id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15632 Crash changing Mac display configuration andreapellegrini6698@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6-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 0x0000000204a1c240 (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, 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""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 250000003 }, { ""rolloutId"" : ""6425c75e4327780c10cc4252"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE"" : ""642600a457e7664b1698eb32"" }, ""deploymentId"" : 250000006 } ], ""experiments"" : [ { ""treatmentId"" : ""3dff9c91-a8fb-424e-a656-c8d6e6037574"", ""experimentId"" : ""662152ede2d11d1408c4db33"", ""deploymentId"" : 400000014 }, { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF89CD9EA78)"" ] } ===== Log before crash start ===== 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 > open /Users/andrea/Desktop/scratch/berny.3_berny-new-ss.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.3_berny- new-ss.out --- notes | berny.3_berny-new-ss.out has 4 imaginary harmonic vibrational modes 46.78i 19.56i 16.42i 12.26i Opened berny.3_berny-new-ss.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close > open /Users/andrea/Desktop/scratch/geometries/si_ts '/Users/andrea/Desktop/scratch/geometries/si_ts' has no suffix > open /Users/andrea/Desktop/scratch/geometries/si_ts.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/si_ts.out --- notes | si_ts.out has 1 imaginary harmonic vibrational mode 190.37i Opened si_ts.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/si_pre.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/si_pre.out --- note | si_pre.out has 0 imaginary harmonic vibrational modes Opened si_pre.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/si_post.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/si_post.out --- note | si_post.out has 0 imaginary harmonic vibrational modes Opened si_post.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/re_ts.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/re_ts.out --- notes | re_ts.out has 1 imaginary harmonic vibrational mode 187.83i Opened re_ts.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/re_pre.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/re_pre.out --- note | re_pre.out has 0 imaginary harmonic vibrational modes Opened re_pre.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/re_post.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/re_post.out --- note | re_post.out has 0 imaginary harmonic vibrational modes Opened re_post.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/pinacol_ts.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/pinacol_ts.out.out --- notes | pinacol_ts.out.out has 1 imaginary harmonic vibrational mode 181.77i Opened pinacol_ts.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/pinacol_pre.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/pinacol_pre.out.out --- note | pinacol_pre.out.out has 0 imaginary harmonic vibrational modes Opened pinacol_pre.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/pinacol_post.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/pinacol_post.out.out --- note | pinacol_post.out.out has 0 imaginary harmonic vibrational modes Opened pinacol_post.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/meme_ts.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/meme_ts.out.out --- notes | meme_ts.out.out has 1 imaginary harmonic vibrational mode 162.44i Opened meme_ts.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/meme_pre.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/meme_pre.out.out --- note | meme_pre.out.out has 0 imaginary harmonic vibrational modes Opened meme_pre.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/meme_post.out.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/meme_post.out.out --- note | meme_post.out.out has 0 imaginary harmonic vibrational modes Opened meme_post.out.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_si_ts.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_si_ts.out --- notes | iodo_si_ts.out has 1 imaginary harmonic vibrational mode 193.27i Opened iodo_si_ts.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_si_pre.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_si_pre.out --- notes | iodo_si_pre.out has 1 imaginary harmonic vibrational mode 5.04i Opened iodo_si_pre.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_si_post.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_si_post.out --- note | iodo_si_post.out has 0 imaginary harmonic vibrational modes Opened iodo_si_post.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_re_ts.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_re_ts.out --- notes | iodo_re_ts.out has 1 imaginary harmonic vibrational mode 167.53i Opened iodo_re_ts.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_re_pre.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_re_pre.out --- note | iodo_re_pre.out has 0 imaginary harmonic vibrational modes Opened iodo_re_pre.out as an ORCA output file > open /Users/andrea/Desktop/scratch/geometries/iodo_re_post.out Summary of feedback from opening /Users/andrea/Desktop/scratch/geometries/iodo_re_post.out --- note | iodo_re_post.out has 0 imaginary harmonic vibrational modes Opened iodo_re_post.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!1 models > hide #2 models > hide #3 models > hide #!4 models > hide #5 models > hide #6 models > hide #!7 models > hide #8 models > hide #9 models > hide #!10 models > hide #11 models > hide #12 models > hide #!13 models > hide #14 models > hide #15 models > hide #!16 models > hide #17 models > hide #18 models > show #8 models > show #!7 models > hide #!7 models > hide #8 models > show #9 models > show #!7 models > hide #9 models > select add #8 66 atoms, 65 bonds, 1 residue, 1 model selected > show #8 models > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.88175,0.17769,0.43697,0.35907,-0.29007,-0.52627,0.79932,-0.26655,0.37199,-0.83155,-0.41249,-1.2889 > view matrix models > #8,0.89253,0.12312,0.43387,0.33127,-0.35716,-0.39445,0.84667,-0.17806,0.27538,-0.91063,-0.30808,-1.2709 > select subtract #8 Nothing selected > hide #8 models > show #9 models > select add #9 66 atoms, 66 bonds, 1 residue, 1 model selected > view matrix models > #9,0.59412,0.61885,0.51386,0.69995,-0.69617,0.71562,-0.056917,0.15729,-0.40295,-0.32392,0.85599,-0.032456 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.59412,0.61885,0.51386,-1.1377,-0.69617,0.71562,-0.056917,-1.2507,-0.40295,-0.32392,0.85599,-0.15371 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.75876,-0.12956,0.63835,-1.6842,0.13289,-0.92862,-0.34643,-2.7895,0.63767,0.34769,-0.68738,-0.52366 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.75876,-0.12956,0.63835,-0.60405,0.13289,-0.92862,-0.34643,-1.2459,0.63767,0.34769,-0.68738,-1.3942 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.72117,0.18771,0.66684,-0.37398,0.14688,-0.98214,0.11761,-1.2037,0.677,0.013131,-0.73586,-1.64 > view matrix models > #9,0.87129,-0.011308,0.49064,-0.61097,-0.086993,-0.98746,0.13172,-1.0863,0.483,-0.15745,-0.86135,-1.6753 > hide #9 models > ui mousemode right tsbond > tsbond #7/a:1@N1 #7/a:1@C1 radius 0.160 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""translate selected models"" > view matrix models > #9,0.87129,-0.011308,0.49064,-0.50259,-0.086993,-0.98746,0.13172,-1.1539,0.483,-0.15745,-0.86135,-1.4921 > select subtract #9 Nothing selected > select add #7 66 atoms, 65 bonds, 2 pseudobonds, 1 residue, 2 models selected > view matrix models #7,1,0,0,0.086582,0,1,0,-0.096985,0,0,1,0.19236 > view matrix models #7,1,0,0,0.34834,0,1,0,-0.18667,0,0,1,0.55614 > select subtract #7 Nothing selected > save /Users/andrea/Desktop/scratch/geometries/pinacol_ts.png width 1207 > height 850 supersample 4 transparentBackground true > hide #!7 models > show #8 models > hide #8 models > show #8 models > show #!7 models > hide #!7 models > ui mousemode right ""move picked models"" > save /Users/andrea/Desktop/scratch/geometries/pinacol_pre.png width 1207 > height 850 supersample 4 transparentBackground true > hide #8 models > show #9 models > save /Users/andrea/Desktop/scratch/geometries/pinacol_post.png width 1207 > height 850 supersample 4 transparentBackground true > close #8-9#7 > show #!10 models > ui mousemode right ""select fragment"" > ui mousemode right bond > ui mousemode right tsbond > tsbond #10/a:1@N1 #10/a:1@C1 radius 0.160 > ui mousemode right distance > distance #10/a:1@O3 #10/a:1@H4 Distance between meme_ts.out #10/a UNK 1 O3 and H4: 3.491Å > distance #10/a:1@O4 #10/a:1@H3 Distance between meme_ts.out #10/a UNK 1 O4 and H3: 2.891Å > ~distance #10/a:1@O4 #10/a:1@H3 > distance #10/a:1@C2 #10/a:1@O3 Distance between meme_ts.out #10/a UNK 1 C2 and O3: 3.676Å > ~distance #10/a:1@O3 #10/a:1@H4 > distance #10/a:1@O3 #10/a:1@C2 Distance already exists; modify distance properties with 'distance style' > ~distance #10/a:1@C2 #10/a:1@O3 > distance #10/a:1@O3 #10/a:1@N1 Distance between meme_ts.out #10/a UNK 1 O3 and N1: 2.363Å > distance #10/a:1@C1 #10/a:1@N1 Distance between meme_ts.out #10/a UNK 1 C1 and N1: 2.695Å > distance #10/a:1@O3 #10/a:1@N1 Distance already exists; modify distance properties with 'distance style' > ~distance #10/a:1@O3 #10/a:1@N1 > distance #10/a:1@N1 #10/a:1@C1 Distance already exists; modify distance properties with 'distance style' > distance #10/a:1@O1 #10/a:1@H7 Distance between meme_ts.out #10/a UNK 1 O1 and H7: 2.822Å > ~distance #10/a:1@O1 #10/a:1@H7 > hide #7.1 models > hide #!7 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!10 models > show #!16 models > show #!13 models > hide #!16 models > ui mousemode right ""move picked models"" > hide #!13 models > show #!16 models > select add #16/a:1@C16 1 atom, 1 residue, 1 model selected > select add #16/a:1@C15 2 atoms, 1 residue, 1 model selected > select add #16/a:1@C14 3 atoms, 1 residue, 1 model selected > select add #16/a:1@C17 4 atoms, 1 residue, 1 model selected > ui tool show Angles/Torsions > select clear > hide #!16 models > show #!13 models > select add #13/a:1@C11 1 atom, 1 residue, 1 model selected > select add #13/a:1@C10 2 atoms, 1 bond, 1 residue, 1 model selected > select add #13/a:1@C9 3 atoms, 1 bond, 1 residue, 1 model selected > select add #13/a:1@C12 4 atoms, 1 bond, 1 residue, 1 model selected > hide #!13 models > select add #13 74 atoms, 75 bonds, 1 pseudobond, 1 residue, 2 models selected > select subtract #13 Nothing selected > show #!4 models > select add #4/a:1@C17 1 atom, 1 residue, 1 model selected > select add #4/a:1@C14 2 atoms, 1 residue, 1 model selected > select add #4/a:1@C15 3 atoms, 1 residue, 1 model selected > select add #4/a:1@C16 4 atoms, 1 residue, 1 model selected > select add #4 74 atoms, 75 bonds, 1 pseudobond, 1 residue, 2 models selected > hide #!4 models > select subtract #4 Nothing selected > show #!1 models > select add #1/a:1@C11 1 atom, 1 residue, 1 model selected > select add #1/a:1@C10 2 atoms, 1 residue, 1 model selected > select add #1/a:1@C9 3 atoms, 1 bond, 1 residue, 1 model selected > select add #1/a:1@C12 4 atoms, 1 residue, 1 model selected > label sel atoms attribute mullikenCharge > select clear > select add #1/a:1@C1 1 atom, 1 residue, 1 model selected > label sel atoms attribute mullikenCharge > hide #!1 models > show #!4 models > select #4/a:1@C1 1 atom, 1 residue, 1 model selected > label sel atoms attribute mullikenCharge > hide #!4 models > select add #4 74 atoms, 75 bonds, 1 pseudobond, 1 residue, 3 models selected > select subtract #4 Nothing selected > show #!13 models > select #13/a:1@C1 1 atom, 1 residue, 1 model selected > label sel atoms attribute mullikenCharge > select add #13 74 atoms, 75 bonds, 1 pseudobond, 1 residue, 3 models selected > select subtract #13 Nothing selected > hide #!13 models > show #!16 models > select #16/a:1@C1 1 atom, 1 residue, 1 model selected > label sel atoms attribute mullikenCharge > ui mousemode right distance > distance #16/a:1@N1 #16/a:1@C1 Distance between iodo_re_ts #16/a UNK 1 N1 and C1: 2.955Å > distance #16/a:1@N1 #16/a:1@C1 Window position QRect(1510,-678 600x300) outside any known screen, using primary screen Distance already exists; modify distance properties with 'distance style' > distance #16/a:1@N1 #16/a:1@C1 Distance already exists; modify distance properties with 'distance style' > show #7.1 models > hide #!16 models > select add #16 74 atoms, 75 bonds, 2 pseudobonds, 1 residue, 4 models selected > select subtract #16 Nothing selected > show #!13 models > distance #13/a:1@N1 #13/a:1@C1 Distance between iodo_si_ts #13/a UNK 1 N1 and C1: 2.802Å > hide #!13 models > show #!4 models > hide #!4 models > show #!4 models > distance #4/a:1@N1 #4/a:1@C2 Distance between re_ts #4/a UNK 1 N1 and C2: 2.836Å > ~distance #4/a:1@N1 #4/a:1@C2 > distance #4/a:1@C1 #4/a:1@N1 Distance between re_ts #4/a UNK 1 C1 and N1: 2.759Å > ~distance #4/a:1@C1 #4/a:1@N1 > hide #!4 models > show #!1 models > distance #1/a:1@N1 #1/a:1@C1 Distance between si_ts #1/a UNK 1 N1 and C1: 2.774Å > hide #!1 models > show #!13 models > show #17 models > hide #17 models > show #!16 models > hide #!13 models > hide #!7 models > show #!7 models > hide #7.1 models > open /Users/andrea/Desktop/scratch/opt_i2-cat.out Summary of feedback from opening /Users/andrea/Desktop/scratch/opt_i2-cat.out --- notes | opt_i2-cat.out has 1 imaginary harmonic vibrational mode 7.62i Opened opt_i2-cat.out as an ORCA output file > hide #!16 models > select add #8/a:1@C7 1 atom, 1 residue, 1 model selected > select add #8/a:1@C6 2 atoms, 1 pseudobond, 1 residue, 2 models selected > select add #8/a:1@C5 3 atoms, 1 pseudobond, 1 residue, 2 models selected > select add #8/a:1@C8 4 atoms, 1 pseudobond, 1 residue, 2 models selected > open /Users/andrea/Desktop/scratch/meme_13diol.1_meme_13diol.out Summary of feedback from opening /Users/andrea/Desktop/scratch/meme_13diol.1_meme_13diol.out --- note | meme_13diol.1_meme_13diol.out has 0 imaginary harmonic vibrational modes Opened meme_13diol.1_meme_13diol.out as an ORCA output file > hide #8 models > select add #9/a:1@C6 5 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@C7 6 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H11 7 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H13 8 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H12 9 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H9 10 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H10 11 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H8 12 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H3 13 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #9/a:1@H4 14 atoms, 1 pseudobond, 2 residues, 3 models selected > delete atoms (#9 & sel) > delete bonds (#9 & sel) > close #9 > show #!16 models > select add #16/a:1@N2 5 atoms, 1 pseudobond, 2 residues, 3 models selected > select add #16/a:1@B1 6 atoms, 2 pseudobonds, 2 residues, 4 models selected > select add #16/a:1@C4 7 atoms, 2 pseudobonds, 2 residues, 4 models selected Either three or four atoms must be selected! > select clear > select add #16/a:1@N2 1 atom, 1 residue, 1 model selected > select add #16/a:1@B1 2 atoms, 1 residue, 1 model selected > select add #16/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #16 74 atoms, 75 bonds, 2 pseudobonds, 1 residue, 4 models selected > select subtract #16 Nothing selected > show #5 models > hide #!16 models > hide #5 models > show #!4 models > select add #4/a:1@N2 1 atom, 1 residue, 1 model selected > select add #4/a:1@B1 2 atoms, 1 residue, 1 model selected > select add #4/a:1@C4 3 atoms, 1 residue, 1 model selected > select clear > hide #!4 models > show #!1 models > select #1/a:1@N2 1 atom, 1 residue, 1 model selected > select add #1/a:1@B1 2 atoms, 1 residue, 1 model selected > select add #1/a:1@C4 3 atoms, 1 residue, 1 model selected > select clear > hide #!1 models > show #!13 models > select add #13/a:1@N2 1 atom, 1 residue, 1 model selected > select add #13/a:1@B1 2 atoms, 1 residue, 1 model selected > select add #13/a:1@C4 3 atoms, 1 residue, 1 model selected > select clear > select #13/a:1@O5 1 atom, 1 residue, 1 model selected > select #13/a:1@O6 1 atom, 1 residue, 1 model selected > select #13/a:1@O5 1 atom, 1 residue, 1 model selected > select add #13/a:1@O6 2 atoms, 1 residue, 1 model selected > select add #13/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #13/a:1@B1 4 atoms, 1 residue, 1 model selected > hide #!13 models > show #!16 models > select add #13 74 atoms, 75 bonds, 2 pseudobonds, 1 residue, 4 models selected > select subtract #13 Nothing selected > select #16/a:1@O6 1 atom, 1 residue, 1 model selected > select add #16/a:1@O5 2 atoms, 1 residue, 1 model selected > select add #16/a:1@B1 3 atoms, 1 residue, 1 model selected > select clear > select #16/a:1@O6 1 atom, 1 residue, 1 model selected > select add #16/a:1@O5 2 atoms, 1 residue, 1 model selected > select add #16/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #16/a:1@B1 4 atoms, 1 residue, 1 model selected > select add #16 74 atoms, 75 bonds, 2 pseudobonds, 1 residue, 4 models selected > select subtract #16 Nothing selected > hide #!16 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > select #4/a:1@O6 1 atom, 1 residue, 1 model selected > select add #4/a:1@O5 2 atoms, 1 residue, 1 model selected > select add #4/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #4/a:1@B1 4 atoms, 1 residue, 1 model selected > select clear > hide #!4 models > show #!1 models > select #1/a:1@O5 1 atom, 1 residue, 1 model selected > select add #1/a:1@O6 2 atoms, 1 residue, 1 model selected > select add #1/a:1@C4 3 atoms, 1 residue, 1 model selected > select add #1/a:1@B1 4 atoms, 1 residue, 1 model selected > hide #!1 models > show #18 models > distance #18/a:1@B1 #18/a:1@N2 Distance between iodo_re_post #18/a UNK 1 B1 and N2: 1.450Å > show #7.1 models > hide #7.1 models > show #7.1 models > distance #18/a:1@N1 #18/a:1@C1 Distance between iodo_re_post #18/a UNK 1 N1 and C1: 1.488Å > select #18/a:1@C16 1 atom, 1 residue, 1 model selected > select add #18/a:1@C15 2 atoms, 1 residue, 1 model selected > select add #18/a:1@C14 3 atoms, 1 residue, 1 model selected > select add #18/a:1@C17 4 atoms, 1 residue, 1 model selected > select clear > distance #18/a:1@H32 #18/a:1@C25 Distance between iodo_re_post #18/a UNK 1 H32 and C25: 5.455Å > distance #18/a:1@H30 #18/a:1@C25 Distance between iodo_re_post #18/a UNK 1 H30 and C25: 4.756Å > ~distance #18/a:1@H32 #18/a:1@C25 > ~distance #18/a:1@H30 #18/a:1@C25 > hide #18 models > show #15 models > select add #15/a:1@C12 1 atom, 1 residue, 1 model selected > select add #15/a:1@C9 2 atoms, 1 residue, 1 model selected > select add #15/a:1@C10 3 atoms, 1 residue, 1 model selected > select add #15/a:1@C11 4 atoms, 1 residue, 1 model selected > ui mousemode right ""translate selected atoms"" > undo > ui mousemode right ""move picked models"" > hide #15 models > select add #15 74 atoms, 76 bonds, 1 residue, 1 model selected > select subtract #15 Nothing selected > show #18 models > show #17 models > show #!16 models > hide #!16 models > hide #18 models > ui mousemode right distance > distance #17/a:1@H30 #17/a:1@C25 Distance between iodo_re_pre #17/a UNK 1 H30 and C25: 3.013Å > distance #17/a:1@H21 #17/a:1@C16 Distance between iodo_re_pre #17/a UNK 1 H21 and C16: 3.635Å > ~distance #17/a:1@H21 #17/a:1@C16 > ~distance #17/a:1@H30 #17/a:1@C25 > hide #17 models > show #!16 models > ~distance #16/a:1@N1 #16/a:1@C1 > distance #17/a:1@N2 #16/a:1@H30 Distance between iodo_re_pre #17/a UNK 1 N2 and iodo_re_ts #16/a UNK 1 H30: 4.856Å > distance #16/a:1@C21 #16/a:1@H30 Distance between iodo_re_ts #16/a UNK 1 C21 and H30: 3.382Å > ui mousemode right ""move picked models"" > ui mousemode right distance > distance #16/a:1@H30 #16/a:1@C20 Distance between iodo_re_ts #16/a UNK 1 H30 and C20: 2.966Å > ~distance #16/a:1@C21 #16/a:1@H30 > hide #!16 models > show #!16 models > hide #!16 models > show #!13 models > ~distance #1/a:1@N1 #1/a:1@C1 > ~distance #13/a:1@N1 #13/a:1@C1 > distance #13/a:1@H26 #13/a:1@C13 Distance between iodo_si_ts #13/a UNK 1 H26 and C13: 4.918Å > distance #13/a:1@C14 #13/a:1@H26 Distance between iodo_si_ts #13/a UNK 1 C14 and H26: 4.730Å > ~distance #13/a:1@H26 #13/a:1@C13 > ~distance #13/a:1@C14 #13/a:1@H26 > hide #!13 models > show #!4 models > distance #4/a:1@H34 #4/a:1@C27 Distance between re_ts #4/a UNK 1 H34 and C27: 3.351Å > distance #4/a:1@H34 #4/a:1@C26 Distance between re_ts #4/a UNK 1 H34 and C26: 3.208Å > ~distance #4/a:1@H34 #4/a:1@C27 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/andrea/Desktop/scratch/berny.3_berny-new-ss.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.3_berny- new-ss.out --- notes | berny.3_berny-new-ss.out has 5 imaginary harmonic vibrational modes 90.77i 46.85i 11.94i 7.15i 4.28i Opened berny.3_berny-new-ss.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!4 models > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #9/a:1@O2 1 atom, 1 residue, 1 model selected > select #9/a:1@C23 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add #9/a:1@O2 2 atoms, 1 residue, 1 model selected > select add #9/a:1@O1 3 atoms, 1 residue, 1 model selected > select add #9/a:1@H31 4 atoms, 1 residue, 1 model selected > select subtract #9/a:1@H31 3 atoms, 1 residue, 1 model selected > select subtract #9/a:1@O1 2 atoms, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close #9 > close #8 > show #!10 models > hide #!7 models > save /Users/andrea/Desktop/scratch/geometries/meme_ts.png width 1207 height > 849 supersample 4 transparentBackground true > hide #!10 models > show #!4 models > ~label #4 atoms > close #1.2 > close #13.2 > close #16.2 > ui mousemode right tsbond > tsbond #4/a:1@N1 #4/a:1@C1 radius 0.160 > ui mousemode right ""translate selected atoms"" > save /Users/andrea/Desktop/scratch/geometries/ch_re_ts.png width 1207 height > 849 supersample 4 transparentBackground true > hide #!4 models > show #!1 models > ui mousemode right bond > ui mousemode right tsbond > tsbond #1/a:1@N1 #1/a:1@C1 radius 0.160 > save /Users/andrea/Desktop/scratch/geometries/ch_si_ts.png width 1207 height > 849 supersample 4 transparentBackground true > hide #!1 models > show #!13 models > tsbond #13/a:1@N1 #13/a:1@C1 radius 0.160 > save /Users/andrea/Desktop/scratch/geometries/ci_si_ts.png width 1207 height > 849 supersample 4 transparentBackground true > hide #!13 models > show #!16 models > tsbond #16/a:1@N1 #16/a:1@C1 radius 0.160 > save /Users/andrea/Desktop/scratch/geometries/ci_re_ts.png width 1207 height > 849 supersample 4 transparentBackground true > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/ts_re_ii- > grad.cube Opened ts_re_ii-grad.cube as #8, grid size 256,267,198, pixel 0.05, shown at level -100,100, step 1, values float32 > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/ts_re_ii- > dens.cube Opened ts_re_ii-dens.cube as #9, grid size 256,267,198, pixel 0.05, shown at level -101,101, step 1, values float32 > hide #!9 models > ui tool show ""Surface Color"" > volume #8 level 0.5 level 100 > color radial #8.1#8.2 palette -2,#0000ff:0,#00ff00:2,#ff0000 > color gradient #8.1#8.2 map #9 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum 0.001488, mean 5.85, maximum 220.2 > color sample #8.1#8.2 map #9 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum -4.999, mean 0.1927, maximum 4.999 > ui mousemode right distance > distance #16/a:1@H11 #16/a:1@O3 Distance between iodo_re_ts #16/a UNK 1 H11 and O3: 2.297Å > distance #16/a:1@H11 #16/a:1@O3 Distance already exists; modify distance properties with 'distance style' > show #!7 models > distance #16/a:1@H23 #16/a:1@C24 Distance between iodo_re_ts #16/a UNK 1 H23 and C24: 3.172Å > distance #16/a:1@H23 #16/a:1@C16 Distance between iodo_re_ts #16/a UNK 1 H23 and C16: 3.284Å > ~distance #16/a:1@H23 #16/a:1@C16 > ui mousemode right ""bond rotation"" > torsion #16/a:1@O3,C6,N1,N2 61.79 > undo > torsion #16/a:1@O3,C6,N1,N2 48.41 > torsion #16/a:1@O3,C6,N1,N2 68.09 > volume #8 level 1 level 100 > volume #8 orthoplanes xyz positionPlanes 128,133,99 style image region all > mousemode rightMode ""move planes"" > volume #8 orthoplanes xyz positionPlanes 128,135,99 > volume #8 orthoplanes xyz positionPlanes 128,135,86 > volume #8 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0.4137 tiltedSlabSpacing 0.05 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #8 tiltedSlabAxis -0.8005,0.07286,0.5948 tiltedSlabOffset 0.6469 > volume #8 tiltedSlabAxis -0.7138,0.06251,-0.6975 tiltedSlabOffset -1.951 > volume #8 tiltedSlabAxis -0.9219,-0.01166,-0.3872 tiltedSlabOffset -2.693 > volume #8 tiltedSlabAxis -0.9438,-0.00706,-0.3303 tiltedSlabOffset -2.89 > volume #8 tiltedSlabAxis -0.5441,-0.8384,-0.03171 tiltedSlabOffset -0.0497 > volume #8 tiltedSlabAxis -0.2315,-0.2587,0.9378 tiltedSlabOffset -3.101 > volume #8 tiltedSlabAxis -0.9542,-0.2778,0.1113 tiltedSlabOffset 0.278 > volume #8 tiltedSlabAxis -0.9591,-0.2819,0.02617 tiltedSlabOffset 0.5058 > volume #8 tiltedSlabAxis -0.981,-0.1694,-0.09421 tiltedSlabOffset 1.339 > volume #!8 planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #8 region 0,0,88,255,266,88 > volume #8 region 0,0,106,255,266,106 > volume #8 region 0,0,108,255,266,108 > volume #8 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 0.4137 tiltedSlabSpacing 0.05 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #8 tiltedSlabAxis -0.9944,-0.05813,-0.0884 tiltedSlabOffset -2.078 > volume #8 tiltedSlabAxis -0.9961,-0.08731,-0.01482 tiltedSlabOffset -2.045 > volume #8 tiltedSlabAxis -0.9948,-0.04999,-0.08918 tiltedSlabOffset -1.877 > volume #8 tiltedSlabAxis -0.9214,0.3701,-0.1188 tiltedSlabOffset 0.04135 > volume #8 tiltedSlabAxis -0.903,-0.05237,0.4265 tiltedSlabOffset -1.455 > volume #8 tiltedSlabAxis -0.4332,-0.2115,0.8762 tiltedSlabOffset -0.5024 > hide #!7 models > volume #8 tiltedSlabAxis -0.04975,-0.2703,0.9615 tiltedSlabOffset -1.081 > color sample #8.1#8.2 map #9 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum -5.002, mean 0.7202, maximum 5.003 > color sample #8.1#8.2 map #9 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum -5.002, mean 0.7202, maximum 5.003 > volume #8 level 0.01311,1 level 0.01311,0.8 level 0,0 level 0,0 level > 100,0.8 level 100,1 > volume #8 level 0.01311,1 level 0.898,0.2559 level 0,0 level 0,0 level > 100,0.8 level 100,1 > volume #8 level 0.01311,1 level 0.2,0.2559 level 0,0 level 0,0 level 100,0.8 > level 100,1 > volume #8 style mesh > volume #8 style image colorMode opaque8 positionPlanes 127,133,98 imageMode > orthoplanes > volume #8 colorMode auto8 imageMode ""tilted slab"" tiltedSlabAxis > 0.1098,0.1971,-0.9742 tiltedSlabOffset -1.561 tiltedSlabSpacing 0.05 > tiltedSlabPlaneCount 39 > volume #8 tiltedSlabAxis 0.3911,0.23,-0.8912 tiltedSlabOffset -2.13 > volume #8 tiltedSlabAxis 0.2893,0.2331,-0.9284 tiltedSlabOffset -1.98 > save ""/Users/andrea/OneDrive - Alma Mater Studiorum Università di > Bologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/slab-interaction.png"" width > 1087 height 896 supersample 4 transparentBackground true > hide #!16 models > show #!13 models > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/ts_si_ii- > grad.cube Opened ts_si_ii-grad.cube as #19, grid size 292,224,186, pixel 0.05, shown at level -100,100, step 1, values float32 > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/ts_si_ii- > dens.cube Opened ts_si_ii-dens.cube as #20, grid size 292,224,186, pixel 0.05, shown at level -103,103, step 1, values float32 > hide #!20 models > volume #19 style image showOutlineBox true imageMode ""tilted slab"" > tiltedSlabAxis 0.2318,0.2808,-0.9314 tiltedSlabOffset -0.5634 > tiltedSlabSpacing 0.05 tiltedSlabPlaneCount 37 > volume #19 color #17375e color #4d0000 color #4d0000 color #b3ffff color > #b3ffff color #b3ffff > volume #19 color black color #4d0000 color #4d0000 color #b3ffff color > #b3ffff color #b3ffff > volume #19 tiltedSlabAxis 0.1688,0.2809,-0.9448 tiltedSlabOffset -0.4059 > volume #19 tiltedSlabAxis 0.01115,-0.1532,-0.9881 tiltedSlabOffset -0.3413 > ui mousemode right ""translate selected atoms"" > ui mousemode right ""translate selected models"" > ui mousemode right ""move planes"" > ui mousemode right ""rotate slab"" > ui mousemode right ""tape measure"" > marker segment #21 position 1.142,1.692,0.489 toPosition -2.309,3.699,0.5885 > color yellow radius 0.1 label 3.994 labelHeight 0.3994 labelColor yellow > marker segment #21 position 3.467,2.755,-0.06636 toPosition > -2.309,3.699,0.5885 color yellow radius 0.0125 label 5.889 labelHeight > 0.5889 labelColor yellow > marker delete #21 > marker segment #21 position 2.233,-3.548,0.9208 toPosition > 4.467,-2.304,0.753 color yellow radius 0.0125 label 2.563 labelHeight 0.2563 > labelColor yellow > marker delete #21 > marker segment #21 position 1.737,3.354,2.235 toPosition -2.309,3.699,0.5885 > color yellow radius 0.0125 label 4.382 labelHeight 0.4382 labelColor yellow > marker segment #21 position 1.142,1.692,0.489 toPosition -2.309,3.699,0.5885 > color yellow radius 0.0125 label 3.994 labelHeight 0.3994 labelColor yellow > marker delete #21 > volume #19 color black color black color #4d0000 color #b3ffff color #b3ffff > color #b3ffff > volume #19 color black color black color #4d0000 color #b3ffff color white > color #b3ffff > volume #19 color white color black color #4d0000 color #b3ffff color white > color #b3ffff > volume #19 color black color black color #4d0000 color #b3ffff color white > color #b3ffff > volume #19 color white color black color #4d0000 color #b3ffff color white > color #b3ffff > volume #19 color black color black color #4d0000 color #b3ffff color white > color #b3ffff > volume #19 level 0.001658,1 level 2.067,0.7706 level 0,0 level 0,0 level > 100,0.8 level 100,1 > volume #19 level 0.001658,1 level 2.067,0.7706 level 0,0 level 0.001658,0 > level 100,0.8 level 100,1 > volume #19 color black color black color #4d0000 color white color white > color #b3ffff > volume #19 color black color black color #4d0000 color black color white > color #b3ffff > volume #19 color black color black color #4d0000 color black color white > color white > ui mousemode right ""rotate slab"" > ui mousemode right ""move planes"" > volume #19 tiltedSlabOffset -0.3413 tiltedSlabPlaneCount 37 > save ""/Users/andrea/OneDrive - Alma Mater Studiorum Università di > Bologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/slab-interaction.png"" width > 1087 height 954 supersample 4 transparentBackground true > hide #!19 models > hide #!13 models Cell requested for row 10 is out of bounds for table with 23 rows! Resizing table model. > show #11 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""translate selected atoms"" > save /Users/andrea/Desktop/scratch/geometries/meme_pre.png width 1207 height > 850 supersample 4 transparentBackground true > hide #11 models > show #12 models > save /Users/andrea/Desktop/scratch/geometries/meme_post.png width 1207 > height 850 supersample 4 transparentBackground true > close #11-12#10 > show #2 models > save /Users/andrea/Desktop/scratch/geometries/ch_si_pre.png width 1207 > height 850 supersample 4 transparentBackground true > hide #2 models > show #3 models > save /Users/andrea/Desktop/scratch/geometries/ch_si_post.png width 1207 > height 850 supersample 4 transparentBackground true > hide #3 models > close #2-3#1 > show #5 models > save /Users/andrea/Desktop/scratch/geometries/ch_re_pre.png width 1207 > height 850 supersample 4 transparentBackground true > hide #5 models > show #6 models > save /Users/andrea/Desktop/scratch/geometries/ch_re_post.png width 1207 > height 850 supersample 4 transparentBackground true > hide #6 models > close #5-6#4 > close #8-9 > close #19-20 > show #14 models > save /Users/andrea/Desktop/scratch/geometries/ci_si_pre.png width 1207 > height 850 supersample 4 transparentBackground true > hide #14 models > show #15 models > hide #15 models > show #15 models > save /Users/andrea/Desktop/scratch/geometries/ci_si_post.png width 1207 > height 850 supersample 4 transparentBackground true > hide #15 models > show #!16 models > show #17 models > hide #!16 models > save /Users/andrea/Desktop/scratch/geometries/ci_re_pre.png width 1207 > height 850 supersample 4 transparentBackground true > hide #17 models > show #18 models > save /Users/andrea/Desktop/scratch/geometries/ci_re_post.png width 1207 > height 850 supersample 4 transparentBackground true > hide #18 models > show #18 models > hide #18 models > show #18 models > hide #18 models > open /Users/andrea/Desktop/scratch/berny.3_berny-new-ss.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.3_berny- new-ss.out --- notes | berny.3_berny-new-ss.out has 2 imaginary harmonic vibrational modes 9.73i 9.43i Opened berny.3_berny-new-ss.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/si/ts_si.xyz > format xyz opened ts_si.xyz as an XYZ coordinate file > close > open /Users/andrea/Desktop/scratch/opt_cat-ilide.out Summary of feedback from opening /Users/andrea/Desktop/scratch/opt_cat- ilide.out --- note | opt_cat-ilide.out has 0 imaginary harmonic vibrational modes Opened opt_cat-ilide.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/andrea/Desktop/scratch/berny_not_cheling_berny_ii_aldolic.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_not_cheling_berny_ii_aldolic.out --- notes | berny_not_cheling_berny_ii_aldolic.out has 2 imaginary harmonic vibrational modes 247.72i 4.61i Opened berny_not_cheling_berny_ii_aldolic.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #1 models > close > open /Users/andrea/Desktop/scratch/berny_berny_ii_aldolic.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_berny_ii_aldolic.out --- warnings | error or warning in berny_berny_ii_aldolic.out: The optimization did not converge but reached the maximum possible hint: add more optimization cycles or compute Hessians during optimization Opened berny_berny_ii_aldolic.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right hbonds > open /Users/andrea/Desktop/scratch/berny_not_cheling_berny_ii_aldolic.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_not_cheling_berny_ii_aldolic.out --- notes | berny_not_cheling_berny_ii_aldolic.out has 2 imaginary harmonic vibrational modes 247.72i 4.61i Opened berny_not_cheling_berny_ii_aldolic.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!1 models > ui mousemode right distance > distance #2/a:1@O7 #2/a:1@H11 Distance between berny_not_cheling_berny_ii_aldolic #2/a UNK 1 O7 and H11: 2.359Å > ui mousemode right bond > ui mousemode right ""bond rotation"" > torsion #2/a:1@C2,C1,S1,O3 -8.01 > torsion #2/a:1@O2,C2,C1,H2 -91.01 > torsion #2/a:1@C2,C1,S1,O3 15.06 > open /Users/andrea/Desktop/scratch/berny_berny_r.log Opened berny_berny_r.log as a Gaussian output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!2 models > hide #!3 models > show #!3 models > close > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/ts_si_ii- > grad.cube Opened ts_si_ii-grad.cube as #1, grid size 292,224,186, pixel 0.05, shown at level -100,100, step 1, values float32 > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/ts_si_ii- > dens.cube Opened ts_si_ii-dens.cube as #2, grid size 292,224,186, pixel 0.05, shown at level -103,103, step 1, values float32 > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/ts_si_ii.xyz opened ts_si_ii.xyz as an XYZ coordinate file > volume #1 level 0.5 level 100 > color sample #1.1#1.2 map #2 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum -4.998, mean 0.2304, maximum 4.999 > ui mousemode right ""translate selected atoms"" > save ""/Users/andrea/OneDrive - Alma Mater Studiorum Università di > Bologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/boc_ar_up.png"" width 1207 > height 852 supersample 4 transparentBackground true > hide #!1 models > hide #3 models > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/te_re_ii.xyz opened te_re_ii.xyz as an XYZ coordinate file > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/ts_re_ii- > grad.cube Opened ts_re_ii-grad.cube as #5, grid size 256,267,198, pixel 0.05, shown at level -100,100, step 1, values float32 > open /Users/andrea/Library/CloudStorage/OneDrive- > AlmaMaterStudiorumUniversitàdiBologna/PhD/BoroCrotyl/images/iodio/re_ii_nci/ts_re_ii- > dens.cube Opened ts_re_ii-dens.cube as #6, grid size 256,267,198, pixel 0.05, shown at level -101,101, step 1, values float32 > volume #5 level -0.5 level 100 > volume #5 level 0.5 level 100 > color sample #5.1#5.2 map #6 palette -2,#0000ff:0,#00ff00:2,#ff0000 Map values for surface ""surface"": minimum -4.999, mean 0.1927, maximum 4.999 > open /Users/andrea/Desktop/scratch/berny_berny_r.log Opened berny_berny_r.log as a Gaussian output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #7 models > ui tool show ""Side View"" > save ""/Users/andrea/OneDrive - Alma Mater Studiorum Università di > Bologna/PhD/BoroCrotyl/images/iodio/si_ii_nci/hb_CO_ar.png"" width 1207 > height 850 supersample 4 transparentBackground true > hide #!5 models > hide #4 models > show #7 models > close > open /Users/andrea/Downloads/cluster.xyz opened cluster.xyz as an XYZ coordinate file > select add /a:1@C1 1 atom, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/andrea/Desktop/scratch/berny.3_berny-new-ss.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny.3_berny- new-ss.out --- notes | berny.3_berny-new-ss.out has 2 imaginary harmonic vibrational modes 17.92i 3.32i Opened berny.3_berny-new-ss.out as an ORCA output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!1 models > close > open /Users/andrea/Downloads/cluster.xyz format xyz opened cluster.xyz as an XYZ coordinate file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select add /a:1@Fe2 1 atom, 1 residue, 1 model selected > select add /a:1@Fe5 2 atoms, 1 residue, 1 model selected > select add /a:1@Fe4 3 atoms, 1 residue, 1 model selected > select add /a:1@Fe3 4 atoms, 1 residue, 1 model selected > select add /a:1@Fe6 5 atoms, 1 residue, 1 model selected > select add /a:1@Fe1 6 atoms, 1 residue, 1 model selected > select add /a:1@C1 7 atoms, 1 residue, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/andrea/Desktop/scratch/qm_all_crest_clustered.xyz opened qm_all_crest_clustered.xyz as an XYZ coordinate file movie The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #1 #3f9fff80 > select add #1 48 atoms, 26 bonds, 27 pseudobonds, 1 residue, 2 models selected > select subtract #1 Nothing selected > select add #2 48 atoms, 26 bonds, 27 pseudobonds, 1 residue, 2 models selected > open /Users/andrea/Desktop/scratch/berny_berny_r.log Opened berny_berny_r.log as a Gaussian output file The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > hide #!2 models > hide #!1 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. ===== 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 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple 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: MacBookPro18,3 Model Number: MKGP3T/A Chip: Unknown Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.140.18 OS Loader Version: 10151.140.18 Software: System Software Overview: System Version: macOS 14.6 (23G5052d) Kernel Version: Darwin 23.6.0 Time since boot: 6 days, 6 hours, 16 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal E24-29: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes E24-29: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes 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-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-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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 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-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 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 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: 1.8.8 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