88601,-0.41122,-0.21422,91.725,-0.38472,-0.90986,0.15541,294.03,-0.25882,-0.055284,-0.96434,306.38 > view matrix models > #1,0.88601,-0.41122,-0.21422,90.734,-0.38472,-0.90986,0.15541,294.35,-0.25882,-0.055284,-0.96434,306.01 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98592,-0.10775,-0.12785,16.255,-0.09588,-0.99079,0.095617,273.05,-0.13697,-0.082013,-0.98717,295.53 > view matrix models > #1,0.98551,-0.16953,0.0050399,6.0428,-0.169,-0.97906,0.11345,279.4,-0.014299,-0.11266,-0.99353,283.07 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.98551,-0.16953,0.0050399,5.9321,-0.169,-0.97906,0.11345,277.71,-0.014299,-0.11266,-0.99353,287.18 > fitmap #1 inMap #2 Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 19295 atoms average map value = 0.07046, steps = 100 shifted from previous position = 5.39 rotated from previous position = 7.18 degrees atoms outside contour = 11385, contour level = 0.069238 Position of 9gz1.cif (#1) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99158233 -0.12125120 -0.04541645 3.24555244 -0.12097831 -0.99261687 0.00872005 288.02278951 -0.04613845 -0.00315224 -0.99893009 281.38024575 Axis -0.99789333 0.06068614 0.02293668 Axis point 0.00000000 144.52872247 140.30004746 Rotation angle (degrees) 179.65916390 Shift along axis 20.69420526 > select subtract #1 Nothing selected > select add #1 19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected > show sel cartoons > hide sel atoms > select subtract #1 Nothing selected > transparency 50 > volume #2 level 0.0488 > surface dust #2 size 8.3 > volume #2 color #402fbf80 > set bgColor white > molmap #1 3.0 Opened 9gz1.cif map 3 as #3, grid size 101,163,179, pixel 1, shown at level 0.114, step 1, values float32 > hide #!1 models > select add #3 2 models selected > fitmap #3 inMap #2 Fit map 9gz1.cif map 3 in map cryosparc_P30_J395_004_volume_map_sharp.mrc using 205156 points correlation = 0.5697, correlation about mean = 0.09812, overlap = 8071 steps = 44, shift = 0.0516, angle = 0.0562 degrees Position of 9gz1.cif map 3 (#3) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99149066 -0.12176240 -0.04604579 3.40454784 -0.12146155 -0.99255271 0.00928665 287.96926309 -0.04683364 -0.00361484 -0.99889617 281.51410436 Axis -0.99787036 0.06093675 0.02326914 Axis point 0.00000000 144.54374258 140.33239670 Rotation angle (degrees) 179.62960799 Shift along axis 20.70120293 > select subtract #3 Nothing selected > show #!1 models > transparency 0 > transparency 50 > color #1 #cc77f6ff > hide #!2 models > ui mousemode right translate > ui tool show ""Side View"" > color #3 #f0c1ff80 models > color #3 #e7d7ff80 models > color #3 #b427fd80 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > show #!2 models > hide #!3 models > select add #1 19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected > fitmap #1 inMap #2 Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 19295 atoms average map value = 0.07045, steps = 44 shifted from previous position = 0.015 rotated from previous position = 0.00755 degrees atoms outside contour = 8166, contour level = 0.048797 Position of 9gz1.cif (#1) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99158183 -0.12125347 -0.04542118 3.24815351 -0.12098664 -0.99261700 0.00858869 288.03518042 -0.04612724 -0.00302104 -0.99893101 281.37146891 Axis -0.99789321 0.06068879 0.02293504 Axis point 0.00000000 144.52573033 140.30511965 Rotation angle (degrees) 179.66670158 Shift along axis 20.69246105 > volume #2 level 0.06602 > fitmap #1 inMap #2 Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 19295 atoms average map value = 0.07045, steps = 48 shifted from previous position = 0.0217 rotated from previous position = 0.0194 degrees atoms outside contour = 10972, contour level = 0.066016 Position of 9gz1.cif (#1) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99157472 -0.12127842 -0.04550984 3.26449705 -0.12099626 -0.99261295 0.00891444 287.99740656 -0.04625479 -0.00333282 -0.99892413 281.41657675 Axis -0.99789142 0.06069759 0.02298930 Axis point 0.00000000 144.52990454 140.30505582 Rotation angle (degrees) 179.64839804 Shift along axis 20.69270623 > volume #2 level 0.03923 > fitmap #1 inMap #2 Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 19295 atoms average map value = 0.07045, steps = 48 shifted from previous position = 0.00628 rotated from previous position = 0.0107 degrees atoms outside contour = 6625, contour level = 0.03923 Position of 9gz1.cif (#1) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99159658 -0.12111529 -0.04546788 3.23505125 -0.12083698 -0.99263310 0.00883072 287.99238790 -0.04620246 -0.00326231 -0.99892678 281.40206425 Axis -0.99789690 0.06061648 0.02296554 Axis point 0.00000000 144.52090217 140.30298325 Rotation angle (degrees) 179.65282797 Shift along axis 20.69138696 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97365,0.0095,-0.22786,13.225,0.0021253,-0.99947,-0.032589,277.27,-0.22805,0.031246,-0.97315,298.85 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.97365,0.0095,-0.22786,16.181,0.0021253,-0.99947,-0.032589,270.07,-0.22805,0.031246,-0.97315,296.87 > fitmap #1 inMap #2 Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 19295 atoms average map value = 0.07046, steps = 160 shifted from previous position = 7.72 rotated from previous position = 13 degrees atoms outside contour = 6631, contour level = 0.03923 Position of 9gz1.cif (#1) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99156366 -0.12139731 -0.04543366 3.26340974 -0.12111950 -0.99259869 0.00882860 288.01653169 -0.04616916 -0.00325122 -0.99892836 281.39811629 Axis -0.99788865 0.06075841 0.02294881 Axis point 0.00000000 144.53360363 140.30174561 Rotation angle (degrees) 179.65320439 Shift along axis 20.70066034 > ui mousemode right translate > select subtract #1 Nothing selected > hide #!1 models > volume #2 level 0.0775 > show #!1 models > volume #2 level 0.0488 > volume #2 level 0.08706 > open > /Users/ruchigautamsharma/Desktop/25HepE525K/RealSpaceRefine_84/25HepE525_M_real_space_refined_084.pdb Chain information for 25HepE525_M_real_space_refined_084.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > select add #4 18857 atoms, 19214 bonds, 9 pseudobonds, 2338 residues, 2 models selected > show sel cartoons > hide sel atoms > hide #!1 models > fitmap #4 inMap #2 Fit molecule 25HepE525_M_real_space_refined_084.pdb (#4) to map cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 18857 atoms average map value = 0.09264, steps = 64 shifted from previous position = 1.12 rotated from previous position = 2.3 degrees atoms outside contour = 11249, contour level = 0.087062 Position of 25HepE525_M_real_space_refined_084.pdb (#4) relative to cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99969266 0.00720946 -0.02371925 1.51432228 -0.00795331 0.99947471 -0.03141731 4.89782055 0.02348029 0.03159630 0.99922487 -5.74779050 Axis 0.78592698 -0.58868858 -0.18911516 Axis point 0.00000000 189.00969684 141.37752898 Rotation angle (degrees) 2.29753035 Shift along axis -0.60614996 > show #!1 models > select subtract #4 Nothing selected > hide #!2 models > dssp > save > /Users/ruchigautamsharma/Desktop/25HepE525K/RealSpaceRefine_84/25HepE525Kand9gz1.cxs > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!3 models > select add #4 18857 atoms, 19214 bonds, 9 pseudobonds, 2338 residues, 2 models selected > fitmap #4 inMap #3 Fit molecule 25HepE525_M_real_space_refined_084.pdb (#4) to map 9gz1.cif map 3 (#3) using 18857 atoms average map value = 0.4154, steps = 76 shifted from previous position = 1.04 rotated from previous position = 2.67 degrees atoms outside contour = 6314, contour level = 0.1138 Position of 25HepE525_M_real_space_refined_084.pdb (#4) relative to 9gz1.cif map 3 (#3) coordinates: Matrix rotation and translation 0.99606454 -0.07196877 -0.05172920 37.16173616 -0.07082037 -0.99720741 0.02370289 277.92100606 -0.05329061 -0.01994612 -0.99837981 281.98258680 Axis -0.99901554 0.03573683 0.02628380 Axis point 0.00000000 141.16977199 139.95674169 Rotation angle (degrees) 178.74821600 Shift along axis -19.78156122 > select subtract #4 Nothing selected > molmap #4 3.0 Opened 25HepE525_M_real_space_refined_084.pdb map 3 as #5, grid size 101,172,182, pixel 1, shown at level 0.117, step 1, values float32 > hide #!4 models > select add #5 2 models selected > fitmap #5 inMap #3 Fit map 25HepE525_M_real_space_refined_084.pdb map 3 in map 9gz1.cif map 3 using 198965 points correlation = 0.6139, correlation about mean = 0.1296, overlap = 4.535e+04 steps = 64, shift = 0.149, angle = 0.23 degrees Position of 25HepE525_M_real_space_refined_084.pdb map 3 (#5) relative to 9gz1.cif map 3 (#3) coordinates: Matrix rotation and translation 0.99576399 -0.07550650 -0.05246730 37.82510827 -0.07443085 -0.99697982 0.02216441 278.48945656 -0.05398240 -0.01816533 -0.99837663 281.75419629 Axis -0.99894033 0.03752804 0.02664320 Axis point 0.00000000 141.38144577 139.97071458 Rotation angle (degrees) 178.84333368 Shift along axis -19.82703012 > select subtract #5 Nothing selected > show #!2 models > hide #!3 models > volume #2 level 0.06793 > show #!3 models > open > /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/cryosparc_P32_J238_map_sharp.ccp4 Opened cryosparc_P32_J238_map_sharp.ccp4 as #6, grid size 340,340,340, pixel 0.824, shown at level 0.00398, step 2, values float32 > select add #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,1.3737,0,1,0,2.1838,0,0,1,14.346 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view matrix models #6,1,0,0,5.8519,0,1,0,1.9654,0,0,1,47.451 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.84923,-0.51065,0.13432,343.57,0.44513,-0.8292,-0.33805,291.05,0.28401,-0.22729,0.93149,53.587 > view matrix models > #6,-0.97151,-0.095409,0.21692,280.27,0.013174,-0.9357,-0.35254,373.79,0.23661,-0.33964,0.91031,82.268 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.97151,-0.095409,0.21692,292.09,0.013174,-0.9357,-0.35254,319.62,0.23661,-0.33964,0.91031,69.854 > view matrix models > #6,-0.97151,-0.095409,0.21692,289.22,0.013174,-0.9357,-0.35254,319.25,0.23661,-0.33964,0.91031,32.472 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.97151,-0.095409,0.21692,263.17,0.013174,-0.9357,-0.35254,304.38,0.23661,-0.33964,0.91031,-6.7661 > view matrix models > #6,-0.97151,-0.095409,0.21692,264.54,0.013174,-0.9357,-0.35254,302.04,0.23661,-0.33964,0.91031,-0.13825 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.97856,-0.10049,0.17976,271.31,0.040104,-0.94915,-0.31227,295.11,0.202,-0.29837,0.93283,-5.0426 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.97856,-0.10049,0.17976,248.82,0.040104,-0.94915,-0.31227,288.51,0.202,-0.29837,0.93283,-12.033 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.99321,-0.077804,-0.086483,282.06,0.1096,-0.87511,-0.47136,286.76,-0.039008,-0.47764,0.87769,60.584 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.99321,-0.077804,-0.086483,282.11,0.1096,-0.87511,-0.47136,293.55,-0.039008,-0.47764,0.87769,66.939 > select add #6 3 models selected > hide #!5 models > hide #!2 models > fitmap #6 inMap #3 Fit map cryosparc_P32_J238_map_sharp.ccp4 in map 9gz1.cif map 3 using 48792 points correlation = 0.5714, correlation about mean = 0.2739, overlap = 3767 steps = 176, shift = 6.29, angle = 12 degrees Position of cryosparc_P32_J238_map_sharp.ccp4 (#6) relative to 9gz1.cif map 3 (#3) coordinates: Matrix rotation and translation -0.98705424 -0.15347550 -0.04657448 313.25053616 -0.15837539 0.88683136 0.43410522 -14.96375182 -0.02532080 0.43586165 -0.89965741 224.60374361 Axis 0.08026911 -0.97129511 -0.22392562 Axis point 155.38113418 0.00000000 114.91132655 Rotation angle (degrees) 179.37312029 Shift along axis -10.61597105 > hide #!3 models > show #!3 models > select add #6 4 models selected > select subtract #6 Nothing selected > show #!1 models > hide #!3 models > transparency #6.1 50 > select add #6 4 models selected > fitmap #1 inMap #6 Fit molecule 9gz1.cif (#1) to map cryosparc_P32_J238_map_sharp.ccp4 (#6) using 19295 atoms average map value = 0.1538, steps = 44 shifted from previous position = 0.175 rotated from previous position = 0.425 degrees atoms outside contour = 4244, contour level = 0.0039782 Position of 9gz1.cif (#1) relative to cryosparc_P32_J238_map_sharp.ccp4 (#6) coordinates: Matrix rotation and translation -0.98581921 -0.16532541 -0.02877541 313.70000276 -0.16128802 0.88612176 0.43448179 -35.11481203 -0.04633236 0.43296162 -0.90022085 223.35351858 Axis -0.08408408 0.97111249 0.22331680 Axis point 155.85507876 0.00000000 114.98629567 Rotation angle (degrees) 179.48206162 Shift along axis -10.59901475 > select subtract #6 Nothing selected > volume #6 level 0.0163 > show #!3 models > hide #!3 models > volume #6 level 0.1231 > show #!2 models > hide #!2 models > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > select ::name=""XB2"" 40 atoms, 42 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 40 atom styles > show #!2 models > volume #2 level 0.09663 > show #!3 models > hide #!2 models > volume #3 level 0.8202 > select add #1 19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected > select subtract #1 Nothing selected > save ""/Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/mava9gZ1 and > 25HepE525K.cxs"" > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!2 models > hide #!6 models > show #!3 models > hide #!3 models > show #!6 models > hide #!2 models > show #!2 models > save ""/Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/mava9gZ1 and > 25HepE525Kand.cxs"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!6 models > volume #2 level 0.05836 > show #!6 models > hide #!2 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.12 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,4 Processor Name: Quad-Core Intel Core i7 Processor Speed: 1.7 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0) OS Loader Version: 580.140.1~51 Software: System Software Overview: System Version: macOS 14.7.1 (23H222) Kernel Version: Darwin 23.6.0 Time since boot: 2 days, 2 hours, 19 minutes Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H1F7ZR2 Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Adapter Firmware Version: 15.67 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 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: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMalign: 0.1.1 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-LigandRecognizer: 0.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.7 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 finufft: 2.3.1 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 Send2Trash: 1.8.3 SEQCROW: 1.8.17 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX