id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15950 Crash in event loop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x0000000347a3b000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000346a2f000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File 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""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003409e7000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000033f9db000 (most 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version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_16/RBP_55_cluster_16.pdb Chain information for RBP_55_cluster_16.pdb #1 --- Chain | Description A B C | No description available > close > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_15/RBP_30_cluster_15.pdb Chain information for RBP_30_cluster_15.pdb #1 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_15/RBP_32_cluster_15.pdb Chain information for RBP_32_cluster_15.pdb #2 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_15/RBP_53_cluster_15.pdb Chain information for RBP_53_cluster_15.pdb #3 --- Chain | Description A B C | No description available > tile 3 models tiled > close > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_14/RBP_25_cluster_14.pdb Chain information for RBP_25_cluster_14.pdb #1 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_14/RBP_29_cluster_14.pdb Chain information for RBP_29_cluster_14.pdb #2 --- Chain | Description A B C | No description available > tile 2 models tiled > close > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_13/RBP_12_cluster_13.pdb Chain information for RBP_12_cluster_13.pdb #1 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_13/RBP_61_cluster_13.pdb Chain information for RBP_61_cluster_13.pdb #2 --- Chain | Description A B C | No description available > close > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_11/RBP_14_cluster_11.pdb Chain information for RBP_14_cluster_11.pdb #1 --- Chain | Description A B C | No description available [deleted to fit within ticket limits] > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_11_relax_domain_1.pdb Chain information for RBP_11_relax_domain_1.pdb #25 --- Chain | Description A B C | No description available > ui mousemode right translate > ui mousemode right zoom > close #13,17-25#14-16 > close #1,10#2-9,11-12 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_12.pdb Chain information for RBP_00_relax_domain_12.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_13.pdb Chain information for RBP_00_relax_domain_13.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_10.pdb Chain information for RBP_00_relax_domain_10.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_11.pdb Chain information for RBP_00_relax_domain_11.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_9.pdb Chain information for RBP_00_relax_domain_9.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_8.pdb Chain information for RBP_00_relax_domain_8.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_7.pdb Chain information for RBP_00_relax_domain_7.pdb #7 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_6.pdb Chain information for RBP_00_relax_domain_6.pdb #8 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_5.pdb Chain information for RBP_00_relax_domain_5.pdb #9 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_4.pdb Chain information for RBP_00_relax_domain_4.pdb #10 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_3.pdb Chain information for RBP_00_relax_domain_3.pdb #11 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_1.pdb Chain information for RBP_00_relax_domain_1.pdb #12 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_2.pdb Chain information for RBP_00_relax_domain_2.pdb #13 --- Chain | Description A B C | No description available > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > close #1-3,5-6,10-13#4,7-9 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_16.pdb Chain information for RBP_01_relax_domain_16.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_15.pdb Chain information for RBP_01_relax_domain_15.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_13.pdb Chain information for RBP_01_relax_domain_13.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_14.pdb Chain information for RBP_01_relax_domain_14.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_12.pdb Chain information for RBP_01_relax_domain_12.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_10.pdb Chain information for RBP_01_relax_domain_10.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_11.pdb Chain information for RBP_01_relax_domain_11.pdb #7 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_8.pdb Chain information for RBP_01_relax_domain_8.pdb #8 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_9.pdb Chain information for RBP_01_relax_domain_9.pdb #9 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_7.pdb Chain information for RBP_01_relax_domain_7.pdb #10 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_6.pdb Chain information for RBP_01_relax_domain_6.pdb #11 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_5.pdb Chain information for RBP_01_relax_domain_5.pdb #12 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_4.pdb Chain information for RBP_01_relax_domain_4.pdb #13 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_3.pdb Chain information for RBP_01_relax_domain_3.pdb #14 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_2.pdb Chain information for RBP_01_relax_domain_2.pdb #15 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_1.pdb Chain information for RBP_01_relax_domain_1.pdb #16 --- Chain | Description A B C | No description available > ui mousemode right zoom > close #1,3,6,8,12-14#2,4-5,7,9-11,15-16 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_17.pdb Chain information for RBP_02_relax_domain_17.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_18.pdb Chain information for RBP_02_relax_domain_18.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_16.pdb Chain information for RBP_02_relax_domain_16.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_15.pdb Chain information for RBP_02_relax_domain_15.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_14.pdb > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_13.pdb Chain information for RBP_02_relax_domain_13.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_12.pdb Chain information for RBP_02_relax_domain_12.pdb #7 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_10.pdb Chain information for RBP_02_relax_domain_10.pdb #8 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_11.pdb Chain information for RBP_02_relax_domain_11.pdb #9 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_9.pdb Chain information for RBP_02_relax_domain_9.pdb #10 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_8.pdb Chain information for RBP_02_relax_domain_8.pdb #11 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_7.pdb Chain information for RBP_02_relax_domain_7.pdb #12 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_5.pdb Chain information for RBP_02_relax_domain_5.pdb #13 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_6.pdb Chain information for RBP_02_relax_domain_6.pdb #14 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_4.pdb Chain information for RBP_02_relax_domain_4.pdb #15 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_3.pdb Chain information for RBP_02_relax_domain_3.pdb #16 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_2.pdb Chain information for RBP_02_relax_domain_2.pdb #17 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_1.pdb Chain information for RBP_02_relax_domain_1.pdb #18 --- Chain | Description A B C | No description available > ui mousemode right select Drag select of 2 residues > select up 224 atoms, 223 bonds, 15 residues, 1 model selected > ui mousemode right zoom > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_6.pdb Chain information for RBP_06_relax_domain_6.pdb #19 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_7.pdb Chain information for RBP_06_relax_domain_7.pdb #20 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_5.pdb Chain information for RBP_06_relax_domain_5.pdb #21 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb Chain information for RBP_06_relax_domain_4.pdb #22 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb Chain information for RBP_06_relax_domain_3.pdb #23 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb Chain information for RBP_06_relax_domain_2.pdb #24 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb Chain information for RBP_06_relax_domain_1.pdb #25 --- Chain | Description A B C | No description available > close #1-2,4-5,10,13,19-25#3,6-9,11-12,14-18 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_6.pdb Chain information for RBP_06_relax_domain_6.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_7.pdb Chain information for RBP_06_relax_domain_7.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_5.pdb Chain information for RBP_06_relax_domain_5.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb Chain information for RBP_06_relax_domain_4.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb Chain information for RBP_06_relax_domain_3.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb Chain information for RBP_06_relax_domain_2.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb Chain information for RBP_06_relax_domain_1.pdb #7 --- Chain | Description A B C | No description available > ui mousemode right translate > close > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_12.pdb Chain information for RBP_00_relax_domain_12.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_13.pdb Chain information for RBP_00_relax_domain_13.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_11.pdb Chain information for RBP_00_relax_domain_11.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_10.pdb Chain information for RBP_00_relax_domain_10.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_9.pdb Chain information for RBP_00_relax_domain_9.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_8.pdb Chain information for RBP_00_relax_domain_8.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_7.pdb Chain information for RBP_00_relax_domain_7.pdb #7 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_6.pdb Chain information for RBP_00_relax_domain_6.pdb #8 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_5.pdb Chain information for RBP_00_relax_domain_5.pdb #9 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_4.pdb Chain information for RBP_00_relax_domain_4.pdb #10 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_3.pdb Chain information for RBP_00_relax_domain_3.pdb #11 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_2.pdb Chain information for RBP_00_relax_domain_2.pdb #12 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_1.pdb Chain information for RBP_00_relax_domain_1.pdb #13 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_6.pdb Chain information for RBP_02_relax_domain_6.pdb #14 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_5.pdb Chain information for RBP_02_relax_domain_5.pdb #15 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_3.pdb Chain information for RBP_02_relax_domain_3.pdb #16 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_4.pdb Chain information for RBP_02_relax_domain_4.pdb #17 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_2.pdb Chain information for RBP_02_relax_domain_2.pdb #18 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_1.pdb Chain information for RBP_02_relax_domain_1.pdb #19 --- Chain | Description A B C | No description available > ui mousemode right zoom > close #1-4,6-9,11#5,10,12-13 > close #14,16,18-19#15,17 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_4.pdb Chain information for RBP_03_relax_domain_4.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_5.pdb Chain information for RBP_03_relax_domain_5.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_3.pdb Chain information for RBP_03_relax_domain_3.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_1.pdb Chain information for RBP_03_relax_domain_1.pdb #4 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_2.pdb Chain information for RBP_03_relax_domain_2.pdb #5 --- Chain | Description A B C | No description available > ui mousemode right select Drag select of 334 residues > select up 4539 atoms, 4596 bonds, 336 residues, 1 model selected > select up 6564 atoms, 6645 bonds, 489 residues, 1 model selected > close #1-2,4#3,5 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb Chain information for RBP_06_relax_domain_3.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb Chain information for RBP_06_relax_domain_4.pdb #2 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb Chain information for RBP_06_relax_domain_2.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb Chain information for RBP_06_relax_domain_1.pdb #4 --- Chain | Description A B C | No description available Drag select of 8 residues > select clear > ui mousemode right zoom > ui mousemode right translate > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_3.pdb Chain information for RBP_12_relax_domain_3.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_2.pdb Chain information for RBP_12_relax_domain_2.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_1.pdb Chain information for RBP_12_relax_domain_1.pdb #7 --- Chain | Description A B C | No description available > hide #4 models > hide #3 models > hide #2 models > hide #1 models > close > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_16_relax_domain_2.pdb Chain information for RBP_16_relax_domain_2.pdb #1 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_16_relax_domain_1.pdb Chain information for RBP_16_relax_domain_1.pdb #2 --- Chain | Description A B C | No description available > ui mousemode right zoom > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_6.pdb Chain information for RBP_04_relax_domain_6.pdb #3 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_4.pdb > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_3.pdb Chain information for RBP_04_relax_domain_3.pdb #5 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_2.pdb Chain information for RBP_04_relax_domain_2.pdb #6 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_1.pdb Chain information for RBP_04_relax_domain_1.pdb #7 --- Chain | Description A B C | No description available > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_5.pdb Chain information for RBP_04_relax_domain_5.pdb #8 --- Chain | Description A B C | No description available > hide #!1 models > hide #!2 models > close #3-8#1-2 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_14_relax_domain_1.pdb Chain information for RBP_14_relax_domain_1.pdb #1 --- Chain | Description A B C | No description available > close #1 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_60_relax_domain_2.pdb Chain information for RBP_60_relax_domain_2.pdb #1 --- Chain | Description A B C | No description available > close #1 > open > /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_64_relax_domain_4.pdb Chain information for RBP_64_relax_domain_4.pdb #1 --- Chain | Description A B C | No description available > close #1 > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_15_cluster_17.pdb Chain information for RBP_15_cluster_17.pdb #1 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_40_cluster_17.pdb Chain information for RBP_40_cluster_17.pdb #2 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_46_cluster_17.pdb Chain information for RBP_46_cluster_17.pdb #3 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_47_cluster_17.pdb Chain information for RBP_47_cluster_17.pdb #4 --- Chain | Description A B C | No description available > close > open /Users/shj152/Downloads/uniparc_YP_009966082_2024_09_16.tsv Install the ArtiaX bundle to open ""Generic Particle List"" format files. Failed opening file /Users/shj152/Downloads/uniparc_YP_009966082_2024_09_16.tsv: Opener for format 'Generic Particle List' is not installed; see log for more info > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/docs/fig/bas49_bas54.cxs Opened cryosparc_P310_J84_class_00_00041_volume.mrc as #1, grid size 128,128,128, pixel 7.03, shown at level 2.07, step 1, values float32 Opened cryosparc_P310_J88_001_volume_map_sharp.mrc as #7, grid size 300,300,300, pixel 3, shown at level 0.439, step 1, values float32 Opened cryosparc_P310_J88_001_volume_map_sharp(1).mrc as #9, grid size 300,300,300, pixel 3, shown at level 0.939, step 1, values float32 Opened cryosparc_P310_J114_002_volume_map.mrc as #8, grid size 300,300,300, pixel 3, shown at level 0.424, step 1, values float32 Opened cryosparc_P310_J184_class_00_00062_volume.mrc as #11, grid size 128,128,128, pixel 5.06, shown at level 1.3, step 1, values float32 Opened cryosparc_P310_J187_003_volume_map.mrc as #12, grid size 300,300,300, pixel 2.16, shown at level 0.242, step 1, values float32 Opened cryosparc_P310_J129_002_volume_map_sharp.mrc as #13, grid size 300,300,300, pixel 4.8, shown at level 1.6, step 1, values float32 Opened cryosparc_P310_J320_002_volume_map.mrc as #14, grid size 208,208,208, pixel 4.62, shown at level 0.966, step 1, values float32 Opened cryosparc_P310_J305_002_volume_map.mrc as #15, grid size 208,208,208, pixel 4.62, shown at level 0.922, step 1, values float32 Opened cryosparc_P310_J310_007_volume_map.mrc as #34, grid size 300,300,300, pixel 3.6, shown at level 0.141, step 2, values float32 Opened cryosparc_P310_J310_007_volume_map.mrc z flip as #35, grid size 300,300,300, pixel 3.6, shown at level 1.07, step 1, values float32 opened ChimeraX session > ui mousemode right translate > hide #30 models > show #30 models > hide #31 models > show #31 models > show #29 models > color #13 white models > color #13 #ffffff33 models > color #14 white models > color #14 #ffffff33 models > color #14 #ffffff05 models > color #13 #ffffff05 models > color #13 #ffffff33 models > color #14 #ffffff33 models > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/cluster_D4/RBP_65_1__cluster_D4_TCTC8_.pdb Chain information for RBP_65_1__cluster_D4_TCTC8_.pdb #46 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D34/RBP_65_2__cluster_D34_TCTC8_.pdb Chain information for RBP_65_2__cluster_D34_TCTC8_.pdb #47 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D12/RBP_65_3__cluster_D12_TCTC8_.pdb Chain information for RBP_65_3__cluster_D12_TCTC8_.pdb #48 --- Chain | Description A B C | No description available > open /Users/shj152/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D15/RBP_65_4__cluster_D15_TCTC8_.pdb Chain information for RBP_65_4__cluster_D15_TCTC8_.pdb #49 --- Chain | Description A B C | No description available > show #5 models > hide #5 models > mmaker #46-49 to #5 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 RBP_65_cluster_8.pdb, chain B (#5) with RBP_65_1__cluster_D4_TCTC8_.pdb, chain B (#46), sequence alignment score = 623.7 RMSD between 121 pruned atom pairs is 0.000 angstroms; (across all 121 pairs: 0.000) Matchmaker RBP_65_cluster_8.pdb, chain C (#5) with RBP_65_2__cluster_D34_TCTC8_.pdb, chain C (#47), sequence alignment score = 974.9 RMSD between 190 pruned atom pairs is 0.000 angstroms; (across all 190 pairs: 0.000) Matchmaker RBP_65_cluster_8.pdb, chain C (#5) with RBP_65_3__cluster_D12_TCTC8_.pdb, chain C (#48), sequence alignment score = 628.7 RMSD between 124 pruned atom pairs is 0.000 angstroms; (across all 124 pairs: 0.000) Matchmaker RBP_65_cluster_8.pdb, chain B (#5) with RBP_65_4__cluster_D15_TCTC8_.pdb, chain B (#49), sequence alignment score = 753.3 RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs: 0.000) > hide #!14 models > show #!14 models > hide #!13 models > show #!13 models > select add #46 5616 atoms, 5700 bonds, 363 residues, 1 model selected > select add #47 14214 atoms, 14388 bonds, 933 residues, 2 models selected > fitmap sel inMap #13 Fit molecules RBP_65_1__cluster_D4_TCTC8_.pdb (#46), RBP_65_2__cluster_D34_TCTC8_.pdb (#47) to map cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 14214 atoms average map value = 1.693, steps = 324 shifted from previous position = 7.07 rotated from previous position = 38.1 degrees atoms outside contour = 5075, contour level = 1.5981 Position of RBP_65_1__cluster_D4_TCTC8_.pdb (#46) relative to cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.08020332 0.46207192 0.88320833 787.49707441 0.93966459 0.26057454 -0.22165597 680.37266050 -0.33256261 0.84769714 -0.41329368 798.79993278 Axis 0.63346237 0.72019722 0.28291588 Axis point 268.12464024 0.00000000 258.92186386 Rotation angle (degrees) 122.42925976 Shift along axis 1214.84544472 Position of RBP_65_2__cluster_D34_TCTC8_.pdb (#47) relative to cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.08020333 0.46207193 0.88320833 787.49707456 0.93966458 0.26057454 -0.22165598 680.37266110 -0.33256261 0.84769714 -0.41329368 798.79993335 Axis 0.63346237 0.72019722 0.28291588 Axis point 268.12464109 0.00000000 258.92186690 Rotation angle (degrees) 122.42925958 Shift along axis 1214.84544391 > select subtract #46 8598 atoms, 8688 bonds, 570 residues, 1 model selected > select subtract #47 Nothing selected > select add #48 5418 atoms, 5445 bonds, 372 residues, 1 model selected > select add #49 11913 atoms, 12012 bonds, 810 residues, 2 models selected > fitmap sel inMap #14 Fit molecules RBP_65_3__cluster_D12_TCTC8_.pdb (#48), RBP_65_4__cluster_D15_TCTC8_.pdb (#49) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 11913 atoms average map value = 1.483, steps = 320 shifted from previous position = 1.23 rotated from previous position = 61.4 degrees atoms outside contour = 2738, contour level = 0.96601 Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.94832432 0.00499779 0.31726332 501.68355928 0.28105700 0.47729871 0.83258207 720.05619692 -0.14726830 0.87872690 -0.45403864 667.90439830 Axis 0.08508541 0.85653941 0.50901937 Axis point 227.91704534 0.00000000 86.39106593 Rotation angle (degrees) 164.26623707 Shift along axis 999.41873464 Position of RBP_65_4__cluster_D15_TCTC8_.pdb (#49) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.94832432 0.00499780 0.31726331 501.68356164 0.28105700 0.47729871 0.83258207 720.05619701 -0.14726829 0.87872690 -0.45403864 667.90439787 Axis 0.08508541 0.85653941 0.50901937 Axis point 227.91704447 0.00000000 86.39106791 Rotation angle (degrees) 164.26623779 Shift along axis 999.41873592 > hide #29 models > hide #30 models > hide #31 models > hide #32 models > color #46 lightpink > color #47 lightpink > color #48 lightpink > color #49 lightpink > ui mousemode right select > select clear > select add #48 5418 atoms, 5445 bonds, 372 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #48,-0.77681,0.018412,0.62947,419.9,-0.55339,-0.49701,-0.66839,611.79,0.30054,-0.86755,0.39627,490.94 > view matrix models > #48,-0.79306,0.067894,0.60534,424.58,-0.52916,-0.56904,-0.62943,605.18,0.30173,-0.8195,0.48721,501.34 > fitmap sel inMap #14 Fit molecule RBP_65_3__cluster_D12_TCTC8_.pdb (#48) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 5418 atoms average map value = 1.818, steps = 184 shifted from previous position = 66.9 rotated from previous position = 10.1 degrees atoms outside contour = 544, contour level = 0.96601 Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.83262730 -0.10089186 0.54456644 493.31064875 0.43446374 0.49080692 0.75521509 665.37974065 -0.34347203 0.86540707 -0.36482539 629.91961602 Axis 0.10567282 0.85161845 0.51339972 Axis point 229.52221678 0.00000000 49.36187477 Rotation angle (degrees) 148.57494528 Shift along axis 942.17974308 > view matrix models > #48,-0.78484,0.043217,0.6182,422.29,-0.54141,-0.53317,-0.65008,608.41,0.30151,-0.84491,0.44185,495.98 > view matrix models > #48,-0.79449,0.072103,0.60298,424.96,-0.52703,-0.57515,-0.62565,604.64,0.30169,-0.81487,0.49495,502.29 > view matrix models > #48,-0.79449,0.072103,0.60298,425.37,-0.52703,-0.57515,-0.62565,605.14,0.30169,-0.81487,0.49495,502.72 > view matrix models > #48,-0.8009,0.036131,0.59771,420.84,-0.50476,-0.57775,-0.64142,603.96,0.32215,-0.81541,0.48095,501.88 > fitmap sel inMap #14 Fit molecule RBP_65_3__cluster_D12_TCTC8_.pdb (#48) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 5418 atoms average map value = 1.818, steps = 200 shifted from previous position = 66.4 rotated from previous position = 10.6 degrees atoms outside contour = 535, contour level = 0.96601 Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.84352364 -0.09625942 0.52839567 493.11002571 0.42437878 0.48354720 0.76556173 665.12522520 -0.32919678 0.87000933 -0.36703304 630.17119592 Axis 0.10354865 0.85021139 0.51615721 Axis point 228.97741272 0.00000000 50.22748700 Rotation angle (degrees) 149.71240237 Shift along axis 941.82532701 > select subtract #48 Nothing selected > select add #49 6495 atoms, 6567 bonds, 438 residues, 1 model selected > view matrix models > #49,-0.88832,0.11619,0.44429,422.75,-0.45112,-0.40185,-0.79687,616.21,0.085946,-0.9083,0.40939,487.36 > fitmap sel inMap #14 Fit molecule RBP_65_4__cluster_D15_TCTC8_.pdb (#49) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 6495 atoms average map value = 1.793, steps = 52 shifted from previous position = 1.64 rotated from previous position = 11.3 degrees atoms outside contour = 346, contour level = 0.96601 Position of RBP_65_4__cluster_D15_TCTC8_.pdb (#49) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.90994301 0.06014993 0.41034827 522.13653224 0.40627866 0.32804507 0.85283298 691.25930910 -0.08331488 0.94274515 -0.32293996 693.43280601 Axis 0.14749761 0.80983619 0.56781141 Axis point 208.55320623 0.00000000 68.70579107 Rotation angle (degrees) 162.25435089 Shift along axis 1030.55975395 > select subtract #49 Nothing selected > show #5 models > hide #46 models > hide #47 models > hide #48 models > hide #49 models > select add #5 26127 atoms, 26409 bonds, 1743 residues, 1 model selected > fitmap sel inMap #14 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms average map value = 0.9266, steps = 44 shifted from previous position = 0.11 rotated from previous position = 0.692 degrees atoms outside contour = 17957, contour level = 0.96601 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.23090830 -0.19491842 0.95325136 511.52670757 0.57417104 0.76365264 0.29523254 728.53549205 -0.78549919 0.61550097 -0.06441722 652.45436137 Axis 0.16611120 0.90182460 0.39889781 Axis point 295.35000064 0.00000000 19.41360326 Rotation angle (degrees) 105.41666021 Shift along axis 1002.24416035 > fitmap sel inMap #13 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 26127 atoms average map value = 1.47, steps = 520 shifted from previous position = 1.63 rotated from previous position = 24.4 degrees atoms outside contour = 14806, contour level = 1.5981 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.20469403 0.47569544 0.85546139 788.07259516 0.84420051 0.35653687 -0.40025859 680.30836126 -0.49540472 0.80411149 -0.32860137 799.83935798 Axis 0.65209373 0.73141249 0.19952326 Axis point 349.08428464 0.00000000 295.98470877 Rotation angle (degrees) 112.56214208 Shift along axis 1171.06979176 > fitmap sel inMap #14 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms average map value = 0.9435, steps = 96 shifted from previous position = 1.31 rotated from previous position = 4.53 degrees atoms outside contour = 17676, contour level = 0.96601 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.63901010 -0.12361064 0.75920123 511.53084314 0.52127249 0.65620632 0.54558983 729.06550456 -0.56563335 0.74438812 -0.35488764 653.25955497 Axis 0.13370861 0.89106292 0.43373826 Axis point 255.78677255 0.00000000 54.79414877 Rotation angle (degrees) 131.97803835 Shift along axis 1001.38297857 > fitmap sel inMap #13 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 26127 atoms average map value = 1.481, steps = 56 shifted from previous position = 1.24 rotated from previous position = 3.91 degrees atoms outside contour = 14656, contour level = 1.5981 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates: Matrix rotation and translation 0.15430263 0.46883794 0.86970206 787.99411508 0.88234957 0.33069254 -0.33481589 680.35358621 -0.44457837 0.81904421 -0.36265223 799.72510786 Axis 0.64205296 0.73131711 0.23009406 Axis point 320.14205827 0.00000000 281.92088963 Rotation angle (degrees) 116.02916070 Shift along axis 1187.50017396 > fitmap sel inMap #14 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms average map value = 0.9469, steps = 60 shifted from previous position = 1.21 rotated from previous position = 3.94 degrees atoms outside contour = 17619, contour level = 0.96601 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.68582226 -0.10802606 0.71970702 511.47347502 0.50424604 0.64254559 0.57694981 729.04683610 -0.52477019 0.75859444 -0.38620036 653.38306737 Axis 0.12985899 0.88968533 0.43771755 Axis point 251.86171359 0.00000000 59.90565334 Rotation angle (degrees) 135.62177335 Shift along axis 1001.03894125 > view matrix models > #5,-0.60188,0.037193,0.79772,433.36,-0.65543,-0.59369,-0.46684,608.02,0.45624,-0.80383,0.38171,501.82 > view matrix models > #5,-0.04817,-0.055293,0.99731,432.81,-0.61675,-0.78375,-0.073241,608.76,0.78569,-0.61861,0.0036515,500.47 > fitmap sel inMap #14 Fit molecule RBP_65_cluster_8.pdb (#5) to map cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms average map value = 0.9243, steps = 68 shifted from previous position = 4.1 rotated from previous position = 2.04 degrees atoms outside contour = 17975, contour level = 0.96601 Position of RBP_65_cluster_8.pdb (#5) relative to cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates: Matrix rotation and translation -0.13035021 -0.20085621 0.97090968 511.20698497 0.56875803 0.78696620 0.23916208 728.10289116 -0.81211029 0.58338751 0.01165737 652.20126182 Axis 0.17453018 0.90403196 0.39021205 Axis point 307.52978038 0.00000000 11.61714579 Rotation angle (degrees) 99.54739018 Shift along axis 1001.94611437 > ui mousemode right select > select clear > hide #5 models > show #46 models > show #47 models > show #48 models > show #49 models > show #5 models > color #5 #fa807297 > color #5 #fa8072a8 > color #5 #011993ff > color #5 black > color #5 #000000a5 > color #5 #00000073 > show #5,46-49 atoms > style #5,46-49 sphere Changed 52254 atom styles > hide #5,46-49 atoms > select add #5 26127 atoms, 26409 bonds, 1743 residues, 1 model selected > show sel cartoons > show sel atoms > style sel sphere Changed 26127 atom styles > show sel surfaces > hide sel atoms > color #5 transparent > color #5 #0000003e > hide #!5 models > select subtract #5 3 models selected Drag select of 14 cryosparc_P310_J320_002_volume_map.mrc > select #14 4 models selected > select clear > ui mousemode right zoom > save ""/Users/shj152/OneDrive - University of > Copenhagen/PhD/AtlasPaper/docs/fig/bas54_tail_fiber_TC8png.png"" width 4200 > height 3186 supersample 4 > show #!10 models > save ""/Users/shj152/OneDrive - University of > Copenhagen/PhD/AtlasPaper/docs/fig/bas54_tail_fiber_TC8png.png"" width 4200 > height 3186 supersample 4 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes true width 10 depthJump 10 > graphics silhouettes true width 10 depthJump 1 > graphics silhouettes true width 10 depthJump 0 > graphics silhouettes true width 10 depthJump 100 > graphics silhouettes true width 10 depthJump 10000 > graphics silhouettes true width 10 > graphics silhouettes true width 100 > graphics silhouettes true width 100000 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14V0004GDK/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 13 days, 3 hours, 50 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 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 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 Send2Trash: 1.8.3 SEQCROW: 1.8.8 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX