id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14619 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000117013600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 484 in remember_data_format File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 514 in collated_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 213 in provider_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 131 in cmd_open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 1979 in _open_dropped_file File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 240 in event File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File 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] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/mandywan/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinuc_struc_tails.pdb > format pdb Chain information for Dinuc_struc_tails.pdb #1 --- Chain | Description A a | No description available > open 8JHO 8jho title: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di- nucleosome [more info...] Chain information for 8jho #2 --- Chain | Description | UniProt A E a e | Histone H3 | A0A310TTQ1_XENLA 1-135 B F b f | Histone H4 | A0A8J1LTD2_XENLA 1-102 C G c g | Histone H2A | Q6AZJ8_XENLA 1-129 D H d h | Histone H2B | A0A8J0U496_XENLA 1-122 I | Di-nucleosome template foward | J | Di-nucleosome template reverse | K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536 L | Histone deacetylase RPD3 | RPD3_YEAST 1-433 M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401 N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684 Non-standard residues in 8jho #2 --- ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium ZN — zinc ion > hide #1 models > show #1 models > hide surfaces > hide cartoons > hide atoms > show atoms > style stick Changed 42987 atom styles > nucleotides atoms > style nucleic stick Changed 13940 atom styles > nucleotides atoms > style nucleic stick Changed 13940 atom styles > style stick Changed 42987 atom styles > hide atoms > show cartoons > hide #1 models > show #1 models > hide #1 models > show #1 models > cartoon style nucleic xsection oval width 1.6 thickness 1.6 > color #2/I,J rgb(0.4,0.4,0.4) > nucleotides ladder > nucleotides stubs > show atoms > undo > show #2/I,J atoms > cartoon style #1 thickness 1.6 > ui tool show ""Show Sequence Viewer"" > color #1 rgb(1,1,0.5) > color #1 rgb(1.0,1.0,0.5) > color #2/K slate blue > color #2/M,O dark cyan > hide #1 models > show #1 models > hide #1 models > show #1 models > color #2/N,P deep pink > color #2/L burly wood > color #A,E,a,e rgb(1.0,1.0,0.5) Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /A,E,a,e rgb(1.0,1.0,0.5) > color /B,F,b,f rgb(0.65,0.9,0.65) > color /C,G,c,g rgb(0.0,0.5,1.0) > color /D,H,d,h rgb(1.0,0.75,0.87) Drag select of 3 residues, 2 shapes > save ""/Users/mandywan/OneDrive - The Institute of Cancer > Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs"" > includeMaps true > open 36283 fromDatabase emdb Opened emdb 36283 as #3, grid size 400,400,400, pixel 1.05, shown at level 0.0066, step 2, values float32, fit PDB 8jho > transparency 70% Missing or invalid ""percent"" argument: Expected a number > transparency 70 > volume #3 step 1 > volume #3 level 0.0066 > volume #3 level 0.007564 > volume #3 level 0.00925 > volume #3 level 0.009009 > open 7HXY Fetching url http://files.rcsb.org/download/7hxy.cif failed: HTTP Error 404: Not Found > open 8HXY Summary of feedback from opening 8HXY fetched from pdb --- note | Fetching compressed mmCIF 8hxy from http://files.rcsb.org/download/8hxy.cif 8hxy title: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome [more info...] Chain information for 8hxy #4 --- Chain | Description | UniProt A E | Histone H3 | A0A310TTQ1_XENLA 1-135 B F | Histone H4 | A0A8J1LTD2_XENLA 1-102 C G | Histone H2A | Q6AZJ8_XENLA 1-129 D H | Histone H2B | A0A8J0U496_XENLA 1-122 I | DNA (352-MER) | J | DNA (352-MER) | K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536 L | Histone deacetylase RPD3 | RPD3_YEAST 1-433 M | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401 N P | Transcriptional regulatory protein RCO1 | A0A8H4BXB0_YEASX 1-684 Non-standard residues in 8hxy #4 --- ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium ZN — zinc ion > style sel stick Changed 63 atom styles > hide sel surfaces > hide sel cartoons > hide sel atoms > undo > cartoon style #4 8hxy #4 \- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow scale=2 \- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow scale=2 \- coil xsection=round width=0.4 height=0.4 \- nucleic xsection=square width=0.4 height=2 \- divisions=20 \- oval parameters: sides=12 \- barbell parameters: sides=18 scale=0.5 > cartoon #4 > select add #4 26263 atoms, 27486 bonds, 460 pseudobonds, 2725 residues, 4 models selected > ui tool show ""Fit in Map"" > fitmap #4 inMap #3 Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms average map value = -5.779e-06, steps = 324 shifted from previous position = 55.5 rotated from previous position = 38.9 degrees atoms outside contour = 26263, contour level = 0.0090094 Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.80736002 0.35625844 0.47037190 -134.98102382 -0.22657756 0.92322711 -0.31034546 99.70702296 -0.54482328 0.14398479 0.82609683 95.91162550 Axis 0.36181977 0.80848169 -0.46415925 Axis point 67.84594802 0.00000000 304.94847640 Rotation angle (degrees) 38.89098156 Shift along axis -12.74576899 > select subtract #4 Nothing selected Average map value = -5.779e-06 for 26263 atoms, 26263 outside contour > fitmap #4 inMap #3 Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms average map value = -5.779e-06, steps = 40 shifted from previous position = 0.0119 rotated from previous position = 0.0071 degrees atoms outside contour = 26263, contour level = 0.0090094 Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.80741227 0.35626966 0.47027370 -134.97452409 -0.22657182 0.92320907 -0.31040331 99.72827462 -0.54474823 0.14407267 0.82613100 95.88488871 Axis 0.36196027 0.80839830 -0.46419496 Axis point 67.81678095 0.00000000 304.97599705 Rotation angle (degrees) 38.88786113 Shift along axis -12.74452944 > hide #4 > fitmap #4 inMap #3 Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms average map value = -5.779e-06, steps = 48 shifted from previous position = 0.0166 rotated from previous position = 0.00735 degrees atoms outside contour = 26263, contour level = 0.0090094 Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.80735451 0.35627455 0.47036915 -134.98527098 -0.22659650 0.92322245 -0.31034551 99.70635686 -0.54482357 0.14397485 0.82609837 95.91438897 Axis 0.36180881 0.80847284 -0.46418320 Axis point 67.84459739 0.00000000 304.95593493 Rotation angle (degrees) 38.89137536 Shift along axis -12.75082748 > fitmap #4 inMap #3 Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms average map value = -5.779e-06, steps = 40 shifted from previous position = 0.0153 rotated from previous position = 0.00868 degrees atoms outside contour = 26263, contour level = 0.0090094 Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.80742132 0.35626006 0.47026543 -134.97182215 -0.22655219 0.92320864 -0.31041893 99.72552448 -0.54474297 0.14409920 0.82612984 95.88026602 Axis 0.36199650 0.80839348 -0.46417510 Axis point 67.80906704 0.00000000 304.96819286 Rotation angle (degrees) 38.88752089 