id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17037 ChimeraX bug report submission chimerax-bug-report@… "{{{ 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 > modelfix Changed 25299 atom styles 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected > split #1 Split ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) into 9 models Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb A #1.1 --- Chain | Description A | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb B #1.2 --- Chain | Description B | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb C #1.3 --- Chain | Description C | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb D #1.4 --- Chain | Description D | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb E #1.5 --- Chain | Description E | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb F #1.6 --- Chain | Description F | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb G #1.7 --- Chain | Description G | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb H #1.8 --- Chain | Description H | No description available Chain information for ylODC_54bpOriC061_rev29_PostPhenix.pdb I #1.9 --- Chain | Description I | No description available > hide #!1.1 models > hide #1.2 models > hide #!1.3 models > hide #!1.5 models > show #!1.5 models > hide #!1.6 models > select /G:548 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms Unsupported scale factor (0.000000) detected on Display0 Unsupported scale factor (0.000000) detected on Display1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/ylODC_54bp- > oriC061_complete/cryosparc_P370_J327_even_better_Orc2WHD.mrc"" Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc as #2, grid size 440,440,440, pixel 0.827, shown at level 0.0402, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1468 > select clear > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > vop flip #2 Opened cryosparc_P370_J327_even_better_Orc2WHD.mrc z flip as #3, 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/need to organize > structures/Projects-maps/ylODC_54bp- > oriC061_complete/cryosparc_P370_J327_FLIPPED_even_better_Orc2WHD.mrc"" models > #3 Unsupported scale factor (0.000000) detected on Display1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/ylODC_54bp- > oriC061_complete/cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc"" Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc as #4, grid size 440,440,440, pixel 0.827, shown at level 0.0436, step 2, values float32 > select ~sel & ##selected Nothing selected > vop flip #4 Opened cryosparc_P370_J418_local_refine_even_better_Orc2WHD.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #4 > volume #5 level 0.1372 > volume #3 level 0.14 > volume #5 level 0.14 > volume #5 level 0.1 > volume #3 level 0.1 > volume #3 level 0.0813 > volume #3 level 0.1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/Projects-maps/ylODC_54bp- > oriC061_complete/cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc"" Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc as #4, grid size 440,440,440, pixel 0.827, shown at level 0.0683, step 2, values float32 > close #5 > vop flip #4 Opened cryosparc_P370_J420_even_better_Orc2WHD-sharp.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #4 > volume #5 level 0.1 > volume #5 level 0.12 > volume #5 level 0.1 > volume #5 level 0.095 > volume #5 level 0.08 > hide #!3 models > hide #!1 models > surface dust #5 size 8.27 > close #5 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb #4 --- Chain | Description A | No description available B | No description available Computing secondary structure > select add #4 6005 atoms, 6077 bonds, 374 residues, 1 model selected > ui mousemode right select > select clear > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal > structure.pdb"" 1j7v-crystal structure.pdb title: Human il-10 / il-10R1 complex [more info...] Chain information for 1j7v-crystal structure.pdb #5 --- Chain | Description | UniProt L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160 R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214 13 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #4 to #5 Computing secondary structure 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 1j7v-crystal structure.pdb, chain R (#5) with test_a3d8f_relaxed_rank_001_alphafold2_multimer_v3_model_5_seed_000.pdb, chain B (#4), sequence alignment score = 1073 RMSD between 192 pruned atom pairs is 0.747 angstroms; (across all 205 pairs: 1.150) > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #6 --- Chain | Description A | No description available B | No description available Computing secondary structure > select ~sel & ##selected Nothing selected > matchmaker #6 to #5 Computing secondary structure 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 1j7v-crystal structure.pdb, chain R (#5) with test_a3d8f_relaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb, chain B (#6), sequence alignment score = 1073 RMSD between 191 pruned atom pairs is 0.713 angstroms; (across all 205 pairs: 1.091) > close #4 > close #6 > ui tool show ""Unit Cell"" > unitcell #5 > unitcell delete #5 > unitcell #5 Drag select of 587 residues > delete sel Drag select of 832 residues, 8 pseudobonds > delete sel > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6.result.zip Unrecognized file suffix '.zip' > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb Chain information for test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #6 --- Chain | Description A B | No description available C D | No description available Computing secondary structure > hide #!4 models > show #!4 models > hide #5 models > show #5 models > hide #5 models > hide #!4 models > show #5 models > hide #5 models > show #!4 models > hide #!4 models > show #5 models > hide #5 models > show #!4 models > close #5 > matchmaker #6 to #4 Specify a single 'to' model only > hide #4.1 models > show #4.1 models > hide #4.2 models > show #4.2 models > hide #!4.3 models > show #!4.3 models > hide #4.4 models > show #4.4 models > close #4 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/test_a3d8f/1j7v-crystal > structure.pdb"" format pdb 1j7v-crystal structure.pdb title: Human il-10 / il-10R1 complex [more info...] Chain information for 1j7v-crystal structure.pdb #4 --- Chain | Description | UniProt L | IL-10; cytokine synthesis inhibitory factor; CSIF | IL10_HUMAN 1-160 R | IL-10R1; IL-10R-A | I10R1_HUMAN 1-214 13 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > unitcell #4 > combine #5 Remapping chain ID 'L' in 1j7v-crystal structure.pdb #2 #5.2 to 'M' Remapping chain ID 'R' in 1j7v-crystal structure.pdb #2 #5.2 to 'S' Remapping chain ID 'L' in 1j7v-crystal structure.pdb #3 #5.3 to 'N' Remapping chain ID 'R' in 1j7v-crystal structure.pdb #3 #5.3 to 'T' Remapping chain ID 'L' in 1j7v-crystal structure.pdb #4 #5.4 to 'O' Remapping chain ID 'R' in 1j7v-crystal structure.pdb #4 #5.4 to 'U' Remapping chain ID 'L' in 1j7v-crystal structure.pdb #5 #5.5 to 'P' Remapping chain ID 'R' in 1j7v-crystal structure.pdb #5 #5.5 to 'V' Remapping chain ID 'L' in 1j7v-crystal structure.pdb #6 #5.6 to 'Q' Remapping chain ID 'R' in 1j7v-crystal structure.pdb #6 #5.6 to 'W' > hide #4 models > hide #!5 models > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain C (#6), sequence alignment score = 1073 RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs: 1.044) > select add #6 12010 atoms, 12154 bonds, 748 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #6,0.51645,0.16079,-0.84109,16.615,-0.7222,0.60956,-0.32692,27.053,0.46012,0.77627,0.43093,122.67 > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb, chain C (#6), sequence alignment score = 1073 RMSD between 194 pruned atom pairs is 0.648 angstroms; (across all 205 pairs: 1.044) > view matrix models > #6,0.51645,0.16079,-0.84109,16.006,-0.7222,0.60956,-0.32692,15.467,0.46012,0.77627,0.43093,137.76 > view matrix models > #6,0.51645,0.16079,-0.84109,12.455,-0.7222,0.60956,-0.32692,-15.933,0.46012,0.77627,0.43093,154.19 > view matrix models > #6,0.51645,0.16079,-0.84109,7.4024,-0.7222,0.60956,-0.32692,10.581,0.46012,0.77627,0.43093,164.48 > view matrix models > #6,0.51645,0.16079,-0.84109,77.402,-0.7222,0.60956,-0.32692,32.484,0.46012,0.77627,0.43093,91.425 > close #6 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb #6 --- Chain | Description A B | No description available C D | No description available Computing secondary structure > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb, chain C (#6), sequence alignment score = 1052 RMSD between 190 pruned atom pairs is 0.752 angstroms; (across all 205 pairs: 1.415) > close #6 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb #6 --- Chain | Description A B | No description available C D | No description available Computing secondary structure > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb, chain D (#6), sequence alignment score = 1073 RMSD between 196 pruned atom pairs is 0.731 angstroms; (across all 205 pairs: 1.005) > close #6 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb Chain information for test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb #6 --- Chain | Description A B | No description available C D | No description available Computing secondary structure > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_004_alphafold2_multimer_v3_model_4_seed_000.pdb, chain C (#6), sequence alignment score = 1073 RMSD between 193 pruned atom pairs is 0.707 angstroms; (across all 205 pairs: 1.082) > close #6 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua- > Tor_Lab/test_a3d8f/test_566b6/test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb Chain information for test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb #6 --- Chain | Description A B | No description available C D | No description available Computing secondary structure > matchmaker #6 to #7 Computing secondary structure 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 combination, chain R (#7) with test_566b6_relaxed_rank_005_alphafold2_multimer_v3_model_5_seed_000.pdb, chain C (#6), sequence alignment score = 1073 RMSD between 192 pruned atom pairs is 0.722 angstroms; (across all 205 pairs: 1.163) > close #6 > close #7 > close #5 > close #4 > close #1 > 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"" 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 > hide #!1 models > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb 7jk3-dmODC_GCrich.pdb title: Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] Chain information for 7jk3-dmODC_GCrich.pdb #2 --- Chain | Description | UniProt A | DMORC1 | ORC1_DROME 440-924 B | DMORC2 | ORC2_DROME 1-618 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 D | ORC4 | Q9W102_DROME 1-459 E | ORC5 | ORC5_DROME 1-460 F | ORC6 | ORC6_DROME 1-257 G | CDC6 | Q9VSM9_DROME 242-662 H | DNA (33-mer) | I | DNA (33-mer) | Non-standard residues in 7jk3-dmODC_GCrich.pdb #2 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > close #2 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb Chain information for hsORC1-6_CDC6_60bpDNA.pdb #2 --- 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 46715 atom styles 43798 atoms, 44629 bonds, 22 pseudobonds, 5455 residues, 4 models selected Computing secondary structure > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif 7mca-assembly1.cif title: Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA. [more info...] Chain information for 7mca-assembly1.cif #3 --- Chain | Description A | Origin recognition complex subunit 1 B | Origin recognition complex subunit 2 C | Origin recognition complex subunit 3 D | Origin recognition complex subunit 4 E | Origin recognition complex subunit 5 F | Origin recognition complex subunit 6 G | DNA (85-MER) H | DNA (85-MER) I | Cell division control protein 6 Non-standard residues in 7mca-assembly1.cif #3 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) MG — magnesium ion > modelfix Changed 71407 atom styles 66312 atoms, 67574 bonds, 36 pseudobonds, 8215 residues, 6 models selected > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H > select #1/H,I 1476 atoms, 1654 bonds, 72 residues, 1 model selected > show #!1 models > ui mousemode right select > select clear > matchmaker #2,3 to #1 Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs: 7.882) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > matchmaker #2,3 to #1/C:180-260,/D,/E Invalid ""to"" argument: only initial part ""#1/C:180-260"" of atom specifier valid > matchmaker #2,3 to (#1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain E (#2), sequence alignment score = 281.2 RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs: 3.490) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 312.4 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs: 3.466) > matchmaker #2,3 to (#1/A:300-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 836.2 RMSD between 200 pruned atom pairs is 1.167 angstroms; (across all 283 pairs: 2.305) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 700.3 RMSD between 218 pruned atom pairs is 0.943 angstroms; (across all 276 pairs: 5.480) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs: 2.171) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 312.4 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs: 3.466) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > select ~nucleic 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected > show sel surfaces > transparency 30 surfaces > transparency 70 surfaces > hide sel cartoons > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs: 2.171) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 312.4 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs: 3.466) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > matchmaker #2,3 to #1 Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs: 7.882) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) Drag select of ylODC_54bpOriC061_rev29_PostPhenix.pdb_A SES surface, 7 of 358676 triangles, ylODC_54bpOriC061_rev29_PostPhenix.pdb_D SES surface, 18 of 396086 triangles, hsORC1-6_CDC6_60bpDNA.pdb_D SES surface, 38 of 440036 triangles > select #2/A:901@C5' 1 atom, 1 residue, 1 model selected > select up 31 atoms, 33 bonds, 1 residue, 1 model selected > select up 3061 atoms, 3113 bonds, 385 residues, 1 model selected > select down 31 atoms, 33 bonds, 1 residue, 2 models selected > select clear > matchmaker #2,3 to (#1/A:500-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 284.5 RMSD between 68 pruned atom pairs is 1.060 angstroms; (across all 96 pairs: 2.171) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain E (#1) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 312.4 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs: 3.466) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > matchmaker #2,3 to #1 Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs: 7.882) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > select #2 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected > show sel atoms > undo > show sel cartoons > select clear > matchmaker #2,3 to #1 Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs: 7.882) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #2 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected > hide sel surfaces > select clear > matchmaker #2,3 to #1 Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain C (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain C (#2), sequence alignment score = 967.1 RMSD between 139 pruned atom pairs is 1.275 angstroms; (across all 568 pairs: 7.882) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > matchmaker #2,3 to (#1/A:400-600 | #1/C:140-300 | #1/D:360-end | #1/E:307-end) Computing secondary structure 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 ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#2), sequence alignment score = 582.4 RMSD between 128 pruned atom pairs is 1.051 angstroms; (across all 196 pairs: 2.238) Matchmaker ylODC_54bpOriC061_rev29_PostPhenix.pdb, chain A (#1) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 527.5 RMSD between 164 pruned atom pairs is 0.962 angstroms; (across all 191 pairs: 2.175) > select add #2 21416 atoms, 21948 bonds, 13 pseudobonds, 2551 residues, 2 models selected > select ~nucleic 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected > show sel surfaces > select clear > select ~nucleic 66692 atoms, 67966 bonds, 38 pseudobonds, 8239 residues, 7 models selected > hide sel cartoons > hide sel atoms > select clear > color #1 FFFF80 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1 #FFFF80 > color #1 #FF8080 > color #2 #8080FF > color #2 #0080FF > color #3 #0080FF > color #3 lime > lighting full > graphics silhouettes false > lighting shadows false > lighting shadows true > lighting full > transparency 75 surfaces > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > nucleotides atoms > style nucleic stick Changed 4715 atom styles > nucleotides fill > style nucleic stick Changed 4715 atom styles > nucleotides tube/slab shape box > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > lighting soft > hide #!2 models > hide #!1 models > | #3/I) /Z /Z Expected fewer arguments > Missing or invalid eighth argument: Expected a text string > newcolor /A /B /C /D /E /F #1/G /Z /Z > newcolor /A /B /C /D /E /F #2/G /Z /Z > newcolor /A /B /C /D /E /F #3/I /Z /Z > transparency 75 surfaces > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > color #3 #0080FF > color #2 lime > newcolor /A /B /C /D /E /F #3/I /Z /Z > newcolor /A /B /C /D /E /F #2/G /Z /Z > transparency 75 surfaces > hide #!3 models > hide #!2 models > show #!1 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/ylODC_54oriC_bend_updated.png"" supersample 3 > show #!2 models > hide #!1 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/hsODC_bend_updated.png"" supersample 3 > show #!3 models > hide #!2 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/scODC_bend_updated.png"" supersample 3 > show #!1 models > show #!2 models > transparency 50 surfaces > hide #!2 models > hide #!3 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/ylODC_54oriC_bend_updated2.png"" supersample 3 > show #!2 models > hide #!1 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/hsODC_bend_updated2.png"" supersample 3 > hide #!2 models > show #!3 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/scODC_bend_updated2.png"" supersample 3 > ui tool show ""Side View"" > show #!1 models > hide #!3 models > show #!2 models > hide #!1 models > lighting full > show #!1 models > hide #!2 models > show #!3 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1-2 cartoons > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > close #2-3 > hide surfaces > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > hide sel cartoons > select /D:465 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /G:557 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select /G:548 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > lighting shadows false > modelfix Changed 25299 atom styles 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > hide sel cartoons > select clear > select /D:465 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /G:560 9 atoms, 8 bonds, 1 residue, 1 model selected > select /G:557 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select /G:548 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > nucleotides tube/slab shape box > nucleotides fill > style nucleic stick Changed 1476 atom styles > nucleotides fill > style nucleic stick Changed 1476 atom styles > nucleotides ladder > nucleotides fill > style nucleic stick Changed 1476 atom styles > nucleotides fill > style nucleic stick Changed 1476 atom styles > nucleotides atoms > style nucleic stick Changed 1476 atom styles > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png"" supersample 3 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb"" Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 --- 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 50598 atom styles 47398 atoms, 48290 bonds, 18 pseudobonds, 5940 residues, 4 models selected > select /A,B,C,E,F 33274 atoms, 33942 bonds, 8 pseudobonds, 4146 residues, 6 models selected > hide sel cartoons > select ~nucleic 47646 atoms, 48546 bonds, 22 pseudobonds, 5956 residues, 6 models selected > hide sel atoms > select clear Drag select of 10 residues > select clear Drag select of 2 residues > show sel atoms > select #2/D:465@NZ 1 atom, 1 residue, 1 model selected > ui tool show ""Add Hydrogens"" > addh #!2 Summary of feedback from adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 --- warnings | Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/H DG 8 P because it is missing heavy-atom bond partners Not adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13 P because it is missing heavy-atom bond partners notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined from SEQRES records No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain C; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain D; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain E; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain F; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain G; guessing termini instead Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined from SEQRES records Chain-initial residues that are actual N termini: ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A PRO 299, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B PRO 106, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C THR 6, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D VAL 34, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 1, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F PRO 179, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G PRO 93, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439 Chain-initial residues that are not actual N termini: ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F GLY 316, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ALA 213, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G THR 386, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G VAL 439 Chain-final residues that are actual C termini: ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/A LEU 718, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B LEU 507, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C LEU 685, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D ARG 511, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602 Chain-final residues that are not actual C termini: ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASN 464, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E MET 300, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F LYS 349, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/F THR 307, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G LYS 602, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G GLY 207, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G HIS 335, ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/G ASN 434 Chain-initial residues that are not actual 5' termini: ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 13 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/B LEU 507 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ARG 29 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D SER 123 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D MET 285 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 420 8 messages similar to the above omitted 3052 hydrogen bonds Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/C ASN 72 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D GLN 127 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LEU 296 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D PHE 436 Adding 'H' to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/E ASP 319 4 messages similar to the above omitted 24712 hydrogens added > select #1/D:465@CE 1 atom, 1 residue, 1 model selected > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1 --- warnings | Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/H DG 8 P because it is missing heavy-atom bond partners Not adding hydrogens to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13 P because it is missing heavy-atom bond partners notes | Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain A determined from SEQRES records Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain B determined from SEQRES records No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain C; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain D; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain E; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain F; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain G; guessing termini instead Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain H determined from SEQRES records Termini for ylODC_54bpOriC061_rev29_PostPhenix.pdb (#1) chain I determined from SEQRES records Chain-initial residues that are actual N termini: ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A PRO 299, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B PRO 106, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C THR 6, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D VAL 34, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 1, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F PRO 179, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G PRO 93, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439 Chain-initial residues that are not actual N termini: ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F GLY 316, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ALA 213, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G THR 386, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G VAL 439 Chain-final residues that are actual C termini: ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/A LEU 718, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B LEU 507, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C LEU 685, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D ARG 511, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602 Chain-final residues that are not actual C termini: ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASN 464, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E MET 300, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F LYS 349, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/F THR 307, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G LYS 602, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G GLY 207, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G HIS 335, ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/G ASN 434 Chain-initial residues that are not actual 5' termini: ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 13 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/B LEU 507 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ARG 29 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D SER 123 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D MET 285 Missing OXT added to C-terminal residue ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 420 8 messages similar to the above omitted 3042 hydrogen bonds Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/C ASN 72 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D GLN 127 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LEU 296 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D PHE 436 Adding 'H' to ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/E ASP 319 4 messages similar to the above omitted 24712 hydrogens added > ui tool show H-Bonds > select #1/D:465 22 atoms, 21 bonds, 1 residue, 1 model selected > hbonds sel restrict #1/H,I twoColors true intraRes false reveal true log > true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ylODC_54bpOriC061_rev29_PostPhenix.pdb 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 31 O6 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ1 2.845 1.875 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 NZ ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/I DG 32 N7 ylODC_54bpOriC061_rev29_PostPhenix.pdb #1/D LYS 465 HZ2 3.459 2.599 2 hydrogen bonds found 0 strict hydrogen bonds found > select #2/D:465 22 atoms, 21 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel restrict #2/H,I twoColors true intraRes false reveal true log > true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 ylODC_54bpOriC061_rev30_PostPhenix.pdb 2 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 31 O6 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ1 2.363 1.498 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 NZ ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/I DG 32 O6 ylODC_54bpOriC061_rev30_PostPhenix.pdb #2/D LYS 465 HZ2 2.546 1.684 2 hydrogen bonds found 0 strict hydrogen bonds found > ui tool show ""Side View"" > close #2 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb"" format pdb Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 --- 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 75323 atom styles 71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected > close #1 > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > hide sel cartoons > select clear > select ~nucleic 23823 atoms, 24273 bonds, 11 pseudobonds, 2978 residues, 3 models selected > hide sel atoms > select clear > select /D:465 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /G:548 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select /G:557 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/Orc4-Cdc6-element-54bpOriC061-ver1.png"" supersample 3 > select clear > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > show sel atoms > undo > show sel cartoons > color sel #808080 > color sel #AAAAAA > color sel #BBBBBB > transparency 70 r Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 70 cartoons > select clear > undo > transparency 0 ribbons > transparency 0 r Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 0 sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency sel 70 target c > transparency sel 90 target c > transparency sel 80 target c > transparency sel 75 target c > select clear > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > hide sel cartoons > show sel cartoons > select clear > turn x 2 180 > wait 180 > turn y 2 180 > wait 180 > turn y 2 180 > wait 180 > select /A,B,C,E,F 16637 atoms, 16971 bonds, 4 pseudobonds, 2073 residues, 3 models selected > hide sel cartoons > select up 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected > select up 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected > select clear > turn y 2 180 > wait 180 > turn y 2 180 > wait 180 > turn y 2 180 > wait 180 > turn y 2 180 > wait 180 > turn y 2 180 > wait 180 > select /I:32@O6 1 atom, 1 residue, 1 model selected > turn y 2 180 centerOn sel ; wait 180 Expected a keyword > turn y 2 180 centerOn sel ; wait 180 Expected a keyword > turn y 2 180 center sel > wait 180 > select clear > turn y 2 180 center sel ; wait 180 Invalid ""center"" argument: Center argument no objects specified > select /I:31@O6 1 atom, 1 residue, 1 model selected > turn y 2 180 center sel > wait 180 > turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180 Invalid ""center"" argument: Center argument no objects specified > select clear > turn y 2 180 center (#1/I:31 | #1/H:24) ; wait 180 Invalid ""center"" argument: Center argument no objects specified > turn y 2 180 center #1/I:31 ; wait 180 Invalid ""center"" argument: Center argument no objects specified > turn y 2 180 models #1/I:31 > wait 180 > turn y 2 180 models #1/I:31 > wait 180 > turn y 2 180 models #1/I:31 > turn y 2 180 models #1 center #1/I:31 Invalid ""center"" argument: Center argument no objects specified > select clear > select /I:31@O6 1 atom, 1 residue, 1 model selected > select clear > turn y 2 180 models #1 center #1/I:31@O6 Invalid ""center"" argument: Center argument no objects specified > turn y 2 180 center #1/I:31@O6 Invalid ""center"" argument: Center argument no objects specified > select /I:31@O6 1 atom, 1 residue, 1 model selected > turn y 2 180 center /I:31@O6 > select clear > turn y 2 180 center /I:31@O6 > turn y 1 360 center /I:31@O6 > wait 360 > turn y 1 360 center /I:31@O6 > wait 360 > movie record supersample 3 > turn y 2 180 center /I:31@O6 > wait 180 > movie encode ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/Orc4-Cdc6-binding-region-54bpOriC.mp4"" Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding- region-54bpOriC.mp4 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > turn y 2 180 center /I:31@O6 > wait 180 > movie record supersample 3 > turn y 2 180 center /I:31@O6 > wait 180 > movie encode ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/figures for > posterpub/Orc4-Cdc6-binding-region-54bpOriC-camera2.mp4"" Movie saved to /Users/jtbauer/.../figures for posterpub/Orc4-Cdc6-binding- region-54bpOriC-camera2.mp4 > show cartoons > transparency 0 cartoons > modelfix Changed 25299 atom styles 23699 atoms, 24145 bonds, 9 pseudobonds, 2970 residues, 2 models selected > select nucleic 1476 atoms, 1654 bonds, 72 residues, 1 model selected > ui tool show ""Add Hydrogens"" > addh #!2 Summary of feedback from adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #2 --- warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond partners notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain A determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain B determined from SEQRES records No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain C; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain D; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain E; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain F; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain G; guessing termini instead Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain H determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) chain I determined from SEQRES records Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127, /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL 439 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS 335, /G ASN 434, /G LYS 602 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS 602, /G GLY 207, /G HIS 335, /G ASN 434 Chain-initial residues that are not actual 5' termini: /I DG 13 Missing OXT added to C-terminal residue /B LEU 507 Missing OXT added to C-terminal residue /C ARG 29 Missing OXT added to C-terminal residue /D SER 123 Missing OXT added to C-terminal residue /D MET 285 Missing OXT added to C-terminal residue /D LEU 420 8 messages similar to the above omitted 3052 hydrogen bonds Adding 'H' to /C ASN 72 Adding 'H' to /D GLN 127 Adding 'H' to /D LEU 296 Adding 'H' to /D PHE 436 Adding 'H' to /E ASP 319 4 messages similar to the above omitted 24712 hydrogens added > ui tool show H-Bonds > hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 ylODC_54bpOriC061_rev30_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > split #2 Split ylODC_54bpOriC061_rev30_PostPhenix.pdb (#2) into 9 models Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb A #2.1 --- Chain | Description A | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb B #2.2 --- Chain | Description B | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb C #2.3 --- Chain | Description C | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb D #2.4 --- Chain | Description D | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb E #2.5 --- Chain | Description E | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb F #2.6 --- Chain | Description F | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb G #2.7 --- Chain | Description G | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb H #2.8 --- Chain | Description H | No description available Chain information for ylODC_54bpOriC061_rev30_PostPhenix.pdb I #2.9 --- Chain | Description I | No description available > select add #2.8 1170 atoms, 1262 bonds, 37 residues, 1 model selected > select add #2.9 2291 atoms, 2469 bonds, 72 residues, 2 models selected > hbonds sel restrict #2/A,B,C,D,E,F,G twoColors true intraRes false reveal > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2.7 ylODC_54bpOriC061_rev30_PostPhenix.pdb G 2.9 ylODC_54bpOriC061_rev30_PostPhenix.pdb I 2.8 ylODC_54bpOriC061_rev30_PostPhenix.pdb H 2.1 ylODC_54bpOriC061_rev30_PostPhenix.pdb A 2.2 ylODC_54bpOriC061_rev30_PostPhenix.pdb B 2.3 ylODC_54bpOriC061_rev30_PostPhenix.pdb C 2.4 ylODC_54bpOriC061_rev30_PostPhenix.pdb D 2.5 ylODC_54bpOriC061_rev30_PostPhenix.pdb E 2.6 ylODC_54bpOriC061_rev30_PostPhenix.pdb F 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found 0 strict hydrogen bonds found > close #2 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev30_PostPhenix.pdb"" format pdb Chain information for ylODC_54bpOriC061_rev30_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 > select nucleic 1476 atoms, 1654 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2"" restrict > #2/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true 'restrict' atom specifier selects no atoms > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to ylODC_54bpOriC061_rev30_PostPhenix.pdb #1 --- warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond partners notes | Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain A determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain B determined from SEQRES records No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain C; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain D; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain E; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain F; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain G; guessing termini instead Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain H determined from SEQRES records Termini for ylODC_54bpOriC061_rev30_PostPhenix.pdb (#1) chain I determined from SEQRES records Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127, /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL 439 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS 335, /G ASN 434, /G LYS 602 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS 602, /G GLY 207, /G HIS 335, /G ASN 434 Chain-initial residues that are not actual 5' termini: /I DG 13 Missing OXT added to C-terminal residue /B LEU 507 Missing OXT added to C-terminal residue /C ARG 29 Missing OXT added to C-terminal residue /D SER 123 Missing OXT added to C-terminal residue /D MET 285 Missing OXT added to C-terminal residue /D LEU 420 8 messages similar to the above omitted 3052 hydrogen bonds Adding 'H' to /C ASN 72 Adding 'H' to /D GLN 127 Adding 'H' to /D LEU 296 Adding 'H' to /D PHE 436 Adding 'H' to /E ASP 319 4 messages similar to the above omitted 24712 hydrogens added > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2"" restrict > #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false > reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 74 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 74 hydrogen bonds found 21 strict hydrogen bonds found > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false > select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 74 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 74 hydrogen bonds found 21 strict hydrogen bonds found > select up 1950 atoms, 1998 bonds, 79 residues, 1 model selected > show sel atoms > select clear > select ~nucleic 47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected > hide sel cartoons > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"" > select /G:548@NZ 1 atom, 1 residue, 1 model selected > select /I:29@N3 1 atom, 1 residue, 1 model selected > select /I:30 33 atoms, 35 bonds, 1 residue, 1 model selected > select /I:29 32 atoms, 33 bonds, 1 residue, 1 model selected > select /H:26 32 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Renumber Residues"" > renumber /H start -7 37 residues renumbered > select /H:12 32 atoms, 34 bonds, 1 residue, 1 model selected > select /H:11 32 atoms, 34 bonds, 1 residue, 1 model selected > renumber /H start -16 37 residues renumbered > renumber /H start -16 0 residues renumbered > renumber /H start -16 0 residues renumbered > select /H:3 32 atoms, 34 bonds, 1 residue, 1 model selected > select /H:2 32 atoms, 34 bonds, 1 residue, 1 model selected > renumber /H start -18 37 residues renumbered > select /H:0 32 atoms, 34 bonds, 1 residue, 1 model selected > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"" > select /I:29 32 atoms, 33 bonds, 1 residue, 1 model selected > ui tool show ""Renumber Residues"" > renumber /I start -15 35 residues renumbered > select /I:1 32 atoms, 33 bonds, 1 residue, 1 model selected > renumber /I start -16 35 residues renumbered > renumber /I start -16 0 residues renumbered > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"" > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30"" restrict > #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false select true > reveal true log true Atom specifier selects no atoms > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false > select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 74 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 18 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT -16 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC -15 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 17 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 18 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC -13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA -12 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC -13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC -13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG -10 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 9 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG -10 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 9 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 8 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 8 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 10 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 10 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT -8 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 12 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 11 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DA -11 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT -10 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 11 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA -9 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 6 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /H DC 6 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 6 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT -4 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT -4 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 7 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA -12 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA -12 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA -11 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA -11 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 1 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 2 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 2 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 3 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA -9 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG -10 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG -10 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG -10 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC -9 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT -13 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT -13 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT -13 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 15 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG -10 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG -10 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT -11 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG -10 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 12 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 13 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC -9 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA -8 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /H DA 0 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /H DA 1 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 2 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 3 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 1 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 2 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 0 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 3 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 5 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 5 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA -11 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT -10 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT -10 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT -10 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT -10 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA -9 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 3 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 0 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 0 OP2 /G LYS 581 HZ1 3.143 2.140 74 hydrogen bonds found 21 strict hydrogen bonds found > show sel atoms > select clear > ui tool show ""Change Chain IDs"" > changechains H main Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (main/299/) > changechains H main Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (main/299/) > changechains I opp No residues specified > changechains I opp No residues specified > changechains H main Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (main/299/) > select /H 1170 atoms, 1262 bonds, 37 residues, 1 model selected > changechains sel main Chain IDs of 37 residues changed > select /I 1121 atoms, 1207 bonds, 35 residues, 1 model selected > changechains sel opp Chain IDs of 35 residues changed > select clear > ui tool show H-Bonds > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false > reveal true log true Atom specifier selects no atoms > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true intraRes false > reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 74 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /main DA -11 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /main DC 6 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /main DA -12 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /main DA 0 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /opp DG 2 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /main DA 1 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /main DG 2 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /main DA -11 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /main DT -10 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /main DA 0 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140 74 hydrogen bonds found 21 strict hydrogen bonds found > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver30.cxs"" > select /main:-13 30 atoms, 31 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /A:436@ND2 1 atom, 1 residue, 1 model selected > select /main:-12 32 atoms, 34 bonds, 1 residue, 1 model selected > select /main:-10 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:-11 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:-10 32 atoms, 33 bonds, 1 residue, 1 model selected > select clear > select /main:-9 32 atoms, 34 bonds, 1 residue, 1 model selected > select /main:-9 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:-8 32 atoms, 33 bonds, 1 residue, 1 model selected > select /main:-9 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel cartoons > select /main:-8 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:-9@C3' 1 atom, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 32 atoms, 34 bonds, 1 residue, 1 model selected > show sel cartoons > select clear > select /main:0 32 atoms, 34 bonds, 1 residue, 1 model selected > select /main:0 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:1 32 atoms, 34 bonds, 1 residue, 1 model selected > select /main:6 30 atoms, 31 bonds, 1 residue, 1 model selected > hide sel cartoons > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2"" dashes 6 > restrict #1/A,B,C,D,E,F,G twoColors true intraRes false reveal true > retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > ui tool show H-Bonds > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true intraRes false > select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G twoColors true slopColor > #00f900 intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ylODC_54bpOriC061_rev30_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /opp DC 18 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /main DT -16 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /main DC -15 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /opp DT 17 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /opp DC 18 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /main DC -13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /main DA -12 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /main DC -13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /main DC -13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /opp DG -10 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /main DG 9 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /opp DG -10 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /main DG 9 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /main DT 8 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /opp DA 8 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /opp DA 10 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /main DT -8 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /opp DT 12 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /opp DT 11 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /main DA -9 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /main DA 7 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /main DA -12 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /main DA -11 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /main DA -11 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /opp DG 1 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /main DA -9 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /opp DG -10 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /opp DG -10 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /opp DG -10 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /opp DC -9 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /opp DT -13 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /opp DG -10 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /opp DG -10 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /opp DT -11 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /opp DG -10 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /main DT 12 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /opp DC -9 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /opp DA -8 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /main DA 1 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /opp DG 5 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /opp DG 5 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /main DT -10 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /main DT -10 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /main DA -9 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /opp DG 3 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /main DA 0 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > select clear > select /main:7 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:8 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select clear > select /main:12@C2 1 atom, 1 residue, 1 model selected > select /main:15 33 atoms, 35 bonds, 1 residue, 1 model selected > select clear > select /opp:17 32 atoms, 33 bonds, 1 residue, 1 model selected > select /opp:18 31 atoms, 32 bonds, 1 residue, 1 model selected > select /opp:18 31 atoms, 32 bonds, 1 residue, 1 model selected > select /opp:17 32 atoms, 33 bonds, 1 residue, 1 model selected > select /opp:18 31 atoms, 32 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > hide sel cartoons > select /opp:11 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select clear > select /opp:12 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /opp:10 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select /opp:9 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /opp:8 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select /opp:9 32 atoms, 33 bonds, 1 residue, 1 model selected > select /opp:1 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /opp:0 32 atoms, 33 bonds, 1 residue, 1 model selected > select /opp:-2 30 atoms, 31 bonds, 1 residue, 1 model selected > select /opp:-4 32 atoms, 33 bonds, 1 residue, 1 model selected > select /opp:-8 32 atoms, 34 bonds, 1 residue, 1 model selected > select /opp:-9 30 atoms, 31 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /E:363@N 1 atom, 1 residue, 1 model selected > select /opp:-9 30 atoms, 31 bonds, 1 residue, 1 model selected > select /E:362@N 1 atom, 1 residue, 1 model selected > select /opp:-9 30 atoms, 31 bonds, 1 residue, 1 model selected > hide sel cartoons > select /opp:-11 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > select /opp:-10 33 atoms, 35 bonds, 1 residue, 1 model selected > select /E:357@N 1 atom, 1 residue, 1 model selected > select /E:356 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"" Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #2 --- 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 75323 atom styles 71260 atoms, 72152 bonds, 18 pseudobonds, 5940 residues, 4 models selected > close #1 > select nucleic 1476 atoms, 1654 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond- > generation2_ver31_relaxed40"" dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop > 40.0 twoColors true slopColor #ff9300 intraRes false select true reveal true > retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 78 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 no hydrogen 3.042 N/A /A ARG 301 NH1 /H DT 10 O2 no hydrogen 2.780 N/A /A ARG 301 NH1 /H DC 11 O4' no hydrogen 2.808 N/A /A ARG 301 NH2 /I DT 46 O2 no hydrogen 3.419 N/A /A ARG 301 NH2 /I DC 47 OP1 no hydrogen 3.241 N/A /A PHE 303 N /H DC 13 OP1 no hydrogen 2.683 N/A /A LYS 305 NZ /H DA 14 OP1 no hydrogen 3.005 N/A /A ASN 435 ND2 /H DC 13 OP2 no hydrogen 2.896 N/A /A ASN 436 ND2 /H DC 13 OP2 no hydrogen 3.172 N/A /B LYS 148 NZ /I DG 19 OP1 no hydrogen 2.880 N/A /B ARG 150 NH1 /H DG 35 O6 no hydrogen 3.317 N/A /B ARG 150 NH1 /I DG 19 O6 no hydrogen 3.200 N/A /B ARG 150 NH2 /H DG 35 O6 no hydrogen 2.932 N/A /B GLY 153 N /H DT 34 OP2 no hydrogen 2.955 N/A /B LYS 248 NZ /I DA 37 O3' no hydrogen 3.058 N/A /B LYS 279 N /I DA 39 OP1 no hydrogen 3.012 N/A /B ASP 280 N /I DA 39 OP1 no hydrogen 3.419 N/A /C LYS 188 NZ /H DT 18 OP1 no hydrogen 2.597 N/A /C ARG 219 N /I DT 41 OP1 no hydrogen 2.860 N/A /C ARG 219 NH1 /I DT 40 OP1 no hydrogen 2.808 N/A /C ARG 220 NH1 /H DA 15 N3 no hydrogen 3.522 N/A /C ARG 220 NH1 /H DT 16 O2 no hydrogen 3.328 N/A /C ARG 220 NH1 /I DT 40 O2 no hydrogen 3.062 N/A /C TYR 223 OH /H DA 17 O3' no hydrogen 2.926 N/A /C TYR 223 OH /H DT 18 OP1 no hydrogen 2.834 N/A /C TYR 607 OH /H DC 32 OP2 no hydrogen 3.278 N/A /C LYS 671 N /H DC 32 OP1 no hydrogen 2.864 N/A /C ARG 672 N /H DC 32 OP1 no hydrogen 2.895 N/A /C ARG 672 NH1 /I DT 25 O2 no hydrogen 2.707 N/A /C ARG 672 NH2 /I DT 25 O2 no hydrogen 3.408 N/A /C LYS 673 NZ /H DA 33 OP1 no hydrogen 2.886 N/A /D LYS 168 NZ /H DA 14 N3 no hydrogen 2.838 N/A /D SER 169 OG /H DA 14 O3' no hydrogen 3.382 N/A /D SER 169 OG /H DA 15 OP2 no hydrogen 2.801 N/A /D ILE 170 N /H DA 15 OP2 no hydrogen 3.077 N/A /D SER 463 OG /I DG 30 OP1 no hydrogen 2.493 N/A /D LYS 465 NZ /I DG 31 N7 no hydrogen 3.444 N/A /D LYS 465 NZ /I DG 31 O6 no hydrogen 2.363 N/A /D LYS 465 NZ /I DG 32 O6 no hydrogen 2.546 N/A /E ARG 76 NH1 /H DA 17 OP1 no hydrogen 3.235 N/A /E ARG 340 NE /I DG 19 O5' no hydrogen 3.009 N/A /E ARG 340 NE /I DG 19 OP2 no hydrogen 2.873 N/A /E ARG 340 NH2 /I DG 19 OP2 no hydrogen 3.300 N/A /E TYR 341 OH /I DG 19 O3' no hydrogen 3.180 N/A /E TYR 341 OH /I DC 20 OP1 no hydrogen 2.940 N/A /E ARG 356 NH1 /I DT 18 OP2 no hydrogen 2.602 N/A /E ARG 357 NH1 /I DT 16 O2 no hydrogen 2.784 N/A /E ARG 357 NH2 /I DT 16 O2 no hydrogen 2.882 N/A /E ARG 357 NH2 /I DT 16 O4' no hydrogen 3.135 N/A /E GLU 358 N /H DG 41 OP1 no hydrogen 2.888 N/A /E THR 359 OG1 /I DG 19 OP1 no hydrogen 2.802 N/A /E ARG 362 N /I DG 19 O3' no hydrogen 3.350 N/A /E ARG 362 NH1 /I DT 18 O2 no hydrogen 2.975 N/A /E ARG 362 NH1 /I DG 19 O4' no hydrogen 3.022 N/A /E ARG 362 NH2 /H DT 38 O2 no hydrogen 2.881 N/A /E ARG 362 NH2 /H DA 39 O4' no hydrogen 3.366 N/A /E LYS 363 N /I DC 20 OP2 no hydrogen 3.408 N/A /E LYS 363 NZ /I DA 21 OP1 no hydrogen 2.944 N/A /G GLY 543 N /H DA 26 OP1 no hydrogen 2.943 N/A /G GLY 546 N /H DA 27 OP1 no hydrogen 2.915 N/A /G LYS 547 NZ /I DG 31 O3' no hydrogen 2.870 N/A /G LYS 547 NZ /I DG 32 OP1 no hydrogen 2.552 N/A /G LYS 548 NZ /H DA 27 N3 no hydrogen 2.902 N/A /G LYS 548 NZ /H DG 28 O4' no hydrogen 2.987 N/A /G LYS 548 NZ /I DT 29 O2 no hydrogen 3.197 N/A /G ASN 553 N /I DG 32 OP2 no hydrogen 2.957 N/A /G ARG 557 NH1 /I DG 34 O6 no hydrogen 2.913 N/A /G ARG 557 NH1 /I DT 35 O4 no hydrogen 3.519 N/A /G ARG 557 NH2 /I DG 34 N7 no hydrogen 2.372 N/A /G LYS 560 NZ /H DA 15 OP1 no hydrogen 3.180 N/A /G GLY 561 N /H DT 16 OP2 no hydrogen 2.846 N/A /G THR 563 N /H DT 16 OP1 no hydrogen 2.931 N/A /G THR 563 OG1 /H DA 15 O3' no hydrogen 2.798 N/A /G THR 563 OG1 /H DT 16 OP1 no hydrogen 3.027 N/A /G ALA 565 N /H DA 17 OP2 no hydrogen 2.576 N/A /G ARG 574 NH2 /I DG 32 OP1 no hydrogen 3.076 N/A /G LYS 581 NZ /H DA 26 O5' no hydrogen 3.367 N/A /G LYS 581 NZ /H DA 26 OP2 no hydrogen 3.143 N/A 78 hydrogen bonds found 25 strict hydrogen bonds found > select up 1142 atoms, 1192 bonds, 81 residues, 1 model selected > show sel atoms > ui tool show H-Bonds > ui tool show ""Add Hydrogens"" > addh #!2 Summary of feedback from adding hydrogens to ylODC_54bpOriC061_rev31_PostPhenix.pdb #2 --- warnings | Not adding hydrogens to /H DG 8 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DG 13 P because it is missing heavy-atom bond partners notes | Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain A determined from SEQRES records Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain B determined from SEQRES records No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain C; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain D; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain E; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain F; guessing termini instead No usable SEQRES records for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain G; guessing termini instead Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain H determined from SEQRES records Termini for ylODC_54bpOriC061_rev31_PostPhenix.pdb (#2) chain I determined from SEQRES records Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C THR 6, /D VAL 34, /E MET 1, /F PRO 179, /G PRO 93, /C THR 6, /C ASN 72, /D VAL 34, /D GLN 127, /D LEU 296, /D PHE 436, /E MET 1, /E ASP 319, /F PRO 179, /F GLY 316, /G PRO 93, /G ALA 213, /G THR 386, /G VAL 439 Chain-initial residues that are not actual N termini: /C ASN 72, /D GLN 127, /D LEU 296, /D PHE 436, /E ASP 319, /F GLY 316, /G ALA 213, /G THR 386, /G VAL 439 Chain-final residues that are actual C termini: /A LEU 718, /B LEU 507, /C LEU 685, /D ARG 511, /C ARG 29, /C LEU 685, /D SER 123, /D MET 285, /D LEU 420, /D ARG 511, /E MET 300, /E ASN 464, /F THR 307, /F LYS 349, /G GLY 207, /G HIS 335, /G ASN 434, /G LYS 602 Chain-final residues that are not actual C termini: /C ARG 29, /D SER 123, /D MET 285, /D LEU 420, /E ASN 464, /E MET 300, /F LYS 349, /F THR 307, /G LYS 602, /G GLY 207, /G HIS 335, /G ASN 434 Chain-initial residues that are not actual 5' termini: /I DG 13 Missing OXT added to C-terminal residue /B LEU 507 Missing OXT added to C-terminal residue /C ARG 29 Missing OXT added to C-terminal residue /D SER 123 Missing OXT added to C-terminal residue /D MET 285 Missing OXT added to C-terminal residue /D LEU 420 8 messages similar to the above omitted 3054 hydrogen bonds Adding 'H' to /C ASN 72 Adding 'H' to /D GLN 127 Adding 'H' to /D LEU 296 Adding 'H' to /D PHE 436 Adding 'H' to /E ASP 319 4 messages similar to the above omitted 24712 hydrogens added > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond- > generation2_ver31_relaxed40"" restrict #2/A,B,C,D,E,F,G angleSlop 40.0 > twoColors true slopColor #ff9300 intraRes false select true reveal true log > true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 139 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A LYS 300 NZ /A ASN 436 OD1 /A LYS 300 HZ1 3.118 2.399 /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 N /A ARG 431 O /A LYS 305 H 2.798 1.912 /A LYS 305 NZ /A GLU 421 OE1 /A LYS 305 HZ2 3.041 2.143 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /A ASN 436 OD1 /A ASN 435 HD21 3.103 2.697 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /A LYS 439 N /A ASN 435 O /A LYS 439 H 3.001 2.009 /A LEU 440 N /A ASN 436 O /A LEU 440 H 2.894 1.926 /A ARG 696 NH2 /G GLY 546 O /A ARG 696 HH21 3.117 2.584 /B LYS 148 N /B PHE 144 O /B LYS 148 H 2.920 2.035 /B LYS 148 NZ /E ARG 340 O /B LYS 148 HZ1 2.840 1.919 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B ASN 252 N /B LYS 248 O /B ASN 252 H 2.859 1.943 /B ASN 252 ND2 /B LYS 248 O /B ASN 252 HD21 2.823 2.421 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B LYS 279 NZ /B ASN 275 O /B LYS 279 HZ1 3.083 2.418 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /B ASP 282 N /B ASP 280 OD1 /B ASP 282 H 3.192 2.326 /B LEU 284 N /B ASP 280 O /B LEU 284 H 2.837 1.850 /C LYS 188 N /C SER 186 OG /C LYS 188 H 3.325 2.447 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C LYS 192 N /C LYS 188 O /C LYS 192 H 2.878 1.920 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NE /C GLU 212 OE1 /C ARG 219 HE 3.259 2.637 /C ARG 219 NE /C GLU 212 OE2 /C ARG 219 HE 2.841 2.024 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 219 NH2 /C GLU 212 OE1 /C ARG 219 HH21 2.795 2.099 /C ARG 220 N /C ASP 218 OD1 /C ARG 220 H 2.980 2.018 /C ARG 220 NE /C ASP 218 OD1 /C ARG 220 HE 2.810 1.851 /C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C ARG 220 NH2 /C ASP 218 OD2 /C ARG 220 HH21 2.856 1.862 /C LYS 222 N /C ARG 219 O /C LYS 222 H 3.430 2.524 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C THR 670 OG1 /C LYS 673 O /C THR 670 HG1 2.628 1.854 /C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /B ARG 152 O /C LYS 673 HZ3 3.238 2.551 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /C SER 676 N /C LYS 673 O /C SER 676 H 3.091 2.178 /D LYS 144 NZ /G LYS 560 O /D LYS 144 HZ1 3.005 2.080 /D ARG 148 NE /G GLY 561 O /D ARG 148 HE 3.310 2.528 /D ARG 148 NH1 /D LYS 168 O /D ARG 148 HH12 2.488 1.669 /D ARG 148 NH2 /D LYS 168 O /D ARG 148 HH22 2.570 1.792 /D ARG 148 NH2 /G GLY 561 O /D ARG 148 HH21 2.721 1.730 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 N /D ASN 167 OD1 /D SER 169 H 3.368 2.513 /D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D THR 173 N /D SER 169 O /D THR 173 H 2.884 1.953 /D THR 173 OG1 /D SER 169 O /D THR 173 HG1 2.830 1.908 /D LEU 174 N /D ILE 170 O /D LEU 174 H 2.877 1.880 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /D ARG 466 N /D SER 463 O /D ARG 466 H 2.968 2.378 /D ARG 466 N /D SER 463 OG /D ARG 466 H 3.160 2.176 /D VAL 467 N /D SER 463 O /D VAL 467 H 2.848 1.922 /D ALA 468 N /D LYS 465 O /D ALA 468 H 3.107 2.545 /D LYS 469 N /D LYS 465 O /D LYS 469 H 3.084 2.242 /E ARG 76 NE /E GLN 80 OE1 /E ARG 76 HE 2.849 1.855 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 76 NH2 /C ASP 218 OD2 /E ARG 76 HH22 3.505 2.561 /E ARG 76 NH2 /E GLN 80 OE1 /E ARG 76 HH21 3.522 2.773 /E GLN 80 N /E ARG 76 O /E GLN 80 H 2.915 1.931 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 N /E PRO 338 O /E TYR 341 H 3.454 2.618 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 344 N /E TYR 341 O /E ARG 344 H 2.933 2.330 /E ARG 344 NH1 /E THR 359 O /E ARG 344 HH11 3.312 2.421 /E PHE 345 N /E TYR 341 O /E PHE 345 H 3.133 2.333 /E LYS 350 NZ /E GLU 358 OE2 /E LYS 350 HZ1 2.768 1.940 /E ARG 356 NE /B ASP 145 OD1 /E ARG 356 HE 2.892 2.039 /E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912 /E ARG 356 NH2 /B ASP 145 O /E ARG 356 HH21 2.568 1.841 /E ARG 356 NH2 /B ASP 145 OD1 /E ARG 356 HH21 3.006 2.208 /E ARG 356 NH2 /B THR 149 OG1 /E ARG 356 HH22 3.252 2.468 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 N /E ARG 357 O /E THR 359 H 3.010 2.141 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G THR 542 N /G LYS 581 O /G THR 542 H 2.775 1.833 /G THR 542 OG1 /G LYS 581 O /G THR 542 HG1 3.224 2.270 /G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343 /G CYS 545 SG /G GLY 543 O /G CYS 545 HG 3.840 2.525 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ASN 553 ND2 /G GLY 572 O /G ASN 553 HD22 2.832 2.022 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G VAL 570 N /G ASN 553 O /G VAL 570 H 3.200 2.301 /G TYR 571 N /G ASN 553 OD1 /G TYR 571 H 3.237 2.453 /G ARG 574 NH2 /G GLY 551 O /G ARG 574 HH22 2.887 1.879 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G ASP 576 N /G ARG 574 O /G ASP 576 H 2.809 1.912 /G LYS 581 N /G THR 542 O /G LYS 581 H 3.429 2.627 /G LYS 581 N /G GLY 543 O /G LYS 581 H 3.308 2.380 /G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 139 hydrogen bonds found 44 strict hydrogen bonds found > select up 2686 atoms, 2716 bonds, 122 residues, 1 model selected > show sel atoms > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond- > generation2_ver31_relaxed40"" restrict #2/A,B,C,D,E,F,G angleSlop 40.0 > twoColors true slopColor #ff9300 intraRes false select true reveal true log > true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 75 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 75 hydrogen bonds found 21 strict hydrogen bonds found > select up 1974 atoms, 2022 bonds, 80 residues, 1 model selected > show sel atoms > select clear > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/hbond-generation2_ver31"" dashes > 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false > select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > select clear > select ~sel & ##selected Nothing selected > select ~nucleic 47733 atoms, 48183 bonds, 11 pseudobonds, 2978 residues, 3 models selected > hide sel cartoons > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" > select /I:18 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /I:16 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > hide atoms > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G angleSlop 40.0 twoColors true > slopColor #ff9300 intraRes false select true reveal true retainCurrent true > log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 75 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DA 15 N3 /C ARG 220 HH12 3.522 2.929 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C LYS 671 N /H DC 32 OP1 /C LYS 671 H 2.864 2.159 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 14 O3' /D SER 169 HG 3.382 2.801 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 N7 /D LYS 465 HZ1 3.444 2.853 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 356 NH1 /I DT 18 OP2 /E ARG 356 HH11 2.602 1.912 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E ARG 362 NH2 /H DA 39 O4' /E ARG 362 HH21 3.366 2.779 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 543 N /H DA 26 OP1 /G GLY 543 H 2.943 2.343 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 31 O3' /G LYS 547 HZ2 2.870 2.326 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /H DA 27 N3 /G LYS 548 HZ1 2.902 2.236 /G LYS 548 NZ /H DG 28 O4' /G LYS 548 HZ2 2.987 2.212 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G LYS 560 NZ /H DA 15 OP1 /G LYS 560 HZ3 3.180 2.601 /G GLY 561 N /H DT 16 OP1 /G GLY 561 H 3.390 2.598 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 N /H DT 16 OP1 /G THR 563 H 2.931 2.306 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 O5' /G LYS 581 HZ1 3.367 2.792 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 75 hydrogen bonds found 21 strict hydrogen bonds found > select up 1974 atoms, 2022 bonds, 80 residues, 1 model selected > show sel atoms > select nucleic 2291 atoms, 2469 bonds, 72 residues, 1 model selected > show sel atoms > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G twoColors true slopColor > #00f900 intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 2 ylODC_54bpOriC061_rev31_PostPhenix.pdb 61 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ARG 301 NE /I DC 47 OP1 /A ARG 301 HE 3.042 2.096 /A ARG 301 NH1 /H DT 10 O2 /A ARG 301 HH12 2.780 1.937 /A ARG 301 NH1 /H DC 11 O4' /A ARG 301 HH11 2.808 1.918 /A ARG 301 NH2 /I DT 46 O2 /A ARG 301 HH22 3.419 2.726 /A ARG 301 NH2 /I DC 47 OP1 /A ARG 301 HH21 3.241 2.383 /A PHE 303 N /H DC 13 OP1 /A PHE 303 H 2.683 1.713 /A LYS 305 NZ /H DA 14 OP1 /A LYS 305 HZ1 3.005 2.074 /A ASN 435 ND2 /H DC 13 OP2 /A ASN 435 HD22 2.896 1.911 /A ASN 436 ND2 /H DC 13 OP2 /A ASN 436 HD22 3.172 2.251 /B LYS 148 NZ /I DG 19 OP1 /B LYS 148 HZ3 2.880 2.062 /B ARG 150 NH1 /H DG 35 O6 /B ARG 150 HH12 3.317 2.492 /B ARG 150 NH1 /I DG 19 O6 /B ARG 150 HH12 3.200 2.518 /B ARG 150 NH2 /H DG 35 O6 /B ARG 150 HH22 2.932 1.954 /B GLY 153 N /H DT 34 OP2 /B GLY 153 H 2.955 1.965 /B LYS 248 NZ /I DA 37 O3' /B LYS 248 HZ1 3.058 2.307 /B LYS 279 N /I DA 39 OP1 /B LYS 279 H 3.012 2.176 /B ASP 280 N /I DA 39 OP1 /B ASP 280 H 3.419 2.439 /C LYS 188 NZ /H DT 18 OP1 /C LYS 188 HZ1 2.597 1.602 /C ARG 219 N /I DT 41 OP1 /C ARG 219 H 2.860 1.859 /C ARG 219 NH1 /I DT 40 OP1 /C ARG 219 HH11 2.808 2.044 /C ARG 220 NH1 /H DT 16 O2 /C ARG 220 HH11 3.328 2.600 /C ARG 220 NH1 /I DT 40 O2 /C ARG 220 HH11 3.062 2.380 /C TYR 223 OH /H DA 17 O3' /C TYR 223 HH 2.926 2.064 /C TYR 607 OH /H DC 32 OP2 /C TYR 607 HH 3.278 2.327 /C ARG 672 N /H DC 32 OP1 /C ARG 672 H 2.895 1.905 /C ARG 672 NH1 /I DT 25 O2 /C ARG 672 HH12 2.707 1.845 /C ARG 672 NH2 /I DT 25 O2 /C ARG 672 HH22 3.408 2.771 /C LYS 673 NZ /H DA 33 OP1 /C LYS 673 HZ1 2.886 1.972 /D LYS 168 NZ /H DA 14 N3 /D LYS 168 HZ1 2.838 1.847 /D SER 169 OG /H DA 15 OP2 /D SER 169 HG 2.801 1.842 /D ILE 170 N /H DA 15 OP2 /D ILE 170 H 3.077 2.202 /D SER 463 OG /I DG 30 OP1 /D SER 463 HG 2.493 1.565 /D LYS 465 NZ /I DG 31 O6 /D LYS 465 HZ1 2.363 1.498 /D LYS 465 NZ /I DG 32 O6 /D LYS 465 HZ2 2.546 1.684 /E ARG 76 NH1 /H DA 17 OP1 /E ARG 76 HH11 3.235 2.257 /E ARG 340 NE /I DG 19 O5' /E ARG 340 HE 3.009 2.192 /E ARG 340 NE /I DG 19 OP2 /E ARG 340 HE 2.873 1.974 /E ARG 340 NH2 /I DG 19 OP2 /E ARG 340 HH21 3.300 2.551 /E TYR 341 OH /I DC 20 OP1 /E TYR 341 HH 2.940 2.219 /E ARG 357 NH1 /I DT 16 O2 /E ARG 357 HH12 2.784 1.882 /E ARG 357 NH2 /I DT 16 O2 /E ARG 357 HH22 2.882 2.025 /E ARG 357 NH2 /I DT 16 O4' /E ARG 357 HH22 3.135 2.386 /E GLU 358 N /H DG 41 OP1 /E GLU 358 H 2.888 1.905 /E THR 359 OG1 /I DG 19 OP1 /E THR 359 HG1 2.802 2.243 /E ARG 362 N /I DG 19 O3' /E ARG 362 H 3.350 2.344 /E ARG 362 NH1 /I DT 18 O2 /E ARG 362 HH12 2.975 2.081 /E ARG 362 NH1 /I DG 19 O4' /E ARG 362 HH11 3.022 2.183 /E ARG 362 NH2 /H DT 38 O2 /E ARG 362 HH22 2.881 2.130 /E LYS 363 N /I DC 20 OP2 /E LYS 363 H 3.408 2.442 /E LYS 363 NZ /I DA 21 OP1 /E LYS 363 HZ1 2.944 1.968 /G GLY 546 N /H DA 27 OP1 /G GLY 546 H 2.915 2.028 /G LYS 547 NZ /I DG 32 OP1 /G LYS 547 HZ1 2.552 1.558 /G LYS 548 NZ /I DT 29 O2 /G LYS 548 HZ3 3.197 2.248 /G ASN 553 N /I DG 32 OP2 /G ASN 553 H 2.957 2.079 /G ARG 557 NH1 /I DG 34 O6 /G ARG 557 HH12 2.913 1.906 /G ARG 557 NH2 /I DG 34 N7 /G ARG 557 HH22 2.372 1.443 /G GLY 561 N /H DT 16 OP2 /G GLY 561 H 2.846 2.111 /G THR 563 OG1 /H DT 16 OP1 /G THR 563 HG1 3.027 2.078 /G ALA 565 N /H DA 17 OP2 /G ALA 565 H 2.576 1.574 /G ARG 574 NH2 /I DG 32 OP1 /G ARG 574 HH21 3.076 2.128 /G LYS 581 NZ /H DA 26 OP2 /G LYS 581 HZ1 3.143 2.140 61 hydrogen bonds found 21 strict hydrogen bonds found > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" > select /I:17 32 atoms, 34 bonds, 1 residue, 1 model selected > select clear > select /H:26 32 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Renumber Residues"" > renumber /H start -16 37 residues renumbered > renumber /H start -18 37 residues renumbered > renumber /I start -16 35 residues renumbered > select /I 1121 atoms, 1207 bonds, 35 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel opp Chain IDs of 35 residues changed > select /H 1170 atoms, 1262 bonds, 37 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel main Chain IDs of 37 residues changed > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" > select /opp:-13 32 atoms, 33 bonds, 1 residue, 1 model selected > select clear > close #2 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb"" Chain information for ARMori_ODC_ver20_DNAchainfix_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 24882 atom styles 23363 atoms, 23801 bonds, 15 pseudobonds, 2924 residues, 2 models selected > select ~nucleic 23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected > hide sel cartoons > select nucleic 1391 atoms, 1559 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"" > dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor > #ff9300 intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 50 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /I DG 53 O3' no hydrogen 3.342 N/A /A ASN 436 ND2 /H DA 10 OP1 no hydrogen 2.810 N/A /B LYS 148 NZ /I DA 28 OP1 no hydrogen 3.208 N/A /B LYS 279 N /I DA 48 OP1 no hydrogen 3.110 N/A /C LYS 188 NZ /H DC 15 OP1 no hydrogen 3.176 N/A /C ARG 219 NH1 /I DT 49 OP2 no hydrogen 3.015 N/A /C ARG 220 NH1 /H DT 13 O2 no hydrogen 3.388 N/A /C ARG 220 NH1 /I DT 49 O2 no hydrogen 3.296 N/A /C TYR 223 OH /H DC 15 OP1 no hydrogen 2.762 N/A /C TYR 607 OH /H DC 29 OP2 no hydrogen 3.098 N/A /C ARG 672 N /H DC 29 OP1 no hydrogen 3.388 N/A /C ARG 672 NH1 /I DT 34 O2 no hydrogen 2.806 N/A /C ARG 672 NH2 /I DT 34 O2 no hydrogen 2.902 N/A /C ARG 672 NH2 /I DT 34 O4' no hydrogen 3.185 N/A /C LYS 673 NZ /H DT 30 OP1 no hydrogen 3.030 N/A /D LYS 168 NZ /H DT 11 O2 no hydrogen 2.564 N/A /D SER 169 OG /H DA 12 OP1 no hydrogen 3.284 N/A /D SER 463 OG /I DT 39 OP2 no hydrogen 2.803 N/A /D LYS 465 NZ /I DG 40 N7 no hydrogen 3.514 N/A /D LYS 465 NZ /I DG 40 O6 no hydrogen 3.045 N/A /D LYS 465 NZ /I DG 41 O6 no hydrogen 3.189 N/A /E ARG 76 NH1 /H DG 14 OP1 no hydrogen 2.908 N/A /E ARG 340 NH1 /I DA 28 OP2 no hydrogen 3.135 N/A /E ARG 356 NH1 /I DT 27 OP2 no hydrogen 2.946 N/A /E ARG 357 N /I DT 27 OP1 no hydrogen 3.073 N/A /E ARG 357 NH1 /I DT 25 O2 no hydrogen 2.761 N/A /E ARG 357 NH2 /I DT 25 O2 no hydrogen 2.690 N/A /E GLU 358 N /H DG 38 OP1 no hydrogen 3.275 N/A /E THR 359 OG1 /I DA 28 OP1 no hydrogen 2.552 N/A /E ARG 362 N /I DG 29 OP2 no hydrogen 2.892 N/A /E ARG 362 NH1 /H DC 35 O4' no hydrogen 3.369 N/A /E ARG 362 NH2 /H DC 35 O2 no hydrogen 3.076 N/A /E ARG 362 NH2 /H DA 36 O4' no hydrogen 3.065 N/A /E LYS 363 N /I DG 29 OP2 no hydrogen 3.221 N/A /E LYS 363 NZ /I DG 30 OP1 no hydrogen 2.954 N/A /E LYS 363 NZ /I DG 30 OP2 no hydrogen 2.890 N/A /G THR 542 OG1 /H DA 23 OP1 no hydrogen 3.290 N/A /G LYS 547 NZ /I DG 41 OP1 no hydrogen 3.303 N/A /G LYS 548 NZ /H DT 24 O2 no hydrogen 2.747 N/A /G LYS 548 NZ /H DC 25 O4' no hydrogen 2.889 N/A /G LYS 548 NZ /I DT 38 O2 no hydrogen 3.045 N/A /G ASN 553 N /I DG 41 OP2 no hydrogen 3.220 N/A /G ARG 557 NH1 /I DG 44 N7 no hydrogen 3.403 N/A /G ARG 557 NH1 /I DG 44 O6 no hydrogen 2.566 N/A /G ARG 557 NH2 /I DG 44 N7 no hydrogen 3.082 N/A /G LYS 560 NZ /H DA 12 OP2 no hydrogen 2.981 N/A /G GLY 561 N /H DT 13 OP1 no hydrogen 2.977 N/A /G THR 563 N /H DT 13 OP2 no hydrogen 3.051 N/A /G GLY 564 N /H DT 13 OP2 no hydrogen 2.948 N/A /G ALA 565 N /H DG 14 OP2 no hydrogen 3.032 N/A 50 hydrogen bonds found 13 strict hydrogen bonds found > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1 --- warning | Not adding hydrogens to /I DA 22 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain A; guessing termini instead No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain B; guessing termini instead No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain C; guessing termini instead No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain D; guessing termini instead No usable SEQRES records for ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb (#1) chain E; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A PRO 299, /B PRO 106, /C THR 6, /D PRO 33, /E MET 1, /F PRO 179, /G PRO 93 Chain-initial residues that are not actual N termini: /B VAL 396, /B VAL 444, /B LYS 489, /C ASN 72, /D ASN 128, /D GLY 162, /D LEU 296, /D PHE 436, /E GLU 217, /E ASP 319, /F SER 313, /G ALA 213, /G THR 386, /G VAL 439, /G ASN 461 Chain-final residues that are actual C termini: /A LEU 718, /C LEU 685 Chain-final residues that are not actual C termini: /B GLU 504, /B GLU 386, /B HIS 420, /B VAL 479, /C ARG 29, /D ARG 510, /D SER 123, /D LEU 159, /D MET 285, /D LEU 420, /E ASN 464, /E ALA 210, /E LEU 304, /F GLN 351, /F THR 307, /G LEU 604, /G GLY 207, /G HIS 335, /G GLN 433, /G PHE 457 2714 hydrogen bonds Adding 'H' to /B VAL 396 Adding 'H' to /B VAL 444 Adding 'H' to /B LYS 489 Adding 'H' to /C ASN 72 Adding 'H' to /D ASN 128 10 messages similar to the above omitted /B GLU 504 is not terminus, removing H atom from 'C' /D ARG 510 is not terminus, removing H atom from 'C' /E ASN 464 is not terminus, removing H atom from 'C' /F GLN 351 is not terminus, removing H atom from 'C' /G LEU 604 is not terminus, removing H atom from 'C' 24328 hydrogens added > select clear > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > ui tool show H-Bonds > hbonds sel dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true > slopColor #ff9300 intraRes false select true reveal true retainCurrent true > log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 49 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /I DG 53 O3' /A GLN 306 HE22 3.342 2.769 /A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481 /C ARG 220 NH1 /I DT 49 O2 /C ARG 220 HH11 3.296 2.935 /C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200 /C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116 /D LYS 168 NZ /H DT 11 O2 /D LYS 168 HZ1 2.564 2.050 /D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH1 /H DC 35 O4' /E ARG 362 HH12 3.369 2.780 /E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066 /E ARG 362 NH2 /H DA 36 O4' /E ARG 362 HH21 3.065 2.496 /E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /I DG 30 OP1 /E LYS 363 HZ3 2.954 2.284 /E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985 /G GLY 546 N /H DT 24 OP1 /G GLY 546 H 3.276 2.580 /G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /H DC 25 O4' /G LYS 548 HZ2 2.889 2.196 /G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH1 /I DG 44 O6 /G ARG 557 HH12 2.566 1.988 /G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292 /G LYS 560 NZ /H DA 12 OP2 /G LYS 560 HZ1 2.981 2.268 /G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059 49 hydrogen bonds found 8 strict hydrogen bonds found > select clear > hide atoms > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > show sel atoms > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"" > restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor #ff9300 > intraRes false select true reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 49 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /I DG 53 O3' /A GLN 306 HE22 3.342 2.769 /A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481 /C ARG 220 NH1 /I DT 49 O2 /C ARG 220 HH11 3.296 2.935 /C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200 /C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116 /D LYS 168 NZ /H DT 11 O2 /D LYS 168 HZ1 2.564 2.050 /D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH1 /H DC 35 O4' /E ARG 362 HH12 3.369 2.780 /E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066 /E ARG 362 NH2 /H DA 36 O4' /E ARG 362 HH21 3.065 2.496 /E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /I DG 30 OP1 /E LYS 363 HZ3 2.954 2.284 /E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985 /G GLY 546 N /H DT 24 OP1 /G GLY 546 H 3.276 2.580 /G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /H DC 25 O4' /G LYS 548 HZ2 2.889 2.196 /G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH1 /I DG 44 O6 /G ARG 557 HH12 2.566 1.988 /G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292 /G LYS 560 NZ /H DA 12 OP2 /G LYS 560 HZ1 2.981 2.268 /G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059 49 hydrogen bonds found 8 strict hydrogen bonds found > select up 1476 atoms, 1511 bonds, 59 residues, 1 model selected > show sel atoms > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20"" dashes 6 > restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false > select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 39 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ASN 436 ND2 /H DA 10 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /I DA 28 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /I DA 48 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /H DC 15 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 NH1 /I DT 49 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /H DT 13 O2 /C ARG 220 HH11 3.388 2.481 /C TYR 223 OH /H DC 15 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /H DC 29 OP2 /C TYR 607 HH 3.098 2.200 /C ARG 672 N /H DC 29 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /I DT 34 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /I DT 34 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /I DT 34 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /H DT 30 OP1 /C LYS 673 HZ1 3.030 2.116 /D SER 169 OG /H DA 12 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /I DT 39 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /I DG 40 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /I DG 40 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /I DG 41 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /H DG 14 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /I DA 28 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /I DT 27 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /I DT 27 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /I DT 25 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /I DT 25 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /H DG 38 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /I DA 28 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /I DG 29 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH2 /H DC 35 O2 /E ARG 362 HH22 3.076 2.066 /E LYS 363 N /I DG 29 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /I DG 30 OP2 /E LYS 363 HZ1 2.890 1.985 /G LYS 547 NZ /I DG 41 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /H DT 24 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /I DT 38 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /I DG 41 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /I DG 44 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH2 /I DG 44 N7 /G ARG 557 HH22 3.082 2.292 /G GLY 561 N /H DT 13 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /H DT 13 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /H DG 14 OP2 /G ALA 565 H 3.032 2.059 39 hydrogen bonds found 8 strict hydrogen bonds found > select clear > select /I:38 32 atoms, 33 bonds, 1 residue, 1 model selected > select /H:23 32 atoms, 34 bonds, 1 residue, 1 model selected > ui tool show ""Renumber Residues"" > renumber /H start -18 34 residues renumbered > renumber /H start -17 34 residues renumbered > select /I:39 32 atoms, 33 bonds, 1 residue, 1 model selected > select /I:38 32 atoms, 33 bonds, 1 residue, 1 model selected > renumber /I start -16 34 residues renumbered > select /H 1060 atoms, 1139 bonds, 34 residues, 1 model selected > ui tool show ""Change Chain IDs"" > changechains sel main Chain IDs of 34 residues changed > select /I 1098 atoms, 1187 bonds, 34 residues, 1 model selected > changechains sel opp Chain IDs of 34 residues changed > select clear > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"" > dashes 6 restrict #1/A,B,C,D,E,F,G angleSlop 40.0 twoColors true slopColor > #ff9300 intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 49 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769 /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 49 hydrogen bonds found 8 strict hydrogen bonds found > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20"" dashes 6 > restrict #1/A,B,C,D,E,F,G twoColors true slopColor #00f900 intraRes false > select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 39 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 39 hydrogen bonds found 8 strict hydrogen bonds found > select clear > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs"" > select /A:303 20 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select /main:-13 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"" > dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors > true slopColor #ff9300 intraRes false select true reveal true retainCurrent > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 53 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769 /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935 /C TYR 223 OH /main DG -9 O3' /C TYR 223 HH 3.522 2.887 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 53 hydrogen bonds found 8 strict hydrogen bonds found > select up 1530 atoms, 1568 bonds, 61 residues, 1 model selected > show sel atoms > select clear > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20"" dashes 6 > restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900 > intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 42 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 42 hydrogen bonds found 8 strict hydrogen bonds found > select up 1335 atoms, 1364 bonds, 53 residues, 1 model selected > show sel atoms > select clear > select /A:436-436 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > select /A:435-436 28 atoms, 27 bonds, 2 residues, 1 model selected > show sel atoms > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > select clear > show cartoons > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20_relaxed40"" > dashes 6 restrict #1/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 twoColors > true slopColor #ff9300 intraRes false select true reveal true retainCurrent > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 53 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A GLN 306 NE2 /opp DG 15 O3' /A GLN 306 HE22 3.342 2.769 /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C ARG 220 NH1 /opp DT 11 O2 /C ARG 220 HH11 3.296 2.935 /C TYR 223 OH /main DG -9 O3' /C TYR 223 HH 3.522 2.887 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D LYS 168 NZ /main DT -12 O2 /D LYS 168 HZ1 2.564 2.050 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH1 /main DC 12 O4' /E ARG 362 HH12 3.369 2.780 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E ARG 362 NH2 /main DA 13 O4' /E ARG 362 HH21 3.065 2.496 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP1 /E LYS 363 HZ3 2.954 2.284 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G GLY 546 N /main DT 1 OP1 /G GLY 546 H 3.276 2.580 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /main DC 2 O4' /G LYS 548 HZ2 2.889 2.196 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH1 /opp DG 6 O6 /G ARG 557 HH12 2.566 1.988 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G LYS 560 NZ /main DA -11 OP2 /G LYS 560 HZ1 2.981 2.268 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 53 hydrogen bonds found 8 strict hydrogen bonds found > select clear > select ~nucleic 47052 atoms, 47494 bonds, 16 pseudobonds, 2932 residues, 3 models selected > hide sel cartoons > select clear > select /main:-13 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel cartoons > select /A:301,306,303,435,436,305 111 atoms, 108 bonds, 6 residues, 1 model selected > show sel atoms > select /B:279,280,248,153,150,148 109 atoms, 104 bonds, 6 residues, 1 model selected > show sel atoms > select /C:219,220,223,188,671-673 159 atoms, 156 bonds, 7 residues, 1 model selected > show sel atoms > select clear > select /D:168,169,465,463 66 atoms, 63 bonds, 4 residues, 1 model selected > show sel atoms > select clear > select /E:76,341,363,359,362,340,356,357,358 192 atoms, 189 bonds, 9 residues, 1 model selected > show sel atoms > select clear > select /G:560,561,563,565,557,547,548,543,581,546 157 atoms, 150 bonds, 10 residues, 1 model selected > show sel atoms > select clear > select /main:-1 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select /main:0 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select /main:-1 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear Drag select of 2 atoms, 2 bonds > select clear > select /A:305@NZ 1 atom, 1 residue, 1 model selected > select /main:-12 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > select /main:-13@C3' 1 atom, 1 residue, 1 model selected > show sel cartoons > select clear > select /main:-11 32 atoms, 34 bonds, 1 residue, 1 model selected > select nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel saveFile ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_generation_ver20"" dashes 6 > restrict #1/A,B,C,D,E,F,G distSlop 0.5 twoColors true slopColor #00f900 > intraRes false select true reveal true retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb 42 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A ASN 436 ND2 /main DA -13 OP1 /A ASN 436 HD22 2.810 1.833 /B LYS 148 NZ /opp DA -10 OP1 /B LYS 148 HZ3 3.208 2.369 /B LYS 279 N /opp DA 10 OP1 /B LYS 279 H 3.110 2.192 /C LYS 188 NZ /main DC -8 OP1 /C LYS 188 HZ1 3.176 2.193 /C ARG 219 N /opp DA 12 OP1 /C ARG 219 H 3.467 2.499 /C ARG 219 NH1 /opp DT 11 OP2 /C ARG 219 HH11 3.015 2.053 /C ARG 220 NH1 /main DT -10 O2 /C ARG 220 HH11 3.388 2.481 /C TYR 223 OH /main DC -8 OP1 /C TYR 223 HH 2.762 1.806 /C TYR 607 OH /main DC 6 OP2 /C TYR 607 HH 3.098 2.200 /C LYS 671 N /main DC 6 OP1 /C LYS 671 H 3.429 2.701 /C ARG 672 N /main DC 6 OP1 /C ARG 672 H 3.388 2.439 /C ARG 672 NH1 /opp DT -4 O2 /C ARG 672 HH12 2.806 1.902 /C ARG 672 NH2 /opp DT -4 O2 /C ARG 672 HH22 2.902 2.042 /C ARG 672 NH2 /opp DT -4 O4' /C ARG 672 HH22 3.185 2.472 /C LYS 673 NZ /main DT 7 OP1 /C LYS 673 HZ1 3.030 2.116 /D SER 169 OG /main DA -11 OP1 /D SER 169 HG 3.284 2.325 /D SER 463 OG /opp DT 1 OP2 /D SER 463 HG 2.803 1.844 /D LYS 465 NZ /opp DG 2 N7 /D LYS 465 HZ1 3.514 2.654 /D LYS 465 NZ /opp DG 2 O6 /D LYS 465 HZ1 3.045 2.260 /D LYS 465 NZ /opp DG 3 O6 /D LYS 465 HZ2 3.189 2.368 /E ARG 76 NH1 /main DG -9 OP1 /E ARG 76 HH11 2.908 2.005 /E ARG 340 NH1 /opp DA -10 OP2 /E ARG 340 HH11 3.135 2.272 /E ARG 356 NH1 /opp DT -11 OP2 /E ARG 356 HH11 2.946 2.163 /E ARG 357 N /opp DT -11 OP1 /E ARG 357 H 3.073 2.081 /E ARG 357 NH1 /opp DT -13 O2 /E ARG 357 HH12 2.761 1.945 /E ARG 357 NH2 /opp DT -13 O2 /E ARG 357 HH22 2.690 1.846 /E GLU 358 N /main DG 15 OP1 /E GLU 358 H 3.275 2.276 /E THR 359 OG1 /opp DA -10 OP1 /E THR 359 HG1 2.552 1.830 /E ARG 362 N /opp DA -10 O3' /E ARG 362 H 3.515 2.618 /E ARG 362 N /opp DG -9 OP2 /E ARG 362 H 2.892 2.000 /E ARG 362 NH2 /main DC 12 O2 /E ARG 362 HH22 3.076 2.066 /E LYS 363 N /opp DG -9 OP2 /E LYS 363 H 3.221 2.221 /E LYS 363 NZ /opp DG -8 OP2 /E LYS 363 HZ1 2.890 1.985 /G LYS 547 NZ /opp DG 3 OP1 /G LYS 547 HZ1 3.303 2.294 /G LYS 548 NZ /main DT 1 O2 /G LYS 548 HZ1 2.747 2.031 /G LYS 548 NZ /opp DT 0 O2 /G LYS 548 HZ3 3.045 2.142 /G ASN 553 N /opp DG 3 OP2 /G ASN 553 H 3.220 2.217 /G ARG 557 NH1 /opp DG 6 N7 /G ARG 557 HH12 3.403 2.708 /G ARG 557 NH2 /opp DG 6 N7 /G ARG 557 HH22 3.082 2.292 /G GLY 561 N /main DT -10 OP1 /G GLY 561 H 2.977 2.057 /G THR 563 N /main DT -10 OP2 /G THR 563 H 3.051 2.249 /G ALA 565 N /main DG -9 OP2 /G ALA 565 H 3.032 2.059 42 hydrogen bonds found 8 strict hydrogen bonds found > select clear > select /main:-9 33 atoms, 35 bonds, 1 residue, 1 model selected > select /main:-8 30 atoms, 31 bonds, 1 residue, 1 model selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"" Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2 --- 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 > select #2 24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected > show sel atoms > show sel cartoons > style sel stick Changed 24882 atom styles > newcolor #2/A #2/B #2/C #2/D #2/E #2/F #2/G #2/H #2/I > color sel byhetero > hide sel atoms > select clear > select #2 & nucleic 1391 atoms, 1559 bonds, 68 residues, 1 model selected > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true > slopColor #00f900 intraRes false select true reveal true retainCurrent true > log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 46 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 no hydrogen 2.810 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 3.208 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 no hydrogen 3.110 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 3.176 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 no hydrogen 3.467 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 no hydrogen 3.015 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 no hydrogen 3.388 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 2.762 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 no hydrogen 3.098 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 no hydrogen 3.388 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.806 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.902 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' no hydrogen 3.185 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 no hydrogen 3.030 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 no hydrogen 2.564 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 no hydrogen 3.284 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 no hydrogen 2.803 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 no hydrogen 3.514 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 no hydrogen 3.045 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 no hydrogen 3.189 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 no hydrogen 2.908 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 no hydrogen 3.135 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 no hydrogen 2.946 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 no hydrogen 3.073 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.761 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.690 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 no hydrogen 3.275 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 2.552 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' no hydrogen 3.515 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 2.892 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 no hydrogen 3.076 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 3.221 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 no hydrogen 2.890 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1 no hydrogen 3.290 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 no hydrogen 3.276 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 no hydrogen 3.303 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 no hydrogen 2.747 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' no hydrogen 2.889 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 no hydrogen 3.045 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 no hydrogen 3.220 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.403 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.082 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 no hydrogen 2.981 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 no hydrogen 2.977 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 3.051 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 no hydrogen 3.032 N/A 46 hydrogen bonds found 13 strict hydrogen bonds found > select up 840 atoms, 876 bonds, 59 residues, 1 model selected > show sel atoms > select #2 & ~nucleic 23491 atoms, 23933 bonds, 16 pseudobonds, 2932 residues, 3 models selected > hide sel cartoons > select clear > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select #2 & nucleic 1391 atoms, 1559 bonds, 68 residues, 1 model selected > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 > twoColors true slopColor #ff9300 intraRes false select true reveal true > retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 55 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3 no hydrogen 3.290 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3' no hydrogen 3.342 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 no hydrogen 2.810 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 3.208 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 no hydrogen 3.110 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 3.176 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 no hydrogen 3.467 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 no hydrogen 3.015 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 no hydrogen 3.388 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2 no hydrogen 3.296 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3' no hydrogen 3.522 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 no hydrogen 2.762 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 no hydrogen 3.098 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 no hydrogen 3.388 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.806 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 no hydrogen 2.902 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' no hydrogen 3.185 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 no hydrogen 3.030 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 no hydrogen 2.564 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 no hydrogen 3.284 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 no hydrogen 2.803 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 no hydrogen 3.514 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 no hydrogen 3.045 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 no hydrogen 3.189 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 no hydrogen 2.908 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 no hydrogen 3.135 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 no hydrogen 2.946 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 no hydrogen 3.073 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.761 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 no hydrogen 2.690 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 no hydrogen 3.275 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 no hydrogen 2.552 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' no hydrogen 3.515 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 2.892 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4' no hydrogen 3.369 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 no hydrogen 3.076 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4' no hydrogen 3.065 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 no hydrogen 3.221 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1 no hydrogen 2.954 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 no hydrogen 2.890 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 542 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 23 OP1 no hydrogen 3.290 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 no hydrogen 3.276 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 no hydrogen 3.303 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 no hydrogen 2.747 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' no hydrogen 2.889 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 no hydrogen 3.045 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 no hydrogen 3.220 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.403 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6 no hydrogen 2.566 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 no hydrogen 3.082 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 no hydrogen 2.981 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 no hydrogen 2.977 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 3.051 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 564 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 no hydrogen 2.948 N/A ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 no hydrogen 3.032 N/A 55 hydrogen bonds found 13 strict hydrogen bonds found > select up 929 atoms, 972 bonds, 65 residues, 1 model selected > show sel atoms > select clear > ui tool show ""Add Hydrogens"" > addh #!2 Summary of feedback from adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2 --- warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 22 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain A; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain B; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain C; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain D; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#2) chain E; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A PRO 299, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B PRO 106, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C THR 6, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PRO 33, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E MET 1, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F PRO 179, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PRO 93 Chain-initial residues that are not actual N termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D GLY 162, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 296, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D PHE 436, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 217, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASP 319, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F SER 313, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 213, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 386, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G VAL 439, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 461 Chain-final residues that are actual C termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A LEU 718, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LEU 685 Chain-final residues that are not actual C termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 386, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B HIS 420, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 479, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 29, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 123, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 159, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D MET 285, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LEU 420, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ALA 210, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LEU 304, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F THR 307, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 207, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G HIS 335, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLN 433, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G PHE 457 2714 hydrogen bonds Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 396 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B VAL 444 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 489 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ASN 72 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ASN 128 10 messages similar to the above omitted ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B GLU 504 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D ARG 510 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ASN 464 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/F GLN 351 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LEU 604 is not terminus, removing H atom from 'C' 24328 hydrogens added > select #2 & nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 angleSlop 40.0 > twoColors true slopColor #ff9300 intraRes false select true reveal true > retainCurrent true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 54 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 54 N3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ARG 301 HH22 3.290 2.710 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 NE2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 53 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A GLN 306 HE22 3.342 2.769 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22 2.810 1.833 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3 3.208 2.369 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H 3.110 2.192 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1 3.176 2.193 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H 3.467 2.499 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11 3.015 2.053 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.388 2.481 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.296 2.935 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 3.522 2.887 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 2.762 1.806 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH 3.098 2.200 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H 3.429 2.701 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H 3.388 2.439 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12 2.806 1.902 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 2.902 2.042 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 3.185 2.472 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1 3.030 2.116 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 11 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 168 HZ1 2.564 2.050 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG 3.284 2.325 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG 2.803 1.844 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.514 2.654 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.045 2.260 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2 3.189 2.368 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11 2.908 2.005 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11 3.135 2.272 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11 2.946 2.163 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H 3.073 2.081 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12 2.761 1.945 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22 2.690 1.846 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H 3.275 2.276 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1 2.552 1.830 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 3.515 2.618 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 2.892 2.000 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH12 3.369 2.780 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22 3.076 2.066 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 36 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH21 3.065 2.496 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H 3.221 2.221 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ3 2.954 2.284 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1 2.890 1.985 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 546 H 3.276 2.580 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1 3.303 2.294 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1 2.747 2.031 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 25 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ2 2.889 2.196 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3 3.045 2.142 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H 3.220 2.217 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 3.403 2.708 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 2.566 1.988 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22 3.082 2.292 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 560 HZ1 2.981 2.268 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H 2.977 2.057 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H 3.051 2.249 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H 3.032 2.059 54 hydrogen bonds found 8 strict hydrogen bonds found > hide #!1 models > show #!1 models > hide #!1 models > select #2 & nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > show sel atoms > select clear > select #2 & nucleic 2158 atoms, 2326 bonds, 68 residues, 1 model selected > hbonds sel dashes 6 restrict #2/A,B,C,D,E,F,G distSlop 0.5 twoColors true > slopColor #00f900 intraRes false select true reveal true retainCurrent true > log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 42 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 ND2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 10 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/A ASN 436 HD22 2.810 1.833 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 148 HZ3 3.208 2.369 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 48 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/B LYS 279 H 3.110 2.192 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 188 HZ1 3.176 2.193 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 50 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 H 3.467 2.499 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 49 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 219 HH11 3.015 2.053 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 220 HH11 3.388 2.481 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 15 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 223 HH 2.762 1.806 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 OH ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C TYR 607 HH 3.098 2.200 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 671 H 3.429 2.701 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 29 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 H 3.388 2.439 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH12 2.806 1.902 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 2.902 2.042 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 34 O4' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C ARG 672 HH22 3.185 2.472 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 30 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/C LYS 673 HZ1 3.030 2.116 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DA 12 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 169 HG 3.284 2.325 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 OG ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 39 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D SER 463 HG 2.803 1.844 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.514 2.654 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 40 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ1 3.045 2.260 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 O6 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/D LYS 465 HZ2 3.189 2.368 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 76 HH11 2.908 2.005 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 340 HH11 3.135 2.272 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 356 HH11 2.946 2.163 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 27 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 H 3.073 2.081 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH12 2.761 1.945 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 25 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 357 HH22 2.690 1.846 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 38 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E GLU 358 H 3.275 2.276 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 OG1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E THR 359 HG1 2.552 1.830 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DA 28 O3' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 3.515 2.618 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 H 2.892 2.000 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DC 35 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E ARG 362 HH22 3.076 2.066 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 29 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 H 3.221 2.221 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 30 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/E LYS 363 HZ1 2.890 1.985 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 547 HZ1 3.303 2.294 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 24 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ1 2.747 2.031 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 NZ ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DT 38 O2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G LYS 548 HZ3 3.045 2.142 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 41 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ASN 553 H 3.220 2.217 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH12 3.403 2.708 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 NH2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/I DG 44 N7 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ARG 557 HH22 3.082 2.292 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP1 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G GLY 561 H 2.977 2.057 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DT 13 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G THR 563 H 3.051 2.249 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 N ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/H DG 14 OP2 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #2/G ALA 565 H 3.032 2.059 42 hydrogen bonds found 8 strict hydrogen bonds found > select clear > select #2/A:301@HH12 1 atom, 1 residue, 1 model selected > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > 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 > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > select #1/opp:16 33 atoms, 35 bonds, 1 residue, 1 model selected > select #1/D:168@NZ 1 atom, 1 residue, 1 model selected > undo > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/main:-10 32 atoms, 33 bonds, 1 residue, 1 model selected > select #1/main:-11 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > select clear > select #1/main:-9 33 atoms, 35 bonds, 1 residue, 1 model selected > select #1/main:-8 30 atoms, 31 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/B:280@CA 1 atom, 1 residue, 1 model selected > select #1/opp:9 30 atoms, 31 bonds, 1 residue, 1 model selected > select #1/opp:10 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"" Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 --- 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 > hide #3 > show #3/B:248 > style sel stick Changed 32 atom styles > style sel stick Changed 32 atom styles > style sel stick Changed 32 atom styles > select clear > select add #3 24882 atoms, 25492 bonds, 16 pseudobonds, 3000 residues, 3 models selected > style sel stick Changed 24882 atom styles > color sel byhetero > select #1/opp:9 30 atoms, 31 bonds, 1 residue, 1 model selected > select #3/B:248@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors > true slopColor #00f900 intraRes false select true reveal true retainCurrent > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found 0 strict hydrogen bonds found > select #3/B:248@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > hbonds sel dashes 6 restrict #3/H,I distSlop 0.5 angleSlop 40.0 twoColors > true slopColor #00f900 intraRes false select true reveal true retainCurrent > true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 3 ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found 0 strict hydrogen bonds found > select #1/opp:9 30 atoms, 31 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/B:248@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show ""Add Hydrogens"" > addh #!3 Summary of feedback from adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 --- warning | Not adding hydrogens to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/I DA 22 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain A; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain B; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain C; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain D; guessing termini instead No usable SEQRES records for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb (#3) chain E; guessing termini instead 4 messages similar to the above omitted Chain-initial residues that are actual N termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A PRO 299, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B PRO 106, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C THR 6, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PRO 33, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E MET 1, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F PRO 179, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PRO 93 Chain-initial residues that are not actual N termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D GLY 162, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 296, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D PHE 436, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E GLU 217, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASP 319, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F SER 313, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ALA 213, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G THR 386, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G VAL 439, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G ASN 461 Chain-final residues that are actual C termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/A LEU 718, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C LEU 685 Chain-final residues that are not actual C termini: ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 386, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B HIS 420, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 479, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ARG 29, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D SER 123, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 159, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D MET 285, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D LEU 420, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ALA 210, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E LEU 304, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F THR 307, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLY 207, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G HIS 335, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G GLN 433, ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G PHE 457 2713 hydrogen bonds Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 396 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B VAL 444 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B LYS 489 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/C ASN 72 Adding 'H' to ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ASN 128 10 messages similar to the above omitted ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/B GLU 504 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/D ARG 510 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/E ASN 464 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/F GLN 351 is not terminus, removing H atom from 'C' ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LEU 604 is not terminus, removing H atom from 'C' 24328 hydrogens added > select #3/B:248@HZ2 1 atom, 1 residue, 1 model selected > close #3 > select #1/B:279@N 1 atom, 1 residue, 1 model selected > select #1/opp:10@P 1 atom, 1 residue, 1 model selected > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" opened ChimeraX session > select /opp:3 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" format > session opened ChimeraX session > select /G:574 48 atoms, 46 bonds, 2 residues, 2 models selected > show sel & #!1 atoms > select #1/opp:3 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/G:543@N 1 atom, 1 residue, 1 model selected > show #!2 models > hide #!1 models > select #2/H:23 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/G:542@OG1 1 atom, 1 residue, 1 model selected > hide #!2 models > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" opened ChimeraX session > select /G:542 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > select /main:-1 30 atoms, 31 bonds, 1 residue, 1 model selected > select /main:0 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20.cxs"" format session opened ChimeraX session > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" format > session opened ChimeraX session > show #!2 models > hide #!1 models > select /G:542 28 atoms, 26 bonds, 2 residues, 2 models selected > show sel & #!2 atoms > select /G:543 14 atoms, 12 bonds, 2 residues, 2 models selected > show sel & #!2 atoms > select clear > select #2/H:22 32 atoms, 34 bonds, 1 residue, 1 model selected > show sel cartoons > hide sel cartoons > show sel cartoons > select #2/H:23 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel cartoons > show #!1 models > hide #!2 models > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" format > session opened ChimeraX session > select /main:0 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" format > session opened ChimeraX session > select #1/G:581@NZ 1 atom, 1 residue, 1 model selected > select add #1/main:0@OP2 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #1/G:581@NZ #1/main:0@OP2 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ and /main DA 0 OP2: 5.033Å > select #1/G:581@NZ 1 atom, 1 residue, 1 model selected > select add #1/main:0@OP1 2 atoms, 2 residues, 1 model selected > distance #1/G:581@NZ #1/main:0@OP1 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/G LYS 581 NZ and /main DA 0 OP1: 4.742Å > ~distance #1/G:581@NZ #1/main:0@OP1 > ~distance #1/G:581@NZ #1/main:0@OP2 > show #!2 models > hide #!2 models > select add #1 49210 atoms, 49820 bonds, 69 pseudobonds, 3000 residues, 4 models selected > select subtract #1 Nothing selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb"" Chain information for ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3 --- 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 > hide #3 > select /G:548 53 atoms, 50 bonds, 3 residues, 3 models selected > select /G:581 53 atoms, 50 bonds, 3 residues, 3 models selected > show sel & #!1,3 atoms > style sel & #!1,3 stick Changed 31 atom styles > select #3/G:581@NZ 1 atom, 1 residue, 1 model selected > select add #1/main:0@OP1 2 atoms, 2 residues, 2 models selected > distance #3/G:581@NZ #1/main:0@OP1 Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP1: 4.358Å > select #3/G:581@NZ 1 atom, 1 residue, 1 model selected > select add #1/main:0@OP2 2 atoms, 2 residues, 2 models selected > distance #3/G:581@NZ #1/main:0@OP2 Distance between ARMori_ODC_ver21_DNAchainfix_PostPhenix.pdb #3/G LYS 581 NZ and ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/main DA 0 OP2: 4.621Å > ~distance #3/G:581@NZ #1/main:0@OP2 > ~distance #3/G:581@NZ #1/main:0@OP1 > close #3 > select #1/main:6 30 atoms, 31 bonds, 1 residue, 1 model selected > select #1/main:7 32 atoms, 33 bonds, 1 residue, 1 model selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" format > session opened ChimeraX session > select /main:6 30 atoms, 31 bonds, 1 residue, 1 model selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" format > session opened ChimeraX session > select #1/main:7 32 atoms, 33 bonds, 1 residue, 1 model selected > select #1/B:153@CA 1 atom, 1 residue, 1 model selected > select #1/main:8 30 atoms, 31 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select #1/B:153@N 1 atom, 1 residue, 1 model selected > select add #1/main:8@OP1 2 atoms, 2 residues, 1 model selected > select #1/main:7 32 atoms, 33 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/B:153@H 1 atom, 1 residue, 1 model selected > select add #1/main:8@OP1 2 atoms, 2 residues, 1 model selected > select #1/B:153@N 1 atom, 1 residue, 1 model selected > select add #1/main:8@OP1 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #1/B:153@N #1/main:8@OP1 Distance between ARMori_ODC_ver20_DNAchainfix_PostPhenix.pdb #1/B GLY 153 N and /main DC 8 OP1: 3.580Å > ~distance #1/B:153@N #1/main:8@OP1 > select clear > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select #1/B:148@NZ 1 atom, 1 residue, 1 model selected > select #1/opp:-10 32 atoms, 34 bonds, 1 residue, 1 model selected > select #1/opp:-9 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/opp:-10 32 atoms, 34 bonds, 1 residue, 1 model selected > select #1/opp:-11 32 atoms, 33 bonds, 1 residue, 1 model selected > select #1/opp:-10 32 atoms, 34 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/E:358@N 1 atom, 1 residue, 1 model selected > select #1/main:-13 32 atoms, 34 bonds, 1 residue, 1 model selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp-oriC061_complete/new_hbond_ver31.cxs"" format > session opened ChimeraX session > select /main:-14 30 atoms, 31 bonds, 1 residue, 1 model selected > select /main:-13 30 atoms, 31 bonds, 1 residue, 1 model selected > select /opp:18 31 atoms, 32 bonds, 1 residue, 1 model selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_oriA006_complete/hbond_oriA_ver20-21.cxs"" format > session opened ChimeraX session > close > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb 7jk3-dmODC_GCrich.pdb title: Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] Chain information for 7jk3-dmODC_GCrich.pdb #1 --- Chain | Description | UniProt A | DMORC1 | ORC1_DROME 440-924 B | DMORC2 | ORC2_DROME 1-618 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 D | ORC4 | Q9W102_DROME 1-459 E | ORC5 | ORC5_DROME 1-460 F | ORC6 | ORC6_DROME 1-257 G | CDC6 | Q9VSM9_DROME 242-662 H | DNA (33-mer) | I | DNA (33-mer) | Non-standard residues in 7jk3-dmODC_GCrich.pdb #1 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > modelfix Changed 21661 atom styles 20180 atoms, 20524 bonds, 18 pseudobonds, 2528 residues, 2 models selected > close #1 > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/hsORC1-6_CDC6_60bpDNA.pdb > format pdb Chain information for hsORC1-6_CDC6_60bpDNA.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 21416 atom styles 20099 atoms, 20484 bonds, 13 pseudobonds, 2485 residues, 2 models selected Computing secondary structure > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7jk3-dmODC_GCrich.pdb format > pdb 7jk3-dmODC_GCrich.pdb title: Structure of drosophila orc bound to GC-rich DNA and CDC6 [more info...] Chain information for 7jk3-dmODC_GCrich.pdb #2 --- Chain | Description | UniProt A | DMORC1 | ORC1_DROME 440-924 B | DMORC2 | ORC2_DROME 1-618 C | origin recognition complex subunit 3 | Q7K2L1_DROME 1-721 D | ORC4 | Q9W102_DROME 1-459 E | ORC5 | ORC5_DROME 1-460 F | ORC6 | ORC6_DROME 1-257 G | CDC6 | Q9VSM9_DROME 242-662 H | DNA (33-mer) | I | DNA (33-mer) | Non-standard residues in 7jk3-dmODC_GCrich.pdb #2 --- ATP — adenosine-5'-triphosphate MG — magnesium ion > modelfix Changed 43077 atom styles 40279 atoms, 41008 bonds, 31 pseudobonds, 5013 residues, 4 models selected > matchmaker #2 to #1 Computing secondary structure 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 hsORC1-6_CDC6_60bpDNA.pdb, chain C (#1) with 7jk3-dmODC_GCrich.pdb, chain C (#2), sequence alignment score = 1256.2 RMSD between 288 pruned atom pairs is 1.187 angstroms; (across all 575 pairs: 4.218) > select #2/G:623 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select clear > select #2/C:181 6 atoms, 5 bonds, 1 residue, 1 model selected > hide #!2 models > hide #!1 models > show #!1 models > select add #2 21661 atoms, 22172 bonds, 30 pseudobonds, 2602 residues, 3 models selected > select subtract #2 Nothing selected > show #!2 models > hide #!1 models > select #2/C:711 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #2/C:712 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #2/C:710 9 atoms, 8 bonds, 1 residue, 1 model selected > show #!1 models > hide #!2 models > show #!2 models > select clear > matchmaker #2/D to #1/D Computing secondary structure 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 hsORC1-6_CDC6_60bpDNA.pdb, chain D (#1) with 7jk3-dmODC_GCrich.pdb, chain D (#2), sequence alignment score = 1104.3 RMSD between 338 pruned atom pairs is 0.924 angstroms; (across all 410 pairs: 2.005) > select #2/D:410 7 atoms, 6 bonds, 1 residue, 1 model selected > matchmaker #2/E to #1/E Computing secondary structure 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 hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1) with 7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 853.4 RMSD between 290 pruned atom pairs is 1.201 angstroms; (across all 363 pairs: 2.631) > select clear > open /Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/7mca-assembly1.cif format > mmcif 7mca-assembly1.cif title: Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA. [more info...] Chain information for 7mca-assembly1.cif #3 --- Chain | Description A | Origin recognition complex subunit 1 B | Origin recognition complex subunit 2 C | Origin recognition complex subunit 3 D | Origin recognition complex subunit 4 E | Origin recognition complex subunit 5 F | Origin recognition complex subunit 6 G | DNA (85-MER) H | DNA (85-MER) I | Cell division control protein 6 Non-standard residues in 7mca-assembly1.cif #3 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) MG — magnesium ion > modelfix Changed 67769 atom styles 62793 atoms, 63953 bonds, 45 pseudobonds, 7773 residues, 6 models selected > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H > matchmaker /A to #1/A Must use different reference and match structures > matchmaker #2-3/A to #1/A Computing secondary structure 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 hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 1245.5 RMSD between 341 pruned atom pairs is 0.995 angstroms; (across all 383 pairs: 1.387) Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1) with 7mca-assembly1.cif, chain A (#3), sequence alignment score = 707.9 RMSD between 295 pruned atom pairs is 1.089 angstroms; (across all 368 pairs: 4.720) > matchmaker #2-3/B to #1/B Computing secondary structure 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 hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7jk3-dmODC_GCrich.pdb, chain B (#2), sequence alignment score = 879.5 RMSD between 201 pruned atom pairs is 1.032 angstroms; (across all 272 pairs: 2.378) Matchmaker hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1) with 7mca-assembly1.cif, chain B (#3), sequence alignment score = 458.2 RMSD between 130 pruned atom pairs is 0.873 angstroms; (across all 193 pairs: 3.624) > hide #!2 models > hide #!1 models > select #3/C:178 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/C:159 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #3 24692 atoms, 25375 bonds, 14 pseudobonds, 2868 residues, 2 models selected > hide #!3 models > select subtract #3 Nothing selected > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"" Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #4 --- 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 93068 atom styles 86492 atoms, 88098 bonds, 54 pseudobonds, 10743 residues, 8 models selected > newcolor #3/A #3/B #3/C #3/D #3/E #3/F #3/I #3/G #3/H > matchmaker #1-3/A to #4 Computing secondary structure 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 ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4 RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs: 3.152) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2 RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs: 6.101) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > show #!3 models > show #!2 models > show #!1 models > matchmaker #1-3/A to #4/A Computing secondary structure 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 ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with hsORC1-6_CDC6_60bpDNA.pdb, chain A (#1), sequence alignment score = 965.4 RMSD between 213 pruned atom pairs is 1.228 angstroms; (across all 381 pairs: 3.152) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7jk3-dmODC_GCrich.pdb, chain A (#2), sequence alignment score = 962.2 RMSD between 250 pruned atom pairs is 1.152 angstroms; (across all 383 pairs: 6.101) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain A (#4) with 7mca- assembly1.cif, chain A (#3), sequence alignment score = 943 RMSD between 228 pruned atom pairs is 1.005 angstroms; (across all 394 pairs: 5.169) > matchmaker #1-3/B to #4/B Computing secondary structure 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 ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with hsORC1-6_CDC6_60bpDNA.pdb, chain B (#1), sequence alignment score = 635.5 RMSD between 137 pruned atom pairs is 1.099 angstroms; (across all 304 pairs: 5.531) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with 7jk3-dmODC_GCrich.pdb, chain B (#2), sequence alignment score = 558 RMSD between 135 pruned atom pairs is 0.988 angstroms; (across all 284 pairs: 5.027) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain B (#4) with 7mca- assembly1.cif, chain B (#3), sequence alignment score = 609.7 RMSD between 153 pruned atom pairs is 1.065 angstroms; (across all 237 pairs: 4.405) > select #3/B:396 14 atoms, 15 bonds, 1 residue, 1 model selected > hide #!2 models > hide #!3 models > hide #!4 models > select #1/B:367 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/B:365 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/B:367@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > select #1/B:367 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/C:177 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > show #!4 models > hide #!1 models > select #4/B:150 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!3 models > show #!2 models > show #!1 models > select #3/B:255 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:254 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > hide #!4 models > hide #!2 models > hide #!1 models > select clear > color #!3 byhetero > show #!4 models > matchmaker #1-3/E to #4/E Computing secondary structure 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 ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 675 RMSD between 179 pruned atom pairs is 1.291 angstroms; (across all 379 pairs: 4.186) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 567.4 RMSD between 149 pruned atom pairs is 1.290 angstroms; (across all 374 pairs: 4.652) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 646.2 RMSD between 174 pruned atom pairs is 1.399 angstroms; (across all 417 pairs: 4.188) > hide #!4 models > select #3/E:366 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3/E:363 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/E:360 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > matchmaker #1-3/E to #4/E:307-end Computing secondary structure 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 ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with hsORC1-6_CDC6_60bpDNA.pdb, chain E (#1), sequence alignment score = 281.2 RMSD between 99 pruned atom pairs is 0.965 angstroms; (across all 120 pairs: 3.490) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7jk3-dmODC_GCrich.pdb, chain E (#2), sequence alignment score = 198.4 RMSD between 96 pruned atom pairs is 1.015 angstroms; (across all 110 pairs: 1.673) Matchmaker ylODC_54bpOriC061_rev31_PostPhenix.pdb, chain E (#4) with 7mca- assembly1.cif, chain E (#3), sequence alignment score = 312.4 RMSD between 101 pruned atom pairs is 0.945 angstroms; (across all 138 pairs: 3.466) > select #4/E:362 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #4/E:359 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/E:357 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #4/E:354 9 atoms, 8 bonds, 1 residue, 1 model selected > hide #!3 models > select #4/E:355 4 atoms, 3 bonds, 1 residue, 1 model selected > select #4/E:354 9 atoms, 8 bonds, 1 residue, 1 model selected > show #!3 models > hide #!4 models > select #3/E:363 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3/E:358 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/E:439 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:369 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:367 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:365 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > hide #!3 models > hide #!4 models > show #!3 models > close #3 > 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 > volume step 1 > volume level 0.1 > morph #1 Require at least 2 structures for morph > morph #1.1-1.25 Require at least 2 structures for morph > volume morph #1 Opened morph as #2, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #2 > 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 > color #808080 > color grey > color lightgrey > color darkgrey > volume morph #2-26 Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #1 > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_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_J408_component_000/J408_component_000_frame_000.mrc"" Opened J408_component_000_frame_024.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at level 0.135, step 2, values float32 Opened J408_component_000_frame_023.mrc as #1.2, grid size 440,440,440, pixel 0.827, shown at level 0.112, step 2, values float32 Opened J408_component_000_frame_022.mrc as #1.3, grid size 440,440,440, pixel 0.827, shown at level 0.103, step 2, values float32 Opened J408_component_000_frame_021.mrc as #1.4, grid size 440,440,440, pixel 0.827, shown at level 0.0998, step 2, values float32 Opened J408_component_000_frame_020.mrc as #1.5, grid size 440,440,440, pixel 0.827, shown at level 0.0974, step 2, values float32 Opened J408_component_000_frame_019.mrc as #1.6, grid size 440,440,440, pixel 0.827, shown at level 0.0929, step 2, values float32 Opened J408_component_000_frame_018.mrc as #1.7, grid size 440,440,440, pixel 0.827, shown at level 0.0878, step 2, values float32 Opened J408_component_000_frame_017.mrc as #1.8, grid size 440,440,440, pixel 0.827, shown at level 0.0867, step 2, values float32 Opened J408_component_000_frame_016.mrc as #1.9, grid size 440,440,440, pixel 0.827, shown at level 0.092, step 2, values float32 Opened J408_component_000_frame_015.mrc as #1.10, grid size 440,440,440, pixel 0.827, shown at level 0.105, step 2, values float32 Opened J408_component_000_frame_014.mrc as #1.11, grid size 440,440,440, pixel 0.827, shown at level 0.128, step 2, values float32 Opened J408_component_000_frame_013.mrc as #1.12, grid size 440,440,440, pixel 0.827, shown at level 0.167, step 2, values float32 Opened J408_component_000_frame_012.mrc as #1.13, grid size 440,440,440, pixel 0.827, shown at level 0.216, step 2, values float32 Opened J408_component_000_frame_011.mrc as #1.14, grid size 440,440,440, pixel 0.827, shown at level 0.235, step 2, values float32 Opened J408_component_000_frame_010.mrc as #1.15, grid size 440,440,440, pixel 0.827, shown at level 0.205, step 2, values float32 Opened J408_component_000_frame_009.mrc as #1.16, grid size 440,440,440, pixel 0.827, shown at level 0.166, step 2, values float32 Opened J408_component_000_frame_008.mrc as #1.17, grid size 440,440,440, pixel 0.827, shown at level 0.143, step 2, values float32 Opened J408_component_000_frame_007.mrc as #1.18, grid size 440,440,440, pixel 0.827, shown at level 0.133, step 2, values float32 Opened J408_component_000_frame_006.mrc as #1.19, grid size 440,440,440, pixel 0.827, shown at level 0.128, step 2, values float32 Opened J408_component_000_frame_005.mrc as #1.20, grid size 440,440,440, pixel 0.827, shown at level 0.127, step 2, values float32 Opened J408_component_000_frame_004.mrc as #1.21, grid size 440,440,440, pixel 0.827, shown at level 0.124, step 2, values float32 Opened J408_component_000_frame_003.mrc as #1.22, grid size 440,440,440, pixel 0.827, shown at level 0.123, step 2, values float32 Opened J408_component_000_frame_002.mrc as #1.23, grid size 440,440,440, pixel 0.827, shown at level 0.125, step 2, values float32 Opened J408_component_000_frame_001.mrc as #1.24, grid size 440,440,440, pixel 0.827, shown at level 0.135, step 2, values float32 Opened J408_component_000_frame_000.mrc as #1.25, grid size 440,440,440, pixel 0.827, shown at level 0.154, step 2, values float32 > volume step 1 > volume level 0.1 #1 Expected a keyword > vop level 0.2 #1 > volume level 0.2 #1 Expected a keyword > vop level #1 0.2 > volume level #1 0.2 Invalid ""level"" argument: Expected a number > vop level > volume level Missing ""level"" keyword's argument > volume #1.10 level 0.12 > vop #1 level 0.2 > vop #1 level 0.3 > vop #1 level 0.2 > surface dust #1.1 size 8.27 > surface dust #1.2 size 8.27 > surface dust #1.3 size 8.27 > surface dust #1.4 size 8.27 > surface dust #1.5 size 8.27 > surface dust #1.6 size 8.27 > surface dust #1.7 size 8.27 > surface dust #1.8 size 8.27 > surface dust #1.9 size 8.27 > surface dust #1.10 size 8.27 > surface dust #1.11 size 8.27 > surface dust #1.12 size 8.27 > surface dust #1.13 size 8.27 > surface dust #1.14 size 8.27 > surface dust #1.15 size 8.27 > surface dust #1.16 size 8.27 > surface dust #1.17 size 8.27 > surface dust #1.18 size 8.27 > surface dust #1.19 size 8.27 > surface dust #1.20 size 8.27 > surface dust #1.21 size 8.27 > surface dust #1.22 size 8.27 > surface dust #1.23 size 8.27 > surface dust #1.24 size 8.27 > surface dust #1.25 size 8.27 > volume morph #1 Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > surface dust #27 size 8.27 > close #1 > close #27 > volume show > volume hide > volume morph #2-26 Opened morph as #1, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > hide #!1 models > show #!26 models > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/PDBs/ylODC_54bp- > oriC061_complete/ylODC_54bpOriC061_rev31_PostPhenix.pdb"" Chain information for ylODC_54bpOriC061_rev31_PostPhenix.pdb #27 --- 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 > select /C:220 11 atoms, 10 bonds, 1 residue, 1 model selected > show #!1 models > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/cryosparc_P370_J380_005_volume_map.mrc"" Opened cryosparc_P370_J380_005_volume_map.mrc as #28, grid size 440,440,440, pixel 0.827, shown at level 0.0231, step 2, values float32 > vop flip #28 Opened cryosparc_P370_J380_005_volume_map.mrc z flip as #29, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close #28 > volume #29 level 0.09557 > hide #!27 models > select add #27 25299 atoms, 25927 bonds, 11 pseudobonds, 3050 residues, 3 models selected > select subtract #27 Nothing selected > close #29 > close #27 > show #!1 models > save ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/J407_component0_ORC_OPEN-CLOSE.cxs"" > close #1 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_001/J407_component_001_frame_000.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J407_component_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_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_001/J407_component_001_frame_024.mrc"" Opened J407_component_001_frame_000.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at level 0.0267, step 2, values float32 Opened J407_component_001_frame_001.mrc as #1.2, grid size 440,440,440, pixel 0.827, shown at level 0.0266, step 2, values float32 Opened J407_component_001_frame_002.mrc as #1.3, grid size 440,440,440, pixel 0.827, shown at level 0.0265, step 2, values float32 Opened J407_component_001_frame_003.mrc as #1.4, grid size 440,440,440, pixel 0.827, shown at level 0.0264, step 2, values float32 Opened J407_component_001_frame_004.mrc as #1.5, grid size 440,440,440, pixel 0.827, shown at level 0.0264, step 2, values float32 Opened J407_component_001_frame_005.mrc as #1.6, grid size 440,440,440, pixel 0.827, shown at level 0.0263, step 2, values float32 Opened J407_component_001_frame_006.mrc as #1.7, grid size 440,440,440, pixel 0.827, shown at level 0.0264, step 2, values float32 Opened J407_component_001_frame_007.mrc as #1.8, grid size 440,440,440, pixel 0.827, shown at level 0.0264, step 2, values float32 Opened J407_component_001_frame_008.mrc as #1.9, grid size 440,440,440, pixel 0.827, shown at level 0.0264, step 2, values float32 Opened J407_component_001_frame_009.mrc as #1.10, grid size 440,440,440, pixel 0.827, shown at level 0.0265, step 2, values float32 Opened J407_component_001_frame_010.mrc as #1.11, grid size 440,440,440, pixel 0.827, shown at level 0.0266, step 2, values float32 Opened J407_component_001_frame_011.mrc as #1.12, grid size 440,440,440, pixel 0.827, shown at level 0.0266, step 2, values float32 Opened J407_component_001_frame_012.mrc as #1.13, grid size 440,440,440, pixel 0.827, shown at level 0.0267, step 2, values float32 Opened J407_component_001_frame_013.mrc as #1.14, grid size 440,440,440, pixel 0.827, shown at level 0.0268, step 2, values float32 Opened J407_component_001_frame_014.mrc as #1.15, grid size 440,440,440, pixel 0.827, shown at level 0.0269, step 2, values float32 Opened J407_component_001_frame_015.mrc as #1.16, grid size 440,440,440, pixel 0.827, shown at level 0.0269, step 2, values float32 Opened J407_component_001_frame_016.mrc as #1.17, grid size 440,440,440, pixel 0.827, shown at level 0.0269, step 2, values float32 Opened J407_component_001_frame_017.mrc as #1.18, grid size 440,440,440, pixel 0.827, shown at level 0.027, step 2, values float32 Opened J407_component_001_frame_018.mrc as #1.19, grid size 440,440,440, pixel 0.827, shown at level 0.0271, step 2, values float32 Opened J407_component_001_frame_019.mrc as #1.20, grid size 440,440,440, pixel 0.827, shown at level 0.0271, step 2, values float32 Opened J407_component_001_frame_020.mrc as #1.21, grid size 440,440,440, pixel 0.827, shown at level 0.0272, step 2, values float32 Opened J407_component_001_frame_021.mrc as #1.22, grid size 440,440,440, pixel 0.827, shown at level 0.0273, step 2, values float32 Opened J407_component_001_frame_022.mrc as #1.23, grid size 440,440,440, pixel 0.827, shown at level 0.0273, step 2, values float32 Opened J407_component_001_frame_023.mrc as #1.24, grid size 440,440,440, pixel 0.827, shown at level 0.0275, step 2, values float32 Opened J407_component_001_frame_024.mrc as #1.25, grid size 440,440,440, pixel 0.827, shown at level 0.0276, step 2, values float32 > vop flip #1 Opened J407_component_001_frame_000.mrc z flip as #2, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_001.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_002.mrc z flip as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_003.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_004.mrc z flip as #6, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_005.mrc z flip as #7, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_006.mrc z flip as #8, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_007.mrc z flip as #9, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_008.mrc z flip as #10, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_009.mrc z flip as #11, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_010.mrc z flip as #12, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_011.mrc z flip as #13, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_012.mrc z flip as #14, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_013.mrc z flip as #15, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_014.mrc z flip as #16, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_015.mrc z flip as #17, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_016.mrc z flip as #18, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_017.mrc z flip as #19, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_018.mrc z flip as #20, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_019.mrc z flip as #21, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_020.mrc z flip as #22, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_021.mrc z flip as #23, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_022.mrc z flip as #24, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_023.mrc z flip as #25, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J407_component_001_frame_024.mrc z flip as #26, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > vop level 0.1 > hide #!1 models > vop morph #2-26 Opened morph as #27, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 > close > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate results/cryosparc_P370_J339_component_002.zip"" Unrecognized file suffix '.zip' > open ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_000.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_001.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_002.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_003.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_004.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_005.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_006.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_007.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_008.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_009.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_010.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_011.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_012.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_013.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_014.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_015.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_016.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_017.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_018.mrc"" > ""/Users/jtbauer/Library/CloudStorage/OneDrive- > Personal/Documents/ROTATION_WORK/Joshua-Tor_Lab/need to organize > structures/intermediate > results/cryosparc_P370_J339_component_002/J339_component_002_frame_019.mrc"" Opened J339_component_002_frame_000.mrc as #1.1, grid size 440,440,440, pixel 0.827, shown at level 0.0255, step 2, values float32 Opened J339_component_002_frame_001.mrc as #1.2, grid size 440,440,440, pixel 0.827, shown at level 0.0253, step 2, values float32 Opened J339_component_002_frame_002.mrc as #1.3, grid size 440,440,440, pixel 0.827, shown at level 0.0252, step 2, values float32 Opened J339_component_002_frame_003.mrc as #1.4, grid size 440,440,440, pixel 0.827, shown at level 0.025, step 2, values float32 Opened J339_component_002_frame_004.mrc as #1.5, grid size 440,440,440, pixel 0.827, shown at level 0.0248, step 2, values float32 Opened J339_component_002_frame_005.mrc as #1.6, grid size 440,440,440, pixel 0.827, shown at level 0.0248, step 2, values float32 Opened J339_component_002_frame_006.mrc as #1.7, grid size 440,440,440, pixel 0.827, shown at level 0.0247, step 2, values float32 Opened J339_component_002_frame_007.mrc as #1.8, grid size 440,440,440, pixel 0.827, shown at level 0.0246, step 2, values float32 Opened J339_component_002_frame_008.mrc as #1.9, grid size 440,440,440, pixel 0.827, shown at level 0.0247, step 2, values float32 Opened J339_component_002_frame_009.mrc as #1.10, grid size 440,440,440, pixel 0.827, shown at level 0.0247, step 2, values float32 Opened J339_component_002_frame_010.mrc as #1.11, grid size 440,440,440, pixel 0.827, shown at level 0.0248, step 2, values float32 Opened J339_component_002_frame_011.mrc as #1.12, grid size 440,440,440, pixel 0.827, shown at level 0.0249, step 2, values float32 Opened J339_component_002_frame_012.mrc as #1.13, grid size 440,440,440, pixel 0.827, shown at level 0.025, step 2, values float32 Opened J339_component_002_frame_013.mrc as #1.14, grid size 440,440,440, pixel 0.827, shown at level 0.0252, step 2, values float32 Opened J339_component_002_frame_014.mrc as #1.15, grid size 440,440,440, pixel 0.827, shown at level 0.0253, step 2, values float32 Opened J339_component_002_frame_015.mrc as #1.16, grid size 440,440,440, pixel 0.827, shown at level 0.0254, step 2, values float32 Opened J339_component_002_frame_016.mrc as #1.17, grid size 440,440,440, pixel 0.827, shown at level 0.0256, step 2, values float32 Opened J339_component_002_frame_017.mrc as #1.18, grid size 440,440,440, pixel 0.827, shown at level 0.0258, step 2, values float32 Opened J339_component_002_frame_018.mrc as #1.19, grid size 440,440,440, pixel 0.827, shown at level 0.0259, step 2, values float32 Opened J339_component_002_frame_019.mrc as #1.20, grid size 440,440,440, pixel 0.827, shown at level 0.0261, step 2, values float32 > vop flip #1 Opened J339_component_002_frame_000.mrc z flip as #2, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_001.mrc z flip as #3, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_002.mrc z flip as #4, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_003.mrc z flip as #5, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_004.mrc z flip as #6, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_005.mrc z flip as #7, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_006.mrc z flip as #8, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_007.mrc z flip as #9, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_008.mrc z flip as #10, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_009.mrc z flip as #11, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_010.mrc z flip as #12, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_011.mrc z flip as #13, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_012.mrc z flip as #14, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_013.mrc z flip as #15, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_014.mrc z flip as #16, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_015.mrc z flip as #17, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened J339_component_002_frame_016.mrc z flip as #18, grid size 440,440,440, pixel 0.827, shown at step 1, values float32 Opened 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 new normal Unassigned