id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20810 ChimeraX bug report submission iktaekim@… "{{{ The following bug report has been submitted: Platform: macOS-26.5.2-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x00000001edf29d80 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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, 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] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > close all > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/LocalRSR_afterISOLDE/20260728_205440/BranchA_PAB8/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0656, step 1, values float32 > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > volume #4 level 0.2626 > volume #3 level 0.04723 > volume #3 style mesh > volume #4 level 0.1754 > show #1,2/C:1-22 atoms > style #1,2/C:1-22 stick Changed 944 atom styles > view #1,2/C:1-22 > hide #!3 models > hide #!4 models > nucleotides atoms > style nucleic stick Changed 5858 atom styles > nucleotides slab > style nucleic stick Changed 5858 atom styles > nucleotides fill > style nucleic stick Changed 5858 atom styles > show #1,2/C:28-38 atoms > style #1,2/C:28-38 stick Changed 440 atom styles > view #1,2/C:28-38 > show #1,2/C:65-80 atoms > style #1,2/C:65-80 stick Changed 682 atom styles > view #1,2/C:65-80 > color #1,2 bychain > view > show #!3 models > volume #4 style mesh > show #!4 models > hide #!3 models > view #1/B:26 > view > style #1/B:26 sticks Expected a keyword > style #1/B:26 stick Changed 12 atom styles > view #1/B:26 > Unknown command: sequence #1 > Unknown command: sequence #2 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #2/B Alignment identifier is 1 > select #1/B:26 #2/B:26 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/B:26 #2/B:26 24 atoms, 24 bonds, 2 residues, 2 models selected 1 [ID: 1] region 2 chains [26] RMSD: 0.179 > surface hidePatches sel > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > color sel bynucleotide > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > view > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape muffler > surface sel > hide #!2 models > select #1/B:22 #2/B:22 24 atoms, 24 bonds, 2 residues, 2 models selected > select #1/B:22-26 #2/B:22-26 106 atoms, 110 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [22-26] RMSD: 0.113 > surface hidePatches (#!1 & sel) > show (#!1 & sel) target ab > volume #4 level 0.1201 > hide #!4 models > close all > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/LocalRSR_afterISOLDE/20260728_205440/BranchA_PAB8/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0656, step 1, values float32 > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > volume #4 level 0.1284 > info polymers #2/A physical chain #2/A:1 #2/A:274 physical chain #2/A:289 #2/A:740 physical chain #2/A:762 #2/A:1054 > hide #!3 models > volume #4 style mesh > hide #!1 models > hide #!4 models > color #2 bychain > select #2/A:1-274 2226 atoms, 2264 bonds, 274 residues, 1 model selected > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > open /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/input- > af3-hpacas9-snu-SNUseq_raw.pdb Chain information for input-af3-hpacas9-snu-SNUseq_raw.pdb #5 --- Chain | Description A | No description available > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > show #!4 models > volume #4 level 0.1888 > volume #4 level 0.2223 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #4 color #00fdff > volume #4 > volume #4 style surface > volume #4 level 0.1754 > hide #5 models > hide #!4 models > close #1-2 > rename #3 id #1 > rename #4 id #2 > close #5 > show #!1 models > show #!2 models > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif"" Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #3 --- Chain | Description A | . B | . C | . > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif"" Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif #4 --- Chain | Description A | . B | . C | . > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif"" Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif #5 --- Chain | Description A | . B | . C | . > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif"" Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif #6 --- Chain | Description A | . B | . C | . > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif"" Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif #7 --- Chain | Description A | . B | . C | . Computing secondary structure > fitmap #3 inMap #2 search 100 Found 15 unique fits from 100 random placements having fraction of points inside contour >= 0.100 (15 of 100). Average map values and times found: 0.04864 (1), 0.04822 (1), 0.04815 (1), 0.04705 (1), 0.04393 (1), 0.04385 (1), 0.03923 (1), 0.03817 (1), 0.03805 (1), 0.03709 (1), 0.03641 (1), 0.03629 (1), 0.03607 (1), 0.03599 (1), 0.03291 (1) Best fit found: Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms average map value = 0.04864, steps = 136 shifted from previous position = 1.95 rotated from previous position = 9.65 degrees atoms outside contour = 10521, contour level = 0.17536 Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.53421526 -0.52575549 -0.66196319 124.61625561 0.01841852 0.77564049 -0.63090620 112.19412299 0.84514782 -0.34923211 -0.40467536 111.43202151 Axis 0.17313397 -0.92636180 0.33448234 Axis point 37.67263092 0.00000000 112.73145945 Rotation angle (degrees) 125.56492192 Shift along axis -45.08499940 Found 15 fits. Populating font family aliases took 54 ms. Replace uses of missing font family ""Courier"" with one that exists to avoid this cost. > mmaker #4 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif, chain A (#4), sequence alignment score = 5391.3 RMSD between 853 pruned atom pairs is 0.943 angstroms; (across all 1054 pairs: 1.826) > mmaker #5 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif, chain A (#5), sequence alignment score = 5382.3 RMSD between 893 pruned atom pairs is 0.838 angstroms; (across all 1054 pairs: 2.332) > mmaker #6 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif, chain A (#6), sequence alignment score = 5356.5 RMSD between 887 pruned atom pairs is 0.962 angstroms; (across all 1054 pairs: 1.542) > mmaker #7 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif, chain A (#7), sequence alignment score = 5381.1 RMSD between 877 pruned atom pairs is 0.762 angstroms; (across all 1054 pairs: 2.636) > hide #7 models > hide #6 models > hide #5 models > hide #4 models > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #8 --- Chain | Description A | No description available B | No description available C | No description available > mmaker #3 to #8 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 HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb, chain A (#8) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3), sequence alignment score = 4976.3 RMSD between 612 pruned atom pairs is 0.977 angstroms; (across all 1019 pairs: 2.821) > hide #!8 models > show #4 models > mmaker #4 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif, chain A (#4), sequence alignment score = 5391.3 RMSD between 853 pruned atom pairs is 0.943 angstroms; (across all 1054 pairs: 1.826) > mmaker #5 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif, chain A (#5), sequence alignment score = 5382.3 RMSD between 893 pruned atom pairs is 0.838 angstroms; (across all 1054 pairs: 2.332) > mmaker #6 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif, chain A (#6), sequence alignment score = 5356.5 RMSD between 887 pruned atom pairs is 0.962 angstroms; (across all 1054 pairs: 1.542) > mmaker #7 to #3 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 fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif, chain A (#7), sequence alignment score = 5381.1 RMSD between 877 pruned atom pairs is 0.762 angstroms; (across all 1054 pairs: 2.636) > show #5 models > show #6 models > show #7 models > show #!8 models > hide #!1 models > hide #!8 models > hide #!2 models > color #3-7 bychain > close #4-7#8 > show #!2 models > fitmap #3 inMap #2 search 100 Found 18 unique fits from 100 random placements having fraction of points inside contour >= 0.100 (18 of 100). Average map values and times found: 0.0488 (1), 0.04646 (1), 0.04524 (1), 0.04423 (1), 0.04077 (1), 0.04077 (1), 0.04059 (1), 0.03987 (1), 0.03694 (1), 0.03642 (1), 0.03614 (1), 0.03583 (1), 0.03556 (1), 0.03549 (1), 0.03482 (1), 0.03396 (1), 0.03288 (1), 0.03171 (1) Best fit found: Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms average map value = 0.0488, steps = 268 shifted from previous position = 2.32 rotated from previous position = 5.96 degrees atoms outside contour = 10524, contour level = 0.17536 Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.71239231 -0.65770712 -0.24478277 140.51639191 0.05689133 0.29352948 -0.95425570 108.23587887 0.69947173 -0.69373042 -0.17169030 122.84264202 Axis 0.21486733 -0.77877066 0.58936262 Axis point 60.89458733 0.00000000 131.98979156 Rotation angle (degrees) 142.68138405 Shift along axis 18.30031667 Found 18 fits. > fitmap #3 inMap #2 search 500 Found 86 unique fits from 500 random placements having fraction of points inside contour >= 0.100 (86 of 500). Average map values and times found: 0.05878 (1), 0.05087 (1), 0.04773 (1), 0.04748 (1), 0.04735 (1), 0.0455 (1), 0.0454 (1), 0.04492 (1), 0.0449 (1), 0.04468 (1), 0.04435 (1), 0.04341 (1), 0.04328 (1), 0.04273 (1), 0.04262 (1), 0.04261 (1), 0.04246 (1), 0.04238 (1), 0.04225 (1), 0.04188 (1), 0.04123 (1), 0.04107 (1), 0.04072 (1), 0.04061 (1), 0.04052 (1), 0.04035 (1), 0.04021 (1), 0.03981 (1), 0.0396 (1), 0.03932 (1), 0.03895 (1), 0.03889 (1), 0.03883 (1), 0.03852 (1), 0.03814 (1), 0.03811 (1), 0.03805 (1), 0.03773 (1), 0.03767 (1), 0.03767 (1), 0.03757 (1), 0.03757 (1), 0.03754 (1), 0.03735 (1), 0.03696 (1), 0.03674 (1), 0.0366 (1), 0.03657 (1), 0.0365 (1), 0.03645 (1), 0.03624 (1), 0.0362 (1), 0.03614 (1), 0.03613 (1), 0.03584 (1), 0.03583 (1), 0.03574 (1), 0.03573 (1), 0.03568 (1), 0.03548 (1), 0.03528 (1), 0.03519 (1), 0.03504 (1), 0.03459 (1), 0.03437 (1), 0.03432 (1), 0.03429 (1), 0.03426 (1), 0.03422 (1), 0.03401 (1), 0.03389 (1), 0.03376 (1), 0.03357 (1), 0.03355 (1), 0.03315 (1), 0.03284 (1), 0.03269 (1), 0.03268 (1), 0.03263 (1), 0.0325 (1), 0.03228 (1), 0.03215 (1), 0.03202 (1), 0.03193 (1), 0.03182 (1), 0.03058 (1) Best fit found: Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms average map value = 0.05878, steps = 280 shifted from previous position = 7.98 rotated from previous position = 19 degrees atoms outside contour = 10051, contour level = 0.17536 Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.17818556 -0.53481697 -0.82596659 120.60722532 -0.98363881 0.07416627 0.16417716 115.03215752 -0.02654588 0.84170676 -0.53928205 123.76489008 Axis 0.59433316 -0.70125679 -0.39370929 Axis point 86.50756224 0.00000000 64.15074726 Rotation angle (degrees) 145.25037350 Shift along axis -57.71359512 Found 86 fits. > fitmap #3 inMap #1 search 100 Found 92 unique fits from 100 random placements having fraction of points inside contour >= 0.100 (96 of 100). Average map values and times found: 0.1082 (4), 0.05659 (1), 0.05494 (2), 0.05474 (1), 0.05177 (1), 0.05133 (1), 0.04992 (1), 0.04876 (1), 0.0485 (1), 0.04822 (1), 0.04777 (1), 0.04756 (1), 0.04748 (1), 0.04732 (1), 0.04685 (1), 0.04664 (1), 0.04652 (1), 0.04638 (1), 0.04627 (1), 0.04605 (1), 0.04604 (1), 0.04591 (1), 0.04582 (1), 0.04571 (1), 0.0457 (1), 0.0457 (1), 0.04562 (1), 0.04513 (1), 0.04482 (1), 0.04449 (1), 0.04432 (1), 0.04373 (1), 0.04344 (1), 0.04308 (1), 0.04303 (1), 0.04286 (1), 0.04281 (1), 0.04249 (1), 0.04243 (1), 0.04219 (1), 0.04216 (1), 0.04213 (1), 0.04198 (1), 0.04179 (1), 0.0417 (1), 0.04135 (1), 0.04134 (1), 0.04132 (1), 0.04094 (1), 0.04083 (1), 0.04076 (1), 0.04055 (1), 0.04036 (1), 0.03951 (1), 0.03945 (1), 0.03932 (1), 0.03879 (1), 0.03801 (1), 0.03791 (1), 0.03776 (1), 0.03749 (1), 0.03746 (1), 0.03741 (1), 0.03735 (1), 0.03727 (1), 0.03725 (1), 0.03709 (1), 0.03701 (1), 0.03656 (1), 0.03626 (1), 0.03601 (1), 0.03587 (1), 0.03529 (1), 0.03528 (1), 0.03513 (1), 0.03503 (1), 0.03479 (1), 0.03444 (1), 0.03326 (1), 0.03325 (1), 0.03323 (1), 0.03264 (1), 0.03022 (1), 0.03011 (1), 0.03 (1), 0.02964 (1), 0.0293 (1), 0.0281 (1), 0.02785 (1), 0.02724 (1), 0.01914 (1), 0.01896 (1) Best fit found: Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) to map cryosparc_P7_J43_004_volume_map.mrc (#1) using 12193 atoms average map value = 0.1082, steps = 876 shifted from previous position = 62.4 rotated from previous position = 63.5 degrees atoms outside contour = 4237, contour level = 0.065555 Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif (#3) relative to cryosparc_P7_J43_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.33919257 -0.26230761 -0.90340643 125.17077408 -0.91427917 0.13415173 -0.38222635 117.76073271 0.22145441 0.95561399 -0.19431914 124.37948944 Axis 0.71713755 -0.60297176 -0.34948362 Axis point 0.00000000 56.17476383 141.85909093 Rotation angle (degrees) 111.13013240 Shift along axis -24.71032764 Found 92 fits. > show #!1 models > fitmap #3 inMap #1 resolution 3.2 metric correlation Opened fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif map 3.2 as #4, grid size 116,156,111, pixel 1.07, shown at level 0.112, step 1, values float32 Fit map fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif map 3.2 in map cryosparc_P7_J43_004_volume_map.mrc using 114926 points correlation = 0.4462, correlation about mean = 0.003041, overlap = 3170 steps = 216, shift = 14.6, angle = 22.4 degrees Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif map 3.2 (#4) relative to cryosparc_P7_J43_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.19524616 -0.65599666 -0.72907296 126.50585638 0.11731941 0.72242014 -0.68142891 112.44004804 0.97371205 -0.21858079 -0.06408864 126.03166979 Axis 0.24024299 -0.88383673 0.40139251 Axis point 21.21672085 0.00000000 144.79583287 Rotation angle (degrees) 105.57248907 Shift along axis -18.39832990 > close #4 > open /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/input- > af3-hpacas9-snu-SNUseq_raw.pdb Chain information for input-af3-hpacas9-snu-SNUseq_raw.pdb #4 --- Chain | Description A | No description available > mmaker #3 to #4 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 input-af3-hpacas9-snu-SNUseq_raw.pdb, chain A (#4) with fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3), sequence alignment score = 5288.7 RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs: 2.942) > hide #!1 models > hide #!2 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > show #!1 models > volume #1 style mesh > open > /Users/iktae/PhenixProjects/HpaCas9_SNU_J43_validation/input/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #5 --- Chain | Description A | . B | . C | . Computing secondary structure > close #5 > Unknown command: sequence #3 > Unknown command: sequence #3 > Unknown command: sequence #3/C > Unknown command: sequence #3.C > ui tool show ""Show Sequence Viewer"" > sequence chain #3/C Alignment identifier is 3/C > close #4 > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_guide24to20_5OH_SNUproject.cxc > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/00_raw/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/00_raw/NewAF_original_142nt.pdb models #1 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/before_guide_edit.cxs > info chains #1 chain id /A chain_id A chain id /B chain_id B chain id /C chain_id C > info polymers #1/C physical chain /C:1 /C:142 > sequence chain #1/C Alignment identifier is 1/C > delete atoms #1/C:1-4 > renumber #1/C start 1 relative false 138 residues renumbered > swapna #1/C:1-20 G,G,A,A,A,U,U,A,G,G,U,G,C,G,C,U,U,G,G,C preserve true > delete atoms #1/C:1@P,OP1,OP2 > show #1/C:1-24 atoms > style #1/C:1-24 stick Changed 515 atom styles > view #1/C:1-24 > info polymers #1/C physical chain /C:1 /C:138 > distance #1/C:20@O3' #1/C:21@P Distance between /C C 20 O3' and G 21 P: 1.588Å > sequence chain #1/C Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb > models #1 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/after_guide_edit.cxs executed NewAF_guide24to20_5OH_SNUproject.cxc > info chains #1 chain id /A chain_id A chain id /B chain_id B chain id /C chain_id C > info polymers #1/A physical chain /A:1 /A:1054 > info polymers #1/B physical chain /B:1 /B:76 > info polymers #1/C physical chain /C:1 /C:138 > sequence chain #1/C Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > distance #1/C:20@O3' #1/C:21@P Distance already exists; modify distance properties with 'distance style' > nucleotides atoms > style nucleic stick Changed 2929 atom styles > nucleotides fill > style nucleic stick Changed 2929 atom styles > nucleotides slab > style nucleic stick Changed 2929 atom styles > color bynucleotide > nucleotides atoms > style nucleic stick Changed 2929 atom styles > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > info chains #1 chain id /A chain_id A chain id /B chain_id B chain id /C chain_id C > info polymers #1/C physical chain /C:1 /C:138 > sequence chain #1/C Alignment identifier is 1/C > distance #1/C:20@O3' #1/C:21@P Distance between /C C 20 O3' and G 21 P: 1.588Å > open /Users/iktae/Downloads/emd_34919.map Opened emd_34919.map as #3, grid size 184,184,184, pixel 1.04, shown at level 0.0297, step 1, values float32 > select add #3 2 models selected > select subtract #3 Nothing selected > volume #3 level 0.03792 > close #3 > info polymers #1/B physical chain /B:1 /B:76 > info polymers #1/A physical chain /A:1 /A:1054 > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif"" Summary of feedback from opening /Users/iktae/Library/Mobile Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif --- warnings | Unknown polymer entity '1' on line 106 Missing or incorrect sequence information. Inferred polymer connectivity. Unknown polymer entity '1' on line 8883 Missing or incorrect sequence information. Inferred polymer connectivity. Unknown polymer entity '1' on line 9637 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for fitted_model_J43.cif --- Chain | Description 2.1/A | No description available 2.2/B | No description available 2.3/C | No description available Computing secondary structure > mmaker #2 to #1 No matrix compatible with both reference structure and all match structures > matchmaker #2 to #1 No matrix compatible with both reference structure and all match structures > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/maps/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > matchmaker #1 to #2 Specify a single 'to' model only > matchmaker #1/A to #2.1/A 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 fitted_model_J43.cif, chain A (#2.1) with NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb, chain A (#1), sequence alignment score = 5273.8 RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs: 2.942) > volume #3 level 0.37 > hide #!2 models > volume #3 level 0.1687 > view #3 > show #!2 models > hide #!3 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #2 models > show #!3 models > fitmap #1/A inMap #3 resolution 3.2 moveWholeMolecules true Opened NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 as #4, grid size 111,113,99, pixel 1.07, shown at level 0.104, step 1, values float32 Fit map NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 in map cryosparc_P7_J43_004_volume_map_sharp.mrc using 83296 points correlation = 0.4734, correlation about mean = 0.1765, overlap = 6203 steps = 52, shift = 0.498, angle = 1.28 degrees Position of NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 (#4) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.33857473 -0.27000738 -0.90136739 125.19961221 -0.91587880 0.12504575 -0.38148340 117.92280308 0.21571549 0.95470392 -0.20495671 123.88670167 Axis 0.71933522 -0.60138055 -0.34770429 Axis point 0.00000000 56.86598985 140.96411150 Rotation angle (degrees) 111.75682757 Shift along axis -23.93192622 > show #!4 models > view #1/A > hide #!4 models > view #1/B > color #1 bychain > view #1/C:1-20 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > view #1/C:21-138 > volume #3 level 0.1217 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb > models #1 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.cxs > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > info chains #1 chain id /A chain_id A chain id /B chain_id B chain id /C chain_id C > info polymers #1/A physical chain /A:1 /A:1054 > info polymers #1/B physical chain /B:1 /B:76 > info polymers #1/C physical chain /C:1 /C:138 > sequence chain #1/C Alignment identifier is 1/C > select clear > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_guide24to20_stage1_unfixed.cxc > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/00_raw/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif Chain information for fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #1 --- Chain | Description A | . B | . C | . Computing secondary structure > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/00_raw/NewAF_original_142nt.pdb models #1 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/before_guide_edit.cxs > delete atoms #1/C:1-4 > renumber #1/C start 1 relative false 138 residues renumbered > swapna #1/C:1-20 G,G,A,A,A,U,U,A,G,G,U,G,C,G,C,U,U,G,G,C preserve true > delete atoms #1/C:1@P,OP1,OP2 > info chains #1 chain id /A chain_id A chain id /B chain_id B chain id /C chain_id C > info polymers #1/C physical chain /C:1 /C:138 > distance #1/C:20@O3' #1/C:21@P Distance between /C C 20 O3' and G 21 P: 1.588Å > show #1/C:1-24 atoms > style #1/C:1-24 stick Changed 515 atom styles > view #1/C:1-24 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_EDITED_COORDS_UNFIXED_SEQRES.pdb > models #1 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/after_guide_edit_unfixed.cxs executed NewAF_guide24to20_stage1_unfixed.cxc > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > info polymers #1/C physical chain /C:1 /C:138 > sequence chain #1/C Alignment identifier is 1/C > open ""/Users/iktae/Library/Mobile > Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- > Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif"" Summary of feedback from opening /Users/iktae/Library/Mobile Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR- Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif --- warnings | Unknown polymer entity '1' on line 106 Missing or incorrect sequence information. Inferred polymer connectivity. Unknown polymer entity '1' on line 8883 Missing or incorrect sequence information. Inferred polymer connectivity. Unknown polymer entity '1' on line 9637 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for fitted_model_J43.cif --- Chain | Description 2.1/A | No description available 2.2/B | No description available 2.3/C | No description available Computing secondary structure > matchmaker #1/A to #2.1/A 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 fitted_model_J43.cif, chain A (#2.1) with NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb, chain A (#1), sequence alignment score = 5273.8 RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs: 2.942) > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/maps/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > view #3 > fitmap #1/A inMap #3 resolution 3.2 moveWholeMolecules true Opened NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2 as #4, grid size 111,113,99, pixel 1.07, shown at level 0.104, step 1, values float32 Fit map NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2 in map cryosparc_P7_J43_004_volume_map_sharp.mrc using 83296 points correlation = 0.4734, correlation about mean = 0.1765, overlap = 6203 steps = 52, shift = 0.498, angle = 1.28 degrees Position of NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2 (#4) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.33857473 -0.27000738 -0.90136739 125.19961221 -0.91587880 0.12504575 -0.38148340 117.92280308 0.21571549 0.95470392 -0.20495671 123.88670167 Axis 0.71933522 -0.60138055 -0.34770429 Axis point 0.00000000 56.86598985 140.96411150 Rotation angle (degrees) 111.75682757 Shift along axis -23.93192622 > save /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit_SEQRESfixed.pdb > models #1 > show #!4 models > hide #!4 models > hide #2.1 models > hide #2.2 models > hide #2.3 models > hide #!2 models > hide #!3 models > color #1 bychain > show #!3 models > volume #3 style mesh > volume #3 level 0.1781 > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best.pdb Chain information for PredictAndBuild_4_overall_best.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > info #4 2 models #4, NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2, hidden size 111,113,99, step 1, voxel size 1.0667, level 0.1035, value range 0 - 2.6513, value type float32, 0 symmetry operators #4.1, surface, shown, 228360 triangles > info chains #4 > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > volume #3 level 0.116 > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best_superposed_predicted_models.pdb Chain information for PredictAndBuild_4_overall_best_superposed_predicted_models.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > hide #6 models > show #6 models > color #5 by chain Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5 bychain > hide #6 models > hide #!3 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > select #5/B 609 atoms, 621 bonds, 76 residues, 1 model selected > show sel atoms > show #6 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #6 models > hide #1 models > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > select clear > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 2134 atom styles > show #1 models > select #1/B 623 atoms, 636 bonds, 76 residues, 1 model selected > show sel atoms > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > select #5/B 609 atoms, 621 bonds, 76 residues, 1 model selected > hide sel atoms > show #6 models > hide #6 models > close #6#5 > show #1 models > close #2 > rename #3 id #2 > rename #4 id #3 > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_5/PredictAndBuild_5_overall_best.pdb Chain information for PredictAndBuild_5_overall_best.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > color #4 bychain > show #!3 models > hide #!3 models > show #!2 models > volume #2 level 0.2196 > show #1 models > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_5/PredictAndBuild_5_CarryOn/PredictAndBuild_5_rebuilt_3_cycle_1.pdb Chain information for PredictAndBuild_5_rebuilt_3_cycle_1.pdb #5 --- Chain | Description C | No description available Computing secondary structure > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!4 models > hide #5 models > show #5 models > show #!4 models > show #1 models > hide #!4 models > open /Users/iktae/PhenixProjects/SNU-HpaCas9-AcrIIC6-J43-validation/ '/Users/iktae/PhenixProjects/SNU-HpaCas9-AcrIIC6-J43-validation/' has no suffix > 04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/ Unknown command: 04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/ > PAB5_full_untrimmed_rebuilt_ABC.pdb Unknown command: PAB5_full_untrimmed_rebuilt_ABC.pdb > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_untrimmed_rebuilt_ABC.pdb Chain information for PAB5_full_untrimmed_rebuilt_ABC.pdb #6 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > hide #5 models > hide #1 models > select #7/B Nothing selected > select #7.B Expected an objects specifier or a keyword > select #6/B 609 atoms, 621 bonds, 76 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B #4/B #6/B Alignment identifier is 1 > select #1/B:41-49,54-65,69-74 #4/B:41-49,54-65,69-74 #6/B:41-49,54-65,69-74 666 atoms, 672 bonds, 81 residues, 3 models selected > select #1/B:26 #4/B:26 #6/B:26 36 atoms, 36 bonds, 3 residues, 3 models selected > select #1/B:26-34 #4/B:26-34 #6/B:26-34 210 atoms, 216 bonds, 27 residues, 3 models selected 1 [ID: 1] region 3 chains [26-34] RMSD: 2.130 > select add #1 12253 atoms, 12778 bonds, 1286 residues, 3 models selected > select subtract #1 134 atoms, 138 bonds, 18 residues, 2 models selected > select add #4 11265 atoms, 11709 bonds, 4 pseudobonds, 1208 residues, 3 models selected > select subtract #4 67 atoms, 69 bonds, 9 residues, 1 model selected > select add #6 12109 atoms, 12629 bonds, 1268 residues, 1 model selected > select subtract #6 Nothing selected > hide #6 models > show #6 models > select add #6 12109 atoms, 12629 bonds, 1268 residues, 1 model selected > select subtract #6 Nothing selected > select #1/B:26-27 #4/B:26-27 #6/B:26-27 60 atoms, 60 bonds, 6 residues, 3 models selected > select #1/B:26-34 #4/B:26-34 #6/B:26-34 210 atoms, 216 bonds, 27 residues, 3 models selected 1 [ID: 1] region 3 chains [26-34] RMSD: 2.130 > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_untrimmed_rebuilt_ABC.pdb Chain information for PAB5_full_untrimmed_rebuilt_ABC.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_superposed_predicted_reference.pdb Chain information for PAB5_full_superposed_predicted_reference.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc Opened cryosparc_P7_J43_004_volume_map.mrc as #4, grid size 256,256,256, pixel 0.934, shown at level 0.0656, step 1, values float32 Computing secondary structure > volume #3 level 0.1687 > hide #!4 models > hide #!3 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #1 atoms > hide #2 atoms > show #1/B:19-38 atoms > show #2/B:19-38 atoms > style #1/B:19-38 stick Changed 157 atom styles > style #2/B:19-38 stick Changed 171 atom styles > color #1/B:19-38 cyan > color #2/B:19-38 magenta > show #1/A:250,444,446,464 atoms > show #1/C:9 atoms > style #1/A:250,444,446,464 stick Changed 40 atom styles > style #1/C:9 stick Changed 23 atom styles > select #1/B:19-38 | #2/B:19-38 | #1/A:250,444,446,464 | #1/C:9 391 atoms, 400 bonds, 45 residues, 2 models selected > view sel > volume zone #3 nearAtoms #1/B:19-38 range 4 > volume zone #4 nearAtoms #1/B:19-38 range 4 > show #!3 models > show #!4 models > volume #3 style mesh > volume #4 style mesh > distance #1/B:24@C #1/B:25@N Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASN 24 C and HIS 25 N: 3.292Å > distance #1/B:29@C #1/B:30@N Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASN 29 C and ILE 30 N: 4.884Å > distance #2/B:24@C #2/B:25@N Distance between PAB5_full_superposed_predicted_reference.pdb #2/B ASN 24 C and HIS 25 N: 1.337Å > distance #2/B:29@C #2/B:30@N Distance between PAB5_full_superposed_predicted_reference.pdb #2/B ASN 29 C and ILE 30 N: 1.331Å > distance #1/A:464@OE1 #1/B:26@CE2 Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/A GLU 464 OE1 and /B TYR 26 CE2: 0.913Å > distance #1/B:27@OD2 #1/C:9@OP1 Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASP 27 OD2 and /C G 9 OP1: 0.901Å > distance #1/B:18@C #1/B:19@N Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B THR 18 C and PHE 19 N: 1.333Å > distance #1/B:38@C #1/B:39@N Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B LYS 38 C and LEU 39 N: 1.329Å > distance #2/B:18@C #2/B:19@N Distance between PAB5_full_superposed_predicted_reference.pdb #2/B THR 18 C and PHE 19 N: 1.323Å > distance #2/B:38@C #2/B:39@N Distance between PAB5_full_superposed_predicted_reference.pdb #2/B LYS 38 C and LEU 39 N: 1.320Å > hide #2 models > volume #3 style surface > volume #3 style mesh > hide #!4 models > show #2 models > hide #2 models > hide #!3 models > show #!3 models > show #2 models > hide #1 models > close all > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/03_local_repair/PAB5_fullABC_B19-38_reference_graft_raw_v1.pdb Chain information for PAB5_fullABC_B19-38_reference_graft_raw_v1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.934, shown at level 0.0814, step 1, values float32 > open > /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel 0.934, shown at level 0.0656, step 1, values float32 > hide #!2 models > hide #!3 models > show #!2 models > volume #2 level 0.1955 > volume #2 style image region 0,0,127,255,255,127 step 1 showOutlineBox true > volume #2 region 0,0,0,255,255,255 step 1 > volume #2 style mesh region 0,0,0,255,255,255 step 1 > volume #2 change image level -0.02881,0 level 0.1865,0.8 level 1.841,1 > volume #2 level 0.1754 > hide #1 atoms > show #1/B:17-40 atoms > style #1/B:17-40 stick Changed 200 atom styles > select #1/B:17-40 200 atoms, 205 bonds, 24 residues, 1 model selected > view sel > volume zone #2 nearAtoms #1/B:17-40 range 4 > volume zone #3 nearAtoms #1/B:17-40 range 4 > distance #1/B:18@C #1/B:19@N Distance between /B THR 18 C and PHE 19 N: 1.224Å > distance #1/B:24@C #1/B:25@N Distance between /B ASN 24 C and HIS 25 N: 1.337Å > distance #1/B:29@C #1/B:30@N Distance between /B ASN 29 C and ILE 30 N: 1.331Å > distance #1/B:38@C #1/B:39@N Distance between /B LYS 38 C and LEU 39 N: 1.276Å > distance #1/A:464@OE1 #1/B:26@CE2 Distance between /A GLU 464 OE1 and /B TYR 26 CE2: 3.865Å > distance #1/B:27@OD2 #1/C:9@OP1 Distance between /B ASP 27 OD2 and /C G 9 OP1: 1.635Å > open /Users/iktae/PhenixProjects/SNU- > HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/03_local_repair/PAB5_fullABC_B19-38_fromReference_v1.pdb Chain information for PAB5_fullABC_B19-38_fromReference_v1.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available Computing secondary structure > rename #5 id #6 > hide #1 models > hide #!2 models > hide #!4 models > hide #4.1 models > distance #6/B:18@C #6/B:19@N Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B THR 18 C and PHE 19 N: 1.224Å > distance #6/B:24@C #6/B:25@N Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASN 24 C and HIS 25 N: 1.337Å > distance #6/B:29@C #6/B:30@N Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASN 29 C and ILE 30 N: 1.331Å > distance #6/B:38@C #6/B:39@N Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B LYS 38 C and LEU 39 N: 1.276Å > distance #6/A:464@OE1 #6/B:26@CE2 Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/A GLU 464 OE1 and /B TYR 26 CE2: 3.865Å > distance #6/B:27@OD2 #6/C:9@OP1 Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASP 27 OD2 and /C G 9 OP1: 1.635Å > close all > open PAB5_fullABC_B19-38_fromReference_v1.pdb No such file/path: PAB5_fullABC_B19-38_fromReference_v1.pdb > open cryosparc_P7_J43_004_volume_map.mrc No such file/path: cryosparc_P7_J43_004_volume_map.mrc > open cryosparc_P7_J43_004_volume_map_sharp.mrc No such file/path: cryosparc_P7_J43_004_volume_map_sharp.mrc > addh #1 No structures specified > isolde start > set selectionWidth 4 Done loading forcefield > isolde select #1 Missing or invalid ""model"" argument: Must specify exactly one atomic structure, got 0 for #1. > clipper associate #2 toModel #1 Invalid ""toModel"" argument: Must specify 1 model, got 0 > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M4 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,5 Model Number: MX303LL/A Chip: Apple M4 Max Total Number of Cores: 14 (10 Performance and 4 Efficiency) Memory: 36 GB System Firmware Version: 18000.121.3 OS Loader Version: 18000.121.3 Software: System Software Overview: System Version: macOS 26.5.2 (25F84) Kernel Version: Darwin 25.5.0 Time since boot: 8 days, 11 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 2777M: 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: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.26.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 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: 1.19.1 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: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 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sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned