id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20234 Crash in QDockWidget::event() in Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.4.1-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 Thread 0x0000000310c37000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030e833000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000030c2f3000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x00000003035df000 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 331 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 629 in wait File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1399 in run File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000001f64d18c0 (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, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, 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48K 2 Kernel Alloc Once 32K 1 MALLOC 522.9M 157 MALLOC guard page 3200K 4 Mach message 96K 4 Memory Tag 22 64.0M 1 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 1088K 68 Stack 285.7M 69 Stack Guard 56.0M 1 VM_ALLOCATE 246.6M 327 VM_ALLOCATE (reserved) 448.0M 1 reserved VM address space (unallocated) __AUTH 6137K 645 __AUTH_CONST 90.9M 1042 __CTF 824 1 __DATA 42.5M 1128 __DATA_CONST 61.4M 1183 __DATA_DIRTY 8454K 896 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 605.1M 138 __OBJC_RO 79.1M 1 __OBJC_RW 2597K 1 __TEXT 1.5G 1206 __TPRO_CONST 128K 2 dyld private memory 304K 4 mapped file 343.3M 70 page table in kernel 1586K 1 shared memory 3600K 44 =========== ======= ======= TOTAL 4.3G 7195 TOTAL, minus reserved VM space 3.9G 7195 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""a05a390aa82a7db582d69a66b4cff51870e02139"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000041 }, { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== 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 > open /Users/Ania/Desktop/HPI/DALI12_Viridis.cxs format session > view name session-start opened ChimeraX session > matchmaker #2-25 to #1 showAlignment true 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#2), sequence alignment score = 174.9 Alignment identifier is 16 Showing conservation header (""seq_conservation"" residue attribute) for alignment 16 Hiding conservation header for alignment 16 Chains used in RMSD evaluation for alignment 16: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 16 RMSD between 43 pruned atom pairs is 0.933 angstroms; (across all 111 pairs: 6.059) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 17 Showing conservation header (""seq_conservation"" residue attribute) for alignment 17 Hiding conservation header for alignment 17 Chains used in RMSD evaluation for alignment 17: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 17 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#4), sequence alignment score = 516.2 Alignment identifier is 18 Showing conservation header (""seq_conservation"" residue attribute) for alignment 18 Hiding conservation header for alignment 18 Chains used in RMSD evaluation for alignment 18: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 18 RMSD between 108 pruned atom pairs is 0.524 angstroms; (across all 117 pairs: 1.674) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb, chain A (#5), sequence alignment score = 390.3 Alignment identifier is 19 Showing conservation header (""seq_conservation"" residue attribute) for alignment 19 Hiding conservation header for alignment 19 Chains used in RMSD evaluation for alignment 19: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 19 RMSD between 95 pruned atom pairs is 0.708 angstroms; (across all 116 pairs: 2.958) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#6), sequence alignment score = 469.7 Alignment identifier is 20 Showing conservation header (""seq_conservation"" residue attribute) for alignment 20 Hiding conservation header for alignment 20 Chains used in RMSD evaluation for alignment 20: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 20 RMSD between 95 pruned atom pairs is 0.789 angstroms; (across all 116 pairs: 2.259) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#7), sequence alignment score = 158.4 Alignment identifier is 21 Showing conservation header (""seq_conservation"" residue attribute) for alignment 21 Hiding conservation header for alignment 21 Chains used in RMSD evaluation for alignment 21: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #7/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 21 RMSD between 74 pruned atom pairs is 1.067 angstroms; (across all 114 pairs: 6.727) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#8), sequence alignment score = 152.8 Alignment identifier is 22 Showing conservation header (""seq_conservation"" residue attribute) for alignment 22 Hiding conservation header for alignment 22 Chains used in RMSD evaluation for alignment 22: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #8/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 22 RMSD between 51 pruned atom pairs is 0.947 angstroms; (across all 110 pairs: 6.406) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#9), sequence alignment score = 162.9 Alignment identifier is 23 Showing conservation header (""seq_conservation"" residue attribute) for alignment 23 Hiding conservation header for alignment 23 Chains used in RMSD evaluation for alignment 23: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #9/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 23 RMSD between 70 pruned atom pairs is 1.087 angstroms; (across all 114 pairs: 5.182) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#10), sequence alignment score = 145 Alignment identifier is 24 Showing conservation header (""seq_conservation"" residue attribute) for alignment 24 Hiding conservation header for alignment 24 Chains used in RMSD evaluation for alignment 24: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #10/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 24 RMSD between 30 pruned atom pairs is 0.794 angstroms; (across all 111 pairs: 7.058) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#11), sequence alignment score = 130.9 Alignment identifier is 25 Showing conservation header (""seq_conservation"" residue attribute) for alignment 25 Hiding conservation header for alignment 25 Chains used in RMSD evaluation for alignment 25: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #11/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 25 RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 112 pairs: 7.396) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#12), sequence alignment score = 135.5 Alignment identifier is 26 Showing conservation header (""seq_conservation"" residue attribute) for alignment 26 Hiding conservation header for alignment 26 Chains used in RMSD evaluation for alignment 26: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #12/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 26 RMSD between 48 pruned atom pairs is 0.986 angstroms; (across all 110 pairs: 8.206) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#13), sequence alignment score = 190.7 Alignment identifier is 27 Showing conservation header (""seq_conservation"" residue attribute) for alignment 27 Hiding conservation header for alignment 27 Chains used in RMSD evaluation for alignment 27: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #13/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 27 RMSD between 64 pruned atom pairs is 1.020 angstroms; (across all 113 pairs: 7.144) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#14), sequence alignment score = 153.1 Alignment identifier is 28 Showing conservation header (""seq_conservation"" residue attribute) for alignment 28 Hiding conservation header for alignment 28 Chains used in RMSD evaluation for alignment 28: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #14/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 28 RMSD between 51 pruned atom pairs is 0.975 angstroms; (across all 111 pairs: 6.729) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#15), sequence alignment score = 136.5 Alignment identifier is 29 Showing conservation header (""seq_conservation"" residue attribute) for alignment 29 Hiding conservation header for alignment 29 Chains used in RMSD evaluation for alignment 29: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #15/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 29 RMSD between 52 pruned atom pairs is 0.944 angstroms; (across all 110 pairs: 8.095) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#16), sequence alignment score = 377.2 Alignment identifier is 30 Showing conservation header (""seq_conservation"" residue attribute) for alignment 30 Hiding conservation header for alignment 30 Chains used in RMSD evaluation for alignment 30: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #16/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 30 RMSD between 98 pruned atom pairs is 0.757 angstroms; (across all 115 pairs: 1.981) > show #3 models > hide #3 models > show #3 models > matchmaker #2-25 to #1 showAlignment true 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACFOPQ_RS19755__3828___WP_380080940.1_____GCF_042649355.1____Deinococcus_antarcticus_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#2), sequence alignment score = 174.9 RMSD between 43 pruned atom pairs is 0.933 angstroms; (across all 111 pairs: 6.059) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACTQ9L_RS01385__266___WP_456132272.1_____GCF_053878665.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#4), sequence alignment score = 516.2 RMSD between 108 pruned atom pairs is 0.524 angstroms; (across all 117 pairs: 1.674) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACXXDI_RS00680__132___WP_458578950.1_____GCF_054352955.1____Deinococcus_sp_PESE_13_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb, chain A (#5), sequence alignment score = 390.3 RMSD between 95 pruned atom pairs is 0.708 angstroms; (across all 116 pairs: 2.958) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ASF71_RS17770__3596___WP_056302518.1_____GCF_001424185.1____Deinococcus_sp_Leaf326_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#6), sequence alignment score = 469.7 RMSD between 95 pruned atom pairs is 0.789 angstroms; (across all 116 pairs: 2.259) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with B9A95_RS33850__1592___WP_170928682.1_____GCF_900176165.1____Deinococcus_hopiensis_KR_140_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#7), sequence alignment score = 158.4 RMSD between 74 pruned atom pairs is 1.067 angstroms; (across all 114 pairs: 6.727) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with C3K08_RS11605__2296___WP_104991448.1_____GCF_002953415.1____Deinococcus_sp_NW_56_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#8), sequence alignment score = 152.8 RMSD between 51 pruned atom pairs is 0.947 angstroms; (across all 110 pairs: 6.406) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with D3875_RS15995__2322___WP_119765318.1_____GCF_003590815.1____Deinococcus_cavernae_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#9), sequence alignment score = 162.9 RMSD between 70 pruned atom pairs is 1.087 angstroms; (across all 114 pairs: 5.182) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DEIPH_RS07230__1474___WP_034356122.1_____GCF_000599865.1____Deinococcus_phoenicis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#10), sequence alignment score = 145 RMSD between 30 pruned atom pairs is 0.794 angstroms; (across all 111 pairs: 7.058) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with DVJ83_RS10370__1923___WP_162865520.1_____GCF_003345215.1____Deinococcus_wulumuqiensis_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#11), sequence alignment score = 130.9 RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 112 pairs: 7.396) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Q07_RS12670__2466___WP_010889133.1_____GCF_020546805.1____Deinococcus_radiodurans_R1_ATCC_13939_DSM_20539_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#12), sequence alignment score = 135.5 RMSD between 48 pruned atom pairs is 0.986 angstroms; (across all 110 pairs: 8.206) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with E5Z01_RS09650__466___WP_135229161.1_____GCF_004634215.1____Deinococcus_fonticola_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#13), sequence alignment score = 190.7 RMSD between 64 pruned atom pairs is 1.020 angstroms; (across all 113 pairs: 7.144) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with H565_RS0105180__1909___WP_027460105.1_____GCF_000482805.1____Deinococcus_murrayi_DSM_11303_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb, chain A (#14), sequence alignment score = 153.1 RMSD between 51 pruned atom pairs is 0.975 angstroms; (across all 111 pairs: 6.729) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with L1280_RS10800__2128___WP_253582275.1_____GCF_024171495.1____Deinococcus_sp_HSC_46F16_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#15), sequence alignment score = 136.5 RMSD between 52 pruned atom pairs is 0.944 angstroms; (across all 110 pairs: 8.095) Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with WDJ50_RS10175__1983___WP_339094749.1_____GCF_037914965.1____Deinococcus_sp_VB142_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#16), sequence alignment score = 377.2 RMSD between 98 pruned atom pairs is 0.757 angstroms; (across all 115 pairs: 1.981) > matchmaker #3 to #1 showAlignment true 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > hide #2 models > hide #4 models > hide #5 models > hide #6 models > hide #7 models > hide #8 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > hide #13 models > hide #14 models > hide #15 models > hide #16 models > matchmaker #3 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > ui tool show Matchmaker > matchmaker #3 to #1 showAlignment true 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > matchmaker #3 to #1 showAlignment true 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 ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 5 pruned atom pairs is 1.560 angstroms; (across all 99 pairs: 16.760) > matchmaker #3 to #1 cutoffDistance none showAlignment true 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 No iteration Matchmaker ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb, chain A (#1) with ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A (#3), sequence alignment score = 112 Alignment identifier is 4 Showing conservation header (""seq_conservation"" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 RMSD between 99 atom pairs is 15.829 angstroms > open ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain1.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain6.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain7.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain8.pdb"" > ""/Users/Ania/Library/CloudStorage/Dropbox/Ania& > Kacper/HPI_Deinococcaceae_ColabFold_2/HPI_Colabfold/PDB_all_HPI_subdomains_WITH_ADDITIONAL/ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain9.pdb"" Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain1.pdb #18 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain2.pdb #19 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #20 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain5.pdb #22 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain6.pdb #23 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain7.pdb #24 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain8.pdb #25 --- Chain | Description A | No description available Chain information for ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain9.pdb #26 --- Chain | Description A | No description available Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 17: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 1: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 2: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 3: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Associated ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb chain A to ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 4: ABEA67_RS16475__3224___WP_345467308.1_____GCF_039545055.1____Deinococcus_carri_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain3.pdb #1/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #3/A, ACINK0_RS03820__731___WP_414657361.1_____GCF_047523805.1____Deinococcus_sp_VB343_relaxed_rank_001_alphafold2_ptm_model_1_seed_000_subdomain4.pdb #21/A Computing secondary structure > select #3/A:351 #21/A:351 34 atoms, 32 bonds, 2 residues, 2 models selected > hide #1 models > hide #3 models > show #3 models > hide #3 models ===== 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 M5 Pro 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: Mac17,9 Model Number: Z1ML0017VB/A Chip: Apple M5 Pro Total Number of Cores: 18 (6 Super and 12 Performance) Memory: 64 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 1 day, 3 hours, 27 minutes Graphics/Displays: Apple M5 Pro: Chipset Model: Apple M5 Pro Type: GPU Bus: Built-In Total Number of Cores: 20 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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-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-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: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 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 closed normal Window Toolkit duplicate all ChimeraX