id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16976 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x0000000200af0840 (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, 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""6736733a26c1270f5a9ef53d"" }, ""deploymentId"" : 240000045 } ], ""experiments"" : [ { ""treatmentId"" : ""993c66e1-bf83-41fd-a09f-0d8d5906d223"", ""experimentId"" : ""664fc3cd79a61a0b8b557292"", ""deploymentId"" : 500000013 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/mohamed/Documents/Research/Projects/WSCP/2024_reppert/paper_data_2025/With_water/Q57E/CDC/extended_most_occ_pH8.pdb > format pdb Chain information for extended_most_occ_pH8.pdb #1 --- Chain | Description A | No description available B | No description available C D | No description available Computing secondary structure > set bgColor white > color #1 #bfbfbfff > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides stubs > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > surface > color white target s transparency 80 > color :CLA green > color :CHL green > color :BCR #FF8C00 > color :XAT #FF8C00 > color :LUT #FF8C00 > color :NEX #FF8C00 > lighting full > graphics silhouettes true > transparency 80 target r > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > ~worm > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides stubs > select :57, Expected an objects specifier or a keyword > select :57 63 atoms, 59 bonds, 4 residues, 1 model selected > show sel atoms > style sel ball Changed 63 atom styles > color sel byhetero > select :CLA 548 atoms, 556 bonds, 10 pseudobonds, 4 residues, 2 models selected > show sel atoms > style sel ball Changed 548 atom styles > color sel byhetero > help help:credits.html > hide cartoons > ui mousemode right select Drag select of 26 atoms, 25 bonds > select up 28 atoms, 26 bonds, 2 residues, 3 models selected > select up 32 atoms, 30 bonds, 2 residues, 3 models selected > mlp sel Map values for surface ""extended_most_occ_pH8.pdb_C SES surface"": minimum -31.54, mean -5.161, maximum 27.03 Map values for surface ""extended_most_occ_pH8.pdb_D SES surface"": minimum -27.38, mean -5.36, maximum 26.14 To also show corresponding color key, enter the above mlp command and add key true > select clear > select up 4 atoms, 2 bonds, 2 residues, 1 model selected > select up 274 atoms, 278 bonds, 2 residues, 1 model selected > mlp sel mlp: no amino acids specified Drag select of 185 atoms, 5 pseudobonds, 197 bonds > select up 196 atoms, 199 bonds, 5 pseudobonds, 4 residues, 4 models selected > select up 305 atoms, 307 bonds, 5 pseudobonds, 4 residues, 4 models selected > mlp sel Map values for surface ""extended_most_occ_pH8.pdb_A SES surface"": minimum -27.58, mean -4.913, maximum 26.76 Map values for surface ""extended_most_occ_pH8.pdb_B SES surface"": minimum -26.55, mean 8.672e+22, maximum 9.261e+24 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select clear > hide surfaces > ui mousemode right distance > distance /C:1001@OBD /D:1001@OBD Distance between /C CLA 1001 OBD and /D CLA 1001 OBD: 5.559Å > distance /A:1001@OBD /B:1001@OBD Distance between /A CLA 1001 OBD and /B CLA 1001 OBD: 5.785Å > distance /D:57@CD /C:57@CD Distance between /D GLU 57 CD and /C GLU 57 CD: 5.726Å > distance /B:57@CD /A:57@CD Distance between /B GLU 57 CD and /A GLU 57 CD: 4.285Å > show ribons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show cartoons > ui mousemode right select > select /A:59 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:54 19 atoms, 18 bonds, 1 residue, 1 model selected > help help:credits.html > hide cartoons > show /A:54,55,56,57,58,59 > style sel ball Changed 19 atom styles > color sel byhetero > show /B:54,55,56,57,58,59 > color sel byhetero > style sel ball Changed 19 atom styles > show /C:54,55,56,57,58,59 > style sel ball Changed 19 atom styles > color sel byhetero > show /D:54,55,56,57,58,59 > style sel ball Changed 19 atom styles > color sel byhetero > select :CLA 548 atoms, 556 bonds, 12 pseudobonds, 4 residues, 3 models selected > ~select > :CLA@CAD,CBD,OBD,CHA,CHB,CHC,CHD,C1A,C1B,C1C,C1D,N1A,N1B,N1C,N1D,C2A,C2B,C2C,C2D,C3A,C3B,C3C,C3D,C4A,C4B,C4C,C4D,MG 436 atoms, 372 bonds, 4 residues, 1 model selected > delete sel > select :CHL Nothing selected > ~select > :CHL@CAD,CBD,OBD,CHA,CHB,CHC,CHD,C1A,C1B,C1C,C1D,N1A,N1B,N1C,N1D,C2A,C2B,C2C,C2D,C3A,C3B,C3C,C3D,C4A,C4B,C4C,C4D,MG Nothing selected > delete sel > show /D:54,55,56,57,58,59 > style ball Changed 10651 atom styles > color byhetero > ui mousemode right distance > distance /A:57@N /A:54@O Distance between /A GLU 57 N and LEU 54 O: 3.368Å > distance /B:54@O /B:57@N Distance between /B LEU 54 O and GLU 57 N: 3.356Å > distance /C:57@N /C:54@O Distance between /C GLU 57 N and LEU 54 O: 3.366Å > distance /D:57@N /D:54@O Distance between /D GLU 57 N and LEU 54 O: 3.351Å > label height 1.3 > ui mousemode right label > label #1/A:56 > label /A:56 text {0.chain_id}_{0.name}_{0.number} > label /B:56 text {0.chain_id}_{0.name}_{0.number} > label /C:56 text {0.chain_id}_{0.name}_{0.number} > label /D:56 text {0.chain_id}_{0.name}_{0.number} > set stick_trancperency Expected a keyword > label #1/B:57 > label #1/A:57 > ui mousemode right select > ui mousemode right label > label delete residues > hide #!2 models > show #!2 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #1.1 models > hide #1.2 models > hide #1.3 models > hide #1.4 models > hide #1.5 models > hide #1.6 models > view #2 clip false > label /C:56 text {0.chain_id}_{0.name}_{0.number} > label /D:56 text {0.chain_id}_{0.name}_{0.number} > ui mousemode right distance > distance /C:54@O /D:54@O Distance between /C LEU 54 O and /D LEU 54 O: 14.465Å > ui mousemode right label > label #1/C:54 > label #1/D:54 > ui mousemode right distance > distance /B:54@O /A:54@O Distance between /B LEU 54 O and /A LEU 54 O: 14.532Å > ui mousemode right select > transparency -a 0.5 Missing or invalid ""percent"" argument: Expected a number > transparency -a 6 Missing or invalid ""percent"" argument: Expected a number > transparency a 6 Missing or invalid ""percent"" argument: Expected a number > transparency 6 a Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 6 atoms > transparency 90 atoms > transparency 90 atoms sele Expected ',' or a keyword > transparency 90 atoms :57 Expected ',' or a keyword > transparency 90 atoms, :57 Missing or invalid ""what"" argument: Should be one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' > transparency/B 80 target a Unknown command: transparency/B 80 target a > transparency/B 80 target atoms Unknown command: transparency/B 80 target atoms > transparency/B 80 target r Unknown command: transparency/B 80 target r > show cartoons > transparency 90 cartoons > ui tool show ""Side View"" > transparency 90 atoms > transparency 40 atoms > color bychain > color byhetero > hide #!2 models > select clear > color byhetero > ui mousemode right select > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 2 models selected > color sel byhetero > style sel ball Changed 19 atom styles > style sel sphere Changed 19 atom styles > style sel sphere Changed 19 atom styles > style sel stick Changed 19 atom styles > style sel ball Changed 19 atom styles > select /A:55@CD 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > hide sel atoms > select /A:56@CD1 1 atom, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 2 models selected > hide sel atoms > select /A:57@CD 1 atom, 1 residue, 1 model selected > select clear > select /A:58@CD 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel atoms > select @@serial_number=8994 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > hide sel atoms > select /B:56@CZ 1 atom, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 2 models selected > hide sel atoms > ui mousemode right distance > distance /A:54@CG /B:54@CG Distance between /A LEU 54 CG and /B LEU 54 CG: 13.534Å > distance /A:54@CG /B:54@CG Distance already exists; modify distance properties with 'distance style' > show #!2 models > hide #2.1 models > close #2 > distance /B:54@CG /A:54@CG Distance between /B LEU 54 CG and /A LEU 54 CG: 13.534Å > ui mousemode right select > select clear > set bgColor white > color #1 #bfbfbfff > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides stubs > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > surface > color white target s transparency 80 > color :CLA green > color :CHL green > color :BCR #FF8C00 > color :XAT #FF8C00 > color :LUT #FF8C00 > color :NEX #FF8C00 > lighting full > graphics silhouettes true > transparency 80 target r > show nucleic > hide protein|solvent|H > surface hidePatches > style (protein|nucleic|solvent) & @@draw_mode=0 stick Changed 0 atom styles > ~worm > cartoon > cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2 > width 2 thickness 0.4 sides 12 divisions 20 > cartoon style ~(nucleic|strand) xsection round > cartoon style (nucleic|strand) xsection rectangle > cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6 > cartoon style nucleic xsection round width 1.6 thickness 1.6 > nucleotides stubs > show :54,57 > select :54,57 139 atoms, 131 bonds, 1 pseudobond, 8 residues, 2 models selected > style sel ball Changed 139 atom styles > color sel byhetero > hbonds sel reveal true 21 hydrogen bonds found > ~hbonds > color sel bychain > select @@serial_number=27558 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > hide sel atoms > select /A:52@OG1 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > hide sel atoms > select /B:52@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > hide sel atoms > select /B:1001@C4C 1 atom, 1 residue, 1 model selected > select up 28 atoms, 32 bonds, 1 residue, 1 model selected > color sel byhetero > select /A:1001@N1C 1 atom, 1 residue, 1 model selected > select up 28 atoms, 32 bonds, 1 residue, 1 model selected > color sel byhetero > select @@serial_number=28659 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > style sel ball Changed 3 atom styles > color sel byhetero > select up 2 atoms, 1 bond, 1 residue, 1 model selected > color sel byhetero > label height 1.3 > ui mousemode right ""move label"" > color #2.1 #424242ff models > color #2.1 #212121ff models > color #2.1 silver models > color #2.1 #0096ffff models > color #2.1 #00fdffff models > color #2.1 #ffd479ff models > color #2.1 #941100ff models > color #2.1 black models > color #2.1 #212121ff models > color #2.1 #424242ff models > color #2.1 black models > ui mousemode right distance > distance /A:54@CA /B:54@CA Distance between /A LEU 54 CA and /B LEU 54 CA: 15.943Å > hide #1.7 models > show #1.7 models > hide #1.7 models > show #1.7 models > hide #2.1 models > show #2.1 models > hide #2.1 target m > close #2.1 > close #2 > distance /B:54@CA /A:54@CA Distance between /B LEU 54 CA and /A LEU 54 CA: 15.943Å > color #2.1 black models > label height 1.3 > ui mousemode right select > select /A:35 16 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select up 4 atoms, 2 bonds, 2 residues, 1 model selected > select up 31 atoms, 29 bonds, 2 residues, 3 models selected > style sel ball Changed 31 atom styles > color sel byhetero > select clear > ui mousemode right ""move label"" > color #2 #0433ffff models > color #2 #011993ff models > color #2 darkgrey models > color #2 #d6d6d6ff models > color #2 #424242ff models > color #2 black models > color #2 #ff2600ff models > color #2 black models > ui mousemode right label > label #1/A:54 > label #1/B:54 > label #1/B:57 > label #1/A:57 > label #1/B:1001 > label #1/A:1001 > ui mousemode right ""move label"" > label :CLA,54,57 text {0.chain_id}_{0.name} > label :CLA,54,57 text {0.chain_id}_{0.name}_{0.number} > label height 1.3 > label height 1 > ui mousemode right label > label #1/B:1001 > label :54,57 text {0.chain_id}_{0.name}_{0.number} > label :CLA text {0.chain_id}_{0.name} > label height 1.3 > label height 1 > ui mousemode right ""move label"" > label :54,57 text {0.chain_id}/{0.name}{0.number} > save CD_pocket.png transparentBackground true > save /Users/mohamed/Documents/Chimera_working_dir/Q57E_AB_pocket.cxs > ui mousemode right distance > hide #!2 models > show #!2 models > ui mousemode right label > ui mousemode right distance > close #2 > distance /C:54@CA /D:54@CA Distance between /C LEU 54 CA and /D LEU 54 CA: 16.019Å > ui mousemode right select > select /C:52@CG2 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > color sel byhetero > style sel ball Changed 14 atom styles > hbonds sel reveal true 3 hydrogen bonds found > ui mousemode right distance > distance /D:54@CG /C:54@CG Distance between /D LEU 54 CG and /C LEU 54 CG: 13.284Å > hide #2.1 models > show #2.1 models > hide #!2 models > show #!2 models > close #2 > distance /D:54@CG /C:54@CG Distance between /D LEU 54 CG and /C LEU 54 CG: 13.284Å > ui mousemode right select > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > hide sel atoms > select @@serial_number=30833 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > color sel byhetero > select @@serial_number=29627 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > color sel byhetero > select @@serial_number=30521 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > color sel byhetero > ui mousemode right label > label delete residues > label #1/D:54 > label #1/D:57 > label #1/C:54 > label #1/C:57 > label #1/C:1001 > label :54,57 text {0.chain_id}_{0.name}_{0.number} > label :CLA text {0.chain_id}_{0.name} > label height 1.3 > label height 1 > ui mousemode right select > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 2 models selected > hide sel atoms > select /C:1001@CHD 1 atom, 1 residue, 1 model selected > select up 28 atoms, 32 bonds, 1 residue, 1 model selected > select up 2694 atoms, 2727 bonds, 181 residues, 1 model selected > select down 28 atoms, 32 bonds, 1 residue, 2 models selected > style sel ball Changed 28 atom styles > color sel byhetero > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 28 atoms, 32 bonds, 1 residue, 1 model selected > color sel byhetero > color #2 black models > ~hbonds > label :54,57 text {0.chain_id}/{0.name}{0.number} > label :CLA text {0.chain_id}/{0.name} > label height 1 > ui mousemode right ""move label"" > ui mousemode right select > select clear > save CD_pocket.png transparentBackground true > ui mousemode right ""move label"" > ui mousemode right distance > distance /A:54@CG /B:54@CG Distance between /A LEU 54 CG and /B LEU 54 CG: 13.534Å > distance /B:54@CD1 /A:54@CD1 Distance between /B LEU 54 CD1 and /A LEU 54 CD1: 11.511Å > close #2 > distance /B:54@CG /B:54@CD1 Distance between /B LEU 54 CG and CD1: 1.520Å > close #2 > distance /B:54@CD1 /A:54@CD1 Distance between /B LEU 54 CD1 and /A LEU 54 CD1: 11.511Å > distance /C:54@CD1 /D:54@CD1 Distance between /C LEU 54 CD1 and /D LEU 54 CD1: 11.186Å > color #2 black models > color #2.1 black models > ui mousemode right select > select clear > ui mousemode right ""move label"" > ui mousemode right distance > HIDE CARTOON Unknown command: HIDE CARTOON > hide cartoons > distance /D:57@CA /C:57@CA Distance between /D GLU 57 CA and /C GLU 57 CA: 6.840Å > distance /A:57@CA /B:57@CA Distance between /A GLU 57 CA and /B GLU 57 CA: 6.693Å > open > /Users/mohamed/Documents/Research/Projects/WSCP/Alpha_fold/WSCP_Q57E_rank_001.pdb Chain information for WSCP_Q57E_rank_001.pdb #3 --- Chain | Description A | No description available B | No description available C D | No description available Computing secondary structure > hide #!1 models > hide #!2 models > show #!1 models > show cartoons > hide #!1 models > show #!1 models > ui mousemode right select > select #1/A:54 19 atoms, 18 bonds, 1 residue, 1 model selected > hide #3 models > show #3 models > hide #!1 models > select #3/C:108 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > show #!1 models > matchmaker #3 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker extended_most_occ_pH8.pdb, chain D (#1) with WSCP_Q57E_rank_001.pdb, chain C (#3), sequence alignment score = 843.5 RMSD between 164 pruned atom pairs is 0.615 angstroms; (across all 177 pairs: 1.018) > ui mousemode right label > label delete residues > label #3/A:53 > ui mousemode right select > select #3/A:53 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > color sel byhetero > select #3/D:52 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > color sel byhetero > hide #!1 models > ui mousemode right distance > distance #3/A:53@CG #3/D:52@CB Distance between WSCP_Q57E_rank_001.pdb #3/A LEU 53 CG and /D LEU 52 CB: 12.968Å > show #!2 models > close #2 > distance #3/A:53@CG #3/D:52@CB Distance between WSCP_Q57E_rank_001.pdb #3/A LEU 53 CG and /D LEU 52 CB: 12.968Å > show #!1 models > hide #!1 models > show #!1 models > ui mousemode right rotate > ui mousemode right select > select #3/C:52 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select #3/B:51 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > hide #!1 models > ui mousemode right distance > distance #3/C:52@CG #3/B:51@CG Distance between WSCP_Q57E_rank_001.pdb #3/C LEU 52 CG and /B LEU 51 CG: 12.927Å > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > ui mousemode right label > label #1/D:54 > label delete residues > ui mousemode right distance > distance #1/D:54@CG #1/C:54@CG Distance between extended_most_occ_pH8.pdb #1/D LEU 54 CG and /C LEU 54 CG: 13.284Å > show #3 models > hide #3 models > distance #1/B:54@CD1 #1/A:54@CG Distance between extended_most_occ_pH8.pdb #1/B LEU 54 CD1 and /A LEU 54 CG: 12.502Å > show #3 models > hide #!1 models > hide #3 models > show #!1 models > select :cys 48 atoms, 40 bonds, 8 residues, 1 model selected > show #!1 atoms > undo > ui mousemode right select > select clear > select :cys 48 atoms, 40 bonds, 8 residues, 1 model selected > show #!1 atoms > hide #!1 atoms > undo Alignment identifier is 3/A Alignment identifier is 3/B Alignment identifier is 1 > select #3/A:44 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:44 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:30 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:30-64 248 atoms, 254 bonds, 35 residues, 1 model selected > view sel > select #3/A:85 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:72-85 108 atoms, 108 bonds, 14 residues, 1 model selected > view orient > view > select #3/A:23-61 278 atoms, 285 bonds, 39 residues, 1 model selected > select #3/A:23-52 209 atoms, 212 bonds, 30 residues, 1 model selected > select #3/A:66 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:66-102 277 atoms, 284 bonds, 37 residues, 1 model selected > select #3/A:85 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:77-85 70 atoms, 70 bonds, 9 residues, 1 model selected > show #3 models > hide #!1 models > select #3/A:74 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:47-74 201 atoms, 205 bonds, 28 residues, 1 model selected > select #3/A:66-110 345 atoms, 353 bonds, 45 residues, 1 model selected > select #3/A:79-110 254 atoms, 261 bonds, 32 residues, 1 model selected > show #!1 models > hide #3 models Alignment identifier is 3/A > select #3/A:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:62-72 74 atoms, 74 bonds, 11 residues, 1 model selected > select #3/A:117-118 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3/A:117-128 102 atoms, 104 bonds, 12 residues, 1 model selected > select #3/A:34 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:34-172 1065 atoms, 1092 bonds, 139 residues, 1 model selected > select add #3 5353 atoms, 5480 bonds, 2 pseudobonds, 699 residues, 2 models selected > select add #1 16004 atoms, 16262 bonds, 16 pseudobonds, 1412 residues, 5 models selected > select add #2 16004 atoms, 16262 bonds, 16 pseudobonds, 1412 residues, 10 models selected > select #3/A:84-85 19 atoms, 19 bonds, 2 residues, 1 model selected > select #3/A:85-121 286 atoms, 295 bonds, 37 residues, 1 model selected > select #3/A:77 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:21-77 409 atoms, 418 bonds, 57 residues, 1 model selected > select #3/A:40-98 443 atoms, 456 bonds, 59 residues, 1 model selected > select #3/A:40-92 394 atoms, 405 bonds, 53 residues, 1 model selected > select #3/A:107-168 485 atoms, 497 bonds, 62 residues, 1 model selected > select #3/A:40-168 988 atoms, 1014 bonds, 129 residues, 1 model selected > select #1/D:45 10 atoms, 9 bonds, 1 residue, 1 model selected > style sel ball Changed 10 atom styles > show sel atoms > color sel byhetero > select #1/A:45 10 atoms, 9 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 10 atom styles > color sel byhetero > show #3 models > hide #3 models > show #3 models > select #1/D:57@CA 1 atom, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 1 atom style > color sel byhetero > hide #!1 models > select #3/C:55 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > color sel byhetero > close #2 > show #!1 models > hide #!1 models > select #3/B:54 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > color sel byhetero > ui mousemode right distance > distance #3/B:54@CD #3/C:55@CD Distance between WSCP_Q57E_rank_001.pdb #3/B GLU 54 CD and /C GLU 55 CD: 5.378Å > show #!1 models > hide #!1 models > show #!1 models > hide #3 models > show #3 models > ui mousemode right select > select #3/D:55 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > select #3/A:56 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 9 atom styles > hide #!1 models > ui mousemode right distance > distance #3/D:55@CD #3/A:56@CD Distance between WSCP_Q57E_rank_001.pdb #3/D GLU 55 CD and /A GLU 56 CD: 5.384Å > show #!1 models > hide #3 models > ui tool show ""Side View"" > hide cartoons > distance #1/B:57@CD #1/A:57@CD Distance between extended_most_occ_pH8.pdb #1/B GLU 57 CD and /A GLU 57 CD: 4.285Å > show #3 models > hide #!1 models > show #!1 models > hide #3 models > show cartoons > distance #1/D:57@CD #1/D:57@OE2 Distance between extended_most_occ_pH8.pdb #1/D GLU 57 CD and OE2: 1.249Å > distance #1/D:57@OE2 #1/C:57@CD Distance between extended_most_occ_pH8.pdb #1/D GLU 57 OE2 and /C GLU 57 CD: 5.026Å > hide cartoons ===== 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 M2 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 Air Model Identifier: Mac14,15 Model Number: MQKW3LL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 1 day, 22 hours, 35 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LS27D36xG: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX