id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17037 Mac multi-display crash chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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coral ; > color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7 > #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA > alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3 > darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color > $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff > alias removeatom select main ; style stick ; color sel byhetero ; hide sel > atoms ; show sel cartoons ; select clear > alias showATP select ::name=""ATP"" ; show sel ; color sel byhetero ; select > clear > alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color > byhetero ; show cartoons ; select clear ; select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" > ; hide sel atoms ; select clear > lighting soft UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/apo_ylORC1-6_autoinhibited_O1AAA/fragmented from > 2.3A map/apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc"" Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc as #1, grid size 100,75,99, pixel 0.827,0.827,0.827, shown at level 0.351, step 1, values float32 > volume #1 level 0.09834 > volume #1 level 0.1 > ui mousemode right ""map eraser"" > volume erase #1 center 163.89,176.39,145.09 radius 12.448 Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy as #3, grid size 100,75,99, pixel 0.827,0.827,0.827, shown at step 1, values float32 > volume erase #3 center 160.72,178.6,147.14 radius 25.099 > volume erase #3 center 153.84,165.37,159.35 radius 25.099 > volume erase #3 center 186.28,218.17,168.98 radius 18.318 > volume erase #3 center 177.17,206.22,131.59 radius 34.403 > volume erase #3 center 218.68,194.01,175.8 radius 34.403 > volume erase #3 center 189.93,162.62,149.15 radius 34.403 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/ylODC_54bp- > oriC061_complete/ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc"" Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc as #2, grid size 440,440,440, pixel 0.827, shown at level 0.0339, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1 > ui mousemode right select > select #3 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-6.5437,0,1,0,-39.682,0,0,1,32.694 > view matrix models #3,1,0,0,63.882,0,1,0,-59.979,0,0,1,-62.393 > view matrix models #3,1,0,0,38.347,0,1,0,-95.198,0,0,1,-13.033 > view matrix models #3,1,0,0,16.509,0,1,0,-66.14,0,0,1,-0.99619 > view matrix models #3,1,0,0,20.128,0,1,0,-62.33,0,0,1,-2.0463 > close #1 > fitmap #3 inMap #2 Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points correlation = 0.9405, correlation about mean = 0.5992, overlap = 241.7 steps = 200, shift = 2.29, angle = 36.2 degrees Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3) relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates: Matrix rotation and translation 0.84572459 -0.49295295 0.20432158 104.99315114 0.53093078 0.81572589 -0.22957303 -70.02432300 -0.05350170 0.30263617 0.95160334 -43.34359941 Axis 0.45011126 0.21805178 0.86594069 Axis point 185.17878159 160.09585855 0.00000000 Rotation angle (degrees) 36.24202405 Shift along axis -5.54331477 > ui mousemode right select > select clear > vop resample #3 onGrid #2 Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > volume #1 level 0.0764 > volume #1 level 0.1 > volume #1 level 0.15 > volume #2 level 0.05442 > volume #2 level 0.1 > select #1 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.99933,-0.018848,0.031243,-3.0076,0.018589,0.99979,0.0085722,-4.9693,-0.031398,-0.0079858,0.99948,6.9845 > fitmap #3 inMap #2 Fit map apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy in map ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc using 11600 points correlation = 0.9405, correlation about mean = 0.5991, overlap = 241.7 steps = 160, shift = 0.0161, angle = 0.0151 degrees Position of apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy (#3) relative to ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc (#2) coordinates: Matrix rotation and translation 0.84577508 -0.49297133 0.20406808 105.02263727 0.53087390 0.81574712 -0.22962913 -70.01411447 -0.05326738 0.30254901 0.95164420 -43.38215291 Axis 0.45014347 0.21766749 0.86602062 Axis point 185.20083727 160.15397652 0.00000000 Rotation angle (degrees) 36.23656846 Shift along axis -5.53438078 > ui mousemode right select > select #3 2 models selected > volume #3 level 0.15 > ui mousemode right ""rotate selected models"" > ui mousemode right select > select clear > close #1 > vop resample #3 onGrid #2 Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled as #1, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > volume #1 level 0.2 > volume #1 level 0.15 > vop flip #1 Opened apo_O1-6_O1AAA_J112_2.3A_FLIPPED_Orc2density.mrc copy resampled z flip as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > vop flip #2 Opened ODC_SEC_54bpOriC061_P370_J300_FLIPPED.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > save /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/High-Res-ORC2WHD- > mask_BASE_notBinary.mrc models #4 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"" Opened cryosparc_frame4_J411_003_volume_map.mrc as #6, grid size 440,440,440, pixel 0.827, shown at level 0.0169, step 2, values float32 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/frame2_J413.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/cryosparc_P370_J410_005_volume_map.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/cryosparc_frame4_J411_003_volume_map.mrc"" Opened frame2_J413.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at level 0.022, step 2, values float32 Opened cryosparc_P370_J410_005_volume_map.mrc as #1.2, grid size 440,440,440, pixel 0.827, shown at level 0.019, step 2, values float32 Opened cryosparc_frame4_J411_003_volume_map.mrc as #1.3, grid size 440,440,440, pixel 0.827, shown at level 0.0169, step 2, values float32 > vop step 1 > vop level 0.1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/ylORC1-6_oriC061_OPEN_noO1AAA/ORC- > OPEN_DNA_P370_J167_FLIPPED.mrc"" Opened ORC-OPEN_DNA_P370_J167_FLIPPED.mrc as #2, grid size 440,440,440, pixel 0.827, shown at level 0.0182, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1 > vop flip #1 Opened frame2_J413.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened cryosparc_P370_J410_005_volume_map.mrc z flip as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened cryosparc_frame4_J411_003_volume_map.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #1#1.1-3 > fitmap #3 inMap #2 Fit map frame2_J413.mrc z flip in map ORC-OPEN_DNA_P370_J167_FLIPPED.mrc using 209824 points correlation = 0.8749, correlation about mean = 0.6459, overlap = 5044 steps = 348, shift = 6.71, angle = 15.5 degrees Position of frame2_J413.mrc z flip (#3) relative to ORC- OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates: Matrix rotation and translation 0.97446697 0.02860606 0.22270119 -35.49808469 0.00472647 0.98901775 -0.14772120 23.54512380 -0.22448115 0.14500202 0.96362992 17.88035991 Axis 0.54714223 0.83584876 -0.04463441 Axis point 52.95063289 0.00000000 164.14097100 Rotation angle (degrees) 15.51567190 Shift along axis -0.54041832 > fitmap #4 inMap #2 Fit map cryosparc_P370_J410_005_volume_map.mrc z flip in map ORC- OPEN_DNA_P370_J167_FLIPPED.mrc using 160211 points correlation = 0.9112, correlation about mean = 0.6738, overlap = 4054 steps = 220, shift = 2.82, angle = 8.58 degrees Position of cryosparc_P370_J410_005_volume_map.mrc z flip (#4) relative to ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates: Matrix rotation and translation 0.99234355 -0.00562414 0.12338008 -16.99642910 0.01597062 0.99641901 -0.08303075 10.54881173 -0.12247128 0.08436548 0.98887980 8.05853927 Axis 0.56133195 0.82441655 0.07241400 Axis point 53.25288131 0.00000000 139.87627102 Rotation angle (degrees) 8.57513729 Shift along axis -0.26047268 > fitmap #5 inMap #2 Fit map cryosparc_frame4_J411_003_volume_map.mrc z flip in map ORC- OPEN_DNA_P370_J167_FLIPPED.mrc using 154100 points correlation = 0.9198, correlation about mean = 0.6573, overlap = 4122 steps = 120, shift = 1.21, angle = 4.97 degrees Position of cryosparc_frame4_J411_003_volume_map.mrc z flip (#5) relative to ORC-OPEN_DNA_P370_J167_FLIPPED.mrc (#2) coordinates: Matrix rotation and translation 0.99738968 -0.01045075 0.07144651 -9.18473790 0.01387007 0.99877345 -0.04753118 5.34475067 -0.07086214 0.04839807 0.99631129 4.38863766 Axis 0.55342664 0.82099463 0.14030953 Axis point 55.32397495 0.00000000 129.96106991 Rotation angle (degrees) 4.97197356 Shift along axis -0.07929937 > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!5 models > hide #!2 models > show #!4 models > show #!3 models > hide #!5 models > volume #3 level 0.171 > volume #4 level 0.1381 > volume #4 level 0.1 > volume #3 level 0.1 > hide #!3 models > show #!3 models > volume #3 level 0.1121 > volume #3 level 0.08 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylORC1-6_oriC061_closed_noO1AAA/ORC-DNA-closed- > noCdc6-noO1AAA_rev2_sidechains-not-done.pdb"" Chain information for ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not- done.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available H | No description available I | No description available > modelfix Changed 18185 atom styles 16772 atoms, 17104 bonds, 8 pseudobonds, 2086 residues, 2 models selected > hide #!1 models > show #!1 models > fitmap #1 inMap #3 Fit molecule ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1) to map frame2_J413.mrc z flip (#3) using 18185 atoms average map value = 0.1748, steps = 108 shifted from previous position = 3.5 rotated from previous position = 6.13 degrees atoms outside contour = 2411, contour level = 0.08 Position of ORC-DNA-closed-noCdc6-noO1AAA_rev2_sidechains-not-done.pdb (#1) relative to frame2_J413.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99078521 -0.01123591 -0.13497562 25.44161891 0.02375867 0.99551894 0.09152899 -17.35760278 0.13334237 -0.09389241 0.98661240 -3.43448090 Axis -0.56526644 -0.81798084 0.10668273 Axis point 43.71104119 0.00000000 183.20504019 Rotation angle (degrees) 9.43986719 Shift along axis -0.54950672 > select /C:220 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select /D:157 7 atoms, 6 bonds, 1 residue, 1 model selected > select /D:171 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > volume #3 level 0.06943 > close #1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"" Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > modelfix Changed 25299 atom styles 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected > fitmap #1 inMap #3 Fit molecule ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) to map frame2_J413.mrc z flip (#3) using 25299 atoms average map value = 0.124, steps = 184 shifted from previous position = 4.41 rotated from previous position = 6.1 degrees atoms outside contour = 9398, contour level = 0.06943 Position of ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) relative to frame2_J413.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99093954 -0.00429549 -0.13423996 23.99797706 0.01699922 0.99546171 0.09363235 -16.70012343 0.13322855 -0.09506597 0.98651539 -3.03142526 Axis -0.57525720 -0.81539242 0.06491808 Axis point 40.21853239 0.00000000 174.40638339 Rotation angle (degrees) 9.43985245 Shift along axis -0.38464920 > select /D:168 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > volume #3 level 0.06037 > select clear Unsupported scale factor (0.000000) detected on Display0 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects- > maps/apo_ylORC1-6_autoinhibited_O1AAA/cryosparc_P370_J421_map_sharp.mrc"" Opened cryosparc_P370_J421_map_sharp.mrc as #6, grid size 480,480,480, pixel 0.84, shown at level 0.0726, step 2, values float32 > hide #!1 models > volume #6 step 1 > volume #6 level 0.1165 > volume #6 level 0.2042 > vop flip #6 Opened cryosparc_P370_J421_map_sharp.mrc z flip as #7, grid size 480,480,480, pixel 0.84, shown at step 1, values float32 > close #6 > volume #7 level 0.2919 > volume #7 level 0.2656 > close #7 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_024.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_023.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_022.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_021.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_020.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_019.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_018.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_017.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_016.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_015.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_014.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_013.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_012.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_011.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_010.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_009.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_008.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_007.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_006.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_005.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_004.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_003.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_002.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_001.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_000/J407_component_000_frame_000.mrc"" Opened J407_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at level 0.0246, step 2, values float32 Opened J407_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel 0.827, shown at level 0.0247, step 2, values float32 Opened J407_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel 0.827, shown at level 0.0246, step 2, values float32 Opened J407_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel 0.827, shown at level 0.0248, step 2, values float32 Opened J407_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel 0.827, shown at level 0.025, step 2, values float32 Opened J407_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel 0.827, shown at level 0.0253, step 2, values float32 Opened J407_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel 0.827, shown at level 0.0256, step 2, values float32 Opened J407_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel 0.827, shown at level 0.0259, step 2, values float32 Opened J407_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel 0.827, shown at level 0.0262, step 2, values float32 Opened J407_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel 0.827, shown at level 0.0265, step 2, values float32 Opened J407_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel 0.827, shown at level 0.0267, step 2, values float32 Opened J407_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel 0.827, shown at level 0.0268, step 2, values float32 Opened J407_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel 0.827, shown at level 0.0269, step 2, values float32 Opened J407_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel 0.827, shown at level 0.0269, step 2, values float32 Opened J407_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel 0.827, shown at level 0.0268, step 2, values float32 Opened J407_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel 0.827, shown at level 0.0266, step 2, values float32 Opened J407_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel 0.827, shown at level 0.0265, step 2, values float32 Opened J407_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel 0.827, shown at level 0.0263, step 2, values float32 Opened J407_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel 0.827, shown at level 0.0261, step 2, values float32 Opened J407_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel 0.827, shown at level 0.026, step 2, values float32 Opened J407_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel 0.827, shown at level 0.0258, step 2, values float32 Opened J407_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel 0.827, shown at level 0.0257, step 2, values float32 Opened J407_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel 0.827, shown at level 0.0257, step 2, values float32 Opened J407_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel 0.827, shown at level 0.0257, step 2, values float32 Opened J407_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel 0.827, shown at level 0.0258, step 2, values float32 > vop step 1 > vop level 0.1 > fitmap #1.2 inMap #1.1 Fit map J407_component_000_frame_023.mrc in map J407_component_000_frame_024.mrc using 209250 points correlation = 0.9997, correlation about mean = 0.998, overlap = 8175 steps = 44, shift = 0.00683, angle = 0.0107 degrees Position of J407_component_000_frame_023.mrc (#1.2) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999999 -0.00012647 -0.00005333 0.03293876 0.00012647 0.99999998 0.00012643 -0.05198641 0.00005331 -0.00012643 0.99999999 0.01305327 Axis -0.67751845 -0.28572825 0.67773749 Axis point 407.94854492 267.83546595 0.00000000 Rotation angle (degrees) 0.01069187 Shift along axis 0.00138407 > fitmap #1.3 inMap #1.1 Fit map J407_component_000_frame_022.mrc in map J407_component_000_frame_024.mrc using 203717 points correlation = 0.9986, correlation about mean = 0.9908, overlap = 7802 steps = 40, shift = 0.0172, angle = 0.0261 degrees Position of J407_component_000_frame_022.mrc (#1.3) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999990 -0.00019261 -0.00039264 0.12474433 0.00019266 0.99999997 0.00012757 -0.06314784 0.00039262 -0.00012765 0.99999991 -0.04255682 Axis -0.28010520 -0.86182612 0.42284371 Axis point 110.06260037 0.00000000 318.73939640 Rotation angle (degrees) 0.02610266 Shift along axis 0.00148604 > fitmap #1.4 inMap #1.1 Fit map J407_component_000_frame_021.mrc in map J407_component_000_frame_024.mrc using 198335 points correlation = 0.9964, correlation about mean = 0.9756, overlap = 7418 steps = 44, shift = 0.0346, angle = 0.0352 degrees Position of J407_component_000_frame_021.mrc (#1.4) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999985 -0.00028033 -0.00047313 0.15686283 0.00028046 0.99999992 0.00027270 -0.11547011 0.00047306 -0.00027283 0.99999985 -0.00564243 Axis -0.44433259 -0.77067092 0.45676569 Axis point 28.17446960 0.00000000 347.22791612 Rotation angle (degrees) 0.03517232 Shift along axis 0.01671292 > fitmap #1.5 inMap #1.1 Fit map J407_component_000_frame_020.mrc in map J407_component_000_frame_024.mrc using 193267 points correlation = 0.9926, correlation about mean = 0.9494, overlap = 7047 steps = 60, shift = 0.0446, angle = 0.0543 degrees Position of J407_component_000_frame_020.mrc (#1.5) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999970 -0.00057369 -0.00052292 0.22913926 0.00057398 0.99999969 0.00054339 -0.22570178 0.00052261 -0.00054369 0.99999972 0.04101180 Axis -0.57357699 -0.55165719 0.60554420 Axis point 376.23364392 417.12641997 0.00000000 Rotation angle (degrees) 0.05429535 Shift along axis 0.01791546 > fitmap #1.6 inMap #1.1 Fit map J407_component_000_frame_019.mrc in map J407_component_000_frame_024.mrc using 188984 points correlation = 0.9863, correlation about mean = 0.9083, overlap = 6678 steps = 48, shift = 0.0575, angle = 0.0736 degrees Position of J407_component_000_frame_019.mrc (#1.6) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999937 -0.00074520 -0.00084161 0.32749078 0.00074572 0.99999953 0.00062002 -0.28019774 0.00084115 -0.00062065 0.99999945 0.00597028 Axis -0.48315481 -0.65532311 0.58061438 Axis point 13.08513741 0.00000000 405.67912733 Rotation angle (degrees) 0.07356325 Shift along axis 0.02885774 > fitmap #1.7 inMap #1.1 Fit map J407_component_000_frame_018.mrc in map J407_component_000_frame_024.mrc using 185458 points correlation = 0.976, correlation about mean = 0.8493, overlap = 6310 steps = 48, shift = 0.0664, angle = 0.101 degrees Position of J407_component_000_frame_018.mrc (#1.7) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999880 -0.00101281 -0.00116866 0.44242428 0.00101380 0.99999913 0.00084596 -0.38421046 0.00116780 -0.00084714 0.99999896 -0.01109545 Axis -0.48017506 -0.66263457 0.57475851 Axis point 27.45801527 0.00000000 393.24528287 Rotation angle (degrees) 0.10101276 Shift along axis 0.03577283 > fitmap #1.8 inMap #1.1 Fit map J407_component_000_frame_017.mrc in map J407_component_000_frame_024.mrc using 183289 points correlation = 0.9601, correlation about mean = 0.7729, overlap = 5913 steps = 48, shift = 0.0993, angle = 0.147 degrees Position of J407_component_000_frame_017.mrc (#1.8) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999771 -0.00151197 -0.00151334 0.63051172 0.00151411 0.99999786 0.00140855 -0.58580425 0.00151121 -0.00141083 0.99999786 0.05858363 Axis -0.55024534 -0.59028684 0.59058573 Axis point 374.46052800 428.62087361 0.00000000 Rotation angle (degrees) 0.14678795 Shift along axis 0.03345506 > fitmap #1.9 inMap #1.1 Fit map J407_component_000_frame_016.mrc in map J407_component_000_frame_024.mrc using 182675 points correlation = 0.9355, correlation about mean = 0.6834, overlap = 5515 steps = 60, shift = 0.127, angle = 0.201 degrees Position of J407_component_000_frame_016.mrc (#1.9) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999541 -0.00199889 -0.00227570 0.88265488 0.00200291 0.99999644 0.00176426 -0.75951590 0.00227217 -0.00176881 0.99999585 0.00414204 Axis -0.50380000 -0.64850507 0.57063713 Axis point 11.52035137 0.00000000 398.95768312 Rotation angle (degrees) 0.20090381 Shift along axis 0.05023198 > fitmap #1.10 inMap #1.1 Fit map J407_component_000_frame_015.mrc in map J407_component_000_frame_024.mrc using 183507 points correlation = 0.9007, correlation about mean = 0.5875, overlap = 5095 steps = 64, shift = 0.173, angle = 0.289 degrees Position of J407_component_000_frame_015.mrc (#1.10) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99999101 -0.00276858 -0.00321317 1.22924900 0.00277736 0.99999241 0.00273204 -1.11683070 0.00320558 -0.00274094 0.99999111 0.04432005 Axis -0.54214099 -0.63582814 0.54936848 Axis point -1.07295593 0.00000000 394.04766813 Rotation angle (degrees) 0.28920482 Shift along axis 0.06803416 > fitmap #1.11 inMap #1.1 Fit map J407_component_000_frame_014.mrc in map J407_component_000_frame_024.mrc using 185464 points correlation = 0.8576, correlation about mean = 0.4935, overlap = 4658 steps = 68, shift = 0.257, angle = 0.451 degrees Position of J407_component_000_frame_014.mrc (#1.11) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99997838 -0.00387997 -0.00530947 1.90413629 0.00390287 0.99998310 0.00431009 -1.66245856 0.00529266 -0.00433072 0.99997662 0.00352928 Axis -0.54908908 -0.67372352 0.49456830 Axis point 8.07677421 0.00000000 366.48177817 Rotation angle (degrees) 0.45082580 Shift along axis 0.07624247 > fitmap #1.12 inMap #1.1 Fit map J407_component_000_frame_013.mrc in map J407_component_000_frame_024.mrc using 188095 points correlation = 0.8117, correlation about mean = 0.4088, overlap = 4242 steps = 72, shift = 0.438, angle = 0.846 degrees Position of J407_component_000_frame_013.mrc (#1.12) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99992647 -0.00628818 -0.01036874 3.45771106 0.00637521 0.99994455 0.00838211 -2.99419606 0.01031546 -0.00844760 0.99991111 -0.07122117 Axis -0.57011020 -0.70068168 0.42897500 Axis point 13.82106219 -0.00000000 338.66317537 Rotation angle (degrees) 0.84571953 Shift along axis 0.09614987 > fitmap #1.13 inMap #1.1 Fit map J407_component_000_frame_012.mrc in map J407_component_000_frame_024.mrc using 190432 points correlation = 0.826, correlation about mean = 0.4787, overlap = 4037 steps = 116, shift = 2.59, angle = 5.32 degrees Position of J407_component_000_frame_012.mrc (#1.13) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99693363 -0.00485375 -0.07810112 18.39674331 0.00874835 0.99873077 0.04960155 -12.12187935 0.07776124 -0.05013271 0.99571075 -3.59284498 Axis -0.53753568 -0.84004816 0.07331093 Axis point 59.10885375 0.00000000 233.44064050 Rotation angle (degrees) 5.32297724 Shift along axis 0.03066174 > fitmap #1.14 inMap #1.1 Fit map J407_component_000_frame_011.mrc in map J407_component_000_frame_024.mrc using 192986 points correlation = 0.8264, correlation about mean = 0.5097, overlap = 4134 steps = 180, shift = 3.25, angle = 6.55 degrees Position of J407_component_000_frame_011.mrc (#1.14) relative to J407_component_000_frame_024.mrc (#1.1) coordinates: Matrix rotation and translation 0.99536641 -0.00257223 -0.09612019 22.16708898 0.00847171 0.99810069 0.06101846 -14.42324176 0.09578068 -0.06155003 0.99349769 -4.19909428 Axis -0.53764860 -0.84177617 0.04844440 Axis point 59.32007584 0.00000000 227.86856058 Rotation angle (degrees) 6.54512439 Shift along axis 0.01961419 > vop flip #1 Opened J407_component_000_frame_024.mrc z flip as #2, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_023.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_022.mrc z flip as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_021.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_020.mrc z flip as #6, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_019.mrc z flip as #7, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_018.mrc z flip as #8, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_017.mrc z flip as #9, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_016.mrc z flip as #10, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_015.mrc z flip as #11, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_014.mrc z flip as #12, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_013.mrc z flip as #13, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_012.mrc z flip as #14, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_011.mrc z flip as #15, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_010.mrc z flip as #16, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_009.mrc z flip as #17, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_008.mrc z flip as #18, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_007.mrc z flip as #19, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_006.mrc z flip as #20, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_005.mrc z flip as #21, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_004.mrc z flip as #22, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_003.mrc z flip as #23, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_002.mrc z flip as #24, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_001.mrc z flip as #25, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_000.mrc z flip as #26, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #1 > fitmap #3 inMap #2 Fit map J407_component_000_frame_023.mrc z flip in map J407_component_000_frame_024.mrc z flip using 209250 points correlation = 0.9997, correlation about mean = 0.998, overlap = 8159 steps = 44, shift = 0.0122, angle = 0.0166 degrees Position of J407_component_000_frame_023.mrc z flip (#3) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999998 -0.00007198 0.00017080 -0.01218363 0.00007199 1.00000000 -0.00004990 -0.01272519 -0.00017079 0.00004991 0.99999998 0.00861980 Axis 0.26000175 0.88979882 0.37504286 Axis point 75.18576895 0.00000000 54.20442455 Rotation angle (degrees) 0.01099771 Shift along axis -0.01125783 > fitmap #4 inMap #2 Fit map J407_component_000_frame_022.mrc z flip in map J407_component_000_frame_024.mrc z flip using 203717 points correlation = 0.9986, correlation about mean = 0.9908, overlap = 7804 steps = 44, shift = 0.00922, angle = 0.043 degrees Position of J407_component_000_frame_022.mrc z flip (#4) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999993 -0.00018708 0.00032120 -0.00987873 0.00018712 0.99999998 -0.00010622 -0.01960247 -0.00032118 0.00010628 0.99999994 0.03150743 Axis 0.27483331 0.83080943 0.48396524 Axis point 103.74870000 0.00000000 27.56737164 Rotation angle (degrees) 0.02215041 Shift along axis -0.00375242 > fitmap #5 inMap #2 Fit map J407_component_000_frame_021.mrc z flip in map J407_component_000_frame_024.mrc z flip using 198335 points correlation = 0.9964, correlation about mean = 0.9756, overlap = 7433 steps = 48, shift = 0.0353, angle = 0.0607 degrees Position of J407_component_000_frame_021.mrc z flip (#5) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999983 -0.00035430 0.00045957 -0.00246458 0.00035440 0.99999991 -0.00022596 -0.04001364 -0.00045949 0.00022612 0.99999987 0.02969192 Axis 0.36297181 0.73789422 0.56900227 Axis point 81.37020887 0.00000000 -5.29006039 Rotation angle (degrees) 0.03568139 Shift along axis -0.01352564 > fitmap #6 inMap #2 Fit map J407_component_000_frame_020.mrc z flip in map J407_component_000_frame_024.mrc z flip using 193267 points correlation = 0.9926, correlation about mean = 0.9494, overlap = 7051 steps = 48, shift = 0.0572, angle = 0.091 degrees Position of J407_component_000_frame_020.mrc z flip (#6) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999963 -0.00049347 0.00070005 -0.00617347 0.00049379 0.99999977 -0.00046712 -0.02146966 -0.00069982 0.00046747 0.99999965 0.00864692 Axis 0.47894449 0.71738422 0.50593682 Axis point 22.46606534 -0.00000000 -0.73683347 Rotation angle (degrees) 0.05590211 Shift along axis -0.01398395 > fitmap #7 inMap #2 Fit map J407_component_000_frame_019.mrc z flip in map J407_component_000_frame_024.mrc z flip using 188984 points correlation = 0.9863, correlation about mean = 0.9084, overlap = 6677 steps = 44, shift = 0.0751, angle = 0.121 degrees Position of J407_component_000_frame_019.mrc z flip (#7) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999936 -0.00073951 0.00086022 0.01917742 0.00074004 0.99999953 -0.00062080 -0.05247554 -0.00085976 0.00062143 0.99999944 -0.00306149 Axis 0.48025379 0.66495781 0.57200298 Axis point 14.71644850 0.00000000 -37.59932412 Rotation angle (degrees) 0.07410093 Shift along axis -0.02743518 > fitmap #8 inMap #2 Fit map J407_component_000_frame_018.mrc z flip in map J407_component_000_frame_024.mrc z flip using 185458 points correlation = 0.976, correlation about mean = 0.8495, overlap = 6307 steps = 48, shift = 0.0762, angle = 0.166 degrees Position of J407_component_000_frame_018.mrc z flip (#8) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999889 -0.00109466 0.00101112 0.06239608 0.00109572 0.99999885 -0.00105131 -0.05426405 -0.00100997 0.00105242 0.99999894 -0.06011444 Axis 0.57667175 0.55401943 0.60042665 Axis point 34.34276710 72.86216565 0.00000000 Rotation angle (degrees) 0.10450891 Shift along axis -0.03017559 > fitmap #9 inMap #2 Fit map J407_component_000_frame_017.mrc z flip in map J407_component_000_frame_024.mrc z flip using 183289 points correlation = 0.9601, correlation about mean = 0.7729, overlap = 5915 steps = 64, shift = 0.122, angle = 0.236 degrees Position of J407_component_000_frame_017.mrc z flip (#9) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999771 -0.00148690 0.00153937 0.06533420 0.00148900 0.99999796 -0.00136750 -0.08041576 -0.00153733 0.00136979 0.99999788 -0.04587663 Axis 0.53874971 0.60555051 0.58571096 Axis point -14.38402550 0.00000000 -56.59152311 Rotation angle (degrees) 0.14555510 Shift along axis -0.04036747 > fitmap #10 inMap #2 Fit map J407_component_000_frame_016.mrc z flip in map J407_component_000_frame_024.mrc z flip using 182675 points correlation = 0.9352, correlation about mean = 0.6832, overlap = 5522 steps = 52, shift = 0.145, angle = 0.328 degrees Position of J407_component_000_frame_016.mrc z flip (#10) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999558 -0.00205030 0.00215508 0.07345453 0.00205433 0.99999614 -0.00186887 -0.11702549 -0.00215124 0.00187329 0.99999593 -0.03493961 Axis 0.53244610 0.61271628 0.58402047 Axis point -1.76436098 0.00000000 -47.18208786 Rotation angle (degrees) 0.20134459 Shift along axis -0.05299829 > fitmap #11 inMap #2 Fit map J407_component_000_frame_015.mrc z flip in map J407_component_000_frame_024.mrc z flip using 183507 points correlation = 0.9009, correlation about mean = 0.5877, overlap = 5090 steps = 48, shift = 0.208, angle = 0.483 degrees Position of J407_component_000_frame_015.mrc z flip (#11) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99999091 -0.00273836 0.00326767 0.05590994 0.00274708 0.99999267 -0.00266766 -0.12998441 -0.00326034 0.00267661 0.99999110 -0.02714748 Axis 0.53107566 0.64870698 0.54510357 Axis point 3.35863162 0.00000000 -28.38436861 Rotation angle (degrees) 0.28828800 Shift along axis -0.06942757 > fitmap #12 inMap #2 Fit map J407_component_000_frame_014.mrc z flip in map J407_component_000_frame_024.mrc z flip using 185464 points correlation = 0.8578, correlation about mean = 0.4936, overlap = 4655 steps = 56, shift = 0.29, angle = 0.782 degrees Position of J407_component_000_frame_014.mrc z flip (#12) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99997895 -0.00391909 0.00517094 0.00256972 0.00394209 0.99998236 -0.00444391 -0.08633596 -0.00515344 0.00446420 0.99997676 -0.05838787 Axis 0.56595594 0.65593568 0.49944195 Axis point -3.11241061 0.00000000 -9.74033626 Rotation angle (degrees) 0.45092040 Shift along axis -0.08433783 > fitmap #13 inMap #2 Fit map J407_component_000_frame_013.mrc z flip in map J407_component_000_frame_024.mrc z flip using 188095 points correlation = 0.8116, correlation about mean = 0.4086, overlap = 4243 steps = 96, shift = 0.393, angle = 1.53 degrees Position of J407_component_000_frame_013.mrc z flip (#13) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99992688 -0.00630498 0.01031927 -0.30501394 0.00639187 0.99994421 -0.00840964 0.04351622 -0.01026567 0.00847499 0.99991139 0.09565506 Axis 0.57242910 0.69787876 0.43045344 Axis point 13.43257006 0.00000000 23.93624556 Rotation angle (degrees) 0.84504164 Shift along axis -0.10305476 > fitmap #14 inMap #2 Fit map J407_component_000_frame_012.mrc z flip in map J407_component_000_frame_024.mrc z flip using 190432 points correlation = 0.8261, correlation about mean = 0.4787, overlap = 4037 steps = 176, shift = 1.44, angle = 10.6 degrees Position of J407_component_000_frame_012.mrc z flip (#14) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99694118 -0.00490893 0.07800121 -9.93956782 0.00881435 0.99872014 -0.04980352 5.90096487 -0.07765690 0.05033871 0.99570850 5.09045949 Axis 0.53956818 0.83868878 0.07394129 Axis point 58.43220848 0.00000000 129.45965602 Rotation angle (degrees) 5.32462315 Shift along axis -0.03760638 > fitmap #15 inMap #2 Fit map J407_component_000_frame_011.mrc z flip in map J407_component_000_frame_024.mrc z flip using 192986 points correlation = 0.8264, correlation about mean = 0.5098, overlap = 4134 steps = 292, shift = 1.7, angle = 13.1 degrees Position of J407_component_000_frame_011.mrc z flip (#15) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99535227 -0.00254091 0.09626734 -12.75691240 0.00845357 0.99809823 -0.06106117 7.73661469 -0.09592911 0.06159118 0.99348082 6.58346657 Axis 0.53732932 0.84199599 0.04816585 Axis point 59.44846482 0.00000000 135.25518533 Rotation angle (degrees) 6.55353132 Shift along axis -0.02336624 > fitmap #16 inMap #2 Fit map J407_component_000_frame_010.mrc z flip in map J407_component_000_frame_024.mrc z flip using 196011 points correlation = 0.8258, correlation about mean = 0.5264, overlap = 4268 steps = 196, shift = 3.64, angle = 7.16 degrees Position of J407_component_000_frame_010.mrc z flip (#16) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99443723 -0.00129423 0.10532294 -14.14446568 0.00834325 0.99775057 -0.06651460 8.62606466 -0.10499994 0.06702333 0.99221111 7.38173986 Axis 0.53560639 0.84358259 0.03865489 Axis point 60.11494959 0.00000000 137.40139033 Rotation angle (degrees) 7.16115140 Shift along axis -0.01372784 > fitmap #17 inMap #2 Fit map J407_component_000_frame_009.mrc z flip in map J407_component_000_frame_024.mrc z flip using 199261 points correlation = 0.8232, correlation about mean = 0.5306, overlap = 4420 steps = 136, shift = 3.94, angle = 7.55 degrees Position of J407_component_000_frame_009.mrc z flip (#17) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99383750 -0.00051591 0.11084568 -14.99048576 0.00835653 0.99749218 -0.07028168 9.22600775 -0.11053144 0.07077485 0.99134944 7.80629725 Axis 0.53705726 0.84286912 0.03378085 Axis point 59.78820314 0.00000000 138.50939775 Rotation angle (degrees) 7.54608177 Shift along axis -0.01072884 > fitmap #18 inMap #2 Fit map J407_component_000_frame_008.mrc z flip in map J407_component_000_frame_024.mrc z flip using 203831 points correlation = 0.8153, correlation about mean = 0.52, overlap = 4559 steps = 2000, shift = 4.22, angle = 7.99 degrees Position of J407_component_000_frame_008.mrc z flip (#18) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99311478 0.00036012 0.11714484 -15.91996779 0.00844044 0.99717627 -0.07462070 10.01782949 -0.11684093 0.07509567 0.99030745 8.49776599 Axis 0.53873766 0.84197168 0.02907615 Axis point 61.09163915 0.00000000 139.97400207 Rotation angle (degrees) 7.98715498 Shift along axis 0.10512492 > fitmap #19 inMap #2 Fit map J407_component_000_frame_007.mrc z flip in map J407_component_000_frame_024.mrc z flip using 209283 points correlation = 0.8104, correlation about mean = 0.5166, overlap = 4743 steps = 2000, shift = 4.27, angle = 7.92 degrees Position of J407_component_000_frame_007.mrc z flip (#19) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99298926 0.00085186 0.11820153 -16.25189613 0.00754817 0.99747619 -0.07059942 9.40986459 -0.11796335 0.07099668 0.99047671 9.37694002 Axis 0.51406917 0.85740414 0.02431115 Axis point 68.09691265 0.00000000 141.27730169 Rotation angle (degrees) 7.91598383 Shift along axis -0.05857770 > fitmap #20 inMap #2 Fit map J407_component_000_frame_006.mrc z flip in map J407_component_000_frame_024.mrc z flip using 215308 points correlation = 0.803, correlation about mean = 0.509, overlap = 4911 steps = 2000, shift = 4.59, angle = 7.95 degrees Position of J407_component_000_frame_006.mrc z flip (#20) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99338714 0.00062278 0.11481118 -15.65271922 0.00828418 0.99699005 -0.07708568 10.23612069 -0.11451362 0.07752704 0.99039194 7.15534657 Axis 0.55880756 0.82883495 0.02769014 Axis point 50.84212432 0.00000000 138.94807270 Rotation angle (degrees) 7.95189644 Shift along axis -0.06467064 > fitmap #21 inMap #2 Fit map J407_component_000_frame_005.mrc z flip in map J407_component_000_frame_024.mrc z flip using 221943 points correlation = 0.7975, correlation about mean = 0.5036, overlap = 5120 steps = 2000, shift = 4.83, angle = 8.46 degrees Position of J407_component_000_frame_005.mrc z flip (#21) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99245648 0.00133502 0.12259016 -16.74608631 0.00870219 0.99665134 -0.08130423 11.00789413 -0.12228819 0.08175771 0.98912147 8.37528140 Axis 0.55407863 0.83208786 0.02503340 Axis point 55.97483404 -0.00000000 140.45584472 Rotation angle (degrees) 8.46162297 Shift along axis 0.09054828 > fitmap #22 inMap #2 Fit map J407_component_000_frame_004.mrc z flip in map J407_component_000_frame_024.mrc z flip using 228675 points correlation = 0.7942, correlation about mean = 0.505, overlap = 5345 steps = 128, shift = 4.86, angle = 8.35 degrees Position of J407_component_000_frame_004.mrc z flip (#22) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99249124 0.00154071 0.12230601 -16.79973741 0.00809048 0.99690400 -0.07821101 10.55194435 -0.12204785 0.07861326 0.98940602 8.69406762 Axis 0.53998559 0.84137207 0.02255251 Axis point 58.99611311 0.00000000 140.99153578 Rotation angle (degrees) 8.34952877 Shift along axis 0.00256822 > fitmap #23 inMap #2 Fit map J407_component_000_frame_003.mrc z flip in map J407_component_000_frame_024.mrc z flip using 235349 points correlation = 0.7882, correlation about mean = 0.5, overlap = 5547 steps = 212, shift = 4.98, angle = 8.42 degrees Position of J407_component_000_frame_003.mrc z flip (#23) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99239157 0.00173360 0.12310956 -16.93547458 0.00807332 0.99683268 -0.07911654 10.70058751 -0.12285679 0.07950849 0.98923436 8.68387043 Axis 0.54184790 0.84019752 0.02165588 Axis point 58.31141283 -0.00000000 141.17775832 Rotation angle (degrees) 8.41685965 Shift along axis 0.00221262 > fitmap #24 inMap #2 Fit map J407_component_000_frame_002.mrc z flip in map J407_component_000_frame_024.mrc z flip using 242114 points correlation = 0.7826, correlation about mean = 0.4956, overlap = 5752 steps = 208, shift = 5.08, angle = 8.48 degrees Position of J407_component_000_frame_002.mrc z flip (#24) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99225263 0.00189051 0.12422215 -17.10140627 0.00804439 0.99680826 -0.07942660 10.75407774 -0.12397582 0.07981055 0.98907041 8.85014965 Axis 0.53987514 0.84148650 0.02086400 Axis point 58.92464501 0.00000000 141.34912975 Rotation angle (degrees) 8.48068000 Shift along axis 0.00143673 > fitmap #25 inMap #2 Fit map J407_component_000_frame_001.mrc z flip in map J407_component_000_frame_024.mrc z flip using 249113 points correlation = 0.7772, correlation about mean = 0.4915, overlap = 5962 steps = 188, shift = 5.18, angle = 8.55 degrees Position of J407_component_000_frame_001.mrc z flip (#25) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99214829 0.00207808 0.12504976 -17.23705108 0.00803389 0.99673797 -0.08030494 10.89836189 -0.12480873 0.08067904 0.98889518 8.86701028 Axis 0.54150720 0.84045738 0.02003374 Axis point 58.45205449 0.00000000 141.52577979 Rotation angle (degrees) 8.54837308 Shift along axis 0.00326072 > fitmap #26 inMap #2 Fit map J407_component_000_frame_000.mrc z flip in map J407_component_000_frame_024.mrc z flip using 256043 points correlation = 0.7721, correlation about mean = 0.488, overlap = 6173 steps = 148, shift = 5.26, angle = 8.6 degrees Position of J407_component_000_frame_000.mrc z flip (#26) relative to J407_component_000_frame_024.mrc z flip (#2) coordinates: Matrix rotation and translation 0.99206661 0.00217833 0.12569448 -17.33798987 0.00806440 0.99668776 -0.08092267 10.99552196 -0.12545442 0.08129433 0.98876308 8.89667575 Axis 0.54245968 0.83985122 0.01968325 Axis point 58.22890126 -0.00000000 141.63243770 Rotation angle (degrees) 8.59910356 Shift along axis 0.00455761 > color grey > volume morph #2-26 Map positions are not the same, J407_component_000_frame_023.mrc z flip #3 and J407_component_000_frame_024.mrc z flip #2. Use the ""volume resample"" command to make a copy of one map with the same grid as the other map. > volume resample #3-26 onGrid #2 Opened J407_component_000_frame_023.mrc z flip resampled as #1, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_022.mrc z flip resampled as #27, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_021.mrc z flip resampled as #28, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_020.mrc z flip resampled as #29, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_019.mrc z flip resampled as #30, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_018.mrc z flip resampled as #31, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_017.mrc z flip resampled as #32, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_016.mrc z flip resampled as #33, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_015.mrc z flip resampled as #34, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_014.mrc z flip resampled as #35, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_013.mrc z flip resampled as #36, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_012.mrc z flip resampled as #37, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_011.mrc z flip resampled as #38, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_010.mrc z flip resampled as #39, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_009.mrc z flip resampled as #40, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_008.mrc z flip resampled as #41, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_007.mrc z flip resampled as #42, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_006.mrc z flip resampled as #43, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_005.mrc z flip resampled as #44, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_004.mrc z flip resampled as #45, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_003.mrc z flip resampled as #46, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_002.mrc z flip resampled as #47, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_001.mrc z flip resampled as #48, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_000_frame_000.mrc z flip resampled as #49, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #3-26 > rename #2 id #500 > rename #1 id #2 > rename #500 id #1 > color grey > volume morph #2-49 Opened morph as #3, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > hide #!1 models > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false Unsupported scale factor (0.000000) detected on Display1 QPainter::begin: Paint device returned engine == 0, type: 2 QPainter::translate: Painter not active QPainter::setPen: Painter not active QPainter::setBrush: Painter not active QPainter::drawPoints: Painter not active QPainter::end: Painter not active, aborted QPainter::begin: Paint device returned engine == 0, type: 2 QPainter::translate: Painter not active QPainter::setPen: Painter not active QPainter::setBrush: Painter not active QPainter::drawPoints: Painter not active QPainter::end: Painter not active, aborted Unsupported scale factor (0.000000) detected on Display0 Unsupported scale factor (0.000000) detected on Display1 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev29_PostPhenix.pdb"" format pdb Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J339_component_002_frame_017.mrc z flip as #19, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_018.mrc z flip as #20, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_019.mrc z flip as #21, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > vop level 0.1 > hide #!1 models > vop morph #2-21 Opened morph as #22, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > show #!21 models > hide #!22 models > hide #!21 models > show #!20 models > hide #!20 models > show #!20 models > show #!21 models > hide #!20 models > hide #!21 models > close #22 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_45bp- > oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif"" Summary of feedback from opening /Users/jtbauer/Library/CloudStorage/OneDrive- Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize structures/PDBs/ylODC_45bp- oriC061_complete/ODC1-6_45bpOriC061_DNApucker_rev3.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 19 Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for ODC1-6_45bpOriC061_DNApucker_rev3.cif #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > modelfix Changed 25273 atom styles 23792 atoms, 24240 bonds, 9 pseudobonds, 2982 residues, 2 models selected Computing secondary structure > lighting soft > graphics silhouettes true > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/45bp_too_short.png"" supersample 3 transparentBackground true ===== 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 > set bgColor white > graphics silhouettes true > alias newcolor color $1 darkseagreen ; color $2 burlywood ; color $3 coral ; > color $4 #498cff ; color $5 mediumslateblue ; color $6 grey ; color $7 > #ff69b4 ; color $8 #20B2AA ; color $9 #20B2AA > alias propercolor color $1 mediumslateblue ; color $2 lightcoral ; color $3 > darkseagreen ; color $4 burlywood ; color $5 coral ; color $6 grey ; color > $7 #bb57a1ff ; color $8 #0080ffff ; color $9 #004080ff > alias removeatom select main ; style stick ; color sel byhetero ; hide sel > atoms ; show sel cartoons ; select clear > alias showATP select ::name=""ATP"" ; show sel ; color sel byhetero ; select > clear > alias modelfix style stick ; newcolor /A /B /C /D /E /F /G /H /I ; color > byhetero ; show cartoons ; select clear ; select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" > ; hide sel atoms ; select clear > lighting soft UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: Z176000HCLL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 11881.61.3 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.2 (23H311) Kernel Version: Darwin 23.6.0 Time since boot: 51 days, 21 hours, 52 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX