id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16822 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-14.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000001dd3b5ec0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 44 in python_instances_of_class File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 176 in _copy_custom_attrs File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 162 in copy File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py"", line 65 in combine_cmd File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 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crash start ===== UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Corndog-Head- > Cap-C5-2_96A/cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc"" format mrc Opened cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc as #1, grid size 512,512,512, pixel 1.06, shown at level 0.327, step 2, values float32 > set bgColor white Already setting window visible! > volume #1 level 0.3 > volume #1 step 1 > surface dust #1 size 10.6 > transparency 50 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/5mer_TOP- > coot-5.pdb"" Chain information for 5mer_TOP-coot-5.pdb #2 --- Chain | Description A B C D E | No description available > hide atoms > show cartoons > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/6mer_Fit/6mer- > coot-3.pdb"" Chain information for 6mer-coot-3.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > combine #3 > hide atoms > show cartoons > select add #3 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #4 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #4 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #3 Nothing selected > select add #4 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view orient > turn x 180 > turn z 72 models #4 > turn z 72 models #5 > turn z 72 models #6 > turn z 72 models #7 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule 5mer_TOP-coot-5.pdb (#2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5746, steps = 40 shifted from previous position = 0.00495 rotated from previous position = 0.00986 degrees atoms outside contour = 1532, contour level = 0.3 Position of 5mer_TOP-coot-5.pdb (#2) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00016951 -0.00002828 0.04570487 0.00016951 0.99999999 0.00000850 -0.04784961 0.00002828 -0.00000851 1.00000000 -0.00870823 Axis -0.04944154 -0.16438129 0.98515701 Axis point 285.18770002 268.73749466 0.00000000 Rotation angle (degrees) 0.00985854 Shift along axis -0.00297311 > fitmap #2 inMap #1 Fit molecule 5mer_TOP-coot-5.pdb (#2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5745, steps = 40 shifted from previous position = 0.0041 rotated from previous position = 0.0188 degrees atoms outside contour = 1524, contour level = 0.3 Position of 5mer_TOP-coot-5.pdb (#2) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999988 -0.00049499 -0.00006232 0.13572348 0.00049499 0.99999988 -0.00000474 -0.13133342 0.00006232 0.00000471 1.00000000 -0.02187583 Axis 0.00947410 -0.12491656 0.99212202 Axis point 266.40584156 274.20415002 0.00000000 Rotation angle (degrees) 0.02858604 Shift along axis -0.00401192 > fitmap #4 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.2185, steps = 52 shifted from previous position = 1.27 rotated from previous position = 0.575 degrees atoms outside contour = 8456, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30248328 0.95314427 0.00445783 -71.70669631 -0.95312960 0.30250594 -0.00584140 453.30387080 -0.00691622 -0.00248196 0.99997300 1.48002833 Axis 0.00176227 0.00596652 -0.99998065 Axis point 273.86798326 275.65200666 0.00000000 Rotation angle (degrees) 72.39331450 Shift along axis 1.09828182 > fitmap #4 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.2185, steps = 44 shifted from previous position = 0.0239 rotated from previous position = 0.0186 degrees atoms outside contour = 8461, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30268705 0.95307852 0.00467760 -71.79305868 -0.95306368 0.30271152 -0.00594691 453.29025008 -0.00708384 -0.00265800 0.99997138 1.55016020 Axis 0.00172539 0.00617016 -0.99997948 Axis point 273.88514483 275.71563968 0.00000000 Rotation angle (degrees) 72.38105954 Shift along axis 1.12287286 > fitmap #3 inMap #1 Fit molecule 6mer-coot-3.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5943, steps = 40 shifted from previous position = 0.00571 rotated from previous position = 0.00747 degrees atoms outside contour = 1491, contour level = 0.3 Position of 6mer-coot-3.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00005683 -0.00011434 0.03059448 0.00005683 1.00000000 -0.00002643 -0.01115520 0.00011434 0.00002642 0.99999999 -0.03857003 Axis 0.20264296 -0.87691092 0.43584753 Axis point 334.18880113 0.00000000 269.02654273 Rotation angle (degrees) 0.00747063 Shift along axis -0.00082878 > fitmap #3 inMap #1 Fit molecule 6mer-coot-3.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5943, steps = 44 shifted from previous position = 0.00275 rotated from previous position = 0.00159 degrees atoms outside contour = 1492, contour level = 0.3 Position of 6mer-coot-3.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00003765 -0.00013268 0.02952940 0.00003765 1.00000000 -0.00001844 -0.00585603 0.00013268 0.00001843 0.99999999 -0.04400699 Axis 0.13249791 -0.95353864 0.27057046 Axis point 326.78378083 0.00000000 224.95040954 Rotation angle (degrees) 0.00797223 Shift along axis -0.00241046 > view #4 clip false > ui mousemode right ""translate selected models"" > view matrix models > #4,0.30269,0.95308,0.0046776,-71.017,-0.95306,0.30271,-0.0059469,449.13,-0.0070838,-0.002658,0.99997,0.74756 > fitmap #4 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5919, steps = 48 shifted from previous position = 1.87 rotated from previous position = 0.587 degrees atoms outside contour = 1511, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30916575 0.95100817 -0.00004905 -70.66463434 -0.95100817 0.30916575 0.00008446 445.96029112 0.00009549 0.00002053 1.00000000 -0.03417099 Axis -0.00003361 -0.00007599 -1.00000000 Axis point 271.62400540 271.61890830 0.00000000 Rotation angle (degrees) 71.99103821 Shift along axis 0.00265651 > fitmap #4 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5918, steps = 28 shifted from previous position = 0.00874 rotated from previous position = 0.0141 degrees atoms outside contour = 1522, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30935380 0.95094701 -0.00001621 -70.70134731 -0.95094701 0.30935380 -0.00005817 445.93230452 -0.00005030 0.00003341 1.00000000 -0.00410100 Axis 0.00004815 0.00001793 -1.00000000 Axis point 271.65021559 271.64030393 0.00000000 Rotation angle (degrees) 71.97970811 Shift along axis 0.00869008 > select subtract #4 Nothing selected > select add #5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #5 clip false > view matrix models > #5,-0.80902,0.58779,7.1983e-17,331.65,-0.58779,-0.80902,-2.2154e-16,653.29,-7.1983e-17,-2.2154e-16,1,-3.3824 > fitmap #5 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.2212, steps = 100 shifted from previous position = 6.5 rotated from previous position = 2.59 degrees atoms outside contour = 8370, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.79861927 0.60182174 0.00422494 325.21260348 -0.60116890 -0.79804422 0.04148938 641.93463776 0.02834090 0.03059431 0.99913001 -14.78059410 Axis -0.00905446 -0.02004182 -0.99975814 Axis point 270.05098621 266.71628557 0.00000000 Rotation angle (degrees) 143.01249563 Shift along axis -1.03314423 > fitmap #5 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.2212, steps = 36 shifted from previous position = 0.0175 rotated from previous position = 0.0104 degrees atoms outside contour = 8367, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.79858281 0.60187043 0.00418166 325.20023301 -0.60122357 -0.79801165 0.04132344 641.95488587 0.02820838 0.03048608 0.99913707 -14.73933063 Axis -0.00900575 -0.01996598 -0.99976010 Axis point 270.05880881 266.72185157 0.00000000 Rotation angle (degrees) 143.00887229 Shift along axis -1.01013461 > view matrix models > #5,-0.79858,0.60187,0.0041817,326.57,-0.60122,-0.79801,0.041323,644.65,0.028208,0.030486,0.99914,-12.49 > fitmap #5 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5921, steps = 60 shifted from previous position = 1.57 rotated from previous position = 2.57 degrees atoms outside contour = 1506, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80895617 0.58786895 0.00008586 331.65894423 -0.58786895 -0.80895618 0.00007441 651.01114206 0.00011320 0.00000972 0.99999999 -0.02989363 Axis -0.00005502 -0.00002325 -1.00000000 Axis point 271.61126098 271.61482534 0.00000000 Rotation angle (degrees) 143.99407211 Shift along axis -0.00349167 > fitmap #5 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5921, steps = 44 shifted from previous position = 0.00978 rotated from previous position = 0.0147 degrees atoms outside contour = 1508, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80883998 0.58802881 -0.00006016 331.61883628 -0.58802881 -0.80883998 0.00000246 651.04710395 -0.00004721 0.00003736 1.00000000 0.01323287 Axis 0.00002968 -0.00001101 -1.00000000 Axis point 271.63261455 271.62120750 0.00000000 Rotation angle (degrees) 143.98274873 Shift along axis -0.01055792 > select subtract #5 Nothing selected > select add #6 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #6 clip false > view matrix models > #6,-0.80902,-0.58779,-7.1983e-17,651.89,0.58779,-0.80902,-2.2154e-16,333.35,7.1983e-17,-2.2154e-16,1,-2.5685 > fitmap #6 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5918, steps = 56 shifted from previous position = 3.17 rotated from previous position = 0.00943 degrees atoms outside contour = 1506, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80904523 -0.58774638 0.00012829 650.98869529 0.58774637 -0.80904524 -0.00009120 331.72852030 0.00015740 0.00000161 0.99999999 -0.04945172 Axis 0.00007896 -0.00002476 1.00000000 Axis point 271.60619003 271.61513891 0.00000000 Rotation angle (degrees) 144.00275310 Shift along axis -0.00626316 > fitmap #6 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5918, steps = 40 shifted from previous position = 0.022 rotated from previous position = 0.0135 degrees atoms outside contour = 1491, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80915159 -0.58759995 0.00002427 651.01097365 0.58759995 -0.80915159 0.00001711 331.78233396 0.00000959 0.00002810 1.00000000 -0.00064232 Axis 0.00000936 0.00001250 1.00000000 Axis point 271.62518094 271.61310216 0.00000000 Rotation angle (degrees) 144.01312237 Shift along axis 0.00959453 > select subtract #6 Nothing selected > select add #7 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #7 clip false > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,447.19,0.95106,0.30902,-8.4621e-17,-70.294,1.1647e-16,-8.4621e-17,1,-1.614 > fitmap #7 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5915, steps = 52 shifted from previous position = 2.03 rotated from previous position = 0.00838 degrees atoms outside contour = 1507, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30889570 -0.95109592 -0.00004435 446.05077317 0.95109592 0.30889570 -0.00005639 -70.61719053 0.00006733 -0.00002477 1.00000000 -0.01514902 Axis 0.00001662 -0.00005871 1.00000000 Axis point 271.61698264 271.61835377 0.00000000 Rotation angle (degrees) 72.00730735 Shift along axis -0.00358882 > fitmap #7 inMap #1 Fit molecule copy of 6mer-coot-3.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5915, steps = 44 shifted from previous position = 0.0127 rotated from previous position = 0.00363 degrees atoms outside contour = 1510, contour level = 0.3 Position of copy of 6mer-coot-3.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30894025 -0.95108145 -0.00003705 446.04475647 0.95108144 0.30894025 -0.00009842 -70.61106386 0.00010505 -0.00000483 0.99999999 -0.01985016 Axis 0.00004920 -0.00007470 1.00000000 Axis point 271.61215147 271.63239345 0.00000000 Rotation angle (degrees) 72.00462355 Shift along axis 0.00737139 > rename #2 id #2.1 > rename #3 id #2 > rename #4 id #2 > rename #5 id #2 > rename #6 id #2 > rename #7 id #2 > select add #2 70705 atoms, 72000 bonds, 9815 residues, 7 models selected > select subtract #2 Nothing selected > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog /Capsid/Fitting/5mer_side- > coot-3.pdb"" Chain information for 5mer_side-coot-3.pdb #3 --- Chain | Description A B C D E | No description available > select add #2.2 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #2.3 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #2.4 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #2.5 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #2.6 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color sel yellow > select subtract #2.2 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #2.3 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #2.4 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #2.5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #2.6 Nothing selected > select add #2.1 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > color sel red > select subtract #2.1 Nothing selected > combine #3 > view orient > turn x 180 > turn z 72 models #4 > turn z 72 models #5 > turn z 72 models #6 > turn z 72 models #7 > select add #3 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > select add #4 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select add #5 30270 atoms, 30825 bonds, 4200 residues, 3 models selected > select subtract #5 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select subtract #4 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > select subtract #3 Nothing selected > turn z 72 models #7 > turn z 72 models #6 > turn z 72 models #5 > hide atoms > show cartoons > view #3 clip false > fitmap #3 inMap #1 Fit molecule 5mer_side-coot-3.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5473, steps = 44 shifted from previous position = 0.0117 rotated from previous position = 0.0186 degrees atoms outside contour = 1726, contour level = 0.3 Position of 5mer_side-coot-3.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00002215 -0.00015301 0.02781714 -0.00002219 0.99999996 -0.00028533 0.06193389 0.00015300 0.00028534 0.99999995 -0.12860248 Axis 0.87923042 -0.47147350 -0.06831255 Axis point 0.00000000 449.77904545 223.67413627 Rotation angle (degrees) 0.01859403 Shift along axis 0.00404265 > fitmap #3 inMap #1 Fit molecule 5mer_side-coot-3.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5472, steps = 28 shifted from previous position = 0.00729 rotated from previous position = 0.0167 degrees atoms outside contour = 1731, contour level = 0.3 Position of 5mer_side-coot-3.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00013866 -0.00002054 -0.03753810 -0.00013866 0.99999999 -0.00005298 0.02505265 0.00002053 0.00005299 1.00000000 -0.03832388 Axis 0.35358439 -0.13705532 -0.92530747 Axis point 199.18879465 318.56130029 0.00000000 Rotation angle (degrees) 0.00858593 Shift along axis 0.01875489 > select add #4 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > view #4 clip false > view matrix models > #4,0.30902,0.95106,1.1647e-16,-71.399,-0.95106,0.30902,-8.4621e-17,447.52,-1.1647e-16,-8.4621e-17,1,-3.2523 > fitmap #4 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.2068, steps = 60 shifted from previous position = 2.48 rotated from previous position = 0.405 degrees atoms outside contour = 7277, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.31230227 0.94998228 0.00097581 -72.84962326 -0.94996694 0.31229096 0.00609638 443.37861872 0.00548671 -0.00283090 0.99998094 -4.46526791 Axis -0.00469863 -0.00237419 -0.99998614 Axis point 269.83161799 271.99935855 0.00000000 Rotation angle (degrees) 71.80288484 Shift along axis 3.75483522 > fitmap #4 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.2068, steps = 40 shifted from previous position = 0.00993 rotated from previous position = 0.0108 degrees atoms outside contour = 7274, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.31243725 0.94993776 0.00109783 -72.87342047 -0.94992287 0.31242533 0.00607909 443.33089505 0.00543177 -0.00294219 0.99998092 -4.41103155 Axis -0.00474833 -0.00228116 -0.99998612 Axis point 269.83218637 271.99907544 0.00000000 Rotation angle (degrees) 71.79476277 Shift along axis 3.74569009 > view matrix models > #4,0.31244,0.94994,0.0010978,-71.488,-0.94992,0.31243,0.0060791,445.25,0.0054318,-0.0029422,0.99998,-1.2928 > fitmap #4 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5433, steps = 56 shifted from previous position = 2.52 rotated from previous position = 0.413 degrees atoms outside contour = 1829, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30894669 0.95107936 -0.00001575 -70.64582654 -0.95107936 0.30894669 -0.00001668 446.03336539 -0.00001100 0.00002014 1.00000000 -0.01497848 Axis 0.00001936 -0.00000250 -1.00000000 Axis point 271.60936052 271.63072359 0.00000000 Rotation angle (degrees) 72.00423521 Shift along axis 0.01249650 > fitmap #4 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5433, steps = 44 shifted from previous position = 0.0109 rotated from previous position = 0.0181 degrees atoms outside contour = 1818, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30908044 0.95103585 -0.00029432 -70.58437096 -0.95103589 0.30908046 0.00003460 445.97462917 0.00012388 0.00026922 0.99999996 -0.10829380 Axis 0.00012335 -0.00021986 -0.99999997 Axis point 271.64505129 271.56626098 0.00000000 Rotation angle (degrees) 71.99617848 Shift along axis 0.00153335 > select subtract #4 Nothing selected > select add #5 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > view #5 clip false > view matrix models > #5,-0.80902,0.58779,7.1983e-17,330.48,-0.58779,-0.80902,-2.2154e-16,650.48,-7.1983e-17,-2.2154e-16,1,0.48581 > fitmap #5 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5441, steps = 48 shifted from previous position = 1.43 rotated from previous position = 0.0198 degrees atoms outside contour = 1776, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80896651 0.58785474 -0.00000886 331.68597169 -0.58785471 -0.80896646 0.00033513 650.93912608 0.00018984 0.00027632 0.99999994 -0.11085507 Axis -0.00005002 -0.00016900 -0.99999998 Axis point 271.60991350 271.57604549 0.00000000 Rotation angle (degrees) 143.99507919 Shift along axis -0.01574870 > fitmap #5 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5442, steps = 44 shifted from previous position = 0.0105 rotated from previous position = 0.0197 degrees atoms outside contour = 1781, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80904786 0.58774277 0.00000306 331.72626950 -0.58774277 -0.80904786 0.00002040 651.01415915 0.00001446 0.00001470 1.00000000 -0.00523430 Axis -0.00000484 -0.00000970 -1.00000000 Axis point 271.61734803 271.61969457 0.00000000 Rotation angle (degrees) 144.00300854 Shift along axis -0.00268751 > select subtract #5 Nothing selected > select add #6 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > view #6 clip false > view matrix models > #6,-0.80902,-0.58779,-7.1983e-17,684.94,0.58779,-0.80902,-2.2154e-16,382.22,7.1983e-17,-2.2154e-16,1,-6.1306 > view matrix models > #6,-0.80902,-0.58779,-7.1983e-17,686.2,0.58779,-0.80902,-2.2154e-16,383.44,7.1983e-17,-2.2154e-16,1,-6.2078 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.1401, steps = 56 shifted from previous position = 1.15 rotated from previous position = 1.53 degrees atoms outside contour = 8571, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.82210615 -0.56920362 -0.01219518 684.88730917 0.56916581 -0.82219537 0.00671256 389.36387799 -0.01384763 -0.00142264 0.99990310 -3.24689355 Axis -0.00714617 0.00145156 0.99997341 Axis point 281.61597640 301.64771083 0.00000000 Rotation angle (degrees) 145.30555247 Shift along axis -7.57594521 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.14, steps = 44 shifted from previous position = 0.0091 rotated from previous position = 0.017 degrees atoms outside contour = 8571, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.82194382 -0.56943956 -0.01212198 684.92676293 0.56940137 -0.82203207 0.00673498 389.28024654 -0.01379982 -0.00136650 0.99990384 -3.27420197 Axis -0.00711360 0.00147325 0.99997361 Axis point 281.61808863 301.66600220 0.00000000 Rotation angle (degrees) 145.28912968 Shift along axis -7.57290576 > view matrix models > #6,-0.82194,-0.56944,-0.012122,641.92,0.5694,-0.82203,0.006735,359.25,-0.0138,-0.0013665,0.9999,18.711 > view matrix models > #6,-0.82194,-0.56944,-0.012122,636.61,0.5694,-0.82203,0.006735,355.52,-0.0138,-0.0013665,0.9999,21.459 > view matrix models > #6,-0.82194,-0.56944,-0.012122,638.09,0.5694,-0.82203,0.006735,356.83,-0.0138,-0.0013665,0.9999,20.635 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.1363, steps = 176 shifted from previous position = 4.31 rotated from previous position = 4.56 degrees atoms outside contour = 10069, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.82234895 -0.56768768 0.03837832 625.61780927 0.56893687 -0.81954557 0.06823416 347.06917970 -0.00728291 0.07794713 0.99693089 -6.60946675 Axis 0.00853825 0.04013882 0.99915763 Axis point 258.71124977 271.35953489 0.00000000 Rotation angle (degrees) 145.33401027 Shift along axis 12.66872999 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.1363, steps = 64 shifted from previous position = 0.0113 rotated from previous position = 0.0181 degrees atoms outside contour = 10069, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.82244034 -0.56754127 0.03858498 625.53733735 0.56880820 -0.81964809 0.06807527 347.16359190 -0.00700942 0.07793530 0.99693378 -6.63439598 Axis 0.00866963 0.04008981 0.99915847 Axis point 258.67301562 271.36527119 0.00000000 Rotation angle (degrees) 145.34363233 Shift along axis 12.71208783 > view matrix models > #6,-0.82244,-0.56754,0.038585,636.53,0.56881,-0.81965,0.068075,343.84,-0.0070094,0.077935,0.99693,-8.8707 > view matrix models > #6,-0.82244,-0.56754,0.038585,638.69,0.56881,-0.81965,0.068075,332.74,-0.0070094,0.077935,0.99693,-20.124 > view matrix models > #6,-0.82244,-0.56754,0.038585,639.63,0.56881,-0.81965,0.068075,323.8,-0.0070094,0.077935,0.99693,-26.047 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.5451, steps = 84 shifted from previous position = 2.32 rotated from previous position = 4.66 degrees atoms outside contour = 1777, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80904595 -0.58774535 0.00023884 650.94578273 0.58774539 -0.80904593 0.00019874 331.67585787 0.00007642 0.00030116 0.99999995 -0.11550121 Axis 0.00008713 0.00013817 0.99999999 Axis point 271.59340445 271.58162342 0.00000000 Rotation angle (degrees) 144.00282413 Shift along axis -0.01295478 > fitmap #6 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.545, steps = 44 shifted from previous position = 0.012 rotated from previous position = 0.00362 degrees atoms outside contour = 1768, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80903084 -0.58776617 0.00018691 650.96377780 0.58776620 -0.80903082 0.00017364 331.67926666 0.00004916 0.00025034 0.99999997 -0.10489011 Axis 0.00006525 0.00011719 0.99999999 Axis point 271.59948811 271.59087786 0.00000000 Rotation angle (degrees) 144.00135000 Shift along axis -0.02354804 > view #6 clip false > select subtract #6 Nothing selected > select add #7 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > view #7 clip false > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,456.07,0.95106,0.30902,-8.4621e-17,-63.277,1.1647e-16,-8.4621e-17,1,4.6984 > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,454.44,0.95106,0.30902,-8.4621e-17,-61.044,1.1647e-16,-8.4621e-17,1,5.3438 > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,455.63,0.95106,0.30902,-8.4621e-17,-62.455,1.1647e-16,-8.4621e-17,1,5.4122 > fitmap #7 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.546, steps = 172 shifted from previous position = 13.7 rotated from previous position = 0.00723 degrees atoms outside contour = 1737, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30912441 -0.95102161 0.00005389 445.96744065 0.95102161 0.30912441 -0.00001606 -70.67339440 -0.00000139 0.00005622 1.00000000 -0.01270359 Axis 0.00003800 0.00002906 1.00000000 Axis point 271.62628821 271.61051504 0.00000000 Rotation angle (degrees) 71.99352877 Shift along axis 0.00218923 > fitmap #7 inMap #1 Fit molecule copy of 5mer_side-coot-3.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 10090 atoms average map value = 0.546, steps = 44 shifted from previous position = 0.0218 rotated from previous position = 0.0172 degrees atoms outside contour = 1723, contour level = 0.3 Position of copy of 5mer_side-coot-3.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30899264 -0.95106440 0.00024965 445.95832019 0.95106442 0.30899260 -0.00019515 -70.58645385 0.00010846 0.00029774 0.99999995 -0.12943872 Axis 0.00025912 0.00007423 0.99999996 Axis point 271.55482671 271.60299810 0.00000000 Rotation angle (degrees) 72.00146997 Shift along axis -0.01911988 > select add #6 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select add #5 30270 atoms, 30825 bonds, 4200 residues, 3 models selected > select add #4 40360 atoms, 41100 bonds, 5600 residues, 4 models selected > select add #3 50450 atoms, 51375 bonds, 7000 residues, 5 models selected > color sel cyan > select subtract #3 40360 atoms, 41100 bonds, 5600 residues, 4 models selected > select subtract #4 30270 atoms, 30825 bonds, 4200 residues, 3 models selected > select subtract #5 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select subtract #6 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > select subtract #7 Nothing selected > rename #3 id #2 > rename #4 id #2 > rename #5 id #2 > rename #6 id #2 > rename #7 id #2 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/6mer_side_tilt.pdb"" Chain information for 6mer_side_tilt.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > combine #3 > hide atoms > show cartoons > view orient > turn x 180 > turn z 72 models #4 > turn z 72 models #5 > turn z 72 models #6 > turn z 72 models #7 > fitmap #3 inMap #1 Fit molecule 6mer_side_tilt.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4932, steps = 44 shifted from previous position = 0.0283 rotated from previous position = 0.0168 degrees atoms outside contour = 2748, contour level = 0.3 Position of 6mer_side_tilt.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999996 0.00006292 -0.00028620 0.06422893 -0.00006292 1.00000000 0.00001980 0.00341497 0.00028620 -0.00001979 0.99999996 -0.04153750 Axis -0.06739639 -0.97445482 -0.21423241 Axis point 144.23698677 0.00000000 224.69154800 Rotation angle (degrees) 0.01682789 Shift along axis 0.00124215 > fitmap #3 inMap #1 Fit molecule 6mer_side_tilt.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4932, steps = 44 shifted from previous position = 0.0052 rotated from previous position = 0.00055 degrees atoms outside contour = 2756, contour level = 0.3 Position of 6mer_side_tilt.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999996 0.00005646 -0.00028099 0.05940778 -0.00005645 1.00000000 0.00002461 0.00233654 0.00028099 -0.00002460 0.99999996 -0.04233969 Axis -0.08554166 -0.97681294 -0.19626284 Axis point 150.05172261 0.00000000 211.69250221 Rotation angle (degrees) 0.01648147 Shift along axis 0.00094551 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.206, steps = 124 shifted from previous position = 11.4 rotated from previous position = 0.463 degrees atoms outside contour = 8610, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30210051 0.95327238 0.00265637 -71.92273194 -0.95327126 0.30210667 -0.00233876 452.55592822 -0.00303198 -0.00182570 0.99999374 0.79783891 Axis 0.00026910 0.00298358 -0.99999551 Axis point 273.11701354 275.39988126 0.00000000 Rotation angle (degrees) 72.41619455 Shift along axis 0.53304780 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.206, steps = 48 shifted from previous position = 0.0247 rotated from previous position = 0.0168 degrees atoms outside contour = 8609, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30201805 0.95329823 0.00275381 -71.91595471 -0.95329645 0.30202501 -0.00260201 452.61995671 -0.00331221 -0.00183935 0.99999282 0.86901866 Axis 0.00040001 0.00318158 -0.99999486 Axis point 273.13623925 275.42308163 0.00000000 Rotation angle (degrees) 72.42115428 Shift along axis 0.54226748 > view #4 clip false > select add #4 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view matrix models > #4,0.30202,0.9533,0.0027538,-71.605,-0.9533,0.30203,-0.002602,447.85,-0.0033122,-0.0018393,0.99999,0.92881 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4943, steps = 68 shifted from previous position = 1.74 rotated from previous position = 0.477 degrees atoms outside contour = 2741, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30897093 0.95107148 -0.00001681 -70.62524876 -0.95107144 0.30897092 0.00027734 445.94374148 0.00026897 -0.00006971 0.99999996 -0.05107193 Axis -0.00018245 -0.00015024 -0.99999997 Axis point 271.56620362 271.57305768 0.00000000 Rotation angle (degrees) 72.00277649 Shift along axis -0.00303963 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4943, steps = 40 shifted from previous position = 0.00604 rotated from previous position = 0.00301 degrees atoms outside contour = 2750, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30897855 0.95106901 0.00000870 -70.63370923 -0.95106896 0.30897853 0.00032265 445.93619772 0.00030417 -0.00010797 0.99999995 -0.05755084 Axis -0.00022639 -0.00015534 -0.99999996 Axis point 271.55936931 271.57551689 0.00000000 Rotation angle (degrees) 72.00231807 Shift along axis 0.00427142 > select subtract #4 Nothing selected > select add #5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #6 clip false > select subtract #5 Nothing selected > select add #6 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view matrix models > #6,-0.80902,-0.58779,-7.1983e-17,658.82,0.58779,-0.80902,-2.2154e-16,341.37,7.1983e-17,-2.2154e-16,1,-4.0386 > fitmap #6 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4967, steps = 120 shifted from previous position = 13.1 rotated from previous position = 0.0142 degrees atoms outside contour = 2717, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80901313 -0.58779054 0.00020469 650.96066810 0.58779052 -0.80901315 -0.00013915 331.72862387 0.00024739 0.00000774 0.99999997 -0.04790015 Axis 0.00012495 -0.00003632 0.99999999 Axis point 271.58715559 271.62045827 0.00000000 Rotation angle (degrees) 143.99962567 Shift along axis 0.02139052 > select subtract #6 Nothing selected > select add #5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #5 clip false > view matrix models > #5,-0.80902,0.58779,7.1983e-17,336.9,-0.58779,-0.80902,-2.2154e-16,654,-7.1983e-17,-2.2154e-16,1,-0.34927 > view matrix models > #5,-0.80902,0.58779,7.1983e-17,337.66,-0.58779,-0.80902,-2.2154e-16,654.61,-7.1983e-17,-2.2154e-16,1,-0.0069747 > view matrix models > #5,-0.80902,0.58779,7.1983e-17,332.01,-0.58779,-0.80902,-2.2154e-16,650.79,-7.1983e-17,-2.2154e-16,1,-0.57263 > fitmap #6 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4967, steps = 44 shifted from previous position = 0.0111 rotated from previous position = 0.0129 degrees atoms outside contour = 2710, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80903995 -0.58775365 0.00004295 651.00116667 0.58775365 -0.80903995 0.00001049 331.70265119 0.00002858 0.00003373 1.00000000 -0.00655130 Axis 0.00001977 0.00001222 1.00000000 Axis point 271.61580231 271.60584774 0.00000000 Rotation angle (degrees) 144.00223811 Shift along axis 0.01037327 > fitmap #6 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4967, steps = 60 shifted from previous position = 0.00553 rotated from previous position = 0.000212 degrees atoms outside contour = 2714, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80904105 -0.58775214 0.00004612 651.00168158 0.58775214 -0.80904105 0.00001081 331.70368923 0.00003096 0.00003585 1.00000000 -0.00201656 Axis 0.00002131 0.00001290 1.00000000 Axis point 271.61606232 271.60611434 0.00000000 Rotation angle (degrees) 144.00234511 Shift along axis 0.01613125 > fitmap #5 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4947, steps = 48 shifted from previous position = 0.682 rotated from previous position = 0.0185 degrees atoms outside contour = 2735, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80897568 0.58784205 0.00028980 331.61903574 -0.58784204 -0.80897573 0.00012483 650.98037001 0.00030782 -0.00006937 0.99999995 -0.06536667 Axis -0.00016518 -0.00001533 -0.99999999 Axis point 271.58032900 271.60897152 0.00000000 Rotation angle (degrees) 143.99597744 Shift along axis 0.00060910 > fitmap #5 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4947, steps = 40 shifted from previous position = 0.0266 rotated from previous position = 0.0164 degrees atoms outside contour = 2726, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80891994 0.58791881 0.00002481 331.67479975 -0.58791880 -0.80891994 0.00007042 651.02057321 0.00006147 0.00004238 1.00000000 0.00548588 Axis -0.00002385 -0.00003118 -1.00000000 Axis point 271.63180992 271.61131435 0.00000000 Rotation angle (degrees) 143.99054102 Shift along axis -0.03369280 > select subtract #5 Nothing selected > select add #7 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #7 clip false > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,446.65,0.95106,0.30902,-8.4621e-17,-70.746,1.1647e-16,-8.4621e-17,1,-3.4766 > view matrix models > #7,0.30902,-0.95106,-1.1647e-16,447.4,0.95106,0.30902,-8.4621e-17,-70.177,1.1647e-16,-8.4621e-17,1,-0.94653 > fitmap #7 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4947, steps = 72 shifted from previous position = 1.76 rotated from previous position = 0.0194 degrees atoms outside contour = 2721, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30916082 -0.95100977 -0.00007333 445.97824713 0.95100972 0.30916083 -0.00029450 -70.57235918 0.00030274 0.00002132 0.99999995 -0.06070336 Axis 0.00016604 -0.00019772 0.99999997 Axis point 271.56410866 271.68082171 0.00000000 Rotation angle (degrees) 71.99133638 Shift along axis 0.02730226 > fitmap #7 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4947, steps = 44 shifted from previous position = 0.0152 rotated from previous position = 0.00113 degrees atoms outside contour = 2717, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30917795 -0.95100420 -0.00007160 445.98116595 0.95100416 0.30917796 -0.00028664 -70.56478416 0.00029473 0.00002053 0.99999996 -0.05067148 Axis 0.00016150 -0.00019260 0.99999997 Axis point 271.56127256 271.69243470 0.00000000 Rotation angle (degrees) 71.99030391 Shift along axis 0.03494343 > select add #6 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #5 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #4 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #3 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color sel cornflower blue > color sel blue > select subtract #3 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #4 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #5 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #6 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #7 Nothing selected > rename #3 id #2 > rename #4 id #2 > rename #5 id #2 > rename #6 id #2 > rename #7 id #2 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/6mer_side_straight1.pdb"" Chain information for 6mer_side_straight1.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > hide atoms > show cartoons > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4117, steps = 44 shifted from previous position = 0.0138 rotated from previous position = 0.000918 degrees atoms outside contour = 3904, contour level = 0.3 Position of 6mer_side_straight1.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00000348 -0.00001068 0.00363308 0.00000348 1.00000000 0.00001142 -0.00639869 0.00001068 -0.00001142 1.00000000 0.01125876 Axis -0.71283470 -0.66678837 0.21739354 Axis point -0.00000000 907.22367503 319.44989715 Rotation angle (degrees) 0.00091805 Shift along axis 0.00412437 > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4117, steps = 60 shifted from previous position = 0.0181 rotated from previous position = 0.0131 degrees atoms outside contour = 3910, contour level = 0.3 Position of 6mer_side_straight1.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00000700 0.00017224 -0.05617344 -0.00000703 0.99999999 0.00014727 -0.04565547 -0.00017224 -0.00014727 0.99999997 0.07360516 Axis -0.64956245 0.75967840 -0.03094108 Axis point 427.20994172 -0.00000000 327.95476081 Rotation angle (degrees) 0.01299048 Shift along axis -0.00047275 > combine #3 > view orient > turn x 180 > turn z 72 models #4 > turn z 72 models #5 > turn z 72 models #6 > turn z 72 models #7 > view #3 clip false > select add #3 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4117, steps = 44 shifted from previous position = 0.0147 rotated from previous position = 0.00147 degrees atoms outside contour = 3907, contour level = 0.3 Position of 6mer_side_straight1.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999998 0.00000501 0.00019418 -0.06155462 -0.00000503 0.99999999 0.00013425 -0.04156282 -0.00019418 -0.00013425 0.99999997 0.09445635 Axis -0.56856333 0.82236490 -0.02125319 Axis point 486.27068369 0.00000000 320.53350503 Rotation angle (degrees) 0.01352865 Shift along axis -0.00118960 > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4117, steps = 28 shifted from previous position = 0.0207 rotated from previous position = 0.00695 degrees atoms outside contour = 3910, contour level = 0.3 Position of 6mer_side_straight1.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999998 -0.00011008 0.00018399 -0.05731283 0.00011005 0.99999998 0.00017105 -0.10156491 -0.00018401 -0.00017103 0.99999997 0.08051164 Axis -0.62360887 0.67087243 0.40130058 Axis point 437.67017639 0.00000000 311.84316297 Rotation angle (degrees) 0.01571474 Shift along axis -0.00008694 > select subtract #3 Nothing selected > select add #4 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #4 clip false > view matrix models > #4,0.30901,0.95106,0.00019329,-70.367,-0.95106,0.30901,-0.0001183,447.45,-0.00017224,-0.00014727,1,0.52031 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4136, steps = 52 shifted from previous position = 1.51 rotated from previous position = 0.00596 degrees atoms outside contour = 3898, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30899677 0.95106306 0.00020902 -70.70683889 -0.95106308 0.30899678 -0.00001641 446.02160378 -0.00008019 -0.00019372 0.99999998 0.06434696 Axis -0.00009322 0.00015205 -0.99999998 Axis point 271.58775317 271.66952613 0.00000000 Rotation angle (degrees) 72.00121856 Shift along axis 0.01006120 > fitmap #4 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4136, steps = 44 shifted from previous position = 0.019 rotated from previous position = 0.00187 degrees atoms outside contour = 3887, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30897763 0.95106928 0.00022338 -70.69985108 -0.95106930 0.30897763 0.00000492 446.01369415 -0.00006434 -0.00021397 0.99999998 0.04379612 Axis -0.00011508 0.00015127 -0.99999998 Axis point 271.57930451 271.65972906 0.00000000 Rotation angle (degrees) 72.00237224 Shift along axis 0.03180616 > select subtract #4 Nothing selected > select add #5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #4 clip false > view #5 clip false > view matrix models > #5,-0.80902,0.58778,-5.278e-05,325.51,-0.58778,-0.80902,-0.00022039,653.96,-0.00017224,-0.00014727,1,0.79208 > fitmap #5 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4121, steps = 96 shifted from previous position = 6.9 rotated from previous position = 0.0072 degrees atoms outside contour = 3946, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80905265 0.58773617 0.00005914 331.71008018 -0.58773616 -0.80905262 -0.00023994 651.07655959 -0.00009317 -0.00022888 0.99999997 0.07117226 Axis 0.00000941 0.00012958 -0.99999999 Axis point 271.61792281 271.65427679 0.00000000 Rotation angle (degrees) 144.00347598 Shift along axis 0.01631185 > fitmap #5 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.412, steps = 48 shifted from previous position = 0.0218 rotated from previous position = 0.0149 degrees atoms outside contour = 3939, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80908180 0.58769602 0.00019244 331.67529022 -0.58769603 -0.80908181 -0.00002190 650.98235445 0.00014283 -0.00013082 0.99999998 -0.04022438 Axis -0.00009266 0.00004221 -0.99999999 Axis point 271.57629945 271.61736789 0.00000000 Rotation angle (degrees) 144.00631866 Shift along axis 0.03696783 > select add #6 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #6 clip false > view matrix models > #6,-0.80901,-0.58779,-0.00022591,651.73,0.58779,-0.80901,-1.7906e-05,333.18,-0.00017224,-0.00014727,1,0.024087 > fitmap #6 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4091, steps = 76 shifted from previous position = 1.61 rotated from previous position = 0.0091 degrees atoms outside contour = 3967, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80896621 -0.58785508 -0.00029919 651.09603464 0.58785513 -0.80896621 -0.00013440 331.71456469 -0.00016303 -0.00028460 0.99999995 0.10201758 Axis -0.00012776 -0.00011581 0.99999999 Axis point 271.64980837 271.64979242 0.00000000 Rotation angle (degrees) 143.99505236 Shift along axis -0.01958025 > fitmap #6 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4091, steps = 44 shifted from previous position = 0.0145 rotated from previous position = 0.0171 degrees atoms outside contour = 3972, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation -0.80896716 -0.58785384 -0.00000594 651.00390936 0.58785383 -0.80896715 -0.00019175 331.73307327 0.00010792 -0.00015861 0.99999998 -0.02239254 Axis 0.00002819 -0.00009684 0.99999999 Axis point 271.60087767 271.64378633 0.00000000 Rotation angle (degrees) 143.99514281 Shift along axis -0.03616666 > select subtract #6 Nothing selected > select add #7 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > view #7 clip false > view matrix models > #7,0.30902,-0.95105,-8.6839e-05,447.98,0.95105,0.30902,0.00020932,-67.762,-0.00017224,-0.00014727,1,0.85769 > view matrix models > #7,0.30902,-0.95105,-8.6839e-05,448.51,0.95105,0.30902,0.00020932,-70.163,-0.00017224,-0.00014727,1,0.97804 > fitmap #7 inMap #1 Fit molecule copy of 6mer_side_straight1.pdb (#7) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4101, steps = 64 shifted from previous position = 2.7 rotated from previous position = 0.00556 degrees atoms outside contour = 3950, contour level = 0.3 Position of copy of 6mer_side_straight1.pdb (#7) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30900829 -0.95105933 -0.00017662 446.06455192 0.95105933 0.30900825 0.00024245 -70.73183698 -0.00017601 -0.00024289 0.99999996 0.10639615 Axis -0.00025516 -0.00000032 0.99999997 Axis point 271.70883134 271.60871477 0.00000000 Rotation angle (degrees) 72.00052681 Shift along axis -0.00739789 > select add #6 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #5 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #4 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #3 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color sel hot pink > select subtract #7 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #6 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #5 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #4 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #3 Nothing selected > rename #3 id #2 > rename #4 id #2 > rename #5 id #2 > rename #6 id #2 > rename #7 id #2 > hide #!1 models > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" selectedOnly true relModel #1 > hide #!2 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" > show #!2 models > hide #!2 models > show #!2 models > select add #2 242385 atoms, 246825 bonds, 33645 residues, 22 models selected > save ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" selectedOnly true relModel #1 > select subtract #2 Nothing selected > hide #!2 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" Chain information for Capsid_Top.pdb --- Chain | Description 3.1/A 3.2/A 3.3/A 3.4/A 3.5/A 3.6/A 3.7/A 3.8/A 3.9/A 3.10/A 3.11/A 3.12/A 3.13/A 3.14/A 3.15/A 3.16/A 3.17/A 3.18/A 3.19/A 3.20/A 3.21/A 3.1/B 3.2/B 3.3/B 3.4/B 3.5/B 3.6/B 3.7/B 3.8/B 3.9/B 3.10/B 3.11/B 3.12/B 3.13/B 3.14/B 3.15/B 3.16/B 3.17/B 3.18/B 3.19/B 3.20/B 3.21/B 3.1/C 3.7/C 3.8/C 3.9/C 3.10/C 3.11/C 3.1/D 3.2/D 3.3/D 3.4/D 3.5/D 3.6/D 3.7/D 3.8/D 3.9/D 3.10/D 3.11/D 3.12/D 3.13/D 3.14/D 3.15/D 3.16/D 3.17/D 3.18/D 3.19/D 3.20/D 3.21/D 3.1/E 3.7/E 3.8/E 3.9/E 3.10/E 3.11/E | No description available 3.2/C 3.3/C 3.4/C 3.5/C 3.6/C 3.12/C 3.13/C 3.14/C 3.15/C 3.16/C 3.17/C 3.18/C 3.19/C 3.20/C 3.21/C 3.2/E 3.3/E 3.4/E 3.5/E 3.6/E 3.12/E 3.13/E 3.14/E 3.15/E 3.16/E 3.17/E 3.18/E 3.19/E 3.20/E 3.21/E 3.2/F 3.3/F 3.4/F 3.5/F 3.6/F 3.12/F 3.13/F 3.14/F 3.15/F 3.16/F 3.17/F 3.18/F 3.19/F 3.20/F 3.21/F | No description available > hide #3.1-21 atoms > show #3.1-21 cartoons > show #!2 models > select add #3 242385 atoms, 246825 bonds, 33645 residues, 22 models selected > select subtract #3 Nothing selected > hide #!2 models > lighting flat > hide #!3 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/6mer_side_tilt-coot-1.pdb"" Chain information for 6mer_side_tilt-coot-1.pdb #4 --- Chain | Description A B D | No description available C E F | No description available > hide #!2 models > show #!1 models > hide #4 atoms > show #4 cartoons > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.526, steps = 48 shifted from previous position = 0.022 rotated from previous position = 0.0103 degrees atoms outside contour = 2271, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 0.00000973 0.00013685 -0.02991728 -0.00000971 0.99999999 -0.00011588 0.03153964 -0.00013686 0.00011588 0.99999998 0.00070070 Axis 0.64526408 0.76204020 -0.05412026 Axis point 6.94722392 0.00000000 240.73008819 Rotation angle (degrees) 0.01028975 Shift along axis 0.00469201 > fitmap #2.13 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#2.13) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4943, steps = 48 shifted from previous position = 0.00283 rotated from previous position = 0.0182 degrees atoms outside contour = 2748, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#2.13) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30904065 0.95104883 0.00002692 -70.65311634 -0.95104883 0.30904065 0.00001302 446.00761869 0.00000406 -0.00002962 1.00000000 0.00996369 Axis -0.00002242 0.00001202 -1.00000000 Axis point 271.61987983 271.62791696 0.00000000 Rotation angle (degrees) 71.99857504 Shift along axis -0.00302035 > fitmap #2.13 inMap #1 Fit molecule copy of 6mer_side_tilt.pdb (#2.13) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4943, steps = 48 shifted from previous position = 0.0253 rotated from previous position = 0.00162 degrees atoms outside contour = 2748, contour level = 0.3 Position of copy of 6mer_side_tilt.pdb (#2.13) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.30901689 0.95105655 0.00001822 -70.64807980 -0.95105655 0.30901689 0.00002311 445.99243890 0.00001635 -0.00002447 1.00000000 0.02507277 Axis -0.00002502 0.00000098 -1.00000000 Axis point 271.60389034 271.61558431 0.00000000 Rotation angle (degrees) 72.00000610 Shift along axis -0.02286670 > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5261, steps = 36 shifted from previous position = 0.0188 rotated from previous position = 0.0162 degrees atoms outside contour = 2276, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999991 -0.00005062 0.00041037 -0.10073495 0.00005068 0.99999999 -0.00014836 0.02310279 -0.00041037 0.00014838 0.99999990 0.08272392 Axis 0.33775081 0.93414767 0.11529315 Axis point 202.34528280 0.00000000 243.12310910 Rotation angle (degrees) 0.02516996 Shift along axis -0.00290439 > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.526, steps = 40 shifted from previous position = 0.0141 rotated from previous position = 0.00242 degrees atoms outside contour = 2269, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999990 -0.00006508 0.00044993 -0.11415221 0.00006515 0.99999999 -0.00014636 0.02208143 -0.00044992 0.00014638 0.99999989 0.07976850 Axis 0.30647131 0.94206508 0.13634046 Axis point 178.23270166 0.00000000 251.49774612 Rotation angle (degrees) 0.02736437 Shift along axis -0.00330656 > hide #4 models > close #3 > show #!2 models > hide #!2 models > show #!2 models > hide #2.1 models > hide #2.2 models > hide #2.3 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > select add #2.2 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #2.3 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #2.4 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #2.5 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #2.6 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color #1#2.7-21#!2 orange > undo > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > show #2.6 models > color sel orange > select subtract #2.2 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #2.3 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #2.4 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #2.5 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #2.6 Nothing selected > select add #2.7 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > select add #2.8 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select add #2.9 30270 atoms, 30825 bonds, 4200 residues, 3 models selected > select add #2.10 40360 atoms, 41100 bonds, 5600 residues, 4 models selected > select add #2.11 50450 atoms, 51375 bonds, 7000 residues, 5 models selected > color sel yellow > select subtract #2.7 40360 atoms, 41100 bonds, 5600 residues, 4 models selected > select subtract #2.8 30270 atoms, 30825 bonds, 4200 residues, 3 models selected > select subtract #2.9 20180 atoms, 20550 bonds, 2800 residues, 2 models selected > select subtract #2.10 10090 atoms, 10275 bonds, 1400 residues, 1 model selected > select subtract #2.11 Nothing selected > select add #2.12 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #2.13 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #2.14 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #2.15 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #2.16 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color sel forest green > select subtract #2.16 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #2.16 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > select subtract #2.15 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #2.16 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #2.14 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #2.13 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #2.12 Nothing selected > select add #2.17 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #2.18 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #2.19 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #2.20 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #2.21 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > color sel blue > color sel cyan > select subtract #2.17 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select subtract #2.18 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select subtract #2.19 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select subtract #2.20 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #2.21 Nothing selected > hide #2.11 models > hide #2.9 models > hide #2.10 models > hide #2.8 models > hide #2.7 models > hide #2.4 models > hide #2.5 models > hide #2.6 models > hide #2.3 models > hide #2.2 models > hide #2.13 models > hide #2.14 models > hide #2.15 models > hide #2.16 models > hide #2.20 models > hide #2.21 models > hide #2.19 models > show #2.19 models > hide #2.17 models > hide #2.19 models > hide #2.18 models > show #2.13 models > show #2.14 models > show #2.15 models > show #2.16 models > hide #2.13 models > hide #2.14 models > hide #2.15 models > hide #2.16 models > show #2.17 models > show #2.18 models > show #2.19 models > show #2.20 models > show #2.21 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Tail/ValidationCryoEM_68/6mer_side_tilt-coot-2.pdb"" Chain information for 6mer_side_tilt-coot-2.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > hide #3#2.12,17-21 atoms > show #3#2.12,17-21 cartoons > hide #3 models > show #3 models > fitmap #3 inMap #1 Fit molecule 6mer_side_tilt-coot-2.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5261, steps = 48 shifted from previous position = 0.019 rotated from previous position = 0.0301 degrees atoms outside contour = 2278, contour level = 0.3 Position of 6mer_side_tilt-coot-2.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999988 -0.00008820 0.00047934 -0.11806765 0.00008829 0.99999998 -0.00019429 0.02759661 -0.00047933 0.00019433 0.99999987 0.07902974 Axis 0.37033273 0.91354660 0.16818523 Axis point 166.64115701 0.00000000 242.31786352 Rotation angle (degrees) 0.03006294 Shift along axis -0.00522189 > close #3 > show #2.16 models > hide #2.16 models > show #4 models > hide #4 models > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.526, steps = 48 shifted from previous position = 0.00755 rotated from previous position = 0.00275 degrees atoms outside contour = 2265, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999987 -0.00006473 0.00049669 -0.11988880 0.00006481 0.99999999 -0.00015750 0.02324241 -0.00049668 0.00015753 0.99999986 0.09341524 Axis 0.29998036 0.94593535 0.12336164 Axis point 188.62353708 0.00000000 239.94071559 Rotation angle (degrees) 0.03008445 Shift along axis -0.00245461 > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5261, steps = 44 shifted from previous position = 0.00313 rotated from previous position = 0.00458 degrees atoms outside contour = 2269, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999991 -0.00005188 0.00041855 -0.10383628 0.00005194 0.99999999 -0.00014653 0.02409803 -0.00041854 0.00014655 0.99999990 0.07556880 Axis 0.32821222 0.93742066 0.11627232 Axis point 181.24491448 0.00000000 246.00304164 Rotation angle (degrees) 0.02558193 Shift along axis -0.00270379 > hide #2.18 models > hide #2.17 models > hide #2.19 models > show #2.17 models > show #2.19 models > show #2.18 models > hide #2.19 models > hide #2.17 models > hide #2.18 models > hide #2.21 models > hide #2.20 models > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/6mer_side_straight1-coot-0.pdb"" Chain information for 6mer_side_straight1-coot-0.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > hide #3#2.12 atoms > show #3#2.12 cartoons > fitmap #4 inMap #1 Fit molecule 6mer_side_tilt-coot-1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.5261, steps = 44 shifted from previous position = 0.0128 rotated from previous position = 0.0095 degrees atoms outside contour = 2283, contour level = 0.3 Position of 6mer_side_tilt-coot-1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999997 0.00000119 0.00026140 -0.06453009 -0.00000115 0.99999999 -0.00014719 0.03444334 -0.00026140 0.00014719 0.99999995 0.04848789 Axis 0.49064556 0.87135055 -0.00389211 Axis point 185.42249966 0.00000000 243.43632451 Rotation angle (degrees) 0.01718851 Shift along axis -0.00183790 > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1-coot-0.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4505, steps = 48 shifted from previous position = 0.0422 rotated from previous position = 0.0553 degrees atoms outside contour = 3073, contour level = 0.3 Position of 6mer_side_straight1-coot-0.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00008292 0.00011253 -0.00502884 0.00008281 0.99999954 0.00095415 -0.36768399 -0.00011261 -0.00095414 0.99999954 0.12860168 Axis -0.98943881 0.11673248 0.08593233 Axis point 0.00000000 137.01954552 382.12671396 Rotation angle (degrees) 0.05525222 Shift along axis -0.02689389 > fitmap #3 inMap #1 Fit molecule 6mer_side_straight1-coot-0.pdb (#3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 12123 atoms average map value = 0.4504, steps = 44 shifted from previous position = 0.0187 rotated from previous position = 0.0169 degrees atoms outside contour = 3077, contour level = 0.3 Position of 6mer_side_straight1-coot-0.pdb (#3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999999 -0.00004757 -0.00015764 0.09259589 0.00004770 0.99999964 0.00084162 -0.31024068 0.00015760 -0.00084163 0.99999963 0.02964269 Axis -0.98139348 -0.18379876 0.05554139 Axis point 0.00000000 37.18216973 375.67040753 Rotation angle (degrees) 0.04913595 Shift along axis -0.03220475 > select add #3 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #3 Nothing selected > view #3 clip false > select #3/A:410 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 48 atoms, 48 bonds, 7 residues, 1 model selected > select up 2018 atoms, 2055 bonds, 280 residues, 1 model selected > close #3 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/6mer_side_straight1-coot-1.pdb"" Chain information for 6mer_side_straight1-coot-1.pdb #3 --- Chain | Description A B D | No description available C E F | No description available > hide #3#2.12 atoms > show #3#2.12 cartoons > color #3#2.12 bychain > hide #!1 models > show #!1 models > hide #!2 models > volume zone #1 nearAtoms #3 range 6.37 > surface dust #1 size 10.6 > hide #3 models > show #4 models > hide #4 models > show #!2 models > show #2.2 models > view #2.2 clip false Cell requested for row 1 is out of bounds for table with 25 rows! Resizing table model. > save ""/Users/melvinshen/Desktop/Docking of Capsid.cxs"" > hide #!2 models > show #3 models > close #4 > split #3 Split 6mer_side_straight1-coot-1.pdb (#3) into 6 models Chain information for 6mer_side_straight1-coot-1.pdb A #3.1 --- Chain | Description A | No description available Chain information for 6mer_side_straight1-coot-1.pdb B #3.2 --- Chain | Description B | No description available Chain information for 6mer_side_straight1-coot-1.pdb C #3.3 --- Chain | Description C | No description available Chain information for 6mer_side_straight1-coot-1.pdb D #3.4 --- Chain | Description D | No description available Chain information for 6mer_side_straight1-coot-1.pdb E #3.5 --- Chain | Description E | No description available Chain information for 6mer_side_straight1-coot-1.pdb F #3.6 --- Chain | Description F | No description available > hide #3.1 models > show #3.1 models > fitmap #3.1 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb A (#3.1) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.437, steps = 44 shifted from previous position = 0.0423 rotated from previous position = 0.112 degrees atoms outside contour = 557, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb A (#3.1) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999928 0.00015041 0.00118713 -0.38066480 -0.00014857 0.99999880 -0.00154468 0.57846321 -0.00118736 0.00154450 0.99999810 0.22283529 Axis 0.79052326 0.60763421 -0.07650910 Axis point 0.00000000 -145.49278027 361.41449616 Rotation angle (degrees) 0.11194948 Shift along axis 0.03352073 > fitmap #3.1 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb A (#3.1) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.437, steps = 48 shifted from previous position = 0.00374 rotated from previous position = 0.0034 degrees atoms outside contour = 557, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb A (#3.1) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999934 0.00015190 0.00114294 -0.36738685 -0.00015009 0.99999873 -0.00158417 0.59125924 -0.00114318 0.00158400 0.99999809 0.19702520 Axis 0.80851167 0.58341194 -0.07706741 Axis point 0.00000000 -125.54183552 361.27720989 Rotation angle (degrees) 0.11225741 Shift along axis 0.03272692 > fitmap #3.2 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5, steps = 44 shifted from previous position = 0.111 rotated from previous position = 0.169 degrees atoms outside contour = 406, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999891 0.00017271 0.00146337 -0.41601897 -0.00016897 0.99999672 -0.00255470 0.70205449 -0.00146380 0.00255445 0.99999567 0.17175619 Axis 0.86622559 0.49628343 -0.05793079 Axis point 0.00000000 -66.26775200 279.14779184 Rotation angle (degrees) 0.16897064 Shift along axis -0.02189824 > fitmap #3.2 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5, steps = 40 shifted from previous position = 0.0143 rotated from previous position = 0.0152 degrees atoms outside contour = 408, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999923 0.00023910 0.00121608 -0.35242617 -0.00023591 0.99999653 -0.00262447 0.74466709 -0.00121670 0.00262418 0.99999582 0.09375116 Axis 0.90423613 0.41911852 -0.08183324 Axis point 0.00000000 -34.82559865 286.06055392 Rotation angle (degrees) 0.16628749 Shift along axis -0.01424466 > fitmap #3.3 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb C (#3.3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms average map value = 0.4855, steps = 44 shifted from previous position = 0.118 rotated from previous position = 0.13 degrees atoms outside contour = 435, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb C (#3.3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999869 -0.00115311 -0.00113240 0.54252872 0.00115492 0.99999805 0.00159884 -0.97636010 0.00113055 -0.00160015 0.99999808 -0.29594100 Axis -0.70343238 -0.49760424 0.50751641 Axis point 0.00000000 -171.11015342 624.77147385 Rotation angle (degrees) 0.13028164 Shift along axis -0.04598626 > fitmap #3.3 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb C (#3.3) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms average map value = 0.4855, steps = 28 shifted from previous position = 0.0213 rotated from previous position = 0.0128 degrees atoms outside contour = 436, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb C (#3.3) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999848 -0.00120494 -0.00126364 0.57657629 0.00120674 0.99999825 0.00142621 -0.95663914 0.00126192 -0.00142773 0.99999818 -0.35423721 Axis -0.63280900 -0.55999847 0.53474712 Axis point 0.00000000 -242.01735017 677.75406265 Rotation angle (degrees) 0.12920070 Shift along axis -0.01857353 > fitmap #3.4 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb D (#3.4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4141, steps = 44 shifted from previous position = 0.0444 rotated from previous position = 0.124 degrees atoms outside contour = 569, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb D (#3.4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999786 -0.00189416 -0.00082903 0.49378425 0.00189362 0.99999799 -0.00065435 -0.39949289 0.00083026 0.00065278 0.99999944 -0.29872385 Axis 0.30139391 -0.38259304 0.87337522 Axis point 202.99968297 253.97098105 0.00000000 Rotation angle (degrees) 0.12424465 Shift along axis 0.04076875 > fitmap #3.4 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb D (#3.4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4141, steps = 40 shifted from previous position = 0.0163 rotated from previous position = 0.0031 degrees atoms outside contour = 568, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb D (#3.4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999797 -0.00185278 -0.00079712 0.48973015 0.00185227 0.99999808 -0.00064026 -0.38800231 0.00079830 0.00063878 0.99999948 -0.29774096 Axis 0.30224104 -0.37700265 0.87551091 Axis point 202.89970862 258.61518296 0.00000000 Rotation angle (degrees) 0.12123412 Shift along axis 0.03361899 > fitmap #3.5 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb E (#3.5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms average map value = 0.4055, steps = 40 shifted from previous position = 0.0409 rotated from previous position = 0.0856 degrees atoms outside contour = 616, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb E (#3.5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999934 -0.00054964 0.00100775 -0.26291649 0.00055061 0.99999939 -0.00095716 0.15876004 -0.00100722 0.00095771 0.99999903 0.26717818 Axis 0.64052261 0.67400453 0.36803353 Axis point 251.49543161 0.00000000 284.53339285 Rotation angle (degrees) 0.08564421 Shift along axis 0.03693156 > fitmap #3.6 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb F (#3.6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms average map value = 0.4629, steps = 48 shifted from previous position = 0.0359 rotated from previous position = 0.0209 degrees atoms outside contour = 470, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb F (#3.6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999994 -0.00030487 0.00018331 -0.04075075 0.00030485 0.99999995 0.00007925 -0.13925991 -0.00018333 -0.00007919 0.99999998 0.09502872 Axis -0.21737300 0.50300526 0.83650146 Axis point 486.98873224 -120.71948308 0.00000000 Rotation angle (degrees) 0.02088121 Shift along axis 0.01830131 > fitmap #3.6 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb F (#3.6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2023 atoms average map value = 0.4628, steps = 28 shifted from previous position = 0.00944 rotated from previous position = 0.00352 degrees atoms outside contour = 470, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb F (#3.6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999994 -0.00031683 0.00013660 -0.02033363 0.00031683 0.99999995 0.00004127 -0.13237802 -0.00013661 -0.00004123 0.99999999 0.08461148 Axis -0.11870250 0.39312464 0.91179095 Axis point 451.96403591 -53.95209620 0.00000000 Rotation angle (degrees) 0.01990916 Shift along axis 0.02752057 > fitmap #3.2 inMap #1 Fit molecule 6mer_side_straight1-coot-1.pdb B (#3.2) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5, steps = 40 shifted from previous position = 0.0108 rotated from previous position = 0.0124 degrees atoms outside contour = 406, contour level = 0.3 Position of 6mer_side_straight1-coot-1.pdb B (#3.2) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999898 0.00019203 0.00141853 -0.40533668 -0.00018839 0.99999669 -0.00256548 0.71173180 -0.00141902 0.00256521 0.99999570 0.15874346 Axis 0.87324874 0.48295383 -0.06474757 Axis point 0.00000000 -60.89431212 281.36465168 Rotation angle (degrees) 0.16831833 Shift along axis -0.02050440 > select add #3.2 2018 atoms, 2055 bonds, 280 residues, 1 model selected > save /Users/melvinshen/Desktop/Monomer_side_straight1.pdb models #3.2 > selectedOnly true relModel #1 > select subtract #3.2 Nothing selected > hide #3.2 models > open /Users/melvinshen/Desktop/Monomer_side_straight1.pdb Chain information for Monomer_side_straight1.pdb #4 --- Chain | Description B | No description available > open /Users/melvinshen/Desktop/Monomer_side_straight1-coot-0.pdb Chain information for Monomer_side_straight1-coot-0.pdb #5 --- Chain | Description B | No description available > fitmap #5 inMap #1 Fit molecule Monomer_side_straight1-coot-0.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5056, steps = 28 shifted from previous position = 0.0323 rotated from previous position = 0.0702 degrees atoms outside contour = 409, contour level = 0.3 Position of Monomer_side_straight1-coot-0.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999972 -0.00068085 -0.00029814 0.14577918 0.00068114 0.99999929 0.00097466 -0.52468195 0.00029748 -0.00097486 0.99999948 -0.02188757 Axis -0.79519980 -0.24295240 0.55554604 Axis point -0.00000000 -22.39100891 538.45900886 Rotation angle (degrees) 0.07023357 Shift along axis -0.00061039 > fitmap #5 inMap #1 Fit molecule Monomer_side_straight1-coot-0.pdb (#5) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5056, steps = 36 shifted from previous position = 0.0157 rotated from previous position = 0.0121 degrees atoms outside contour = 406, contour level = 0.3 Position of Monomer_side_straight1-coot-0.pdb (#5) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999969 -0.00063823 -0.00045391 0.18632471 0.00063861 0.99999944 0.00083799 -0.47121580 0.00045338 -0.00083828 0.99999955 -0.07454433 Axis -0.73065356 -0.39547111 0.55655007 Axis point 0.00000000 -95.02120348 558.13731478 Rotation angle (degrees) 0.06572400 Shift along axis 0.00872578 > fitmap #4 inMap #1 Fit molecule Monomer_side_straight1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5, steps = 40 shifted from previous position = 0.0127 rotated from previous position = 0.0125 degrees atoms outside contour = 407, contour level = 0.3 Position of Monomer_side_straight1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999998 0.00005007 -0.00020496 0.05327346 -0.00005008 1.00000000 -0.00005805 0.03347037 0.00020496 0.00005806 0.99999998 -0.06389558 Axis 0.26528006 -0.93662212 -0.22883507 Axis point 314.67801034 0.00000000 263.24627490 Rotation angle (degrees) 0.01253787 Shift along axis -0.00259515 > fitmap #4 inMap #1 Fit molecule Monomer_side_straight1.pdb (#4) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.5, steps = 40 shifted from previous position = 0.0141 rotated from previous position = 0.0124 degrees atoms outside contour = 406, contour level = 0.3 Position of Monomer_side_straight1.pdb (#4) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00000061 -0.00000188 0.00068200 0.00000061 1.00000000 -0.00000042 -0.00002207 0.00000188 0.00000042 1.00000000 -0.00214976 Axis 0.20816097 -0.93014162 0.30249889 Axis point 1063.89232921 0.00000000 416.34300259 Rotation angle (degrees) 0.00011593 Shift along axis -0.00048781 > hide #5 models > hide #4 models > show #4 models > show #5 models > hide #4 models > view #5 clip false > combine #5 > hide #3.1 models > show #3.1 models > hide #3.3 models > show #3.3 models > hide #3.3 models > select add #6 2018 atoms, 2055 bonds, 280 residues, 1 model selected > view matrix models > #6,0.93892,-0.033931,-0.34247,124.48,-0.043039,0.97574,-0.21467,79.976,0.34144,0.2163,0.91468,-114.96 > view matrix models > #6,0.93892,-0.033931,-0.34247,142.78,-0.043039,0.97574,-0.21467,91.566,0.34144,0.2163,0.91468,-114.76 > view matrix models > #6,0.95995,-0.099497,-0.2619,119.38,0.010079,0.94647,-0.32263,108.31,0.27998,0.30707,0.90957,-102.48 > view matrix models > #6,0.93168,-0.11922,-0.34315,154.89,0.054093,0.97961,-0.19346,51.979,0.35922,0.16169,0.91914,-116.04 > view matrix models > #6,0.93168,-0.11922,-0.34315,154.87,0.054093,0.97961,-0.19346,51.968,0.35922,0.16169,0.91914,-116.05 > view matrix models > #6,0.81503,-0.17036,-0.55381,261.65,-0.02304,0.94552,-0.32475,120.26,0.57897,0.27744,0.7667,-158.94 > view matrix models > #6,0.81503,-0.17036,-0.55381,266.85,-0.02304,0.94552,-0.32475,123.54,0.57897,0.27744,0.7667,-157.65 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.2044, steps = 84 shifted from previous position = 2.36 rotated from previous position = 8.59 degrees atoms outside contour = 1437, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.82085740 -0.23415757 -0.52092548 263.05237063 0.10961917 0.95972686 -0.25866580 55.35184890 0.56051473 0.15522432 0.81346705 -152.34785664 Axis 0.34265522 -0.89531283 0.28460910 Axis point 393.95927097 0.00000000 371.32038387 Rotation angle (degrees) 37.15299510 Shift along axis -2.78053997 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.2044, steps = 40 shifted from previous position = 0.0128 rotated from previous position = 0.00459 degrees atoms outside contour = 1436, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.82087891 -0.23410646 -0.52091456 263.03436240 0.10961112 0.95974705 -0.25859428 55.33660322 0.56048481 0.15517656 0.81349678 -152.35267786 Axis 0.34258321 -0.89534889 0.28458234 Axis point 393.96226657 0.00000000 371.31551944 Rotation angle (degrees) 37.14960680 Shift along axis -2.79129083 > view matrix models > #6,0.82088,-0.23411,-0.52091,267.54,0.10961,0.95975,-0.25859,58.333,0.56048,0.15518,0.8135,-152.26 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.2131, steps = 80 shifted from previous position = 4.32 rotated from previous position = 5.14 degrees atoms outside contour = 1390, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.79706764 -0.31996333 -0.51215881 281.54700629 0.17737611 0.93473412 -0.30791208 50.71174493 0.57725288 0.15458202 0.80180017 -150.60790463 Axis 0.36026246 -0.84860355 0.38740544 Axis point 395.82453886 0.00000000 392.85328241 Rotation angle (degrees) 39.93251920 Shift along axis 0.05032707 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.2131, steps = 60 shifted from previous position = 0.00116 rotated from previous position = 0.00204 degrees atoms outside contour = 1390, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.79704644 -0.31997599 -0.51218389 281.56237176 0.17738579 0.93473251 -0.30791138 50.70942425 0.57727918 0.15456553 0.80178441 -150.61045749 Axis 0.36023614 -0.84861312 0.38740894 Axis point 395.81957821 0.00000000 392.85096972 Rotation angle (degrees) 39.93424008 Shift along axis 0.04842121 > view matrix models > #6,0.71314,-0.33187,-0.61749,342.11,0.1107,0.9231,-0.36827,92.257,0.69223,0.19427,0.69504,-162.85 > view matrix models > #6,0.71314,-0.33187,-0.61749,344.73,0.1107,0.9231,-0.36827,93.911,0.69223,0.19427,0.69504,-161.79 > view matrix models > #6,0.71314,-0.33187,-0.61749,341.99,0.1107,0.9231,-0.36827,91.682,0.69223,0.19427,0.69504,-165.9 > view matrix models > #6,0.71314,-0.33187,-0.61749,342.67,0.1107,0.9231,-0.36827,92.032,0.69223,0.19427,0.69504,-166.09 > view matrix models > #6,0.63138,-0.37067,-0.68115,393.3,0.077771,0.9042,-0.41997,120.4,0.77156,0.21218,0.59972,-167.16 > view matrix models > #6,0.63138,-0.37067,-0.68115,395.46,0.077771,0.9042,-0.41997,121.82,0.77156,0.21218,0.59972,-165.91 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4003, steps = 76 shifted from previous position = 3.31 rotated from previous position = 7.46 degrees atoms outside contour = 709, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58689173 -0.44065636 -0.67924964 419.13040141 0.03811572 0.85303287 -0.52046337 172.71149149 0.80876776 0.27956556 0.51743387 -160.67916205 Axis 0.45560260 -0.84740011 0.27265239 Axis point 415.87944292 0.00000000 363.58724462 Rotation angle (degrees) 61.40082400 Shift along axis 0.79160636 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4003, steps = 36 shifted from previous position = 0.000931 rotated from previous position = 0.0107 degrees atoms outside contour = 710, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58690544 -0.44063957 -0.67924869 419.12309219 0.03795795 0.85298755 -0.52054917 172.79464093 0.80876523 0.27973025 0.51734881 -160.67134051 Axis 0.45572874 -0.84736743 0.27254312 Axis point 415.90019722 0.00000000 363.56965736 Rotation angle (degrees) 61.40463076 Shift along axis 0.79602061 > view matrix models > #6,0.58691,-0.44064,-0.67925,418.92,0.037958,0.85299,-0.52055,172.52,0.80877,0.27973,0.51735,-160.82 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4004, steps = 44 shifted from previous position = 0.367 rotated from previous position = 0.0106 degrees atoms outside contour = 707, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58679042 -0.44063777 -0.67934922 419.18046826 0.03784352 0.85297983 -0.52057014 172.83248517 0.80885405 0.27975660 0.51719567 -160.65245021 Axis 0.45571668 -0.84740271 0.27245360 Axis point 415.88247035 0.00000000 363.53904513 Rotation angle (degrees) 61.41363133 Shift along axis 0.79847554 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4003, steps = 28 shifted from previous position = 0.0174 rotated from previous position = 0.0128 degrees atoms outside contour = 710, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58690275 -0.44065349 -0.67924197 419.12466053 0.03801033 0.85299570 -0.52053198 172.77191519 0.80876472 0.27968345 0.51737491 -160.67420099 Axis 0.45569677 -0.84737162 0.27258354 Axis point 415.89635255 0.00000000 363.57725016 Rotation angle (degrees) 61.40360055 Shift along axis 0.79459358 > select subtract #6 Nothing selected > select add #7 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select subtract #7 Nothing selected > select add #6 2018 atoms, 2055 bonds, 280 residues, 1 model selected > close #2 > show #4 models > hide #4 models > save /Users/melvinshen/Desktop/Monomer_side_straight2-coot-0.pdb models #6 > selectedOnly true relModel #1 > open /Users/melvinshen/Desktop/Monomer_side_straight2-coot-1.pdb Chain information for Monomer_side_straight2-coot-1.pdb #2 --- Chain | Description B | No description available > close #3 > close #4 > rename #2 id #8 > rename #5 id #2 > color #2 #0433ffff > select subtract #6 Nothing selected > select add #6 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select subtract #6 Nothing selected > select add #8 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select subtract #8 Nothing selected > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4004, steps = 28 shifted from previous position = 0.0215 rotated from previous position = 0.0244 degrees atoms outside contour = 708, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58671199 -0.44066026 -0.67940237 419.22261349 0.03769000 0.85293029 -0.52066245 172.91475289 0.80891811 0.27987223 0.51703291 -160.63802185 Axis 0.45579397 -0.84739302 0.27235443 Axis point 415.89230056 0.00000000 363.51625513 Rotation angle (degrees) 61.42311646 Shift along axis 0.80190822 > fitmap #6 inMap #1 Fit molecule copy of Monomer_side_straight1-coot-0.pdb (#6) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.4003, steps = 28 shifted from previous position = 0.0232 rotated from previous position = 0.0215 degrees atoms outside contour = 711, contour level = 0.3 Position of copy of Monomer_side_straight1-coot-0.pdb (#6) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.58690614 -0.44062006 -0.67926073 419.12672897 0.03793988 0.85299606 -0.52053653 172.79784811 0.80876557 0.27973502 0.51734570 -160.67268808 Axis 0.45572513 -0.84737609 0.27252223 Axis point 415.90206430 0.00000000 363.56859088 Rotation angle (degrees) 61.40443132 Shift along axis 0.79493773 > fitmap #8 inMap #1 Fit molecule Monomer_side_straight2-coot-1.pdb (#8) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.493, steps = 48 shifted from previous position = 0.033 rotated from previous position = 0.0603 degrees atoms outside contour = 425, contour level = 0.3 Position of Monomer_side_straight2-coot-1.pdb (#8) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999948 0.00062603 -0.00080026 0.15726136 -0.00062581 0.99999977 0.00027749 0.15407411 0.00080043 -0.00027699 0.99999964 -0.29775941 Axis -0.26323900 -0.75993338 -0.59431177 Axis point 358.36840956 0.00000000 202.36012461 Rotation angle (degrees) 0.06034277 Shift along axis 0.01847854 > fitmap #8 inMap #1 Fit molecule Monomer_side_straight2-coot-1.pdb (#8) to map cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) using 2018 atoms average map value = 0.493, steps = 28 shifted from previous position = 0.0186 rotated from previous position = 0.0058 degrees atoms outside contour = 429, contour level = 0.3 Position of Monomer_side_straight2-coot-1.pdb (#8) relative to cryosparc_P2_J247_007_volume_map_sharp-2_96A.mrc (#1) coordinates: Matrix rotation and translation 0.99999957 0.00058051 -0.00071753 0.13406403 -0.00058028 0.99999978 0.00031392 0.13225338 0.00071771 -0.00031350 0.99999969 -0.24506049 Axis -0.32181446 -0.73616458 -0.59539665 Axis point 337.04560150 0.00000000 189.06541714 Rotation angle (degrees) 0.05585234 Shift along axis 0.00540419 > rename #8 id #3 > select add #3 2018 atoms, 2055 bonds, 280 residues, 1 model selected > view #3 clip false > hide #6 models > select subtract #3 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/B Alignment identifier is 3/B > select #3/B:208-209 15 atoms, 14 bonds, 2 residues, 1 model selected > select #3/B:201-209 72 atoms, 71 bonds, 9 residues, 1 model selected > view #2 clip false > select sequence ELDSQKMVI 288 atoms, 284 bonds, 36 residues, 4 models selected > select clear > select #3/B:201 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/B:201-208 64 atoms, 63 bonds, 8 residues, 1 model selected > select #3/B:264 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:264-265 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3/B:202-264 461 atoms, 464 bonds, 63 residues, 1 model selected > select #3/B:191 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:191-208 128 atoms, 127 bonds, 18 residues, 1 model selected > volume zone #1 nearAtoms sel & #3 range 6.37 > surface dust #1 size 10.6 > close #3 > open /Users/melvinshen/Desktop/Monomer_side_straight2-coot-1.pdb Chain information for Monomer_side_straight2-coot-1.pdb #3 --- Chain | Description B | No description available > view #3 clip false > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" Chain information for Capsid_Top.pdb --- Chain | Description 4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A 4.21/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B 4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B 4.17/B 4.18/B 4.19/B 4.20/B 4.21/B 4.1/C 4.7/C 4.8/C 4.9/C 4.10/C 4.11/C 4.1/D 4.2/D 4.3/D 4.4/D 4.5/D 4.6/D 4.7/D 4.8/D 4.9/D 4.10/D 4.11/D 4.12/D 4.13/D 4.14/D 4.15/D 4.16/D 4.17/D 4.18/D 4.19/D 4.20/D 4.21/D 4.1/E 4.7/E 4.8/E 4.9/E 4.10/E 4.11/E | No description available 4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.12/C 4.13/C 4.14/C 4.15/C 4.16/C 4.17/C 4.18/C 4.19/C 4.20/C 4.21/C 4.2/E 4.3/E 4.4/E 4.5/E 4.6/E 4.12/E 4.13/E 4.14/E 4.15/E 4.16/E 4.17/E 4.18/E 4.19/E 4.20/E 4.21/E 4.2/F 4.3/F 4.4/F 4.5/F 4.6/F 4.12/F 4.13/F 4.14/F 4.15/F 4.16/F 4.17/F 4.18/F 4.19/F 4.20/F 4.21/F | No description available > hide #2-3,7#4.1-21 cartoons > show #2-3,7#4.1-21 cartoons > hide #2-3,7#4.1-21 atoms > show #6 models > hide #6 models > select add #3 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.4 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > select subtract #4.4 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.8 12108 atoms, 12330 bonds, 1680 residues, 2 models selected > select subtract #4.8 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.19 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > select subtract #4.19 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.19 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > select add #4.20 26264 atoms, 26745 bonds, 3646 residues, 3 models selected > select add #4.21 38387 atoms, 39090 bonds, 5329 residues, 4 models selected > close #4.21 > close #4.19 > close #4.20 > select add #4.18 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > select subtract #4.18 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.16 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > select subtract #4.16 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select add #4.17 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > close #4.16 > close #4.17 > select add #4.18 14141 atoms, 14400 bonds, 1963 residues, 2 models selected > close #4.18 > close #4 > open ""/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage > Proteins/Structure/CryoEM/cryosparc/Corndog > /Capsid/Fitting/6mer_Fit/Capsid_Top.pdb"" Chain information for Capsid_Top.pdb --- Chain | Description 4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A 4.21/A 4.1/B 4.2/B 4.3/B 4.4/B 4.5/B 4.6/B 4.7/B 4.8/B 4.9/B 4.10/B 4.11/B 4.12/B 4.13/B 4.14/B 4.15/B 4.16/B 4.17/B 4.18/B 4.19/B 4.20/B 4.21/B 4.1/C 4.7/C 4.8/C 4.9/C 4.10/C 4.11/C 4.1/D 4.2/D 4.3/D 4.4/D 4.5/D 4.6/D 4.7/D 4.8/D 4.9/D 4.10/D 4.11/D 4.12/D 4.13/D 4.14/D 4.15/D 4.16/D 4.17/D 4.18/D 4.19/D 4.20/D 4.21/D 4.1/E 4.7/E 4.8/E 4.9/E 4.10/E 4.11/E | No description available 4.2/C 4.3/C 4.4/C 4.5/C 4.6/C 4.12/C 4.13/C 4.14/C 4.15/C 4.16/C 4.17/C 4.18/C 4.19/C 4.20/C 4.21/C 4.2/E 4.3/E 4.4/E 4.5/E 4.6/E 4.12/E 4.13/E 4.14/E 4.15/E 4.16/E 4.17/E 4.18/E 4.19/E 4.20/E 4.21/E 4.2/F 4.3/F 4.4/F 4.5/F 4.6/F 4.12/F 4.13/F 4.14/F 4.15/F 4.16/F 4.17/F 4.18/F 4.19/F 4.20/F 4.21/F | No description available > hide sel atoms > show sel cartoons > select subtract #3 Nothing selected > hide #2-3,7#4.1-21 atoms > show #2-3,7#4.1-21 cartoons > select add #4.21 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select add #4.20 24246 atoms, 24690 bonds, 3366 residues, 2 models selected > select add #4.19 36369 atoms, 37035 bonds, 5049 residues, 3 models selected > select add #4.18 48492 atoms, 49380 bonds, 6732 residues, 4 models selected > select add #4.17 60615 atoms, 61725 bonds, 8415 residues, 5 models selected > close #4.21 > close #4.17-20 > select add #4.16 12123 atoms, 12345 bonds, 1683 residues, 1 model selected > select subtract #4.16 Nothing selected > select add #3 2018 atoms, 2055 bonds, 280 residues, 1 model selected > select subtract #3 Nothing selected > select add #2 2018 atoms, 2055 bonds, 280 residues, 1 model selected > hide #!4 models > hide #7 models > show #7 models > hide #7 models > show #6 models > hide #6 models > show #6 models > close #6 > show #7 models > select subtract #2 Nothing selected > select add #7 2018 atoms, 2055 bonds, 280 residues, 1 model selected > view #7 clip false > turn z 30 models #7 > turn y 30 models #7 > turn x 30 models #7 > turn z 30 models #7 > turn z 52 models #7 > turn z 72 models #7 > view orient > view sel > view orient > turn x 180 > turn x 90 > turn x 180 > turn y 180 > turn y 30 > turn z 72 models #7 > turn z 70 models #7 > turn z -70 models #7 > turn x 72 > turn x 72 models #7 > view matrix models > #7,0.51736,0.80053,-0.30249,153.66,0.80002,-0.32693,0.50308,-279.25,0.30384,-0.50227,-0.80958,504.58 > view matrix models > #7,0.64059,0.75597,-0.13477,67.803,0.73298,-0.54966,0.40077,-201.92,0.22889,-0.35551,-0.90621,541.96 > view matrix models > #7,0.81789,0.56845,0.089027,-36.929,0.5721,-0.81993,-0.02048,5.6588,0.061354,0.067682,-0.99582,578.06 > view matrix models > #7,0.65826,0.48291,0.57749,-115.91,0.45933,-0.86543,0.20012,-15.443,0.59641,0.13353,-0.79149,329.51 > view matrix models > #7,0.65826,0.48291,0.57749,-124.59,0.45933,-0.86543,0.20012,-21.173,0.59641,0.13353,-0.79149,352.68 > view matrix models > #7,0.65826,0.48291,0.57749,-122.98,0.45933,-0.86543,0.20012,-20.26,0.59641,0.13353,-0.79149,350.62 > view matrix models > #7,0.45091,0.66089,0.59992,-78.89,0.66034,-0.69921,0.27396,-128.47,0.60053,0.27262,-0.75169,322.17 > view matrix models > #7,0.3075,0.58085,0.7537,-66.251,0.58096,-0.74191,0.33474,-114.55,0.75361,0.33494,-0.56559,208.97 > view #7 clip false > view matrix models > #7,0.3075,0.58085,0.7537,-66.749,0.58096,-0.74191,0.33474,-114.6,0.75361,0.33494,-0.56559,206.88 > view matrix models > #7,0.29412,0.69051,0.66083,-47.247,0.30515,-0.72306,0.61973,-106.31,0.90575,0.019378,-0.42338,148.71 > view matrix models > #7,0.29412,0.69051,0.66083,-42.413,0.30515,-0.72306,0.61973,-104.64,0.90575,0.019378,-0.42338,140.37 > undo > close #7 > rename #4 id #10 > combine #2 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16U0000PTA/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B74) Kernel Version: Darwin 23.1.0 Time since boot: 46 days, 1 hour, 18 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403220040 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4.2 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.0 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect new normal Unassigned