id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9974 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit 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: Segmentation fault Thread 0x000070001ca3b000 (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 0x000070001ba38000 (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 ""/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 0x000070001aa35000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers 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 0x0000700019a32000 (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 0x0000700018a2f000 (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 0x0000700017a2c000 (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 0x0000700016a29000 (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 0x0000700015a26000 (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 0x0000700014a23000 (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 0x0000700013a20000 (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 0x0000700012a1d000 (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 Current thread 0x00007ff847f80640 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: ""P"", ""arch"" : ""x86_64"", ""base"" : 140703201247232, ""size"" : 624080, ""uuid"" : ""5db85b72-c63a-3182-91e5-5c942ec30e48"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" } ], ""sharedCache"" : { ""base"" : 140703200624640, ""size"" : 21474836480, ""uuid"" : ""e15dc6ac-9320-3b97-95de-b6e917a43ec4"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=2.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 9088K 11 \nCG image 284K 28 \nColorSync 264K 30 \nCoreAnimation 204K 26 \nCoreGraphics 16K 3 \nCoreUI image data 560K 8 \nFoundation 36K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.5G 868 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 140K 35 \nStack 331.3M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 292.4M 279 \n__CTF 824 1 \n__DATA 47.5M 774 \n__DATA_CONST 41.1M 396 \n__DATA_DIRTY 1802K 226 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.7M 153 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 946.5M 776 \ndyld private memory 292K 4 \nmapped file 214.4M 59 \nshared memory 3004K 30 \n=========== ======= ======= \nTOTAL 3.9G 3775 \nTOTAL, minus reserved VM space 3.7G 3775 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4a5cf050672ae1fbf75a2a0cdef146f29a5901d5"", ""trialInfo"" : { ""rollouts"" : [ ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/jeongmin/Desktop/A3A_Cas9.cxs Opened cryosparc_P4_J65_003_volume_map_sharp.mrc as #1, grid size 128,128,128, pixel 1.74, shown at level 0.306, step 1, values float32 Opened cryosparc_P4_J65_003_volume_map_sharp.mrc z flip as #2, grid size 128,128,128, pixel 1.74, shown at level 0.203, step 1, values float32 Opened cryosparc_P4_J87_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.87, shown at level 0.0788, step 1, values float32 Opened cryosparc_P4_J87_004_volume_map_sharp.mrc z flip as #5, grid size 256,256,256, pixel 0.87, shown at level 0.06, step 1, values float32 Log from Mon May 1 13:44:56 2023 Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/jeongmin/Downloads/cryosparc_P4_J65_003_volume_map_sharp.mrc Opened cryosparc_P4_J65_003_volume_map_sharp.mrc as #1, grid size 128,128,128, pixel 1.74, shown at level 0.228, step 1, values float32 > volume flip #1 Opened cryosparc_P4_J65_003_volume_map_sharp.mrc z flip as #2, grid size 128,128,128, pixel 1.74, shown at step 1, values float32 > open 5f9r Summary of feedback from opening 5f9r fetched from pdb --- notes | Fetching compressed mmCIF 5f9r from http://files.rcsb.org/download/5f9r.cif Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif 5f9r title: Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage [more info...] Chain information for 5f9r #3 --- Chain | Description | UniProt A | RNA (116-MER) | B | CRISPR-associated endonuclease Cas9/Csn1 | CAS9_STRP1 C | DNA (30-MER) | D | DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') | Non-standard residues in 5f9r #3 --- GTP — guanosine-5'-triphosphate SO4 — sulfate ion > ui mousemode right ""translate selected models"" > select add #3 13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected > view matrix models #3,1,0,0,83.021,0,1,0,101.2,0,0,1,174.08 > select subtract #3 Nothing selected > select add #3 13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected > view matrix models > #3,-0.82856,-0.29632,-0.47506,-9.641,-0.54532,0.61943,0.56474,115.79,0.12692,0.72698,-0.67482,91.359 > view matrix models > #3,-0.82856,-0.29632,-0.47506,47.527,-0.54532,0.61943,0.56474,141.63,0.12692,0.72698,-0.67482,85.91 > view matrix models > #3,-0.92924,-0.10474,-0.35432,55.835,-0.29773,0.78016,0.55018,145.39,0.2188,0.61674,-0.75614,87.65 > view matrix models > #3,-0.98368,-0.021961,-0.17858,73.63,-0.10124,0.88807,0.44843,157.62,0.14875,0.45919,-0.8758,73.018 > select subtract #3 Nothing selected > fitmap #3 inMap #2 Fit molecule 5f9r (#3) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) using 13652 atoms average map value = 0.2545, steps = 140 shifted from previous position = 13.3 rotated from previous position = 26.5 degrees atoms outside contour = 6701, contour level = 0.22835 Position of 5f9r (#3) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) coordinates: Matrix rotation and translation -0.89649491 -0.44014457 -0.05069144 75.17382605 -0.40363710 0.76419720 0.50307030 136.66721882 -0.18268540 0.47146091 -0.86275759 61.03807044 Axis -0.22489751 0.93912335 0.25974687 Axis point 54.47513854 0.00000000 9.67472743 Rotation angle (degrees) 175.97021224 Shift along axis 127.29541780 > transparency #2.1 50 > lighting soft > set bgColor white > graphics silhouettes true > lighting simple > volume #2 level 0.1366 > volume #2 level 0.1999 > select :1048 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 7 atom styles > view matrix models > #3,-0.89649,-0.44014,-0.050691,84.036,-0.40364,0.7642,0.50307,108.81,-0.18269,0.47146,-0.86276,41.021 > ui mousemode right translate [Repeated 1 time(s)] > volume #2 level 0.2283 > volume #2 level 0.1461 > surface dust #2 size 17.4 > volume #2 level 0.03855 > volume #2 level 0.06702 > sel:1065 Unknown command: sel:1065 > select :1065 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 7 atom styles > volume #2 level 0.1334 > volume #2 level 0.05437 > volume #1 level 0.2568 > hide #!1 models > volume #2 level 0.1588 > volume #2 level 0.07018 [Repeated 1 time(s)] > volume #2 level 0.1145 > volume #2 level 0.105 > volume #2 level 0.1746 > volume #2 level 0.1461 > volume #2 level 0.105 > volume #2 level 0.1271 > volume #2 level 0.1018 [Repeated 1 time(s)] > volume #2 level 0.05437 > volume #2 level 0.124 > volume #2 level 0.09233 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #2 level -0.07533 > volume #2 level -0.03737 > volume #2 level 0.01008 > volume #2 level 0.03222 > volume #2 level 0.086 > open /Users/jeongmin/Downloads/cryosparc_P4_J87_004_volume_map_sharp.mrc Opened cryosparc_P4_J87_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.87, shown at level 0.0788, step 1, values float32 > hide #!2 models > volume flip #4 Opened cryosparc_P4_J87_004_volume_map_sharp.mrc z flip as #5, grid size 256,256,256, pixel 0.87, shown at step 1, values float32 > hide #!3 models > volume #5 level 0.05529 > volume #5 level 0.0905 > show #!3 models > ui mousemode right ""translate selected atoms"" > undo > select add #3 13652 atoms, 14243 bonds, 146 pseudobonds, 1530 residues, 2 models selected > lighting simple > fitmap #3 inMap #5 Fit molecule 5f9r (#3) to map cryosparc_P4_J87_004_volume_map_sharp.mrc z flip (#5) using 13652 atoms average map value = 0.09574, steps = 164 shifted from previous position = 4.98 rotated from previous position = 16.7 degrees atoms outside contour = 7777, contour level = 0.090496 Position of 5f9r (#3) relative to cryosparc_P4_J87_004_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.98429173 -0.16938333 -0.04979038 72.55794778 -0.17288153 0.86752810 0.46637642 138.85420298 -0.03580183 0.46765829 -0.88318398 64.46642418 Axis 0.08855022 -0.96631423 -0.24165197 Axis point 42.58520987 0.00000000 15.03080350 Rotation angle (degrees) 179.58528399 Shift along axis -143.33020794 > select subtract #3 Nothing selected > show #!2 models > hide #!2 models > volume #5 level 0.05998 > color #5 #99ffffff models > surface dust #5 size 8.7 > transparency #5.1 50 > volume #5 level 0.03885 > volume #5 level 0.02242 > volume #5 level 0.07406 > volume #5 level 0.04824 > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting soft [Repeated 1 time(s)] > lighting simple > show #!2 models > hide #!3 models > ui mousemode right ""move picked models"" > view matrix models > #2,-0.98909,0.13297,-0.063354,217.89,-0.14623,-0.83499,0.53048,164.38,0.017637,0.53396,0.84532,-46.764 > fitmap #2 inMap #5 Fit map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip in map cryosparc_P4_J87_004_volume_map_sharp.mrc z flip using 54341 points correlation = 0.885, correlation about mean = 0.7625, overlap = 1342 steps = 148, shift = 6.26, angle = 12.6 degrees Position of cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) relative to cryosparc_P4_J87_004_volume_map_sharp.mrc z flip (#5) coordinates: Matrix rotation and translation -0.99935737 -0.03549261 -0.00501284 227.02537480 0.02404855 -0.76758983 0.64049007 123.43320020 -0.02658046 0.63995792 0.76795010 -42.17253956 Axis -0.00840296 0.34056344 0.94018399 Axis point 112.28605897 71.26671330 0.00000000 Rotation angle (degrees) 178.18544722 Shift along axis 0.47920364 > volume #2 level 0.1381 > volume #5 level 0.05998 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > ui mousemode right translate > hide #!5 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!5 models > volume #1 level 0.3057 > hide #!1 models > volume #2 level 0.2098 > show #!5 models > volume #5 level 0.07641 > hide #!2 models > show #!2 models > show #!3 models > open 6VPC Summary of feedback from opening 6VPC fetched from pdb --- notes | Fetching compressed mmCIF 6vpc from http://files.rcsb.org/download/6vpc.cif Fetching CCD 8AZ from http://ligand-expo.rcsb.org/reports/8/8AZ/8AZ.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif 6vpc title: Structure of the SpCas9 DNA adenine base editor - ABE8e [more info...] Chain information for 6vpc #6 --- Chain | Description | UniProt A | Cas9 (SpCas9) single-guide RNA (sgRNA) | B | CRISPR-associated endonuclease Cas9 | A0A4U7H5M9_STRPY C | DNA target strand (TS) | D | DNA non-target strand (NTS) | E F | t-RNA adenine deaminase A v8e (TadA-8e) | Non-standard residues in 6vpc #6 --- 8AZ — 8-aza-nebularine-5'-monophosphate MG — magnesium ion ZN — zinc ion > hide #!2 models > hide #!3 models > hide #!6 models > show #!6 models > ui mousemode right ""translate selected atoms"" [Repeated 1 time(s)] > hide #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > show #!5 models > select add #6 16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected > ui mousemode right ""translate selected atoms"" > hide #!5 models > select subtract #6 Nothing selected > volume flip #6 [Repeated 1 time(s)] > show #!5 models > hide #!6 models > show #!3 models > lighting simple > view > volume #2 level 0.1707 > volume #2 level 0.1349 > volume #5 level 0.09519 > volume #5 level 0.121 > volume #5 level 0.03651 > volume #5 level 0.04824 > volume #5 level 0.05998 > hide #!5 models > show #!3 cartoons [Repeated 2 time(s)] > style #!3 sphere Changed 13652 atom styles > style #!3 sphere Changed 13652 atom styles > style #!3 sphere Changed 13652 atom styles > style #!3 stick Changed 13652 atom styles > show #!3 surfaces [Repeated 1 time(s)] > style #!3 sphere Changed 13652 atom styles > style #!3 sphere Changed 13652 atom styles > show #!3 surfaces > show #!3 cartoons > show #!3 atoms > undo [Repeated 2 time(s)] > show #!3 atoms [Repeated 1 time(s)] > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > style #!3 stick Changed 13652 atom styles > style #!3 stick Changed 13652 atom styles > show #!3 surfaces > style #!3 stick Changed 13652 atom styles > show #!3 surfaces > nucleotides #!3 atoms > style nucleic & #!3 stick Changed 3491 atom styles > rainbow #!3 [Repeated 1 time(s)] > view #3 clip false > show #!3 cartoons [Repeated 1 time(s)] > show #!3 target m > style #!3 sphere Changed 13652 atom styles > hide #!3 target m > view #3 clip false > show #!3 models > hide #!3 models > show #!3 models > select :1063 13 atoms, 11 bonds, 2 residues, 2 models selected > style sel & #!3 sphere Changed 8 atom styles > style sel & #!3 sphere Changed 8 atom styles > open 5f9r 5f9r title: Crystal structure of catalytically-active Streptococcus pyogenes CRISPR-Cas9 in complex with single-guided RNA and double-stranded DNA primed for target DNA cleavage [more info...] Chain information for 5f9r #7 --- Chain | Description | UniProt A | RNA (116-MER) | B | CRISPR-associated endonuclease Cas9/Csn1 | CAS9_STRP1 C | DNA (30-MER) | D | DNA (5'-D(P*AP*TP*GP*AP*GP*AP*CP*GP*CP*TP*GP*GP*AP*GP*TP*AP*CP*AP*C)-3') | Non-standard residues in 5f9r #7 --- GTP — guanosine-5'-triphosphate SO4 — sulfate ion > style sel & #!3 sphere Changed 8 atom styles > style sel & #!3 stick Changed 8 atom styles > select add #3 13657 atoms, 14247 bonds, 146 pseudobonds, 1531 residues, 4 models selected > select subtract #3 5 atoms, 4 bonds, 1 residue, 5 models selected > style #!3,7 stick Changed 27304 atom styles > style #!3,7 sphere Changed 27304 atom styles > style #!3,7 ball Changed 27304 atom styles > nucleotides #!3,7 atoms > style nucleic & #!3,7 stick Changed 6982 atom styles > select :1048 20 atoms, 17 bonds, 3 residues, 3 models selected > hide #!7 models > hide #!3 models > show #!3 models > show sel & #!3 atoms [Repeated 2 time(s)] > style sel & #!3 sphere Changed 7 atom styles > style sel & #!3 sphere Changed 7 atom styles > style sel & #!3 sphere Changed 7 atom styles > hide #!2 models > hide sel & #!3 surfaces [Repeated 6 time(s)] > select add #3 13665 atoms, 14254 bonds, 146 pseudobonds, 1532 residues, 5 models selected > select subtract #3 13 atoms, 11 bonds, 2 residues, 6 models selected > select add #3 13665 atoms, 14254 bonds, 146 pseudobonds, 1532 residues, 4 models selected > hide sel & #!3 surfaces [Repeated 1 time(s)] > hide sel & #!3 atoms > show #!2 models > select subtract #3 13 atoms, 11 bonds, 2 residues, 6 models selected > hide #!3 models > show #!6 models > hide sel & #!6 atoms > select add #6 16316 atoms, 16932 bonds, 157 pseudobonds, 1793 residues, 5 models selected > select add #7 29961 atoms, 31169 bonds, 303 pseudobonds, 3322 residues, 6 models selected > select subtract #7 16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected > select subtract #6 Nothing selected > select add #6 16309 atoms, 16926 bonds, 157 pseudobonds, 1792 residues, 4 models selected > hide sel atoms > show sel cartoons > fitmap #6 inMap #2 Fit molecule 6vpc (#6) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) using 16309 atoms average map value = 0.09211, steps = 144 shifted from previous position = 12.2 rotated from previous position = 5.57 degrees atoms outside contour = 11604, contour level = 0.13485 Position of 6vpc (#6) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) coordinates: Matrix rotation and translation -0.99780088 0.00375893 0.06617603 221.43948330 0.03833365 -0.78176037 0.62239959 129.04354049 0.05407335 0.62356763 0.77989709 -60.16807777 Axis 0.03186975 0.33021967 0.94336593 Axis point 111.09796843 76.12908193 0.00000000 Rotation angle (degrees) 178.94998492 Shift along axis -7.09057903 > hide #!2 models > show #!2 models > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.15601,0.52519,0.83656,-40.238,0.96317,0.26866,0.010959,-37.785,-0.21899,0.80747,-0.54776,125.53 > view matrix models > #6,0.41847,-0.87223,0.25319,133.94,0.033701,-0.26367,-0.96402,264.39,0.90761,0.41195,-0.080941,-23.145 > view matrix models > #6,-0.85794,-0.3921,0.33197,218.68,-0.019499,-0.62084,-0.78369,279.42,0.51339,-0.67883,0.525,70.677 > view matrix models > #6,-0.85794,-0.3921,0.33197,235.82,-0.019499,-0.62084,-0.78369,277.37,0.51339,-0.67883,0.525,65.184 > view matrix models > #6,-0.95854,-0.2833,0.030828,262.48,0.14341,-0.57305,-0.80688,257.13,0.24625,-0.769,0.58991,106.19 > fitmap #6 inMap #2 Fit molecule 6vpc (#6) to map cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) using 16309 atoms average map value = 0.2222, steps = 128 shifted from previous position = 10.2 rotated from previous position = 18.9 degrees atoms outside contour = 6064, contour level = 0.13485 Position of 6vpc (#6) relative to cryosparc_P4_J65_003_volume_map_sharp.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99458213 0.01889308 0.10222251 -22.63766958 -0.09874880 -0.13554974 0.98583718 27.10701277 0.03248173 -0.99059039 -0.13294968 237.70773492 Axis -0.99761454 0.03520211 -0.05938050 Axis point 0.00000000 117.19763526 107.83568756 Rotation angle (degrees) 97.87189415 Shift along axis 9.42268886 > ui mousemode right translate [Repeated 2 time(s)] > select subtract #6 Nothing selected > hide #!6 models > show #!3 models > show #!3 atoms > hide #!3 atoms > select :1048 20 atoms, 17 bonds, 3 residues, 3 models selected > show sel & #!3 atoms > select :1063 21 atoms, 18 bonds, 3 residues, 3 models selected > show sel & #!3 atoms > select :1063 21 atoms, 18 bonds, 3 residues, 3 models selected > show sel & #!3 atoms [Repeated 1 time(s)] > style sel & #!3 sphere Changed 8 atom styles > show #!6 models > hide #!6 models > volume #2 level 0.07949 > volume #2 level 0.2032 > save /Users/jeongmin/Desktop/A3A_Cas9.cxs ——— End of log from Mon May 1 13:44:56 2023 ——— opened ChimeraX session > save /Users/jeongmin/Desktop/image1.png supersample 3 > save /Users/jeongmin/Desktop/image2.png supersample 3 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!5 models > hide #!5 models > show #!5 models > hide #!2 models > open /Users/jeongmin/Downloads/cryosparc_P4_J118_class_01_final_volume.mrc Opened cryosparc_P4_J118_class_01_final_volume.mrc as #8, grid size 128,128,128, pixel 1.66, shown at level 1.29, step 1, values float32 > hide #!5 models > volume #2 level 0.1446 > volume #2 level 0.1186 > hide #!2 models > volume #2 level 0.1316 > volume flip #8 Opened cryosparc_P4_J118_class_01_final_volume.mrc z flip as #9, grid size 128,128,128, pixel 1.66, shown at step 1, values float32 > volume #2 level 0.1609 > volume #2 level 0.1804 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!2 models > show #!8 models > volume #8 level 1.596 > volume #8 level 1.388 > volume #9 level 1.405 > hide #!8 models > show #!2 models > hide #!3 models > show #!3 models > hide #!9 models > show #!8 models > hide #!8 models > hide #!2 models > show #!4 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > show #!7 models > hide #!7 models > hide #!2 models > show #!5 models > hide #!4 models > volume #5 level 0.0459 > save /Users/jeongmin/Desktop/image3.png supersample 3 > volume #5 level 0.05763 > open ""/Users/jeongmin/Downloads/5keg (1).pdb"" 5keg (1).pdb title: Crystal structure of APOBEC3A In complex with A single-stranded DNA [more info...] Chain information for 5keg (1).pdb #10 --- Chain | Description | UniProt A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199 B | DNA (5'-D(*TP*TP*CP*TP*T)-3') | Non-standard residues in 5keg (1).pdb #10 --- CA — calcium ion CL — chloride ion ZN — zinc ion > open ""/Users/jeongmin/Downloads/5keg (1).pdb"" 5keg (1).pdb title: Crystal structure of APOBEC3A In complex with A single-stranded DNA [more info...] Chain information for 5keg (1).pdb #11 --- Chain | Description | UniProt A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199 B | DNA (5'-D(*TP*TP*CP*TP*T)-3') | Non-standard residues in 5keg (1).pdb #11 --- CA — calcium ion CL — chloride ion ZN — zinc ion > open ""/Users/jeongmin/Downloads/5keg (1).pdb"" 5keg (1).pdb title: Crystal structure of APOBEC3A In complex with A single-stranded DNA [more info...] Chain information for 5keg (1).pdb #12 --- Chain | Description | UniProt A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199 B | DNA (5'-D(*TP*TP*CP*TP*T)-3') | Non-standard residues in 5keg (1).pdb #12 --- CA — calcium ion CL — chloride ion ZN — zinc ion > open ""/Users/jeongmin/Downloads/5keg (2).pdb"" 5keg (2).pdb title: Crystal structure of APOBEC3A In complex with A single-stranded DNA [more info...] Chain information for 5keg (2).pdb #13 --- Chain | Description | UniProt A | DNA DC->du-editing enzyme apobec-3A | ABC3A_HUMAN 1-199 B | DNA (5'-D(*TP*TP*CP*TP*T)-3') | Non-standard residues in 5keg (2).pdb #13 --- CA — calcium ion CL — chloride ion ZN — zinc ion QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields 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 Updating list of available bundles failed: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129) OpenGL version: 4.1 INTEL-20.6.1 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 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: 8 GB System Firmware Version: 1968.120.12.0.0 (iBridge: 20.16.5060.0.0,0) OS Loader Version: 577~170 Software: System Software Overview: System Version: macOS 13.4.1 (22F82) Kernel Version: Darwin 22.5.0 Time since boot: 33 days, 4 hours, 42 minutes 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 Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) 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-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-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-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 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 duplicate Tom Goddard all ChimeraX