Shift along axis -12.74709612 > fitmap #4 inMap #3 Fit molecule 8hxy (#4) to map emdb 36283 (#3) using 26263 atoms average map value = -5.778e-06, steps = 40 shifted from previous position = 0.0152 rotated from previous position = 0.00415 degrees atoms outside contour = 26263, contour level = 0.0090094 Position of 8hxy (#4) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.80739356 0.35625613 0.47031607 -134.97645811 -0.22656535 0.92321956 -0.31037685 99.70516412 -0.54477865 0.14403895 0.82611682 95.89614245 Axis 0.36190433 0.80843838 -0.46416876 Axis point 67.82497140 0.00000000 304.95208714 Rotation angle (degrees) 38.88888349 Shift along axis -12.75507699 > ui tool show Matchmaker > matchmaker #!4 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 Dinuc_struc_tails.pdb, chain A (#1) with 8hxy, chain A (#4), sequence alignment score = 48.4 RMSD between 10 pruned atom pairs is 0.173 angstroms; (across all 10 pairs: 0.173) > undo > redo > open 35082 fromDatabase emdb Summary of feedback from opening 35082 fetched from emdb --- notes | Fetching compressed map 35082 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35082/map/emd_35082.map.gz Fetching map header 35082 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35082/header/emd-35082.xml Opened emdb 35082 as #5, grid size 256,256,256, pixel 1.05, shown at level 0.03, step 1, values float32, fit PDB 8hxy > fitmap #4 inMap #5 Fit molecule 8hxy (#4) to map emdb 35082 (#5) using 26263 atoms average map value = 0.0008659, steps = 288 shifted from previous position = 66.4 rotated from previous position = 24.1 degrees atoms outside contour = 26263, contour level = 0.03 Position of 8hxy (#4) relative to emdb 35082 (#5) coordinates: Matrix rotation and translation 0.18211634 -0.62546900 -0.75869768 427.26680800 -0.91436876 -0.39149278 0.10326262 461.95502534 -0.36161223 0.67492365 -0.64320655 190.94153111 Axis 0.75855799 -0.52690725 -0.38335169 Axis point 0.00000000 354.38060411 263.50739153 Rotation angle (degrees) 157.86391425 Shift along axis 7.50144247 > hide #!5 models > hide #!4 models > show #!4 models > hide #!4 models > close #5 > volume #3 level 0.007564 > surface #2/ Expected an atoms specifier or a keyword > surface #2/L > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > set bgColor white > lighting simple > lighting soft > lighting full > color /C,G,c,g royal blue > color /D,H,d,h (1.0,0.75,0.87) Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /D,H,d,h rgb(1.0,0.75,0.87) > transparency #2 50 > transparency #2 70 > transparency #2 20 > transparency #2 30 > transparency #2 40 > color #2/L rgb(0.99,0.82,0.65) > transparency #2 40 > transparency #2 30 > transparency #2 20 > transparency #2 10 > transparency #2 50 > transparency #2 40 > lighting simple > lighting soft > lighting full > transparency #3 40 > transparency #3 50 > transparency #3 70 > transparency #3 30 > transparency #3 40 > transparency #3 30 > transparency #3 50 > surface #2/N,M,L,K > surface #2/N,M,L,K,O,P > undo > surface #2/N,M,L,K > hide surfaces #2/O,P Expected ',' or a keyword > hide surfaces #2/O,P Expected ',' or a keyword > ~surface #2/O,P > ~surface #2/N,M,L,K > open 35081 fromDatabase emdb Summary of feedback from opening 35081 fetched from emdb --- notes | Fetching compressed map 35081 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35081/map/emd_35081.map.gz Fetching map header 35081 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35081/header/emd-35081.xml Opened emdb 35081 as #5, grid size 256,256,256, pixel 1.05, shown at level 0.0135, step 1, values float32, fit PDB 8hxx > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.01303, steps = 84 shifted from previous position = 1.49 rotated from previous position = 1.15 degrees atoms outside contour = 13151, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.99981319 -0.01519254 -0.01194854 5.69483194 0.01525831 0.99986883 0.00543239 -3.32790881 0.01186444 -0.00561369 0.99991386 -2.16352830 Axis -0.27475368 -0.59230995 0.75741623 Axis point 268.94024873 349.25268408 0.00000000 Rotation angle (degrees) 1.15182564 Shift along axis -1.23221400 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 77178 points correlation = 0.7408, correlation about mean = 0.133, overlap = 2.29 steps = 628, shift = 124, angle = 12.2 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98920703 0.12489032 0.07662806 -14.23972201 -0.11171858 0.98124879 -0.15706611 59.98940524 -0.09480723 0.14681012 0.98461077 115.50987072 Axis 0.72083386 0.40666677 -0.56126703 Axis point 0.00000000 -532.50448220 576.78120646 Rotation angle (degrees) 12.16812733 Shift along axis -50.70065828 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 77178 points correlation = 0.7409, correlation about mean = 0.133, overlap = 2.29 steps = 44, shift = 0.0172, angle = 0.00855 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98922680 0.12476281 0.07658057 -14.23385105 -0.11160550 0.98127227 -0.15699984 59.96184917 -0.09473413 0.14676164 0.98462504 115.49857769 Axis 0.72101794 0.40663804 -0.56105136 Axis point 0.00000000 -532.81392555 576.74552571 Rotation angle (degrees) 12.16030948 Shift along axis -50.68072740 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 77178 points correlation = 0.7409, correlation about mean = 0.133, overlap = 2.29 steps = 40, shift = 0.00512, angle = 0.0116 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98925306 0.12456976 0.07655558 -14.20980922 -0.11142405 0.98130346 -0.15693374 59.91995306 -0.09467346 0.14671705 0.98463752 115.49234470 Axis 0.72131112 0.40674820 -0.56059447 Axis point -0.00000000 -533.38445172 576.56621718 Rotation angle (degrees) 12.15079427 Shift along axis -50.62173088 > open 35082 fromDatabase emdb Opened emdb 35082 as #6, grid size 256,256,256, pixel 1.05, shown at level 0.03, step 1, values float32, fit PDB 8hxy > fitmap #6 inMap #3 Fit map emdb 35082 in map emdb 36283 using 137879 points correlation = 0.04101, correlation about mean = 0.0363, overlap = 0.1579 steps = 408, shift = 65.8, angle = 34.3 degrees Position of emdb 35082 (#6) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.83002691 0.11306315 0.54614289 -127.05113795 -0.16595560 0.98494900 0.04831368 40.10259507 -0.53246039 -0.13073712 0.83629764 119.92242510 Axis -0.15867614 0.95586619 -0.24726848 Axis point 154.85301937 0.00000000 272.44851364 Rotation angle (degrees) 34.34689659 Shift along axis 28.83966372 > hide #!5 models > close #5 > close #6 > open 35081 fromDatabase emdb Opened emdb 35081 as #5, grid size 256,256,256, pixel 1.05, shown at level 0.0135, step 1, values float32, fit PDB 8hxx > volume #5 level 0.01492 > volume #5 level 0.0135 > volume #5 level 0.01528 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.7501, correlation about mean = 0.1202, overlap = 2.153 steps = 676, shift = 124, angle = 12.1 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98939564 0.12015212 0.08160718 -14.18603821 -0.10620192 0.98173516 -0.15785193 59.27347054 -0.09908288 0.14751118 0.98408487 115.95656871 Axis 0.72555185 0.42932496 -0.53782394 Axis point 0.00000000 -552.69586595 567.85192373 Rotation angle (degrees) 12.14784968 Shift along axis -47.20934497 > fitmap #5 inMap #3 metric correlation Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857 steps = 136, shift = 6.95, angle = 19.2 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.95131278 0.20632824 -0.22898176 11.80469811 -0.25694936 0.94118296 -0.21943486 97.18243585 0.17023812 0.26758791 0.94837529 62.23418195 Axis 0.62295947 -0.51064922 -0.59258660 Axis point 0.00000000 -7.02044215 260.56361502 Rotation angle (degrees) 23.01016501 Shift along axis -79.15142910 > fitmap #5 inMap #3 metric correlation Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857 steps = 40, shift = 0.00643, angle = 0.00133 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.95131514 0.20630820 -0.22899003 11.81311889 -0.25693391 0.94118449 -0.21944641 97.18111392 0.17024827 0.26759800 0.94837062 62.22747418 Axis 0.62298566 -0.51067158 -0.59253979 Axis point 0.00000000 -7.02867722 260.56344632 Rotation angle (degrees) 23.01022287 Shift along axis -79.14048369 > fitmap #5 inMap #3 metric correlation Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.8144, correlation about mean = 0.1298, overlap = 1.857 steps = 48, shift = 0.00512, angle = 0.00617 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.95132248 0.20635803 -0.22891464 11.79566434 -0.25697085 0.94116310 -0.21949487 97.19898510 0.17015148 0.26763479 0.94837761 62.23909035 Axis 0.62308146 -0.51044049 -0.59263818 Axis point 0.00000000 -7.01223637 260.64504895 Rotation angle (degrees) 23.01074024 Shift along axis -79.14989857 Correlation = 0.8144, Correlation about mean = 0.1298, Overlap = 1.857 > fitmap #5 inMap #3 metric cam Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.7826, correlation about mean = 0.1769, overlap = 1.83 steps = 156, shift = 9.68, angle = 15.7 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.96600153 0.16994144 -0.19483569 10.67086071 -0.24444876 0.84574362 -0.47430215 132.80677431 0.08417746 0.50580394 0.85853161 53.47424980 Axis 0.89094092 -0.25362992 -0.37669104 Axis point 0.00000000 -0.94289344 256.61144526 Rotation angle (degrees) 33.36974963 Shift along axis -44.31993584 > fitmap #2 inMap #5 Fit molecule 8jho (#2) to map emdb 35081 (#5) using 42813 atoms average map value = 0.002236, steps = 808 shifted from previous position = 65.2 rotated from previous position = 20.3 degrees atoms outside contour = 41844, contour level = 0.015275 Position of 8jho (#2) relative to emdb 35081 (#5) coordinates: Matrix rotation and translation 0.99723440 0.05928757 0.04481678 -84.00347569 -0.07153422 0.92926586 0.36241939 -127.92858091 -0.02015973 -0.36462301 0.93093697 -71.63525434 Axis -0.98040889 0.08762013 -0.17641179 Axis point 0.00000000 -218.54305667 330.58789023 Rotation angle (degrees) 21.76405662 Shift along axis 83.78593966 > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.01303, steps = 472 shifted from previous position = 65.2 rotated from previous position = 20.3 degrees atoms outside contour = 13154, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.99981479 -0.01515479 -0.01186217 5.68056937 0.01521933 0.99986976 0.00536897 -3.31142014 0.01177926 -0.00554851 0.99991523 -2.15083773 Axis -0.27287765 -0.59090732 0.75918794 Axis point 268.18095539 349.47915962 -0.00000000 Rotation angle (degrees) 1.14624124 Shift along axis -1.22624808 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.7501, correlation about mean = 0.1202, overlap = 2.153 steps = 192, shift = 9.64, angle = 25.7 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98938462 0.12021951 0.08164160 -14.20138256 -0.10625304 0.98171267 -0.15795734 59.30490700 -0.09913815 0.14760589 0.98406510 115.95518391 Axis 0.72560073 0.42928567 -0.53778936 Axis point 0.00000000 -552.30010817 567.68201061 Rotation angle (degrees) 12.15510087 Shift along axis -47.20525068 > fitmap #5 inMap #3 Fit map emdb 35081 in map emdb 36283 using 66947 points correlation = 0.7501, correlation about mean = 0.1203, overlap = 2.153 steps = 44, shift = 0.00958, angle = 0.00986 degrees Position of emdb 35081 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.98940099 0.12011757 0.08159325 -14.18101529 -0.10617263 0.98174301 -0.15782282 59.26271540 -0.09906090 0.14748708 0.98409070 115.95508528 Axis 0.72557774 0.42932978 -0.53778517 Axis point 0.00000000 -552.82488963 567.86588218 Rotation angle (degrees) 12.14526063 Shift along axis -47.20510550 > select add #5 2 models selected Drag select of 5 emdb 35081 > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > ui mousemode right select > ui mousemode right ""translate selected models"" > view matrix models > #5,0.9894,0.12012,0.081593,121.86,-0.10617,0.98174,-0.15782,96.351,-0.099061,0.14749,0.98409,28.646 > select add #4 26263 atoms, 27486 bonds, 460 pseudobonds, 2725 residues, 6 models selected > show #!4 models > select subtract #4 2 models selected > hide #!4 models > open 8HXX Summary of feedback from opening 8HXX fetched from pdb --- note | Fetching compressed mmCIF 8hxx from http://files.rcsb.org/download/8hxx.cif 8hxx title: Cryo-EM structure of the histone deacetylase complex Rpd3S [more info...] Chain information for 8hxx #6 --- Chain | Description | UniProt E | Histone H3 | A0A310TTQ1_XENLA 1-135 K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536 L | Histone deacetylase RPD3 | RPD3_YEAST 1-433 M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401 N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684 Non-standard residues in 8hxx #6 --- ZN — zinc ion > hide surfaces #6 Expected ',' or a keyword > ~surface #6 > show #1#!2,6 cartoons > ~surface #6 > cartoon #6 > ui tool show ""Fit in Map"" > fitmap #6 inMap #3 Fit molecule 8hxx (#6) to map emdb 36283 (#3) using 14873 atoms average map value = 0.007384, steps = 1324 shifted from previous position = 192 rotated from previous position = 84.9 degrees atoms outside contour = 8440, contour level = 0.0075638 Position of 8hxx (#6) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.09978045 0.90768477 0.40761774 38.43434035 -0.96868019 0.18223183 -0.16867202 322.90482788 -0.22738194 -0.37802106 0.89743943 267.95201370 Axis -0.10509844 0.31878567 -0.94198196 Axis point 220.22121701 193.84102671 0.00000000 Rotation angle (degrees) 84.85216422 Shift along axis -153.50792245 > fitmap #6 inMap #5 Fit molecule 8hxx (#6) to map emdb 35081 (#5) using 14873 atoms average map value = -0.0007173, steps = 88 shifted from previous position = 1.17 rotated from previous position = 4.43 degrees atoms outside contour = 14873, contour level = 0.015275 Position of 8hxx (#6) relative to emdb 35081 (#5) coordinates: Matrix rotation and translation 0.23343365 0.91014681 0.34225943 -131.97554074 -0.96245141 0.26641879 -0.05204139 248.64620284 -0.13854965 -0.31725986 0.93816319 203.78654595 Axis -0.13590868 0.24638603 -0.95959510 Axis point 100.10439965 246.69161615 0.00000000 Rotation angle (degrees) 77.34923611 Shift along axis -116.35299942 > view matrix models > #5,0.9894,0.12012,0.081593,124.47,-0.10617,0.98174,-0.15782,55.166,-0.099061,0.14749,0.98409,52.618 > view matrix models > #5,0.9894,0.12012,0.081593,159.95,-0.10617,0.98174,-0.15782,-42.27,-0.099061,0.14749,0.98409,106.38 > view matrix models > #5,0.9894,0.12012,0.081593,173.46,-0.10617,0.98174,-0.15782,-59.056,-0.099061,0.14749,0.98409,114.9 > ui mousemode right select > select #6/N:92@ND2 1 atom, 1 residue, 1 model selected > select add #6 14873 atoms, 15195 bonds, 36 pseudobonds, 1824 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #6,0.10405,0.90662,0.40893,28.485,-0.9478,0.21499,-0.23549,387.98,-0.30142,-0.36308,0.88166,248.38 > view matrix models > #6,0.10405,0.90662,0.40893,18.191,-0.9478,0.21499,-0.23549,473.12,-0.30142,-0.36308,0.88166,188.87 > hide sel atoms > ui tool show Matchmaker > matchmaker #!2 to #6 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 8hxx, chain K (#6) with 8jho, chain K (#2), sequence alignment score = 6474.3 RMSD between 549 pruned atom pairs is 0.199 angstroms; (across all 549 pairs: 0.199) > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.0001283, steps = 784 shifted from previous position = 96.9 rotated from previous position = 30.9 degrees atoms outside contour = 42813, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.72834200 -0.34573474 -0.59159565 97.43009351 -0.68149783 -0.27570900 -0.67789767 726.41678596 0.07126453 0.89691250 -0.43642792 89.56609192 Axis 0.90438437 -0.38066835 -0.19282253 Axis point 0.00000000 367.61128453 264.28163066 Rotation angle (degrees) 119.46537244 Shift along axis -205.67998503 > undo > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.0001283, steps = 76 shifted from previous position = 0.0488 rotated from previous position = 0.0505 degrees atoms outside contour = 42813, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.72784539 -0.34625506 -0.59190245 97.75586173 -0.68197094 -0.27510514 -0.67766717 726.37739434 0.07181028 0.89689720 -0.43636990 89.39943104 Axis 0.90419473 -0.38113752 -0.19278509 Axis point 0.00000000 367.73688204 264.25423815 Rotation angle (degrees) 119.45993471 Shift along axis -205.69421913 > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.0001283, steps = 100 shifted from previous position = 0.0103 rotated from previous position = 0.00923 degrees atoms outside contour = 42813, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.72792795 -0.34616908 -0.59185123 97.70017775 -0.68189432 -0.27523035 -0.67769344 726.38710680 0.07170109 0.89689198 -0.43639859 89.43861713 Axis 0.90422774 -0.38105421 -0.19279492 Axis point 0.00000000 367.71402087 264.25938814 Rotation angle (degrees) 119.46228226 Shift along axis -205.69296922 > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.0001283, steps = 104 shifted from previous position = 0.0227 rotated from previous position = 0.0246 degrees atoms outside contour = 42813, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.72817642 -0.34590544 -0.59169970 97.53792390 -0.68165589 -0.27550674 -0.67782098 726.40298652 0.07144470 0.89690884 -0.43640599 89.50967529 Axis 0.90432102 -0.38082433 -0.19281161 Axis point 0.00000000 367.65295955 264.27238549 Rotation angle (degrees) 119.46344435 Shift along axis -205.68483847 > close #5 > hide #!6 models > fitmap #2 inMap #3 Fit molecule 8jho (#2) to map emdb 36283 (#3) using 42813 atoms average map value = 0.0001283, steps = 96 shifted from previous position = 0.0376 rotated from previous position = 0.0322 degrees atoms outside contour = 42813, contour level = 0.0075638 Position of 8jho (#2) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.72785905 -0.34628785 -0.59186648 97.74913213 -0.68195792 -0.27517534 -0.67765177 726.39972736 0.07179551 0.89686301 -0.43644260 89.42971413 Axis 0.90420416 -0.38112436 -0.19276687 Axis point 0.00000000 367.73677550 264.25461763 Rotation angle (degrees) 119.46418729 Shift along axis -205.70254289 Opened 8jho map 5 as #5, grid size 124,118,186, pixel 1.67, shown at level 0.101, step 1, values float32 > fitmap #2 inMap #3 resolution 5 Fit map 8jho map 5 in map emdb 36283 using 156378 points correlation = 0.3254, correlation about mean = -0.00831, overlap = 5.777 steps = 68, shift = 0.472, angle = 0.523 degrees Position of 8jho map 5 (#5) relative to emdb 36283 (#3) coordinates: Matrix rotation and translation 0.73203849 -0.34017073 -0.59025717 94.63424804 -0.67819095 -0.28168408 -0.67875703 726.98647447 0.06462722 0.89718334 -0.43690430 91.26196499 Axis 0.90584462 -0.37642509 -0.19429276 Axis point 0.00000000 366.66005673 264.64136770 Rotation angle (degrees) 119.55606255 Shift along axis -205.66356583 Average map value = 0.0001285 for 32643 atoms, 42813 outside contour > open 8JHO 8jho title: Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di- nucleosome [more info...] Chain information for 8jho #7 --- Chain | Description | UniProt A E a e | Histone H3 | A0A310TTQ1_XENLA 1-135 B F b f | Histone H4 | A0A8J1LTD2_XENLA 1-102 C G c g | Histone H2A | Q6AZJ8_XENLA 1-129 D H d h | Histone H2B | A0A8J0U496_XENLA 1-122 I | Di-nucleosome template foward | J | Di-nucleosome template reverse | K | Transcriptional regulatory protein SIN3 | SIN3_YEAST 1-1536 L | Histone deacetylase RPD3 | RPD3_YEAST 1-433 M O | Chromatin modification-related protein EAF3 | A0A8H4F719_YEASX 1-401 N P | RCO1 isoform 1 | A0A8H4BXB0_YEASX 1-684 Non-standard residues in 8jho #7 --- ML3 — 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium ZN — zinc ion > hide #!2 models > hide #1#!7 atoms > show #1#!7 atoms > show #1#!7 cartoons > hide #1#!7 atoms > color #2/L rgb(0.99,0.82,0.65) > color /C,G,c,g royal blue > cartoon style nucleic xsection oval width 1.6 thickness 1.6 > color #2/I,J rgb(0.4,0.4,0.4) > show #2/I,J atoms > cartoon style #1 thickness 1.6 > color #1 rgb(1,1,0.5) > color #1 rgb(1.0,1.0,0.5) > color #2/K slate blue > color #2/M,O dark cyan > color #2/N,P deep pink > color #2/L burly wood > color /A,E,a,e rgb(1.0,1.0,0.5) > color /B,F,b,f rgb(0.65,0.9,0.65) > color /C,G,c,g rgb(0.0,0.5,1.0) > color /D,H,d,h rgb(1.0,0.75,0.87) > color #/D,H,d,h rgb(1.0,0.75,0.87) Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #7/D,H,d,h rgb(1.0,0.75,0.87) > color #7/C,G,c,g rgb(0.0,0.5,1.0) > color #7/B,F,b,f rgb(0.65,0.9,0.65) > color #7/A,E,a,e rgb(1.0,1.0,0.5) > color #7/L burly wood > color #7/N,P deep pink > color #7/M,O dark cyan > cartoon style 71 thickness 1.6 Expected an atoms specifier or a keyword > cartoon style #7/1 thickness 1.6 > color #7/I,J rgb(0.4,0.4,0.4) > color #7/K slate blue > nucleotides #1#!7 stubs > nucleotides stubs > show #1#!7 atoms > hide #1#!7 atoms > show #7/I,J atoms > save ""/Users/mandywan/OneDrive - The Institute of Cancer > Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs"" > lighting full > lighting simple > lighting soft > lighting full > lighting simple > lighting soft > lighting full > set bgColor white > transparency 50 > transparency 40 > transparency 70 > transparency 80 > transparency 90 > transparency 80 > close #5 > volume #3 level 0.007443 > save ""/Users/mandywan/OneDrive - The Institute of Cancer > Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc.png"" > width 1038 height 932 supersample 3 transparentBackground true > lighting simple > lighting soft > lighting full > lighting simple > save ""/Users/mandywan/OneDrive - The Institute of Cancer > Research/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.png"" > width 1038 height 932 supersample 3 transparentBackground true > open /Users/mandywan/Library/CloudStorage/OneDrive- > TheInstituteofCancerResearch/Sin3B_Project/Writing/Thesis/Thesis_figures/Discussion_figs/Dinucleosome_struc2.cxs ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16066.0.0,0) OS Loader Version: 540.120.3~19 Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 4 days 5:58 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2717D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: J0XYN7CL625S Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 5.04 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX