id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14719 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.1-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000204518600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/orderedset.py"", line 53 in __iter__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 294 in list_handlers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 489 in trigger_handlers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1027 in _fire_trigger File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1017 in _cpp_rename File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 120 in set_prop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 98 in clone_seq File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 60 in matches_to_gapped_seqs File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py"", line 55 in nw File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 78 in align File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 406 in match File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py"", line 742 in cmd_match File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/tool.py"", line 303 in run_matchmaker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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, 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How to cite UCSF ChimeraX > open > /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb #3 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb #4 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd/HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb #5 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #2-5 to #1 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 HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#2), sequence alignment score = 1245.7 RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs: 0.541) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#3), sequence alignment score = 1243.9 RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs: 0.494) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#4), sequence alignment score = 1256.5 RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs: 0.375) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#5), sequence alignment score = 1247.5 RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs: 0.365) > color bfactor 10460 atoms, 1290 residues, atom bfactor range 17.3 to 98.9 > open > /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #6 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #8 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb #9 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5/HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #10 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #2-10 to #1 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 HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#2), sequence alignment score = 1245.7 RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs: 0.541) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#3), sequence alignment score = 1243.9 RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs: 0.494) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#4), sequence alignment score = 1256.5 RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs: 0.375) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#5), sequence alignment score = 1247.5 RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs: 0.365) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#6), sequence alignment score = 1249.3 RMSD between 235 pruned atom pairs is 0.523 angstroms; (across all 243 pairs: 0.869) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#7), sequence alignment score = 1243.9 RMSD between 237 pruned atom pairs is 0.385 angstroms; (across all 243 pairs: 0.635) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#8), sequence alignment score = 1252.9 RMSD between 238 pruned atom pairs is 0.379 angstroms; (across all 243 pairs: 0.514) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#9), sequence alignment score = 1243.9 RMSD between 240 pruned atom pairs is 0.340 angstroms; (across all 243 pairs: 0.428) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#10), sequence alignment score = 1227.7 RMSD between 235 pruned atom pairs is 0.324 angstroms; (across all 243 pairs: 0.858) > hide #5 models > hide #4 models > hide #3 models > hide #2 models > color #1,6-10 bychain > color bfactor #1,6-10 12257 atoms, 1523 residues, atom bfactor range 16.9 to 98.9 > show #2 models > show #3 models > show #4 models > show #5 models > select #1/B#2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B 19640 atoms, 19950 bonds, 2430 residues, 10 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface #1.1: minimum, -14.25, mean -0.67, maximum 13.96 Coulombic values for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #2.1: minimum, -18.46, mean -0.67, maximum 13.67 Coulombic values for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb_B SES surface #3.1: minimum, -14.29, mean -0.64, maximum 14.99 Coulombic values for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb_B SES surface #4.1: minimum, -13.81, mean -0.59, maximum 14.25 Coulombic values for HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb_B SES surface #5.1: minimum, -17.36, mean -0.66, maximum 14.37 Coulombic values for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb_B SES surface #6.1: minimum, -14.90, mean -0.53, maximum 13.49 Coulombic values for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb_B SES surface #7.1: minimum, -13.99, mean -0.60, maximum 13.50 Coulombic values for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb_B SES surface #8.1: minimum, -14.14, mean -0.69, maximum 13.50 Coulombic values for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb_B SES surface #9.1: minimum, -14.46, mean -0.64, maximum 14.71 Coulombic values for HsFAM3Ctail_GOLPH3_E_U_12_0_560b5_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface #10.1: minimum, -17.43, mean -0.71, maximum 14.57 To also show corresponding color key, enter the above coulombic command and add key true > hide #!5 models > show #!5 models > hide #!7 models > hide #!6 models > hide #!8 models > hide #!9 models > hide #!10 models > show #!10 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!10 models > hide #!5 models > close #6-10 Alignment identifier is 1 > select clear Alignment identifier is 2 Alignment identifier is 3 > select #1/A:2 #2/A:2 #3/A:2 #4/A:2 #5/A:2 55 atoms, 50 bonds, 5 residues, 5 models selected > select #1/A:2 #2/A:2 #3/A:2 #4/A:2 #5/A:2 55 atoms, 50 bonds, 5 residues, 5 models selected 2 [ID: 2] region 5 chains [2] RMSD: 3.967 > select #1/A:2,4-5 #2/A:2,4-5 #3/A:2,4-5 #4/A:2,4-5 #5/A:2,4-5 165 atoms, 155 bonds, 15 residues, 5 models selected 2 [ID: 2] region 5 chains [2] + 1 other block RMSD: 3.652 > select #1/A:2,4-5,9-10 #2/A:2,4-5,9-10 #3/A:2,4-5,9-10 #4/A:2,4-5,9-10 > #5/A:2,4-5,9-10 260 atoms, 245 bonds, 25 residues, 5 models selected 2 [ID: 2] region 5 chains [2] + 2 other blocks RMSD: 3.026 > select #1/A:12 #2/A:12 #3/A:12 #4/A:12 #5/A:12 55 atoms, 50 bonds, 5 residues, 5 models selected > select #1/A:12-13 #2/A:12-13 #3/A:12-13 #4/A:12-13 #5/A:12-13 110 atoms, 105 bonds, 10 residues, 5 models selected 2 [ID: 2] region 5 chains [12-13] RMSD: 1.724 > select #1/A:9,12-13 #2/A:9,12-13 #3/A:9,12-13 #4/A:9,12-13 #5/A:9,12-13 165 atoms, 155 bonds, 15 residues, 5 models selected 2 [ID: 2] region 5 chains [12-13] + 1 other block RMSD: 1.787 > select #1/A:4-5,9,12-13 #2/A:4-5,9,12-13 #3/A:4-5,9,12-13 #4/A:4-5,9,12-13 > #5/A:4-5,9,12-13 275 atoms, 260 bonds, 25 residues, 5 models selected 2 [ID: 2] region 5 chains [12-13] + 2 other blocks RMSD: 2.602 > select #1/A:2,4-5,9,12-13 #2/A:2,4-5,9,12-13 #3/A:2,4-5,9,12-13 > #4/A:2,4-5,9,12-13 #5/A:2,4-5,9,12-13 330 atoms, 310 bonds, 30 residues, 5 models selected 2 [ID: 2] region 5 chains [12-13] + 3 other blocks RMSD: 2.875 > show sel & #!1-4 atoms > color (#!1-4 & sel) orange > select #1/A:7 #2/A:7 #3/A:7 #4/A:7 #5/A:7 40 atoms, 35 bonds, 5 residues, 5 models selected > select #1/A:7-8 #2/A:7-8 #3/A:7-8 #4/A:7-8 #5/A:7-8 80 atoms, 75 bonds, 10 residues, 5 models selected 2 [ID: 2] region 5 chains [7-8] RMSD: 3.111 > select #1/A:7-8,10 #2/A:7-8,10 #3/A:7-8,10 #4/A:7-8,10 #5/A:7-8,10 120 atoms, 110 bonds, 15 residues, 5 models selected 2 [ID: 2] region 5 chains [7-8] + 1 other block RMSD: 2.678 > show sel & #!1-4 atoms > color (#!1-4 & sel) lime > select clear > hide #!4 models > select #1/B:18 #2/B:18 #3/B:18 #4/B:18 #5/B:18 40 atoms, 35 bonds, 5 residues, 5 models selected > select #1/B:18 #2/B:18 #3/B:18 #4/B:18 #5/B:18 40 atoms, 35 bonds, 5 residues, 5 models selected 1 [ID: 1] region 5 chains [18] RMSD: 0.535 > select #1/B:18,20 #2/B:18,20 #3/B:18,20 #4/B:18,20 #5/B:18,20 85 atoms, 75 bonds, 10 residues, 5 models selected 1 [ID: 1] region 5 chains [18] + 1 other block RMSD: 0.774 > hide #!3 models > hide #!2 models > select #1/B#2/B#3/B#4/B#5/B 9820 atoms, 9975 bonds, 1215 residues, 5 models selected > mlp sel & #!1 Map values for surface ""HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb_B SES surface"": minimum -28.78, mean -4.602, maximum 25.34 To also show corresponding color key, enter the above mlp command and add key true > hide sel & #!1 surfaces > open ""/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat > Collaboration/ConFold/HsGOLPH3ConFold_b471d_weblogo.pdb"" Chain information for HsGOLPH3ConFold_b471d_weblogo.pdb #6 --- Chain | Description A | No description available > select #6/A 2370 atoms, 2401 bonds, 298 residues, 1 model selected > show sel surfaces > ui tool show ""Render by Attribute"" > color byattribute a:bfactor #!1-6 target cabs palette > 0.04,#0fc7cf:25.1605,#b2b2b2:98.88,#9e205e 12830 atoms, 1588 residues, 6 surfaces, atom bfactor range 0.04 to 98.9 > color byattribute a:bfactor #!6 target cabs palette > 0.04,#0fc7cf:2.94081,#b2b2b2:5.09488,#9e205e 2370 atoms, 298 residues, 1 surfaces, atom bfactor range 0.04 to 17.3 > color byattribute a:bfactor #!6 target cabs palette > 0.04,#0fc7cf:2.94081,#b2b2b2:5.09488,#9e205e 2370 atoms, 298 residues, 1 surfaces, atom bfactor range 0.04 to 17.3 > select clear > ui tool show Matchmaker > matchmaker #!2-6 to #1 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 HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#2), sequence alignment score = 1245.7 RMSD between 236 pruned atom pairs is 0.344 angstroms; (across all 243 pairs: 0.541) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_003_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#3), sequence alignment score = 1243.9 RMSD between 239 pruned atom pairs is 0.373 angstroms; (across all 243 pairs: 0.494) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_004_alphafold2_multimer_v3_model_2_seed_000.pdb, chain B (#4), sequence alignment score = 1256.5 RMSD between 242 pruned atom pairs is 0.343 angstroms; (across all 243 pairs: 0.375) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb, chain B (#5), sequence alignment score = 1247.5 RMSD between 241 pruned atom pairs is 0.311 angstroms; (across all 243 pairs: 0.365) Matchmaker HsB4GALT5tail_GOLPH3_E_U_12_0_cd9cd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb, chain B (#1) with HsGOLPH3ConFold_b471d_weblogo.pdb, chain A (#6), sequence alignment score = 1256.5 RMSD between 224 pruned atom pairs is 0.689 angstroms; (across all 243 pairs: 1.083) > open > /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb #8 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_003_alphafold2_multimer_v3_model_3_seed_000.pdb #9 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #10 --- Chain | Description A | No description available B | No description available > open > /Users/sean/Downloads/HsGALNT2tail_GOLPH3_E_U_12_0_a277a/HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for HsGALNT2tail_GOLPH3_E_U_12_0_a277a_unrelaxed_rank_005_alphafold2_multimer_v3_model_1_seed_000.pdb #11 --- Chain | Description A | No description available B | No description available > hide #!1 models > hide #!6 models > ui tool show Matchmaker > matchmaker #8-11#!2-6 to #7 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.6.1 (21G217) Kernel Version: Darwin 21.6.0 Time since boot: 55 days 4:00 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX