id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9646 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 lgebert@… 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 0x000000031ddac000 (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 0x000000031cda9000 (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 0x000000031bda6000 (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 0x000000031ada3000 (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 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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 0x0000000317d9a000 (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 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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 0x0000000313d8e000 (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 0x0000000312d8b000 (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 0x0000000311d88000 (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 0x0000000200d4e280 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", 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""64a84dae90d82611a0bd7d3d"", ""deploymentId"" : 400000010 }, { ""treatmentId"" : ""a092db1b-c401-44fa-9c54-518b7d69ca61"", ""experimentId"" : ""64a844035c85000c0f42398a"", ""deploymentId"" : 400000018 } ] } } ===== Log before crash start ===== 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 > open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00500_volume.mrc Opened cryosparc_P338_J28_class_00_00500_volume.mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.793, step 1, values float32 > volume #1 level 1.09 > close session > open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00600_volume.mrc Opened cryosparc_P338_J28_class_00_00600_volume.mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.756, step 1, values float32 > volume #1 level 1.282 > close session > open /Users/luca/Downloads/cryosparc_P338_J28_class_00_00700_volume.mrc Opened cryosparc_P338_J28_class_00_00700_volume.mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.744, step 1, values float32 > volume #1 level 1.432 > close session > open /Users/luca/Downloads/cryosparc_P338_J28_class_00_final_volume.mrc Opened cryosparc_P338_J28_class_00_final_volume.mrc as #1, grid size 128,128,128, pixel 1.82, shown at level 0.267, step 1, values float32 > volume #1 level 0.3339 > volume #1 level 0.3743 > open /Users/luca/Downloads/cryosparc_P338_J29_002_volume_map_sharp.mrc Opened cryosparc_P338_J29_002_volume_map_sharp.mrc as #2, grid size 128,128,128, pixel 1.82, shown at level 0.908, step 1, values float32 > volume #2 level 1.124 > open /Users/luca/Downloads/cryosparc_P338_J26_003_volume_map_sharp.mrc Opened cryosparc_P338_J26_003_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 0.91, shown at level 0.081, step 1, values float32 > volume #3 level 0.08355 > open /Users/luca/Downloads/cryosparc_P338_J25_class_00_final_volume.mrc Opened cryosparc_P338_J25_class_00_final_volume.mrc as #4, grid size 128,128,128, pixel 1.82, shown at level 0.186, step 1, values float32 > hide #!3 models > volume #4 level 0.3723 > open /Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume.mrc Opened cryosparc_P338_J33_class_00_00000_volume.mrc as #5, grid size 64,64,64, pixel 3.64, shown at level 0.673, step 1, values float32 > volume #5 level 0.4716 > close session > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume > (1).mrc"" Opened cryosparc_P338_J33_class_00_00000_volume (1).mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.673, step 1, values float32 > volume #1 level 0.3924 > close session > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00000_volume > (2).mrc"" Opened cryosparc_P338_J33_class_00_00000_volume (2).mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.673, step 1, values float32 > volume #1 level 0.3776 > volume #1 level 0.7543 > close session > open /Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume.mrc Opened cryosparc_P338_J33_class_00_00400_volume.mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #1 level 0.5567 > volume #1 level 0.5658 > volume #1 level 0.7706 > volume #1 level 1.13 > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume > (1).mrc"" Opened cryosparc_P338_J33_class_00_00400_volume (1).mrc as #2, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #2 level 0.9799 > volume #2 level 1.044 > volume #2 level 0.7524 > volume #2 level 1.253 > volume #2 level 0.4793 > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume > (2).mrc"" Opened cryosparc_P338_J33_class_00_00400_volume (2).mrc as #3, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #3 level 0.7363 > close #3 > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume > (3).mrc"" Opened cryosparc_P338_J33_class_00_00400_volume (3).mrc as #3, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #3 level 0.502 > volume #2 level 0.3669 > close #3 > close #2 > close #1 > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume > (3).mrc"" Opened cryosparc_P338_J33_class_00_00400_volume (3).mrc as #1, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #1 level 0.4975 > volume #1 level 0.9753 > open ""/Users/luca/Downloads/cryosparc_P338_J33_class_00_00400_volume > (4).mrc"" Opened cryosparc_P338_J33_class_00_00400_volume (4).mrc as #2, grid size 64,64,64, pixel 3.64, shown at level 0.821, step 1, values float32 > volume #2 level 0.9298 > open /Users/luca/Downloads/cryosparc_P338_J33_class_00_final_volume.mrc Opened cryosparc_P338_J33_class_00_final_volume.mrc as #3, grid size 128,128,128, pixel 1.82, shown at level 0.274, step 1, values float32 > close #1 > close #2 > volume #3 level 0.3548 > oepn 4w5r Unknown command: oepn 4w5r > open 4w5r 4w5r title: The Crystal Structure of Human Argonaute2 Bound to a Guide and Target RNA Containing Seed Pairing from 2-8 (Long Target) [more info...] Chain information for 4w5r #1 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 B | RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*UP*U)-3') | D | RNA (5'-R(P*AP*AP*UP*GP*UP*GP*AP*AP*A)-3') | Non-standard residues in 4w5r #1 --- IPA — isopropyl alcohol (2-propanol) IPH — phenol MG — magnesium ion > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-3.071,0,1,0,7.3938,0,0,1,4.26 > select add #1 7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 6 models selected > view matrix models > #3,1,0,0,-9.0761,0,1,0,17.328,0,0,1,19.342,#1,1,0,0,-6.0051,0,1,0,9.9338,0,0,1,15.082 > select subtract #3 7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 4 models selected > view matrix models #1,1,0,0,-47.563,0,1,0,101.28,0,0,1,85.733 > view matrix models #1,1,0,0,31.974,0,1,0,134.67,0,0,1,130.29 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.18479,-0.03013,0.98232,66.496,-0.86517,-0.47913,0.14806,171.07,0.46619,-0.87723,-0.11461,110.4 > view matrix models > #1,-0.12749,0.92727,0.35201,101.81,-0.82843,0.095606,-0.55188,183.41,-0.5454,-0.36197,0.75599,162.76 > view matrix models > #1,-0.28882,0.89363,0.34353,111.18,-0.70482,0.044373,-0.708,177.79,-0.64793,-0.44661,0.61703,169.99 > fitmap #1 inMap #3 Fit molecule 4w5r (#1) to map cryosparc_P338_J33_class_00_final_volume.mrc (#3) using 7005 atoms average map value = 0.4065, steps = 104 shifted from previous position = 23.7 rotated from previous position = 27.8 degrees atoms outside contour = 2578, contour level = 0.35475 Position of 4w5r (#1) relative to cryosparc_P338_J33_class_00_final_volume.mrc (#3) coordinates: Matrix rotation and translation -0.52514277 0.65064588 0.54852986 145.60182305 -0.80600685 -0.17342691 -0.56592938 175.56091051 -0.27308978 -0.73931255 0.61549892 114.73456628 Axis -0.10312104 0.48866491 -0.86635596 Axis point 125.63093130 75.24083125 0.00000000 Rotation angle (degrees) 122.78822009 Shift along axis -28.62512920 > volume #3 color #b2ffff80 > ui mousemode right translate > select subtract #1 Nothing selected > volume #3 level 0.3369 > volume #3 level 0.2458 > volume #3 level 0.2423 > open /Users/luca/Downloads/cryosparc_P338_J36_002_volume_map_sharp.mrc Opened cryosparc_P338_J36_002_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.91, shown at level 0.118, step 1, values float32 > select add #1 7005 atoms, 7070 bonds, 32 pseudobonds, 956 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.52514,0.65065,0.54853,148.78,-0.80601,-0.17343,-0.56593,191.85,-0.27309,-0.73931,0.6155,112.75 > select subtract #1 Nothing selected > fitmap #1 inMap #2 Fit molecule 4w5r (#1) to map cryosparc_P338_J36_002_volume_map_sharp.mrc (#2) using 7005 atoms average map value = 0.1592, steps = 124 shifted from previous position = 16.9 rotated from previous position = 2.43 degrees atoms outside contour = 1324, contour level = 0.11795 Position of 4w5r (#1) relative to cryosparc_P338_J36_002_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.49299766 0.65561043 0.57195128 143.24545670 -0.82256967 -0.13707364 -0.55189668 176.50503678 -0.28342978 -0.74255355 0.60686224 115.38981914 Axis -0.11094751 0.49776542 -0.86018616 Axis point 126.98745031 75.31060187 0.00000000 Rotation angle (degrees) 120.77076574 Shift along axis -27.29134749 > volume #2 color #b2b2ff80 > volume #2 level 0.01723 > volume #2 level 0.1324 > open 7ki3 7ki3 title: Human Argonaute2:miR-122 bound to the HCV genotype 1a site-1 RNA [more info...] Chain information for 7ki3 #4 --- Chain | Description | UniProt A D | Protein argonaute-2 | AGO2_HUMAN 1-859 B E | miR-122 | C F | HCV genotype 1a miR-122 site-1 | Non-standard residues in 7ki3 #4 --- BA — barium ion 7ki3 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > split #4 Split 7ki3 (#4) into 6 models Chain information for 7ki3 A #4.1 --- Chain | Description A | No description available Chain information for 7ki3 B #4.2 --- Chain | Description B | No description available Chain information for 7ki3 C #4.3 --- Chain | Description C | No description available Chain information for 7ki3 D #4.4 --- Chain | Description D | No description available Chain information for 7ki3 E #4.5 --- Chain | Description E | No description available Chain information for 7ki3 F #4.6 --- Chain | Description F | No description available > hide #!4.2 models > hide #!4.3 models > hide #!4.5 models > hide #!4.4 models > hide #!4.6 models > select add #4.1 6434 atoms, 6585 bonds, 5 pseudobonds, 805 residues, 3 models selected > hide sel atoms > show sel cartoons > view matrix models #4.1,1,0,0,2.6709,0,1,0,104.26,0,0,1,70.271 > view matrix models #4.1,1,0,0,82.075,0,1,0,110.05,0,0,1,77.832 > ui mousemode right ""rotate selected models"" > view matrix models > #4.1,-0.22254,-0.95733,0.1844,111.5,0.65048,-0.28669,-0.70334,128.1,0.72619,-0.036575,0.68653,71.712 > view matrix models > #4.1,-0.69944,0.61905,-0.35715,127.96,-0.077958,-0.56284,-0.82288,150.86,-0.71042,-0.54772,0.44193,116.63 > fitmap #4.1 inMap #3 Fit molecule 7ki3 A (#4.1) to map cryosparc_P338_J33_class_00_final_volume.mrc (#3) using 6434 atoms average map value = 0.4019, steps = 168 shifted from previous position = 32.9 rotated from previous position = 33.3 degrees atoms outside contour = 1133, contour level = 0.24226 Position of 7ki3 A (#4.1) relative to cryosparc_P338_J33_class_00_final_volume.mrc (#3) coordinates: Matrix rotation and translation -0.63240895 0.74930610 0.19646703 120.50726057 -0.48292867 -0.18306497 -0.85631018 166.49236275 -0.60567220 -0.63641778 0.47763332 115.53081255 Axis 0.14790952 0.53955496 -0.82885657 Axis point 113.57066268 88.94396613 -0.00000000 Rotation angle (degrees) 131.98378749 Shift along axis 11.89747755 > fitmap #4.1 inMap #2 Fit molecule 7ki3 A (#4.1) to map cryosparc_P338_J36_002_volume_map_sharp.mrc (#2) using 6434 atoms average map value = 0.1587, steps = 172 shifted from previous position = 27.7 rotated from previous position = 0.742 degrees atoms outside contour = 1691, contour level = 0.13245 Position of 7ki3 A (#4.1) relative to cryosparc_P338_J36_002_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.63650877 0.74738436 0.19045526 120.86109405 -0.47178353 -0.18194298 -0.86273811 166.44771829 -0.61014497 -0.63899403 0.46841194 115.83778862 Axis 0.15162932 0.54255947 -0.82621896 Axis point 113.55858005 89.56375972 0.00000000 Rotation angle (degrees) 132.45569595 Shift along axis 12.92649548 > select subtract #4.1 Nothing selected > ui mousemode right translate > hide #!1 models > open /Users/luca/Downloads/cryosparc_P338_J38_002_volume_map_sharp.mrc Opened cryosparc_P338_J38_002_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 0.91, shown at level 0.14, step 1, values float32 > volume #5 level 0.1773 > show #!1 models > volume #5 color #ffb2ff80 > fitmap #1 inMap #5 Fit molecule 4w5r (#1) to map cryosparc_P338_J38_002_volume_map_sharp.mrc (#5) using 7005 atoms average map value = 0.2189, steps = 56 shifted from previous position = 0.736 rotated from previous position = 2.67 degrees atoms outside contour = 2815, contour level = 0.17731 Position of 4w5r (#1) relative to cryosparc_P338_J38_002_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation -0.51150010 0.65824658 0.55233964 144.10619490 -0.81999133 -0.18176091 -0.54274965 175.51076010 -0.25686935 -0.73053022 0.63272722 113.62226947 Axis -0.11074177 0.47722318 -0.87177652 Axis point 125.34716977 74.16246341 0.00000000 Rotation angle (degrees) 122.02348987 Shift along axis -31.25399912 > hide #!4 models > volume #5 level 0.3491 > volume #5 level 0.2406 > open ""/Users/luca/Downloads/cryosparc_P338_J38_002_volume_map_sharp (1).mrc"" Opened cryosparc_P338_J38_002_volume_map_sharp (1).mrc as #6, grid size 256,256,256, pixel 0.91, shown at level 0.119, step 1, values float32 > volume #6 level 0.1603 > close #5 > volume #6 level 0.1467 > volume #6 level 0.1535 Must specify one map, got 0 Must specify one map, got 0 > volume #6 level 0.1239 > volume #6 color #ffb2b280 > close #2 > close #3 > close #4 > volume #6 level 0.2367 > volume #6 level 0.1681 > open > /Users/luca/Downloads/cryosparc_P338_J81_class_00_00142_volume_sharp.mrc Opened cryosparc_P338_J81_class_00_00142_volume_sharp.mrc as #2, grid size 128,128,128, pixel 1.82, shown at level 0.288, step 1, values float32 > open > /Users/luca/Downloads/cryosparc_P338_J81_class_01_00142_volume_sharp.mrc Opened cryosparc_P338_J81_class_01_00142_volume_sharp.mrc as #3, grid size 128,128,128, pixel 1.82, shown at level 0.37, step 1, values float32 > open > /Users/luca/Downloads/cryosparc_P338_J81_class_02_00142_volume_sharp.mrc Opened cryosparc_P338_J81_class_02_00142_volume_sharp.mrc as #4, grid size 128,128,128, pixel 1.82, shown at level 0.18, step 1, values float32 > open > /Users/luca/Downloads/cryosparc_P338_J81_class_03_00142_volume_sharp.mrc Opened cryosparc_P338_J81_class_03_00142_volume_sharp.mrc as #5, grid size 128,128,128, pixel 1.82, shown at level 0.224, step 1, values float32 > hide #!1 models > hide #!6 models > tile #2-5 4 models tiled > ui hideFloating toggle > ~tile #2-5 > hide #!2 models > hide #!4 models > hide #!5 models > volume #3 level 0.3259 > show #!1 models > open 6n4o 6n4o title: Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more info...] Chain information for 6n4o #7 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 C | RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') | D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') | > hide #!1 models > view > select add #7 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > color #7 silver > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,134.41,0,1,0,86.47,0,0,1,145.57 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.92303,-0.3844,-0.015891,137.82,-0.33201,-0.775,-0.53772,87.264,0.19438,0.50161,-0.84297,81.09 > view matrix models > #7,0.8078,-0.33082,-0.48786,120.04,-0.27178,-0.94347,0.18975,114.19,-0.52306,-0.02069,-0.85205,77.825 > select subtract #7 Nothing selected > view > fitmap #7 inMap #3 Fit molecule 6n4o (#7) to map cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) using 7064 atoms average map value = 0.5235, steps = 76 shifted from previous position = 12.1 rotated from previous position = 6.89 degrees atoms outside contour = 1179, contour level = 0.32585 Position of 6n4o (#7) relative to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.64862780 0.66298115 -0.37381541 105.48492075 -0.24663666 0.64773526 0.72083938 126.01241295 0.72003634 -0.37535987 0.58365455 152.38074407 Axis -0.61036037 -0.60905330 -0.50647240 Axis point 0.00000000 65.30435132 41.55386414 Rotation angle (degrees) 63.89555715 Shift along axis -218.30873293 > volume #3 color #e5bf9980 > show #!4 models > show #!5 models > show #!6 models > hide #!6 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > show #!3 models > select add #2 2 models selected > view matrix models > #2,-0.57006,0.78117,-0.25456,129.4,0.63265,0.61504,0.47062,-87.102,0.5242,0.10724,-0.84482,140.11 > view matrix models > #2,0.22379,-0.50724,-0.83224,244.28,0.77159,-0.42949,0.46924,11.616,-0.59546,-0.74716,0.29526,234.51 > view matrix models > #2,-0.63442,0.71251,0.29972,80.286,0.71648,0.39651,0.57396,-84.953,0.29011,0.57888,-0.76206,106.3 > view matrix models > #2,-0.59942,0.60826,0.52031,62.035,0.80007,0.4356,0.41249,-80.423,0.024257,0.66353,-0.74775,126.79 > hide #!3 models > hide #!7 models > view matrix models > #2,-0.27642,-0.95564,0.10168,244.54,-0.71411,0.27505,0.64373,89.698,-0.64314,0.10533,-0.75847,268.51 > view matrix models > #2,-0.41526,-0.87606,-0.24509,292.44,0.84008,-0.26594,-0.47281,94.768,0.34903,-0.40223,0.8464,20.781 > view matrix models > #2,-0.26903,-0.90879,-0.31894,287.3,0.93496,-0.16692,-0.31303,54.101,0.23124,-0.38241,0.89459,26.955 > show #!3 models > view matrix models > #2,0.065034,0.94046,0.33363,-31.554,-0.74388,0.26854,-0.61198,239.59,-0.66514,-0.20838,0.71706,134.51 > view matrix models > #2,-0.93809,0.08739,-0.3352,258.71,0.28792,-0.34132,-0.89476,217.38,-0.1926,-0.93588,0.29503,207.62 > volume #2 flipNormals Missing ""flipNormals"" keyword's argument > volume #2 flipNormals z Invalid ""flipNormals"" argument: Expected true or false (or 1 or 0) > volume #2 flipz Expected a keyword > volume flip #2 Opened cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip as #8, grid size 128,128,128, pixel 1.82, shown at step 1, values float32 > select subtract #2 Nothing selected > select add #8 2 models selected > view matrix models > #8,-0.26322,0.94827,0.1775,24.99,-0.6288,-0.029099,-0.77702,277.98,-0.73166,-0.31614,0.60393,167.63 > view matrix models > #8,-0.44751,0.89256,0.055398,67.001,0.52616,0.2127,0.82335,-69.664,0.72311,0.3976,-0.56482,51.394 > view matrix models > #8,-0.43927,0.64907,0.62109,27.696,0.84768,0.070549,0.5258,-57.813,0.29746,0.75745,-0.5812,64.052 > view matrix models > #8,-0.27642,0.71873,0.63799,-1.1989,0.92354,0.015032,0.3832,-44.263,0.26583,0.69513,-0.66793,84.646 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.27642,0.71873,0.63799,-9.0153,0.92354,0.015032,0.3832,-43.882,0.26583,0.69513,-0.66793,76.115 > select subtract #8 Nothing selected > ui mousemode right translate > fitmap #8 inMap #3 Fit map cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip in map cryosparc_P338_J81_class_01_00142_volume_sharp.mrc using 20966 points correlation = 0.9155, correlation about mean = 0.3598, overlap = 5706 steps = 108, shift = 2.95, angle = 13.2 degrees Position of cryosparc_P338_J81_class_00_00142_volume_sharp.mrc z flip (#8) relative to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.99567086 0.06298972 0.06835091 217.19583721 -0.07382409 -0.98271577 -0.16976376 259.76578932 0.05647615 -0.17407477 0.98311161 19.46765305 Axis -0.03137660 0.08642742 -0.99576393 Axis point 112.78241990 126.97925006 0.00000000 Rotation angle (degrees) 176.06079682 Shift along axis -3.74916630 > hide #!3 models > volume #8 level 0.4246 > show #!2 models > hide #!8 models > volume #8 level 0.4524 > hide #!8 models > volume #2 level 0.4942 > show #!3 models > hide #!3 models > show #!4 models > show #!5 models > hide #!4 models > show #!3 models > select add #5 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.50566,-0.47369,-0.72105,305.97,0.69708,0.26811,-0.66498,67.807,0.50832,-0.83889,0.19462,132.82 > view matrix models > #5,-0.1187,-0.29358,-0.94854,264.66,0.77891,0.56492,-0.27232,-19.749,0.61579,-0.77115,0.16162,115.96 > fitmap #5 inMap #3 Fit map cryosparc_P338_J81_class_03_00142_volume_sharp.mrc in map cryosparc_P338_J81_class_01_00142_volume_sharp.mrc using 20953 points correlation = 0.8656, correlation about mean = 0.3181, overlap = 4732 steps = 120, shift = 6.76, angle = 22.4 degrees Position of cryosparc_P338_J81_class_03_00142_volume_sharp.mrc (#5) relative to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.65589195 -0.72842587 0.19799370 255.15172882 -0.40663589 0.56193744 0.72032880 12.64178605 -0.63596621 0.39194651 -0.66477434 216.39418224 Axis -0.34483118 0.87573352 0.33790866 Axis point 161.55241525 0.00000000 69.03857300 Rotation angle (degrees) 151.56578913 Shift along axis -3.79196762 > select subtract #5 Nothing selected > volume #5 level 0.1967 > open 7KX9 Summary of feedback from opening 7KX9 fetched from pdb --- notes | Fetching compressed mmCIF 7kx9 from http://files.rcsb.org/download/7kx9.cif Fetching CCD OMG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif 7kx9 title: Cryo-EM structure of Ephydatia fluviatilis PiwiA-piRNA-target complex [more info...] Chain information for 7kx9 #9 --- Chain | Description | UniProt A | Piwi-A | D5MRY8_9METZ 220-987 B | RNA (5'-R(P*UP*CP*UP*CP*UP*UP*GP*AP*GP*UP*UP*GP*GP*AP*CP*AP*AP*AP*UP*GP*GP*CP*AP*(OMG))-3') | C | RNA (5'-R(P*UP*GP*UP*CP*CP*AP*AP*CP*UP*CP*AP*AP*GP*AP*GP*A)-3') | Non-standard residues in 7kx9 #9 --- MG — magnesium ion > select add #9 12424 atoms, 12646 bonds, 43 pseudobonds, 776 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #9,1,0,0,37.459,0,1,0,79.187,0,0,1,49.245 > view matrix models #9,1,0,0,72.428,0,1,0,63.017,0,0,1,45.299 > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.071579,-0.47086,-0.8793,198.84,0.37597,0.8038,-0.46103,78.537,0.92386,-0.36359,0.11949,63.578 > view matrix models > #9,-0.95277,-0.14204,0.26845,165.79,-0.25182,0.86358,-0.43682,106.54,-0.16978,-0.48379,-0.85856,178.64 > view matrix models > #9,-0.95632,0.28493,0.065261,154.99,0.12818,0.60943,-0.78241,118.53,-0.2627,-0.73987,-0.61934,183.72 > fitmap #9 inMap #3 Fit molecule 7kx9 (#9) to map cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) using 12424 atoms average map value = 0.4928, steps = 116 shifted from previous position = 13.7 rotated from previous position = 24 degrees atoms outside contour = 2529, contour level = 0.32585 Position of 7kx9 (#9) relative to cryosparc_P338_J81_class_01_00142_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.64716431 -0.08501905 0.75759495 115.36697829 0.74746078 -0.26621230 0.60863239 59.60477086 0.14993574 0.96015768 0.23583151 50.79616015 Axis 0.32280710 0.55801592 0.76446962 Axis point 47.23097824 26.77123450 0.00000000 Rotation angle (degrees) 147.01073029 Shift along axis 109.33381277 > select subtract #9 Nothing selected > hide #!5 models > close #9 > volume #3 level 0.3148 > volume #3 level 0.3617 > show #!1 models > hide #!1 models > volume #3 level 0.414 > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!3 models > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/structures and > maps/221027_Ago2-ON1_modified_guide_modelled_WIP.pdb"" Chain information for 221027_Ago2-ON1_modified_guide_modelled_WIP.pdb #9 --- Chain | Description A | No description available B | No description available > view #9 clip false > open /Users/luca/Downloads/cryosparc_P338_J137_004_volume_map_sharp.mrc Opened cryosparc_P338_J137_004_volume_map_sharp.mrc as #10, grid size 128,128,128, pixel 1.82, shown at level 0.372, step 1, values float32 > close session > open /Users/luca/Downloads/cryosparc_P338_J137_004_volume_map_sharp.mrc > format mrc Opened cryosparc_P338_J137_004_volume_map_sharp.mrc as #1, grid size 128,128,128, pixel 1.82, shown at level 0.372, step 1, values float32 > volume #1 level 0.9025 > volume #1 color #b2b2b280 > open 6n4o 6n4o title: Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more info...] Chain information for 6n4o #2 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 C | RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') | D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') | > select add #2 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,149.19,0,1,0,80.787,0,0,1,143.45 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.10865,-0.99388,0.020007,147.68,-0.7006,0.090839,0.70775,106.34,-0.70523,0.062882,-0.70618,76.954 > fitmap #2 inMap #1 Fit molecule 6n4o (#2) to map cryosparc_P338_J137_004_volume_map_sharp.mrc (#1) using 7064 atoms average map value = 0.6122, steps = 228 shifted from previous position = 27 rotated from previous position = 54.8 degrees atoms outside contour = 5152, contour level = 0.90246 Position of 6n4o (#2) relative to cryosparc_P338_J137_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.67901032 -0.52854607 0.50949390 129.14480096 -0.11621978 0.76265161 0.63628256 123.56513617 -0.72487099 0.37282915 -0.57927582 80.16845187 Axis -0.19841209 0.92962518 0.31053127 Axis point 86.89605717 0.00000000 -11.56484224 Rotation angle (degrees) 138.40165473 Shift along axis 114.14018341 > ui mousemode right translate > select subtract #2 Nothing selected > volume #1 level 0.8371 > open /Users/luca/Downloads/cryosparc_P318_J65_005_volume_map_sharp.mrc Opened cryosparc_P318_J65_005_volume_map_sharp.mrc as #3, grid size 128,128,128, pixel 1.82, shown at level 0.352, step 1, values float32 > hide #!2 models > volume #3 level 0.9178 > close #3 > open /Users/luca/Downloads/cryosparc_P338_J142_003_volume_map_sharp.mrc Opened cryosparc_P338_J142_003_volume_map_sharp.mrc as #3, grid size 128,128,128, pixel 1.82, shown at level 0.356, step 1, values float32 > hide #!1 models > volume #3 level 0.5851 > volume #3 level 0.6044 > show #!1 models > volume #1 level 0.6772 > open /Users/luca/Downloads/cryosparc_P338_J150_003_volume_map_sharp.mrc Opened cryosparc_P338_J150_003_volume_map_sharp.mrc as #4, grid size 128,128,128, pixel 1.82, shown at level 0.301, step 1, values float32 > volume #4 level 0.5582 > open /Users/luca/Downloads/cryosparc_P338_J149_004_volume_map_sharp.mrc Opened cryosparc_P338_J149_004_volume_map_sharp.mrc as #5, grid size 128,128,128, pixel 1.82, shown at level 0.314, step 1, values float32 > hide #!4 models > volume #5 level 0.8024 > show #!2 models > fitmap #2 inMap #5 Fit molecule 6n4o (#2) to map cryosparc_P338_J149_004_volume_map_sharp.mrc (#5) using 7064 atoms average map value = 0.5297, steps = 80 shifted from previous position = 2.7 rotated from previous position = 7.28 degrees atoms outside contour = 5392, contour level = 0.80242 Position of 6n4o (#2) relative to cryosparc_P338_J149_004_volume_map_sharp.mrc (#5) coordinates: Matrix rotation and translation -0.74089486 -0.42110233 0.52320898 125.49275417 -0.03059541 0.79937714 0.60005009 124.93352663 -0.67092379 0.42856623 -0.60513821 80.77151964 Axis -0.13523831 0.94173588 0.30796775 Axis point 79.70912723 0.00000000 -7.08664080 Rotation angle (degrees) 140.65368478 Shift along axis 125.55797880 > volume #5 level 0.4616 > volume #5 level 0.6182 > open /Users/luca/Downloads/cryosparc_P338_J146_005_volume_map_sharp.mrc Opened cryosparc_P338_J146_005_volume_map_sharp.mrc as #6, grid size 128,128,128, pixel 1.82, shown at level 0.363, step 1, values float32 > hide #!5 models > volume #6 level 0.4134 > open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb Chain information for ranked_0.pdb #7 --- Chain | Description A | No description available > close session > open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb > format pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > ui tool show ""AlphaFold Error Plot"" Must choose path to predicted aligned file > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/confidence_model_1_multimer_v3_pred_0.json JSON file ""/Users/luca/Documents/my_alphafold/230811_VEE- nsP1234_XtoG/confidence_model_1_multimer_v3_pred_0.json"" is not AlphaFold predicted aligned error data, expected a top level list > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/pae_model_1_multimer_v3_pred_0.json > color #1:511-1675 lime > color #1:1022-1022 lime > color #1:1978-1978 magenta > color #1:734-734 lime > color #1:1164-1164 magenta > color #1:557-557 lime > color #1:820-820 magenta > color #1:537-537 lime > color #1:754-754 magenta > color #1:511-992 lime > color #1:491-491 lime > color #1:506-506 magenta > color #1:56-289 lime > color #1:385-385 lime > color #1:486-486 magenta > color #1:1-501 lime > color #1:1270-1270 lime > color #1:537-537 magenta > color #1:466-466 lime > color #1:785-785 magenta > color #1:527-1675 lime > color #1:1073-1073 lime > color #1:1316-1316 magenta > color #1:1326-1508 lime > color #1:525-1674 lime > color #1:532-532 lime > color #1:1543-1543 magenta > color #1:1853-2491 lime > color #1:1853-1853 lime > color #1:2041-2041 magenta > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/features.pkl File /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/features.pkl does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold ""monomer"" preset does not compute PAE. Run AlphaFold with the ""monomer_ptm"" or ""multimer"" presets to get PAE values. > hide #1 models > show #1 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/pae_model_3_multimer_v3_pred_0.json > color #1:129-566 lime > color #1:896-896 lime > color #1:384-384 magenta > color #1:5-519 lime > color #1:634-634 lime > color #1:394-394 magenta > color #1:510-1689 lime > color #1:488-488 lime > color #1:677-677 magenta > color #1:492-1682 lime > color #1:1104-1104 lime > color #1:1974-1974 magenta > color #1:519-1671 lime > color #1:1863-2499 magenta > color #1:1148-1148 lime > color #1:2010-2010 magenta > color #1:532-1006 lime > color #1:1838-2494 magenta > color #1:1884-1884 lime > color #1:1808-1808 magenta > color #1:1818-2474 lime > color #1:1374-1374 lime > color #1:1641-1641 magenta > color #1:488-990 lime > color #1:116-116 lime > color #1:970-970 magenta > color #1:490-997 lime > color #1:390-390 lime > color #1:1788-1788 magenta > color #1:510-1689 lime > color #1:351-351 lime > color #1:854-854 magenta > color #1:1838-2499 lime > color #1:500-995 lime > color #1:448-448 lime > color #1:1863-1863 magenta > open /Users/luca/Downloads/cryosparc_P338_J141_003_volume_map_sharp.mrc Opened cryosparc_P338_J141_003_volume_map_sharp.mrc as #2, grid size 128,128,128, pixel 1.82, shown at level 0.35, step 1, values float32 > open /Users/luca/Downloads/cryosparc_P338_J141_003_volume_mask_refine.mrc Opened cryosparc_P338_J141_003_volume_mask_refine.mrc as #3, grid size 128,128,128, pixel 1.82, shown at level 1, step 1, values float32 > hide #1 models > volume #3 level 1 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 1 > volume #2 level 0.1019 > volume #2 level 0.08281 > open /Users/luca/Downloads/cryosparc_P338_J143_003_volume_map_sharp.mrc Opened cryosparc_P338_J143_003_volume_map_sharp.mrc as #4, grid size 128,128,128, pixel 1.82, shown at level 0.368, step 1, values float32 > hide #!2 models > volume #4 level 0.219 > volume #4 level 0.4265 > open 6n4o 6n4o title: Human Argonaute2-miR-122 bound to a seed and supplementary paired target [more info...] Chain information for 6n4o #5 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 C | RNA (5'-R(P*UP*GP*GP*AP*GP*UP*GP*UP*GP*AP*CP*AP*AP*UP*GP*GP*UP*GP*UP*UP*U)-3') | D | RNA (5'-R(*CP*CP*AP*UP*UP*GP*UP*CP*AP*CP*AP*CP*UP*CP*CP*AP*AP*A)-3') | > ui mousemode right zoom > ui mousemode right ""translate selected models"" > select add #5 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > view matrix models #5,1,0,0,91.347,0,1,0,108,0,0,1,173.46 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.8277,-0.36026,0.43027,85.377,-0.092838,0.84407,0.52813,126.13,-0.55344,0.39719,-0.73208,103.84 > fitmap #5 inMap #4 Fit molecule 6n4o (#5) to map cryosparc_P338_J143_003_volume_map_sharp.mrc (#4) using 7064 atoms average map value = 0.643, steps = 204 shifted from previous position = 45.4 rotated from previous position = 13.9 degrees atoms outside contour = 2486, contour level = 0.4265 Position of 6n4o (#5) relative to cryosparc_P338_J143_003_volume_map_sharp.mrc (#4) coordinates: Matrix rotation and translation -0.68599554 -0.51093406 0.51803139 128.74194912 -0.10048106 0.77166942 0.62803652 123.52402063 -0.72063422 0.37877790 -0.58070098 79.94218834 Axis -0.18762507 0.93238390 0.30896132 Axis point 85.80712635 0.00000000 -11.16278108 Rotation angle (degrees) 138.37545014 Shift along axis 115.71563536 > select subtract #5 Nothing selected > ui mousemode right zoom > volume #4 color silver > volume #4 color #c0c0c080 > volume #4 level 0.5261 > open /Users/luca/Documents/my_xray/hago2_af2_adjusted-and-aligned.pdb Chain information for hago2_af2_adjusted-and-aligned.pdb #6 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #!6 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 6n4o, chain A (#5) with hago2_af2_adjusted-and-aligned.pdb, chain A (#6), sequence alignment score = 4072.6 RMSD between 517 pruned atom pairs is 0.608 angstroms; (across all 796 pairs: 6.100) > matchmaker #!6 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 6n4o, chain A (#5) with hago2_af2_adjusted-and-aligned.pdb, chain A (#6), sequence alignment score = 4072.6 RMSD between 517 pruned atom pairs is 0.608 angstroms; (across all 796 pairs: 6.100) > hide #!5 models > hide #!6 models > show #!5 models > select add #5 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > show sel atoms > select subtract #5 Nothing selected > select add #5 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > hide sel atoms > select subtract #5 Nothing selected > molmap #6 4 Opened hago2_af2_adjusted-and-aligned.pdb map 4 as #7, grid size 70,88,79, pixel 1.33, shown at level 0.0977, step 1, values float32 > hide #!5 models > volume #7 level 0.5598 > volume #7 level 0.5872 > volume #4 level 0.6257 > volume #4 level 0.8083 > hide #!7 models > hide #!4 models > show #1 models > view > color #1:244-244 lime > color #1:1387-1387 magenta > color #1:67-67 lime > color #1:2143-2143 magenta > color #1:191-191 lime > color #1:862-862 magenta > alphafold pae #1 colorDomains true > color bfactor #1 palette alphafold 39157 atoms, 2499 residues, atom bfactor range 12.7 to 97 > color #1:505-1684 lime > color #1:510-1675 lime > color #1:1888-2499 magenta > color #1:435-435 lime > color #1:1905-1905 magenta > color #1:501-1020 lime > color #1:1894-2499 magenta > color #1:541-541 lime > color #1:501-501 magenta > color #1:1-537 lime > color #1:531-1006 lime > color #1:1028-1028 lime > color #1:1055-1055 magenta > color #1:997-1671 lime > color #1:1228-1228 lime > color #1:1410-1410 magenta > color #1:1317-1498 lime > color #1:1507-1667 lime > color #1:1835-2499 lime > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final > structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- > DFc_no_fill_no_fill.ccp4"" Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- DFc_no_fill_no_fill.ccp4 as #8, grid size 154,171,167, pixel 0.585,0.595,0.571, shown at level 3.14, step 1, values float32 > close #8 > color #1:488-1690 lime > color #1:510-1667 lime > color #1:1873-2499 magenta > color #1:466-466 lime > color #1:1881-1881 magenta > color #1:497-993 lime > color #1:1873-2499 magenta > open /Users/luca/Downloads/AF-Q9VUQ5-F1-model_v4.pdb AF-Q9VUQ5-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for protein argonaute-2 (Q9VUQ5) [more info...] Chain information for AF-Q9VUQ5-F1-model_v4.pdb #8 --- Chain | Description | UniProt A | protein argonaute-2 | AGO2_DROME 1-1214 > hide #8 models > show #!5 models > hide #1 models > show #8 models > ui tool show Matchmaker > matchmaker #8 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 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8), sequence alignment score = 1533.4 RMSD between 493 pruned atom pairs is 1.010 angstroms; (across all 756 pairs: 4.353) > matchmaker #8 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 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8), sequence alignment score = 1533.4 RMSD between 493 pruned atom pairs is 1.010 angstroms; (across all 756 pairs: 4.353) > view > hide #8 models Drag select of 116 residues, 5 pseudobonds > show #8 models > ui tool show Matchmaker > matchmaker #8 to #5 & sel 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 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8), sequence alignment score = 196.2 RMSD between 76 pruned atom pairs is 0.839 angstroms; (across all 100 pairs: 2.505) > matchmaker #8 to #5 & sel 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 6n4o, chain A (#5) with AF-Q9VUQ5-F1-model_v4.pdb, chain A (#8), sequence alignment score = 196.2 RMSD between 76 pruned atom pairs is 0.839 angstroms; (across all 100 pairs: 2.505) > select clear > hide #!5 models > hide #8 models > show #!5 models Drag select of 120 residues, 5 pseudobonds > show sel atoms > select clear > select add #5 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 3 models selected > hide sel cartoons > show #8 models > select add #8 16696 atoms, 17127 bonds, 38 pseudobonds, 2043 residues, 4 models selected > select subtract #5 9632 atoms, 9840 bonds, 1214 residues, 1 model selected > select subtract #8 Nothing selected Drag select of 406 atoms, 1 pseudobonds, 411 bonds, 77 residues > select clear Drag select of 953 atoms, 5 pseudobonds, 972 bonds, 12 shapes, 196 residues > show sel atoms > select add #5 8626 atoms, 7287 bonds, 38 pseudobonds, 1025 residues, 4 models selected > select subtract #5 1562 atoms, 196 residues, 1 model selected > select add #8 9632 atoms, 9840 bonds, 1214 residues, 1 model selected > select subtract #8 Nothing selected > select add #8 9632 atoms, 9840 bonds, 1214 residues, 1 model selected > hide sel cartoons > select clear Drag select of 130 atoms, 130 bonds Drag select of 9 atoms, 11 bonds > select clear Drag select of 135 atoms, 136 bonds > hide sel atoms Drag select of 247 atoms, 253 bonds > select clear Drag select of 249 atoms, 255 bonds > hide sel atoms Drag select of 2 atoms > hide sel atoms Drag select of 1853 atoms, 5 pseudobonds, 1899 bonds, 12 shapes > nucleotides sel atoms > style nucleic & sel stick Changed 75 atom styles > select clear > hide #8 models > select clear > select #5/C:18@C1' 1 atom, 1 residue, 1 model selected > select clear > select #5/B:17-18 Nothing selected > select #5/C:17-18 43 atoms, 47 bonds, 2 residues, 1 model selected > hide sel atoms > select clear > select #5/C 411 atoms, 457 bonds, 2 pseudobonds, 19 residues, 2 models selected > color #5/C cornflower blue > select clear > open /Users/luca/Documents/my_alphafold/230816_VEE-nsP123/230816_VEE- > nsP123_ranked_0.pdb Chain information for 230816_VEE-nsP123_ranked_0.pdb #9 --- Chain | Description A | No description available > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230816_VEE- > nsP123/pae_model_4_multimer_v3_pred_0.json Number of residues in structure ""ranked_0.pdb #1"" is 2499 which does not match PAE matrix size 1885. This can happen if chains were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error. > close #9 > close #1 > open /Users/luca/Documents/my_alphafold/230816_VEE-nsP123/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > ui tool show ""AlphaFold Error Plot"" Must choose structure to associate with predicted aligned error > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230816_VEE- > nsP123/pae_model_4_multimer_v3_pred_0.json > hide #1 models > hide #!5 models > show #1 models > view > color #1:525-993 lime > color #1:515-986 lime > color #1:1320-1668 magenta > color #1:525-986 lime > color #1:1019-1293 magenta > color #1:993-1624 lime > color #1:1170-1170 lime > color #1:1494-1498 magenta > color #1:983-1642 lime > color #1:1180-1180 lime > color #1:1511-1511 magenta > color #1:542-970 lime > color #1:976-1280 magenta > color #1:970-970 lime > color #1:1280-1280 magenta > color #1:455-719 lime > color #1:836-1080 magenta > color #1:425-425 lime > color #1:1150-1150 magenta > color #1:540-990 lime > color #1:996-1314 lime > color #1:539-1314 lime > color #1:989-1658 lime > close #1 > open /Users/luca/Documents/my_alphafold/230811_VEE-nsP1234_XtoG/ranked_0.pdb Chain information for ranked_0.pdb #1 --- Chain | Description A | No description available > open /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json confidence_model_3_multimer_v3_pred_0.json does not look like Mole Online json file, does not contain Channels. > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json JSON file ""/Users/luca/Documents/my_alphafold/230811_VEE- nsP1234_XtoG/confidence_model_3_multimer_v3_pred_0.json"" is not AlphaFold predicted aligned error data, expected a top level list > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file /Users/luca/Documents/my_alphafold/230811_VEE- > nsP1234_XtoG/pae_model_3_multimer_v3_pred_0.json > color #1:510-984 lime > color #1:1884-2484 magenta > hide #1 models > show #8 models > show #!5 models > view > zone #5/C:21 > view > hide #5 > hide #5 cartoons > zone #5/C:21 > hide #5 cartoons > zone #5/C:21 residueDistance 10 > select add #5 7064 atoms, 7287 bonds, 38 pseudobonds, 829 residues, 4 models selected > hide sel cartoons > select subtract #5 Nothing selected > open /Users/luca/Downloads/AF-B4ESF5-F1-model_v4.pdb AF-B4ESF5-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for papain-like cysteine proteinase (B4ESF5) [more info...] Chain information for AF-B4ESF5-F1-model_v4.pdb #9 --- Chain | Description | UniProt A | papain-like cysteine proteinase | B4ESF5_HORVV 1-355 > hide #!5 models > hide #8 models > show #1 models > view > ui tool show Matchmaker > matchmaker #9 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 ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A (#9), sequence alignment score = 88.1 RMSD between 12 pruned atom pairs is 1.304 angstroms; (across all 297 pairs: 63.656) > matchmaker #9 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 ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A (#9), sequence alignment score = 88.1 RMSD between 12 pruned atom pairs is 1.304 angstroms; (across all 297 pairs: 63.656) > color #1:503-1254 lime > color #1:510-989 lime > select #1:500-990 7694 atoms, 7772 bonds, 491 residues, 1 model selected > select #1:500-900 6269 atoms, 6329 bonds, 401 residues, 1 model selected > select #1:600-900 4764 atoms, 4812 bonds, 301 residues, 1 model selected > select #1:550-900 5537 atoms, 5593 bonds, 351 residues, 1 model selected > ui tool show Matchmaker > matchmaker #9 to #1 & sel 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 ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A (#9), sequence alignment score = 13.4 RMSD between 8 pruned atom pairs is 1.211 angstroms; (across all 225 pairs: 30.953) > matchmaker #9 to #1 & sel 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 ranked_0.pdb, chain A (#1) with AF-B4ESF5-F1-model_v4.pdb, chain A (#9), sequence alignment score = 13.4 RMSD between 8 pruned atom pairs is 1.211 angstroms; (across all 225 pairs: 30.953) > hide #9 models > show #9 models > hide #9 models > select #1:510,511,546,706 69 atoms, 67 bonds, 4 residues, 1 model selected > color #1:510,511,546,706 firebrick > color #1:204-204 lime > color #1:1310-1310 magenta > select #1:510,511,546,706 firebrick Expected a keyword > select #1:510,511,546,706 69 atoms, 67 bonds, 4 residues, 1 model selected > select clear > select #1:510,511,546,706 69 atoms, 67 bonds, 4 residues, 1 model selected > view #1:536 > open /Users/luca/Documents/my_alphafold/230819_VEE-nsP2/ranked_0.pdb Chain information for ranked_0.pdb #10 --- Chain | Description A | No description available > view > hide #1 models > hide #10 models > show #10 models > show #1 models > ui tool show Matchmaker > matchmaker #10 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 ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#10), sequence alignment score = 3912 RMSD between 529 pruned atom pairs is 0.841 angstroms; (across all 794 pairs: 2.898) > matchmaker #10 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 ranked_0.pdb, chain A (#1) with ranked_0.pdb, chain A (#10), sequence alignment score = 3912 RMSD between 529 pruned atom pairs is 0.841 angstroms; (across all 794 pairs: 2.898) > select clear > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > open /Users/luca/Documents/my_alphafold/230821_VEE-nsP1/230821_VEE- > nsP1_ranked_0.pdb Chain information for 230821_VEE-nsP1_ranked_0.pdb #11 --- Chain | Description A | No description available > ui tool show Matchmaker > matchmaker #11 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 ranked_0.pdb, chain A (#1) with 230821_VEE-nsP1_ranked_0.pdb, chain A (#11), sequence alignment score = 2645.2 RMSD between 452 pruned atom pairs is 0.424 angstroms; (across all 535 pairs: 30.415) > show #1 models > hide #1 models > show #1 models > hide #1 models > close session > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final > structures and maps/unmod YX_Ago2-122-21mer_refine_2.pdb"" Chain information for unmod YX_Ago2-122-21mer_refine_2.pdb #1 --- Chain | Description A | No description available B | No description available > set bgColor white > set bgColor #ffffff00 > lighting soft > select #1/B 219 atoms, 242 bonds, 1 pseudobond, 11 residues, 2 models selected > hide sel cartoons > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 219 atom styles > select clear > hide pseudobonds > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final > structures and maps/unmod YX_Ago2-122-21mer_refine_2_2mFo- > DFc_no_fill_no_fill.ccp4"" Opened unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size 194,236,212, pixel 0.468,0.449,0.459, shown at level 3.26, step 1, values float32 > volume cover #2 atomBox #1 Extended map unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 to box of size (182, 223, 198), cell size (135, 240, 150) grid points, 1 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 0 Opened unmod YX_Ago2-122-21mer_refine_2_2mFo-DFc_no_fill_no_fill.ccp4 extended as #3, grid size 182,223,198, pixel 0.468,0.449,0.459, shown at step 1, values float32 > close #2 > volume zone #3 nearAtoms #1 range 5 > volume #3 level 1.5 > volume #3 style mesh > volume #3 color #76d6ff > volume zone #3 nearAtoms #1/B range 5 > volume zone #3 nearAtoms #1/B range 2 > volume zone #3 nearAtoms #1/B:21 range 5 > volume zone #3 nearAtoms #1/B:21 range 10 > color #1/A silver > color #1/B firebrick > view > view name front > volume zone #3 nearAtoms #1/B:21 range 5 > volume zone #3 nearAtoms #1/B:21 range 8 > volume zone #3 nearAtoms #1/B:21 range 7 > select (intersect) zone #1/B:21 8 Expected an objects specifier or a keyword > select zone #1/B:21 8 Selected 203 atoms, 1 surfaces > select zone #1/B:21 8 AND #1A Expected an objects specifier or a keyword > select zone #1/B:21 8,#1A Missing or invalid ""range"" argument: Expected a number > select zone #1/B:21 8 & #1/A Expected an objects specifier or a keyword > select intersect zone #1/B:21 8 & #1/A Missing or invalid ""objects"" argument: invalid objects specifier > select intersect (zone #1/B:21 8 & #1/A) Missing or invalid ""objects"" argument: invalid objects specifier > select zone #1/B:21 8 & #1/A Expected an objects specifier or a keyword > select #1/B & :21 20 atoms, 21 bonds, 1 residue, 1 model selected > select (zone #1/B:21 5) & #1/A Expected an objects specifier or a keyword > select (zone #1/B:21 5) Expected an objects specifier or a keyword > select zone #1/B:21 5 Selected 76 atoms, 1 surfaces > select zone #1/B:21 5 & #1/A Expected an objects specifier or a keyword > select #1/A & zone #1/B:21 5 Expected a keyword > select zone #1/B:21 5 Selected 76 atoms, 1 surfaces > select intersect #1/A 59 atoms, 14 residues, 1 model selected > show sel atoms > view name PAZ-view > select zone #1/B:21 5 residues Missing ""residues"" keyword's argument > select zone #1/B:21 5 residues true Selected 154 atoms, 1 surfaces > select intersect #1/A 133 atoms, 14 residues, 1 model selected > show sel atoms > ~select Nothing selected > rename #3 id #2 > save ""/Users/luca/Desktop/230822 modified siRNAs session.cxs"" includeMaps > true > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final > structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34.pdb"" Chain information for ON1 apo-Ago_dials_220928_509_A9_r2_refine_34.pdb #3 --- Chain | Description A | No description available B | No description available > open ""/Users/luca/Dropbox (Scripps Research)/Modified_Guides/final > structures and maps/ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- > DFc_no_fill_no_fill.ccp4"" Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- DFc_no_fill_no_fill.ccp4 as #4, grid size 154,171,167, pixel 0.585,0.595,0.571, shown at level 3.14, step 1, values float32 > volume cover #4 atomBox #3 Extended map ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- DFc_no_fill_no_fill.ccp4 to box of size (146, 165, 159), cell size (108, 180, 120) grid points, 1 symmetry operations, 0 points not covered by any symmetry, maximum value difference where symmetric map copies overlap = 0 Opened ON1 apo-Ago_dials_220928_509_A9_r2_refine_34_2mFo- DFc_no_fill_no_fill.ccp4 extended as #5, grid size 146,165,159, pixel 0.585,0.595,0.571, shown at step 1, values float32 > volume zone #5 nearAtoms #3/B:21 range 8 > close #4 > rename #5 id #4 > volume #4 level 1.5 > volume #4 style mesh > color #3/A dim grey > color #3/B sea green > color #3/B dark orange > hide #!1 models > hide #!2 models > select #3/A 6386 atoms, 6534 bonds, 7 pseudobonds, 795 residues, 2 models selected > hide sel atoms > select zone #3/B:21 5 residues true Selected 327 atoms, 2 surfaces > select intersect #3/A 147 atoms, 16 residues, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide pseudobonds > view PAZ-view > view name PAZ-view > hide #!3 models > hide #!4 models > show #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > show #!3 models > hide #!3 models > show #!2 models > show #!4 models > show #!3 models > hide #!2 models > hide #!1 models > hide #!3 models > hide #!4 models > show #!1 models > show #!2 models > save ""/Users/luca/Desktop/230822 WT-PAZ-view.jpg"" width 1344 height 908 > supersample 3 > hide #!2 models > show #!3 models > show #!4 models > hide #!1 models > save ""/Users/luca/Desktop/230822 ON1-PAZ-view.jpg"" width 1344 height 908 > supersample 3 > hide #!3 models > show #!2 models > show #!3 models > show #!1 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!1 models > view PAZ-view > select #1/A 6497 atoms, 6650 bonds, 4 pseudobonds, 810 residues, 2 models selected > hide sel atoms > hide sel cartoons > volume zone #2 nearAtoms #1/B:21 range 1 > volume zone #2 nearAtoms #1/B:21 range 2 > volume zone #2 nearAtoms #1/B:21 range 1.5 > select #1/B:22 Nothing selected > select #1/B:20 20 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > view name nucleotide > hide #!1 models > hide #!2 models > show #!3 models > show #!4 models > select up 219 atoms, 242 bonds, 11 residues, 1 model selected > select #3/A 6386 atoms, 6534 bonds, 7 pseudobonds, 795 residues, 2 models selected > hide sel cartoons > hide sel atoms > volume zone #4 nearAtoms #3/B:21 range 1.5 > show #!1 models > show #!2 models > hide #!4 models > hide #!3 models > save ""/Users/luca/Desktop/230822 WT-nt21-view.jpg"" width 1344 height 908 > supersample 3 > hide #!2 models > hide #!1 models > show #!3 models > show #!4 models > save ""/Users/luca/Desktop/230822 ON1-nt21-view.jpg"" width 1344 height 908 > supersample 3 > show #!1 models > show #!2 models > select #1/A 6497 atoms, 6650 bonds, 4 pseudobonds, 810 residues, 2 models selected > show sel cartoons > select #1/,3A Expected an objects specifier or a keyword > select #1,3/A 12883 atoms, 13184 bonds, 11 pseudobonds, 1605 residues, 4 models selected > show sel cartoons > select zone #3/B:21 5 residues true Selected 327 atoms, 2 surfaces > select intersect #3/A 147 atoms, 16 residues, 1 model selected > show sel atoms > select zone #1/B:21 5 residues true Selected 298 atoms, 2 surfaces > select intersect #1/A 133 atoms, 14 residues, 1 model selected > show sel atoms > select clear > open 4w5n Summary of feedback from opening 4w5n fetched from pdb --- note | Fetching compressed mmCIF 4w5n from http://files.rcsb.org/download/4w5n.cif 4w5n title: The Crystal Structure of Human Argonaute2 Bound to a Defined Guide RNA [more info...] Chain information for 4w5n #5 --- Chain | Description | UniProt A | Protein argonaute-2 | AGO2_HUMAN 1-859 B | RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*CP*AP*AP*GP*UP*CP*UP*CP*UP*U)-3') | Non-standard residues in 4w5n #5 --- IPH — phenol MG — magnesium ion > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models Drag select of 112 atoms, 104 residues, 107 bonds > ui tool show Matchmaker > matchmaker #!5 to #1 & sel 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 unmod YX_Ago2-122-21mer_refine_2.pdb, chain A (#1) with 4w5n, chain A (#5), sequence alignment score = 523 RMSD between 100 pruned atom pairs is 0.414 angstroms; (across all 102 pairs: 0.544) > show #!5 models > select #5/B 360 atoms, 392 bonds, 1 pseudobond, 23 residues, 2 models selected > hide sel cartoons > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 355 atom styles > hide waters Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ligands Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select clear > hide pseudobonds > hide #!1 models > select zone #5/B:21 5 residues true Selected 480 atoms, 2 surfaces > select intersect #5/A 124 atoms, 13 residues, 1 model selected > show sel atoms > select clear > select zone #5/B:21 5 residues true Selected 480 atoms, 2 surfaces > select intersect #5:cys Nothing selected > select zone #5/B:21 20 residues true Selected 2792 atoms, 2 surfaces > select intersect #5:cys 30 atoms, 5 residues, 1 model selected > show sel atoms > color sel yellow > select clear > view #5/B:21 > ui tool show ""Side View"" Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 83.1 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: MacBookPro18,4 Model Number: MKH53LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 41 days, 13 hours, 42 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: 3024 x 1964 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-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: 2022.9.26 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