id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16713 Crash in QDockWidget event handling chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000386473000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e66d3840 (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, 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2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/jabarro/Documents/collin/set2/1654.xyz format xyz opened 1654.xyz as an XYZ coordinate file > style ball Changed 70 atom styles > lighting soft > lighting simple > lighting full > lighting simple > lighting flat > lighting simple > lighting shadows true > lighting simple > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > view > preset seqcrow ball-stick-endcap Using preset: SEQCROW / Ball-Stick-Endcap Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow sticks Using preset: SEQCROW / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > ui tool show ""Buried Volume"" > ui mousemode right ""select fragment"" > ui mousemode right select > select add /a:1@C4 61 atoms, 60 bonds, 1 residue, 1 model selected > select add /a:1@C1 62 atoms, 60 bonds, 1 residue, 1 model selected > select add /a:1@N1 63 atoms, 60 bonds, 1 residue, 1 model selected > select add /a:1@C3 64 atoms, 61 bonds, 1 residue, 1 model selected > select add /a:1@C2 65 atoms, 62 bonds, 1 residue, 1 model selected > select clear > select /a:1@N2 1 atom, 1 residue, 1 model selected > color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1654 /a:1@N2 83.0 > ui mousemode right ""color key"" > ui mousemode right select > ui mousemode right ""color key"" > key delete > ui mousemode right select > ui mousemode right ""contour level"" > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting full > view sel > view > transparency 0 > volume hide No volumes specified > volume style surface No volumes specified > transparency 0 > transparecy 9 Unknown command: transparecy 9 > transparency 9 > transparency 20 > transparency 100 > transparency 50 > transparency 60 > open /Users/jabarro/Documents/collin/set2/1654.xyz opened 1654.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select add #1/a:1@C2 85 atoms, 84 bonds, 2 residues, 2 models selected > select add #1/a:1@C4 86 atoms, 84 bonds, 2 residues, 2 models selected > select add #3/a:1@H3 87 atoms, 84 bonds, 2 residues, 2 models selected > open /Users/jabarro/Documents/collin/set2/1654.xyz opened 1654.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > select clear > ui mousemode right ""select similar fragments"" > ui mousemode right select > select add #1/a:1@C2 205 atoms, 204 bonds, 3 residues, 3 models selected > select add #4/a:1@H4 206 atoms, 204 bonds, 3 residues, 3 models selected > select add #1/a:1@C3 207 atoms, 205 bonds, 3 residues, 3 models selected > select add #1/a:1@N1 208 atoms, 205 bonds, 3 residues, 3 models selected > select add #1/a:1@C1 209 atoms, 205 bonds, 3 residues, 3 models selected > select add #1/a:1@C4 210 atoms, 206 bonds, 3 residues, 3 models selected Traceback (most recent call last): File ""/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/SEQCROW/tools/percent_Vbur.py"", line 655, in calc_vbur info = percent_vbur_cmd( ^^^^^^^^^^^^^^^^^ File ""/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/SEQCROW/commands/percent_Vbur.py"", line 314, in percent_vbur targets = rescol.find([AtomSpec(a.atomspec) for a in ligand_atoms]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'NoneType' object is not iterable TypeError: 'NoneType' object is not iterable File ""/Users/jabarro/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/SEQCROW/commands/percent_Vbur.py"", line 314, in percent_vbur targets = rescol.find([AtomSpec(a.atomspec) for a in ligand_atoms]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > select clear > select #1/a:1@N2 1 atom, 1 residue, 1 model selected > color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1654 #1/a:1@N2 83.0 > transparency 60 > select clear > ui mousemode right rotate > ui mousemode right translate > ui mousemode right rotate > transparency 80 > save /Users/jabarro/Documents/collin/set2/sp/image3d.png width 1024 height > 665 supersample 3 > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting flat > graphics silhouettes false > lighting soft > lighting flat > lighting full > graphics silhouettes false > lighting simple > graphics silhouettes true > graphics silhouettes false > lighting full > save /Users/jabarro/Documents/collin/set2/sp/3d-1654.png width 1024 height > 665 supersample 3 > ui mousemode right ""select similar fragments"" > ui mousemode right select > select #4/a:1@H4 1 atom, 1 residue, 1 model selected > ui mousemode right ""select similar fragments"" > ui mousemode right select > select add #1/a:1@C2 206 atoms, 204 bonds, 3 residues, 3 models selected > select add #1/a:1@C3 207 atoms, 204 bonds, 3 residues, 3 models selected > select add #3/a:1@H2 208 atoms, 204 bonds, 3 residues, 3 models selected > select add #1/a:1@N1 209 atoms, 204 bonds, 3 residues, 3 models selected > select add #1/a:1@C4 210 atoms, 204 bonds, 3 residues, 3 models selected > select add #3/a:1@H3 211 atoms, 204 bonds, 3 residues, 3 models selected > select add #3/a:1@H1 212 atoms, 205 bonds, 3 residues, 3 models selected > select clear > select #1/a:1@N2 1 atom, 1 residue, 1 model selected > color radial #1.1 center 8.3327,7.4627,9.5307 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1654 #1/a:1@N2 81.2 > transparency 80 > select clear > open /Users/jabarro/Documents/collin/set2/1528a.xyz opened 1528a.xyz as an XYZ coordinate file Drag select of 3 atoms > select clear > hide #4 models > hide #3 models > hide #1 models > ui mousemode right translate > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > ui mousemode right select > select add #5/a:1@C5 39 atoms, 38 bonds, 1 residue, 1 model selected > select add #5/a:1@H5 40 atoms, 38 bonds, 1 residue, 1 model selected > select add #5/a:1@H6 41 atoms, 38 bonds, 1 residue, 1 model selected > select add #5/a:1@H4 42 atoms, 41 bonds, 1 residue, 1 model selected > select add #5/a:1@C1 43 atoms, 41 bonds, 1 residue, 1 model selected > select add #5/a:1@C2 44 atoms, 43 bonds, 1 residue, 1 model selected > select add #5/a:1@H1 45 atoms, 44 bonds, 1 residue, 1 model selected > select add #5/a:1@N2 46 atoms, 45 bonds, 1 residue, 1 model selected > select add #5/a:1@C3 47 atoms, 46 bonds, 1 residue, 1 model selected > select add #5/a:1@H2 48 atoms, 47 bonds, 1 residue, 1 model selected > select add #5/a:1@C4 49 atoms, 48 bonds, 1 residue, 1 model selected > select add #5/a:1@H3 50 atoms, 48 bonds, 1 residue, 1 model selected > select clear > select add #5/a:1@N1 1 atom, 1 residue, 1 model selected > color radial #5.1 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50 > coordinateSystem #5 > transparency #5.1 30 model center %Vbur 1528a #5/a:1@N1 88.0 > transparency 80 > save /Users/jabarro/Documents/collin/set2/sp/3d-1528a.png width 1024 height > 665 supersample 3 > color radial #5.2 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50 > coordinateSystem #5 > transparency #5.2 30 model center %Vbur 1528a #5/a:1@N1 88.0 > hide #5 models > select add #1 71 atoms, 70 bonds, 2 residues, 2 models selected > close > open /Users/jabarro/Documents/collin/set2/1528b.xyz opened 1528b.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > ui mousemode right select > select /a:1@H14 1 atom, 1 residue, 1 model selected > select add /a:1@C14 2 atoms, 1 bond, 1 residue, 1 model selected > select add /a:1@C13 3 atoms, 1 bond, 1 residue, 1 model selected > select add /a:1@H13 4 atoms, 1 bond, 1 residue, 1 model selected > select add /a:1@N6 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /a:1@C12 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /a:1@H18 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /a:1@C11 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /a:1@C15 9 atoms, 8 bonds, 1 residue, 1 model selected > select add /a:1@H17 10 atoms, 9 bonds, 1 residue, 1 model selected > select add /a:1@H15 11 atoms, 10 bonds, 1 residue, 1 model selected > select add /a:1@H16 12 atoms, 11 bonds, 1 residue, 1 model selected > ui mousemode right ""select fragment"" > ui mousemode right select > select subtract /a:1@N5 12 atoms, 11 bonds, 1 residue, 1 model selected > color radial #1.1 center 4.4826,8.4268,15.9536 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 > color radial #1.2 center 3.8680,7.5177,18.0786 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.2 30 > color radial #1.3 center 4.0928,8.5865,17.2102 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.3 30 > color radial #1.4 center 4.6473,7.1598,15.5569 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.4 30 > color radial #1.5 center 4.9406,6.9931,14.6692 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.5 30 > color radial #1.6 center 4.4065,6.0957,16.3879 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.6 30 > color radial #1.7 center 4.5130,5.2136,16.0504 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.7 30 > color radial #1.8 center 3.4754,7.7454,19.4843 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.8 30 > color radial #1.9 center 4.1829,8.2428,19.9447 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.9 30 > color radial #1.10 center 2.6425,8.2612,19.5112 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.10 30 > color radial #1.11 center 3.3397,6.8827,19.9291 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.11 30 > color radial #1.12 center 3.9421,9.5903,17.5791 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.12 30 model center %Vbur 1528b /a:1@N6 61.5 1528b /a:1@C11 82.3 1528b /a:1@C12 67.8 1528b /a:1@C13 66.3 1528b /a:1@H13 50.9 1528b /a:1@C14 74.8 1528b /a:1@H14 59.7 1528b /a:1@C15 59.5 1528b /a:1@H15 45.8 1528b /a:1@H16 52.7 1528b /a:1@H17 60.7 1528b /a:1@H18 47.7 > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select subtract /a:1@N5 12 atoms, 11 bonds, 1 residue, 1 model selected > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N5 1 atom, 1 residue, 1 model selected > color radial #1.1 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1528b /a:1@N5 87.0 > transparency 80 > select clear > save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height > 665 supersample 3 > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select subtract /a:1@N5 50 atoms, 49 bonds, 1 residue, 1 model selected > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select /a:1@N5 1 atom, 1 residue, 1 model selected > select clear > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select add /a:1@N5 39 atoms, 38 bonds, 1 residue, 1 model selected > color radial #1.1 center 3.5530,3.8159,19.2383 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 > color radial #1.2 center 1.9472,0.6868,24.2120 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.2 30 > color radial #1.3 center 3.9867,0.8261,18.3503 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.3 30 > color radial #1.4 center 2.5437,3.0927,22.1901 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.4 30 > color radial #1.5 center 0.4085,7.8598,17.5553 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.5 30 > color radial #1.6 center 7.6569,7.8598,17.5553 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.6 30 > color radial #1.7 center 0.9491,5.8417,15.7080 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.7 30 > color radial #1.8 center 8.1975,5.8417,15.7080 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.8 30 > color radial #1.9 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.9 30 > color radial #1.10 center 0.3453,6.5909,17.8955 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.10 30 > color radial #1.11 center 7.5937,6.5909,17.8955 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.11 30 > color radial #1.12 center 0.6160,5.5823,16.9688 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.12 30 > color radial #1.13 center 7.8644,5.5823,16.9688 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.13 30 > color radial #1.14 center 0.5604,4.6768,17.2497 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.14 30 > color radial #1.15 center 7.8088,4.6768,17.2497 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.15 30 > color radial #1.16 center 1.0164,7.1324,15.3885 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.16 30 > color radial #1.17 center 8.2648,7.1324,15.3885 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.17 30 > color radial #1.18 center 1.2568,7.3672,14.5001 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.18 30 > color radial #1.19 center 8.5052,7.3672,14.5001 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.19 30 > color radial #1.20 center 0.7535,8.1367,16.2857 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.20 30 > color radial #1.21 center 8.0019,8.1367,16.2857 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.21 30 > color radial #1.22 center 0.8172,9.0430,16.0053 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.22 30 > color radial #1.23 center 8.0656,9.0430,16.0053 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.23 30 > color radial #1.24 center -0.0378,6.2402,19.3259 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.24 30 > color radial #1.25 center 7.2106,6.2402,19.3259 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.25 30 > color radial #1.26 center -0.9114,5.7960,19.3306 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.26 30 > color radial #1.27 center 6.3370,5.7960,19.3306 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.27 30 > color radial #1.28 center 0.6362,5.6394,19.7066 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.28 30 > color radial #1.29 center 7.8846,5.6394,19.7066 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.29 30 > color radial #1.30 center -0.0851,7.0595,19.8615 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.30 30 > color radial #1.31 center 7.1633,7.0595,19.8615 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.31 30 > color radial #1.32 center 3.5155,0.7982,19.6078 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.32 30 > color radial #1.33 center 3.2687,2.0009,20.2457 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.33 30 > color radial #1.34 center 2.8110,1.9384,21.5500 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.34 30 > color radial #1.35 center 2.5893,0.7511,22.2097 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.35 30 > color radial #1.36 center 2.5595,-1.5890,22.1031 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.36 30 > color radial #1.37 center 3.2809,-0.4309,20.2033 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.37 30 > color radial #1.38 center 2.8198,-0.4127,21.4992 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.38 30 > color radial #1.39 center 3.5745,-2.2150,19.1488 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.39 30 model center %Vbur 1528b /a:1@I1 53.9 1528b /a:1@I2 44.6 1528b /a:1@F1 49.3 1528b /a:1@F2 49.5 1528b /a:1@N1 49.6 1528b /a:1@N2 49.2 1528b /a:1@N3 45.4 1528b /a:1@N4 43.3 1528b /a:1@N5 42.8 1528b /a:1@C1 58.8 1528b /a:1@C2 56.1 1528b /a:1@C3 56.1 1528b /a:1@C4 50.9 1528b /a:1@H1 47.9 1528b /a:1@H2 41.1 1528b /a:1@C5 44.5 1528b /a:1@C6 44.5 1528b /a:1@H3 33.5 1528b /a:1@H4 33.5 1528b /a:1@C7 44.8 1528b /a:1@C8 44.8 1528b /a:1@H5 33.3 1528b /a:1@H6 33.3 1528b /a:1@C9 42.9 1528b /a:1@C10 42.6 1528b /a:1@H7 34.5 1528b /a:1@H8 44.2 1528b /a:1@H9 46.0 1528b /a:1@H10 35.5 1528b /a:1@H11 33.7 1528b /a:1@H12 33.8 1528b /a:1@C16 64.6 1528b /a:1@C17 68.0 1528b /a:1@C18 64.3 1528b /a:1@C19 67.8 1528b /a:1@F3 49.1 1528b /a:1@C20 67.8 1528b /a:1@C21 64.5 1528b /a:1@I3 44.6 > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select add /a:1@N5 39 atoms, 38 bonds, 1 residue, 1 model selected > color radial #1.1 center 3.5530,3.8159,19.2383 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 > color radial #1.2 center 1.9472,0.6868,24.2120 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.2 30 > color radial #1.3 center 3.9867,0.8261,18.3503 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.3 30 > color radial #1.4 center 2.5437,3.0927,22.1901 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.4 30 > color radial #1.5 center 0.4085,7.8598,17.5553 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.5 30 > color radial #1.6 center 7.6569,7.8598,17.5553 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.6 30 > color radial #1.7 center 0.9491,5.8417,15.7080 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.7 30 > color radial #1.8 center 8.1975,5.8417,15.7080 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.8 30 > color radial #1.9 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.9 30 > color radial #1.10 center 0.3453,6.5909,17.8955 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.10 30 > color radial #1.11 center 7.5937,6.5909,17.8955 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.11 30 > color radial #1.12 center 0.6160,5.5823,16.9688 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.12 30 > color radial #1.13 center 7.8644,5.5823,16.9688 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.13 30 > color radial #1.14 center 0.5604,4.6768,17.2497 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.14 30 > color radial #1.15 center 7.8088,4.6768,17.2497 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.15 30 > color radial #1.16 center 1.0164,7.1324,15.3885 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.16 30 > color radial #1.17 center 8.2648,7.1324,15.3885 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.17 30 > color radial #1.18 center 1.2568,7.3672,14.5001 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.18 30 > color radial #1.19 center 8.5052,7.3672,14.5001 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.19 30 > color radial #1.20 center 0.7535,8.1367,16.2857 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.20 30 > color radial #1.21 center 8.0019,8.1367,16.2857 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.21 30 > color radial #1.22 center 0.8172,9.0430,16.0053 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.22 30 > color radial #1.23 center 8.0656,9.0430,16.0053 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.23 30 > color radial #1.24 center -0.0378,6.2402,19.3259 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.24 30 > color radial #1.25 center 7.2106,6.2402,19.3259 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.25 30 > color radial #1.26 center -0.9114,5.7960,19.3306 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.26 30 > color radial #1.27 center 6.3370,5.7960,19.3306 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.27 30 > color radial #1.28 center 0.6362,5.6394,19.7066 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.28 30 > color radial #1.29 center 7.8846,5.6394,19.7066 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.29 30 > color radial #1.30 center -0.0851,7.0595,19.8615 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.30 30 > color radial #1.31 center 7.1633,7.0595,19.8615 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.31 30 > color radial #1.32 center 3.5155,0.7982,19.6078 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.32 30 > color radial #1.33 center 3.2687,2.0009,20.2457 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.33 30 > color radial #1.34 center 2.8110,1.9384,21.5500 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.34 30 > color radial #1.35 center 2.5893,0.7511,22.2097 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.35 30 > color radial #1.36 center 2.5595,-1.5890,22.1031 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.36 30 > color radial #1.37 center 3.2809,-0.4309,20.2033 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.37 30 > color radial #1.38 center 2.8198,-0.4127,21.4992 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.38 30 > color radial #1.39 center 3.5745,-2.2150,19.1488 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.39 30 model center %Vbur 1528b /a:1@I1 53.9 1528b /a:1@I2 44.6 1528b /a:1@F1 49.3 1528b /a:1@F2 49.5 1528b /a:1@N1 49.6 1528b /a:1@N2 49.2 1528b /a:1@N3 45.4 1528b /a:1@N4 43.3 1528b /a:1@N5 42.8 1528b /a:1@C1 58.8 1528b /a:1@C2 56.1 1528b /a:1@C3 56.1 1528b /a:1@C4 50.9 1528b /a:1@H1 47.9 1528b /a:1@H2 41.1 1528b /a:1@C5 44.5 1528b /a:1@C6 44.5 1528b /a:1@H3 33.5 1528b /a:1@H4 33.5 1528b /a:1@C7 44.8 1528b /a:1@C8 44.8 1528b /a:1@H5 33.3 1528b /a:1@H6 33.3 1528b /a:1@C9 42.9 1528b /a:1@C10 42.6 1528b /a:1@H7 34.5 1528b /a:1@H8 44.2 1528b /a:1@H9 46.0 1528b /a:1@H10 35.5 1528b /a:1@H11 33.7 1528b /a:1@H12 33.8 1528b /a:1@C16 64.6 1528b /a:1@C17 68.0 1528b /a:1@C18 64.3 1528b /a:1@C19 67.8 1528b /a:1@F3 49.1 1528b /a:1@C20 67.8 1528b /a:1@C21 64.5 1528b /a:1@I3 44.6 > select clear > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select add /a:1@N5 1 atom, 1 residue, 1 model selected > color radial #1.1 center 4.0272,6.2629,17.6591 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1528b /a:1@N5 42.7 > transparency 80 > save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height > 665 supersample 3 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-1528b.png width 1024 height > 665 supersample 3 > close #1 > open /Users/jabarro/Documents/collin/set2/1528a.xyz format xyz opened 1528a.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > ui mousemode right select > select clear > select /a:1@N1 1 atom, 1 residue, 1 model selected > color radial #1.1 center 4.0327,20.3203,17.5553 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1528a /a:1@N1 43.9 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-1528a.png width 1024 height > 665 supersample 3 > open /Users/jabarro/Documents/collin/set2/1654.xyz opened 1654.xyz as an XYZ coordinate file > hide #!1 models > show #!1 models > hide #2 models > show #2 models > hide #!1 models > show #!1 models > hide #2 models > hide #!1 models > select add #1 51 atoms, 51 bonds, 1 residue, 3 models selected > select add #1 51 atoms, 51 bonds, 1 residue, 3 models selected > show #!1 models > close > open /Users/jabarro/Documents/collin/set2/1654.xyz opened 1654.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > select clear > ui mousemode right translate > ui mousemode right ""select fragment"" > ui mousemode right select > select add /a:1@N2 61 atoms, 60 bonds, 1 residue, 1 model selected > select clear > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select clear > select add /a:1@N2 1 atom, 1 residue, 1 model selected > color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 1654 /a:1@N2 46.6 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-1654.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/6677a.xyz opened 6677a.xyz as an XYZ coordinate file > ui mousemode right translate > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N3 1 atom, 1 residue, 1 model selected > color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6677a /a:1@N3 44.6 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6677a.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/6677b.xyz opened 6677b.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > ui mousemode right select > select clear > select /a:1@N6 1 atom, 1 residue, 1 model selected > color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6677b /a:1@N6 44.7 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6677b.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/6647a.xyz opened 6647a.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right translate > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N6 1 atom, 1 residue, 1 model selected > color radial #1.1 center 0.0000,-0.0000,0.0000 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6647a /a:1@N6 41.9 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6647b.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/6647b.xyz opened 6647b.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N3 1 atom, 1 residue, 1 model selected > color radial #1.1 center -0.0000,-0.0000,0.0000 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6647b /a:1@N3 43.0 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6647b.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6680a.xyz opened 6680a.xyz as an XYZ coordinate file > select clear > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false Drag select of 1 atoms, 1 bonds > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select clear > select /a:1@N6 1 atom, 1 residue, 1 model selected > select clear > ui mousemode right ""select fragment"" > ui mousemode right select > select clear > select /a:1@N6 1 atom, 1 residue, 1 model selected > color radial #1.1 center 15.1339,17.1707,20.0486 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680a /a:1@N6 40.7 > transparency 60 > select clear > save /Users/jabarro/Documents/collin/set2/sp/3d-6680a.png width 1024 height > 665 supersample 3 > save /Users/jabarro/Documents/collin/set2/sp/2d-6680a.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6680b.xyz opened 6680b.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > select clear > ui mousemode right ""select fragment"" > lighting full > graphics silhouettes false > select clear > ui mousemode right select > select /a:1@N5 1 atom, 1 residue, 1 model selected > select clear > select /a:1@N5 1 atom, 1 residue, 1 model selected > color radial #1.1 center 10.6213,10.3164,14.2871 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680b /a:1@N5 42.7 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/2d-6680b.png width 1024 height > 665 supersample 3 > save /Users/jabarro/Documents/collin/set2/sp/3d-6680b.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6680c.xyz opened 6680c.xyz as an XYZ coordinate file > lighting full > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N1 1 atom, 1 residue, 1 model selected > color radial #1.1 center 14.0278,11.5147,13.0069 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680c /a:1@N1 42.7 > transparency 60 > color radial #1.2 center 14.0278,11.5147,13.0069 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.2 30 model center %Vbur 6680c /a:1@N1 42.7 > save /Users/jabarro/Documents/collin/set2/sp/2d-6680c.png width 1024 height > 665 supersample 3 > transparency 60 > color radial #1.1 center 14.0278,11.5147,13.0069 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680c /a:1@N1 42.7 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6680c.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6680d.xyz opened 6680d.xyz as an XYZ coordinate file > lighting full > graphics silhouettes true > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N2 1 atom, 1 residue, 1 model selected > color radial #1.1 center 14.7711,8.8695,13.4615 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680d /a:1@N2 41.7 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6680d.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6679a.xyz opened 6679a.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > select clear > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N1 1 atom, 1 residue, 1 model selected > color radial #1.1 center 8.5347,32.6077,4.5766 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6679a /a:1@N1 44.0 > transparency 60 > select clear Drag select of %Vbur for 6679a, 15 of 5539 triangles > select clear > save /Users/jabarro/Documents/collin/set2/sp/3d-6679a.png width 1024 height > 665 supersample 3 > close > open /Users/jabarro/Documents/collin/set2/sp/6679b.xyz opened 6679b.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > select clear > select /a:1@I3 1 atom, 1 residue, 1 model selected > select /a:1@N5 1 atom, 1 residue, 1 model selected > select clear > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select /a:1@N4 1 atom, 1 residue, 1 model selected > color radial #1.1 center 6.6301,30.5894,4.3823 palette rainbow range 0,3.50 > coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6679b /a:1@N4 40.1 > transparency 60 > save /Users/jabarro/Documents/collin/set2/sp/3d-6679b.png width 1024 height > 665 supersample 3 > ui windowfill toggle > show target m > close > open /Users/jabarro/Documents/collin/set2/sp/6680a.xyz format xyz opened 6680a.xyz as an XYZ coordinate file > preset seqcrow ""ball-stick-endcap (displayed only)"" Using preset: SEQCROW / Ball-Stick-Endcap (Displayed Only) Preset implemented in Python; no expansion to individual ChimeraX commands available. > lighting full > graphics silhouettes false > ui mousemode right ""select fragment"" > select clear > ui mousemode right select > select add /a:1@H18 45 atoms, 44 bonds, 1 residue, 1 model selected > select add /a:1@C15 46 atoms, 44 bonds, 1 residue, 1 model selected > select add /a:1@C14 47 atoms, 44 bonds, 1 residue, 1 model selected > select add /a:1@H17 48 atoms, 44 bonds, 1 residue, 1 model selected > select clear > select /a:1@N6 1 atom, 1 residue, 1 model selected > color radial #1.1 center 15.1339,17.1707,20.0486 palette rainbow range > 0,3.50 coordinateSystem #1 > transparency #1.1 30 model center %Vbur 6680a /a:1@N6 71.5 ===== 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 - 89.3 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: 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: Mac15,6 Model Number: MRX33LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 25 days, 6 hours, 1 minute Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2723QE: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 Send2Trash: 1.8.3 SEQCROW: 1.8.17 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 can't reproduce Tom Goddard all ChimeraX