id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17300 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202311280534 (2023-11-28 05:34:38 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001f7f84f40 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1819 in new_bond File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 235 in molecule_from_atoms File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in split_molecule File 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All rights reserved. How to cite UCSF ChimeraX > open /Users/aleon/Downloads/emhancer5G01.mrc Summary of feedback from opening /Users/aleon/Downloads/emhancer5G01.mrc --- notes | open kw {} Opened emhancer5G01.mrc as #1, grid size 512,512,512, pixel 0.833, shown at level 8.22e-05, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1393 > volume #1 level 0.1013 > volume flip #1 Opened emhancer5G01.mrc z flip as #2, grid size 512,512,512, pixel 0.833, shown at step 1, values float32 > open > /Users/aleon/Desktop/ModelBuilding/5G01new/cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc Summary of feedback from opening /Users/aleon/Desktop/ModelBuilding/5G01new/cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc --- notes | open kw {} Opened cryosparc_P323_J565_007_volume_map_sharp_tentativefinal.mrc as #3, grid size 512,512,512, pixel 0.833, shown at level 0.0782, step 2, values float32 > volume #3 step 1 > volume #3 level 0.2023 > show #!1 models > close #2 > volume #3 level 0.2732 > volume #3 level 0.2661 > volume #3 level 0.259 > volume #3 level 0.2448 > volume #3 level 0.3441 > open > /Users/aleon/Desktop/ModelBuilding/5G01new/5G01_5TG8UniProtNumbering_ReadyToBuild- > coot-0.pdb Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb #2 --- Chain | Description A C E | No description available B D F | No description available H | No description available L | No description available > hide atoms > show cartoons > transparency #1.1 50 > volume #1 level 0.06757 > split #2 Split 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb (#2) into 8 models Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb A #2.1 --- Chain | Description A | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb B #2.2 --- Chain | Description B | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb C #2.3 --- Chain | Description C | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb D #2.4 --- Chain | Description D | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb E #2.5 --- Chain | Description E | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb F #2.6 --- Chain | Description F | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H #2.7 --- Chain | Description H | No description available Chain information for 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L #2.8 --- Chain | Description L | No description available > select add #2.8 815 atoms, 835 bonds, 107 residues, 1 model selected > select add #2.7 1759 atoms, 1798 bonds, 230 residues, 2 models selected > ui tool show ""Fit in Map"" > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 56 shifted from previous position = 0.101 rotated from previous position = 0.196 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999580 -0.00163217 0.00239462 -0.27246777 0.00163650 0.99999703 -0.00180616 0.12169443 -0.00239166 0.00181007 0.99999550 0.25598900 Axis 0.52934418 0.70061640 0.47846777 Axis point 94.08668116 0.00000000 127.98856163 Rotation angle (degrees) 0.19570932 Shift along axis 0.06351437 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999580 -0.00163217 0.00239462 -0.27246777 0.00163650 0.99999703 -0.00180616 0.12169443 -0.00239166 0.00181007 0.99999550 0.25598900 Axis 0.52934418 0.70061640 0.47846777 Axis point 94.08668116 0.00000000 127.98856163 Rotation angle (degrees) 0.19570932 Shift along axis 0.06351437 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 28 shifted from previous position = 0.02 rotated from previous position = 0.0484 degrees atoms outside contour = 551, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999301 -0.00217097 0.00304553 -0.32045454 0.00217653 0.99999597 -0.00182310 0.00304205 -0.00304156 0.00182972 0.99999370 0.38436186 Axis 0.43880597 0.73123026 0.52225628 Axis point 115.42840782 0.00000000 114.46891212 Rotation angle (degrees) 0.23847835 Shift along axis 0.06234248 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999301 -0.00217097 0.00304553 -0.32045454 0.00217653 0.99999597 -0.00182310 0.00304205 -0.00304156 0.00182972 0.99999370 0.38436186 Axis 0.43880597 0.73123026 0.52225628 Axis point 115.42840782 0.00000000 114.46891212 Rotation angle (degrees) 0.23847835 Shift along axis 0.06234248 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 36 shifted from previous position = 0.00657 rotated from previous position = 0.0412 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999541 -0.00177525 0.00245609 -0.25233398 0.00178001 0.99999654 -0.00193496 0.11436749 -0.00245265 0.00193932 0.99999511 0.24301384 Axis 0.53858494 0.68239068 0.49423601 Axis point 86.30670547 0.00000000 116.54915899 Rotation angle (degrees) 0.20607729 Shift along axis 0.06224622 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999541 -0.00177525 0.00245609 -0.25233398 0.00178001 0.99999654 -0.00193496 0.11436749 -0.00245265 0.00193932 0.99999511 0.24301384 Axis 0.53858494 0.68239068 0.49423601 Axis point 86.30670547 0.00000000 116.54915899 Rotation angle (degrees) 0.20607729 Shift along axis 0.06224622 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 40 shifted from previous position = 0.00216 rotated from previous position = 0.000596 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999542 -0.00176566 0.00245617 -0.25231218 0.00177042 0.99999655 -0.00193901 0.11655127 -0.00245274 0.00194335 0.99999510 0.24136057 Axis 0.54008155 0.68288782 0.49191071 Axis point 85.72735610 0.00000000 116.52952899 Rotation angle (degrees) 0.20593464 Shift along axis 0.06205014 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999542 -0.00176566 0.00245617 -0.25231218 0.00177042 0.99999655 -0.00193901 0.11655127 -0.00245274 0.00194335 0.99999510 0.24136057 Axis 0.54008155 0.68288782 0.49191071 Axis point 85.72735610 0.00000000 116.52952899 Rotation angle (degrees) 0.20593464 Shift along axis 0.06205014 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 36 shifted from previous position = 0.0166 rotated from previous position = 0.0314 degrees atoms outside contour = 549, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999688 -0.00134332 0.00210700 -0.25644442 0.00134738 0.99999724 -0.00192292 0.20762260 -0.00210441 0.00192575 0.99999593 0.17514859 Axis 0.61014576 0.66765404 0.42656797 Axis point 71.43530146 0.00000000 138.28313613 Rotation angle (degrees) 0.18070499 Shift along axis 0.05686438 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999688 -0.00134332 0.00210700 -0.25644442 0.00134738 0.99999724 -0.00192292 0.20762260 -0.00210441 0.00192575 0.99999593 0.17514859 Axis 0.61014576 0.66765404 0.42656797 Axis point 71.43530146 0.00000000 138.28313613 Rotation angle (degrees) 0.18070499 Shift along axis 0.05686438 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 28 shifted from previous position = 0.0145 rotated from previous position = 0.0483 degrees atoms outside contour = 551, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999455 -0.00201277 0.00261795 -0.24912033 0.00201778 0.99999613 -0.00191407 0.06141263 -0.00261409 0.00191934 0.99999474 0.28064599 Axis 0.50199222 0.68514424 0.52780790 Axis point 93.98833292 0.00000000 107.84631565 Rotation angle (degrees) 0.21876730 Shift along axis 0.06514721 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999455 -0.00201277 0.00261795 -0.24912033 0.00201778 0.99999613 -0.00191407 0.06141263 -0.00261409 0.00191934 0.99999474 0.28064599 Axis 0.50199222 0.68514424 0.52780790 Axis point 93.98833292 0.00000000 107.84631565 Rotation angle (degrees) 0.21876730 Shift along axis 0.06514721 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 28 shifted from previous position = 0.0164 rotated from previous position = 0.0673 degrees atoms outside contour = 547, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999763 -0.00109636 0.00188279 -0.24763072 0.00109999 0.99999753 -0.00192894 0.26007809 -0.00188067 0.00193101 0.99999637 0.12770622 Axis 0.66308077 0.64650529 0.37729936 Axis point 0.00000000 -55.72870457 117.43016303 Rotation angle (degrees) 0.16676615 Shift along axis 0.05212617 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999763 -0.00109636 0.00188279 -0.24763072 0.00109999 0.99999753 -0.00192894 0.26007809 -0.00188067 0.00193101 0.99999637 0.12770622 Axis 0.66308077 0.64650529 0.37729936 Axis point 0.00000000 -55.72870457 117.43016303 Rotation angle (degrees) 0.16676615 Shift along axis 0.05212617 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 28 shifted from previous position = 0.0146 rotated from previous position = 0.0454 degrees atoms outside contour = 551, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999569 -0.00170989 0.00238527 -0.24829433 0.00171453 0.99999664 -0.00194465 0.13112558 -0.00238194 0.00194873 0.99999526 0.22695890 Axis 0.55276001 0.67682041 0.48617950 Axis point 82.42457286 0.00000000 118.57538821 Rotation angle (degrees) 0.20178270 Shift along axis 0.06184406 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999569 -0.00170989 0.00238527 -0.24829433 0.00171453 0.99999664 -0.00194465 0.13112558 -0.00238194 0.00194873 0.99999526 0.22695890 Axis 0.55276001 0.67682041 0.48617950 Axis point 82.42457286 0.00000000 118.57538821 Rotation angle (degrees) 0.20178270 Shift along axis 0.06184406 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 36 shifted from previous position = 0.0141 rotated from previous position = 0.0285 degrees atoms outside contour = 548, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999697 -0.00131750 0.00208084 -0.25656893 0.00132158 0.99999721 -0.00195709 0.22092705 -0.00207826 0.00195983 0.99999592 0.16331478 Axis 0.62239907 0.66088173 0.41935038 Axis point 67.24968512 0.00000000 139.79112949 Rotation angle (degrees) 0.18028882 Shift along axis 0.05480450 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999697 -0.00131750 0.00208084 -0.25656893 0.00132158 0.99999721 -0.00195709 0.22092705 -0.00207826 0.00195983 0.99999592 0.16331478 Axis 0.62239907 0.66088173 0.41935038 Axis point 67.24968512 0.00000000 139.79112949 Rotation angle (degrees) 0.18028882 Shift along axis 0.05480450 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 40 shifted from previous position = 0.0145 rotated from previous position = 0.0398 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999512 -0.00185994 0.00251123 -0.25162157 0.00186472 0.99999645 -0.00190390 0.09065496 -0.00250768 0.00190858 0.99999503 0.26061481 Axis 0.52075660 0.68554735 0.50876064 Axis point 90.77702586 0.00000000 113.58549600 Rotation angle (degrees) 0.20973273 Shift along axis 0.06370524 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999512 -0.00185994 0.00251123 -0.25162157 0.00186472 0.99999645 -0.00190390 0.09065496 -0.00250768 0.00190858 0.99999503 0.26061481 Axis 0.52075660 0.68554735 0.50876064 Axis point 90.77702586 0.00000000 113.58549600 Rotation angle (degrees) 0.20973273 Shift along axis 0.06370524 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 40 shifted from previous position = 0.0014 rotated from previous position = 0.00857 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999554 -0.00174323 0.00242474 -0.25078302 0.00174793 0.99999659 -0.00193992 0.12231065 -0.00242135 0.00194415 0.99999518 0.23581029 Axis 0.54516924 0.68019885 0.49002042 Axis point 84.60086957 0.00000000 117.52840739 Rotation angle (degrees) 0.20410311 Shift along axis 0.06202823 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999554 -0.00174323 0.00242474 -0.25078302 0.00174793 0.99999659 -0.00193992 0.12231065 -0.00242135 0.00194415 0.99999518 0.23581029 Axis 0.54516924 0.68019885 0.49002042 Axis point 84.60086957 0.00000000 117.52840739 Rotation angle (degrees) 0.20410311 Shift along axis 0.06202823 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 40 shifted from previous position = 0.000881 rotated from previous position = 0.0033 degrees atoms outside contour = 550, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999537 -0.00178584 0.00246283 -0.25170210 0.00179060 0.99999653 -0.00193332 0.11156410 -0.00245937 0.00193773 0.99999510 0.24469577 Axis 0.53679736 0.68256059 0.49594318 Axis point 86.68261574 0.00000000 115.96190715 Rotation angle (degrees) 0.20659128 Shift along axis 0.06239144 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999537 -0.00178584 0.00246283 -0.25170210 0.00179060 0.99999653 -0.00193332 0.11156410 -0.00245937 0.00193773 0.99999510 0.24469577 Axis 0.53679736 0.68256059 0.49594318 Axis point 86.68261574 0.00000000 115.96190715 Rotation angle (degrees) 0.20659128 Shift along axis 0.06239144 > fitmap sel inMap #1 Fit molecules 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7), 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 1759 atoms average map value = 0.237, steps = 28 shifted from previous position = 0.0187 rotated from previous position = 0.0282 degrees atoms outside contour = 547, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999664 -0.00149755 0.00211768 -0.23264751 0.00150122 0.99999737 -0.00173413 0.13321376 -0.00211507 0.00173730 0.99999625 0.21382791 Axis 0.55616145 0.67813373 0.48043635 Axis point 86.40837525 0.00000000 126.72067157 Rotation angle (degrees) 0.17881361 Shift along axis 0.06367787 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999664 -0.00149755 0.00211768 -0.23264751 0.00150122 0.99999737 -0.00173413 0.13321376 -0.00211507 0.00173730 0.99999625 0.21382791 Axis 0.55616145 0.67813373 0.48043635 Axis point 86.40837525 0.00000000 126.72067157 Rotation angle (degrees) 0.17881361 Shift along axis 0.06367787 > select clear > select add #2.7 944 atoms, 963 bonds, 123 residues, 1 model selected > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map emhancer5G01.mrc (#1) using 944 atoms average map value = 0.2481, steps = 60 shifted from previous position = 0.0597 rotated from previous position = 0.385 degrees atoms outside contour = 278, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99996119 -0.00356284 0.00805717 -1.25941691 0.00355764 0.99999345 0.00065965 -0.89108197 -0.00805947 -0.00063096 0.99996732 1.94358221 Axis -0.07305309 0.91226010 0.40304435 Axis point 237.39561134 0.00000000 156.88712111 Rotation angle (degrees) 0.50612090 Shift along axis 0.06245561 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map emhancer5G01.mrc (#1) using 944 atoms average map value = 0.2481, steps = 40 shifted from previous position = 0.0124 rotated from previous position = 0.0326 degrees atoms outside contour = 278, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99996295 -0.00355914 0.00783717 -1.21390513 0.00355819 0.99999366 0.00013478 -0.75252091 -0.00783760 -0.00010689 0.99996928 1.79689355 Axis -0.01403674 0.91044210 0.41339830 Axis point 224.71263675 0.00000000 155.81910716 Rotation angle (degrees) 0.49322684 Shift along axis 0.07474528 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map emhancer5G01.mrc (#1) using 944 atoms average map value = 0.2481, steps = 44 shifted from previous position = 0.0153 rotated from previous position = 0.0334 degrees atoms outside contour = 278, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99995988 -0.00381995 0.00810195 -1.22155969 0.00381532 0.99999255 0.00058690 -0.93022822 -0.00810413 -0.00055596 0.99996701 1.93994519 Axis -0.06366544 0.90279235 0.42533832 Axis point 235.44900774 0.00000000 151.44358394 Rotation angle (degrees) 0.51426680 Shift along axis 0.06310124 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map emhancer5G01.mrc (#1) using 944 atoms average map value = 0.2481, steps = 40 shifted from previous position = 0.00154 rotated from previous position = 0.0159 degrees atoms outside contour = 278, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99995860 -0.00366850 0.00832736 -1.30534798 0.00366420 0.99999315 0.00053099 -0.88300432 -0.00832925 -0.00050046 0.99996519 1.97794611 Axis -0.05658458 0.91377191 0.40226743 Axis point 233.78521022 0.00000000 157.49059909 Rotation angle (degrees) 0.52221302 Shift along axis 0.06266132 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) to map emhancer5G01.mrc (#1) using 944 atoms average map value = 0.2481, steps = 40 shifted from previous position = 0.0123 rotated from previous position = 0.0372 degrees atoms outside contour = 278, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb H (#2.7) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99996350 -0.00360409 0.00774711 -1.18284326 0.00360230 0.99999348 0.00024451 -0.79038502 -0.00774794 -0.00021660 0.99996996 1.79775254 Axis -0.02697348 0.90640485 0.42154795 Axis point 227.44457516 0.00000000 153.49824654 Rotation angle (degrees) 0.48974355 Shift along axis 0.07333548 > select add #2.8 1759 atoms, 1798 bonds, 230 residues, 2 models selected > select subtract #2.7 815 atoms, 835 bonds, 107 residues, 1 model selected > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 815 atoms average map value = 0.2252, steps = 40 shifted from previous position = 0.0693 rotated from previous position = 0.158 degrees atoms outside contour = 260, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999597 -0.00230000 0.00166696 -0.00725415 0.00230719 0.99998798 -0.00432575 0.62250308 -0.00165699 0.00432958 0.99998925 -0.39883307 Axis 0.83600220 0.32105405 0.44499956 Axis point 0.00000000 94.14831450 142.43417593 Rotation angle (degrees) 0.29659967 Shift along axis 0.01631211 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 815 atoms average map value = 0.2252, steps = 28 shifted from previous position = 0.00904 rotated from previous position = 0.045 degrees atoms outside contour = 261, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999398 -0.00292874 0.00185970 0.06441551 0.00293756 0.99998438 -0.00475504 0.60402438 -0.00184575 0.00476047 0.99998697 -0.44360852 Axis 0.80799998 0.31464469 0.49813127 Axis point 0.00000000 95.73948955 125.31589554 Rotation angle (degrees) 0.33737735 Shift along axis 0.02112552 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 815 atoms average map value = 0.2252, steps = 40 shifted from previous position = 0.00472 rotated from previous position = 0.0111 degrees atoms outside contour = 261, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999364 -0.00298014 0.00196156 0.04825343 0.00298913 0.99998496 -0.00459933 0.55793122 -0.00194782 0.00460516 0.99998750 -0.39234187 Axis 0.79033112 0.33567310 0.51254296 Axis point 0.00000000 88.22723548 119.24302275 Rotation angle (degrees) 0.33364605 Shift along axis 0.02432662 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 815 atoms average map value = 0.2252, steps = 28 shifted from previous position = 0.0169 rotated from previous position = 0.0437 degrees atoms outside contour = 261, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999580 -0.00229050 0.00177495 -0.04182500 0.00229818 0.99998797 -0.00433342 0.63147239 -0.00176500 0.00433748 0.99998904 -0.37105302 Axis 0.83139268 0.33942150 0.43997643 Axis point 0.00000000 87.56440037 144.20098396 Rotation angle (degrees) 0.29878093 Shift along axis 0.01630772 > fitmap sel inMap #1 Fit molecule 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) to map emhancer5G01.mrc (#1) using 815 atoms average map value = 0.2252, steps = 44 shifted from previous position = 0.0165 rotated from previous position = 0.0252 degrees atoms outside contour = 260, contour level = 0.06757 Position of 5G01_5TG8UniProtNumbering_ReadyToBuild-coot-0.pdb L (#2.8) relative to emhancer5G01.mrc (#1) coordinates: Matrix rotation and translation 0.99999480 -0.00262945 0.00186654 0.00538842 0.00263801 0.99998595 -0.00459763 0.62394266 -0.00185442 0.00460253 0.99998769 -0.41217089 Axis 0.81885345 0.33118137 0.46882611 Axis point 0.00000000 91.72652073 134.14614433 Rotation angle (degrees) 0.32187268 Shift along axis 0.01781403 > select clear > select add #1 2 models selected > select subtract #1 Nothing selected > select add #1 2 models selected > select subtract #1 Nothing selected > select add #2 13444 atoms, 13704 bonds, 1721 residues, 9 models selected > hide #!1 models > combine sel > save /Users/aleon/Desktop/ModelBuilding/5G01new/5G01_EMhancer_Fit.pdb models > #4 relModel #1 > close > open /Users/aleon/Desktop/ModelBuilding/6H4new/emhancer6H4.mrc Summary of feedback from opening /Users/aleon/Desktop/ModelBuilding/6H4new/emhancer6H4.mrc --- notes | open kw {} Opened emhancer6H4.mrc as #1, grid size 512,512,512, pixel 0.833, shown at level 6.59e-05, step 2, values float32 > open > /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_5TG8UniProtNumbering_ReadyToBuild- > Refit-coot-3.pdb Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb #2 --- Chain | Description A C E | No description available B D F | No description available H | No description available L | No description available > volume #1 step 1 > volume #1 level 0.06129 > volume flip #1 Opened emhancer6H4.mrc z flip as #3, grid size 512,512,512, pixel 0.833, shown at step 1, values float32 > hide atoms > show cartoons > transparency #3.1 50 > volume #1 level 0.05484 > volume #3 level 0.03229 > split #2 Split 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb (#2) into 8 models Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb A #2.1 --- Chain | Description A | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb B #2.2 --- Chain | Description B | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb C #2.3 --- Chain | Description C | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb D #2.4 --- Chain | Description D | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb E #2.5 --- Chain | Description E | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb F #2.6 --- Chain | Description F | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H #2.7 --- Chain | Description H | No description available Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L #2.8 --- Chain | Description L | No description available > select add #2.7 1776 atoms, 1800 bonds, 119 residues, 1 model selected > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map emhancer6H4.mrc z flip (#3) using 1776 atoms average map value = 0.1735, steps = 44 shifted from previous position = 0.0434 rotated from previous position = 0.517 degrees atoms outside contour = 545, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to emhancer6H4.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99995934 0.00563431 0.00704100 -3.26382830 -0.00563512 0.99998412 0.00009586 1.23296795 -0.00704035 -0.00013553 0.99997521 1.54295019 Axis -0.01282825 0.78068676 -0.62479086 Axis point 221.10775476 0.00000000 464.74942199 Rotation angle (degrees) 0.51673266 Shift along axis 0.04040980 > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map emhancer6H4.mrc z flip (#3) using 1776 atoms average map value = 0.1735, steps = 40 shifted from previous position = 0.00324 rotated from previous position = 0.0112 degrees atoms outside contour = 545, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to emhancer6H4.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99995847 0.00573222 0.00708490 -3.29773953 -0.00573419 0.99998353 0.00025773 1.21198079 -0.00708331 -0.00029834 0.99997487 1.59072854 Axis -0.03049432 0.77696654 -0.62880291 Axis point 226.64496659 0.00000000 466.60777071 Rotation angle (degrees) 0.52241001 Shift along axis 0.04197612 > select add #2.8 3508 atoms, 3555 bonds, 232 residues, 2 models selected > select subtract #2.7 1732 atoms, 1755 bonds, 113 residues, 1 model selected > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8) to map emhancer6H4.mrc z flip (#3) using 1732 atoms average map value = 0.1623, steps = 40 shifted from previous position = 0.0645 rotated from previous position = 0.374 degrees atoms outside contour = 607, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8) relative to emhancer6H4.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99997982 -0.00622110 -0.00128438 1.69159387 0.00622299 0.99997955 0.00147382 -1.82335538 0.00127518 -0.00148179 0.99999809 0.01313887 Axis -0.22658991 -0.19622703 0.95401885 Axis point 294.30086023 270.48536533 0.00000000 Rotation angle (degrees) 0.37368186 Shift along axis -0.01297176 > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8) to map emhancer6H4.mrc z flip (#3) using 1732 atoms average map value = 0.1623, steps = 40 shifted from previous position = 0.012 rotated from previous position = 0.0397 degrees atoms outside contour = 609, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L (#2.8) relative to emhancer6H4.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99997994 -0.00616294 -0.00146069 1.72985251 0.00616606 0.99997870 0.00214204 -1.99287718 0.00144746 -0.00215100 0.99999664 0.10407725 Axis -0.32097352 -0.21743060 0.92179170 Axis point 325.07881845 278.27480266 0.00000000 Rotation angle (degrees) 0.38316956 Shift along axis -0.02598681 > select clear > select add #2 15193 atoms, 15461 bonds, 1723 residues, 9 models selected > combine sel > save /Users/aleon/Desktop/ModelBuilding/6H4new/EMhancer6H4_FitinMap.pdb > models #4 relModel #3 > save /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_EMHancerMap.mrc models #3 > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #2.7/H #4/H Alignment identifier is 1 > select #2.7/H:1 #4/H:1 34 atoms, 32 bonds, 2 residues, 2 models selected > select #2.7/H:1-2 #4/H:1-2 66 atoms, 64 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [1-2] RMSD: 0.000 > delete atoms sel > delete bonds sel > select #2.7/H:118 #4/H:118 22 atoms, 20 bonds, 2 residues, 2 models selected > select #2.7/H:118-119 #4/H:118-119 46 atoms, 44 bonds, 4 residues, 2 models selected 1 [ID: 1] region 2 chains [118-119] RMSD: 0.000 > delete atoms sel > delete bonds sel > select add #2.7 1720 atoms, 1744 bonds, 115 residues, 1 model selected > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms average map value = 0.1766, steps = 76 shifted from previous position = 0.0148 rotated from previous position = 0.0971 degrees atoms outside contour = 528, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to 6H4_EMHancerMap.mrc (#3) coordinates: Matrix rotation and translation 0.99995069 0.00592546 0.00796941 -3.59102572 -0.00591628 0.99998181 -0.00117582 1.65046679 -0.00797623 0.00112861 0.99996755 1.47852023 Axis 0.11525058 0.79748071 -0.59223460 Axis point 185.51020105 0.00000000 452.13554805 Rotation angle (degrees) 0.57282454 Shift along axis 0.02671680 > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms average map value = 0.1766, steps = 36 shifted from previous position = 0.00154 rotated from previous position = 0.0102 degrees atoms outside contour = 528, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to 6H4_EMHancerMap.mrc (#3) coordinates: Matrix rotation and translation 0.99995114 0.00595014 0.00789336 -3.57567490 -0.00594230 0.99998183 -0.00101626 1.61270024 -0.00789926 0.00096930 0.99996833 1.49765050 Axis 0.09993239 0.79483494 -0.59854068 Axis point 189.90057564 0.00000000 454.52892265 Rotation angle (degrees) 0.56921607 Shift along axis 0.02810001 > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms average map value = 0.1766, steps = 44 shifted from previous position = 0.00235 rotated from previous position = 0.00679 degrees atoms outside contour = 528, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to 6H4_EMHancerMap.mrc (#3) coordinates: Matrix rotation and translation 0.99995002 0.00603993 0.00796669 -3.61581683 -0.00603221 0.99998131 -0.00099239 1.62757059 -0.00797254 0.00094428 0.99996777 1.52079226 Axis 0.09640714 0.79345217 -0.60094868 Axis point 191.09060147 0.00000000 455.41495959 Rotation angle (degrees) 0.57550175 Shift along axis 0.02889075 > ui mousemode right ""rotate selected models"" > view matrix models > #2.7,0.98464,-0.11414,0.1321,-8.1577,0.12924,0.98526,-0.11203,6.526,-0.11736,0.12738,0.98489,1.308 > fitmap sel inMap #3 Fit molecule 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) to map 6H4_EMHancerMap.mrc (#3) using 1720 atoms average map value = 0.1766, steps = 92 shifted from previous position = 0.336 rotated from previous position = 12.1 degrees atoms outside contour = 527, contour level = 0.032288 Position of 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H (#2.7) relative to 6H4_EMHancerMap.mrc (#3) coordinates: Matrix rotation and translation 0.99995430 0.00549588 0.00782213 -3.45421867 -0.00548303 0.99998358 -0.00166319 1.67847744 -0.00783114 0.00162022 0.99996802 1.32821793 Axis 0.16925178 0.80688885 -0.56593658 Axis point 169.10100723 0.00000000 442.97350230 Rotation angle (degrees) 0.55576465 Shift along axis 0.01802498 > select #3 2 models selected > select clear > open > /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_J604_WA79_modelangeloFinal.cif Summary of feedback from opening /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_J604_WA79_modelangeloFinal.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for 6H4_J604_WA79_modelangeloFinal.cif #5 --- Chain | Description Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Af | No description available Ag | No description available Ah | No description available Ai | No description available Aj | No description available Ak | No description available Al | No description available Ba | No description available Bb | No description available Bc | No description available Ca | No description available Cb | No description available Cc | No description available Cd | No description available Ce | No description available Cf | No description available Cg | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available Dg | No description available Dh | No description available Ea | No description available Eb | No description available Ec | No description available Ed | No description available Ee | No description available Ef | No description available Eg | No description available > show atoms > hide atoms > show cartoons > hide #4 models > hide #!2 models > show #!2 models > hide #!2 models Drag select of 74 residues > select up 684 atoms, 699 bonds, 85 residues, 1 model selected Drag select of 1333 residues > select up 12113 atoms, 12301 bonds, 1549 residues, 1 model selected > select up 12701 atoms, 12903 bonds, 1626 residues, 1 model selected Drag select of 90 residues > select down 11982 atoms, 12903 bonds, 1536 residues, 1 model selected > select down 11982 atoms, 12903 bonds, 1536 residues, 1 model selected > select clear Drag select of 1465 residues > select up 11869 atoms, 12053 bonds, 1523 residues, 1 model selected > delete sel Drag select of 16 residues > delete sel Drag select of 86 residues > view matrix models > #5,0.96969,0.17483,-0.17069,16.703,-0.15978,0.98224,0.09837,11.229,0.18485,-0.068115,0.9804,-20.241 > show sel atoms > style sel stick Changed 690 atom styles > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #2.1 models > hide #2.2 models > hide #2.3 models > hide #2.5 models > hide #2.6 models > hide #2.7 models > hide #2.8 models > hide #2.4 models > show #2.8 models > hide #2.8 models > show #2.7 models > hide #2.7 models > select clear > hide #!5 models > show #2.7 models > select aromatic-ring 2464 atoms, 2524 bonds, 392 residues, 10 models selected > show sel & #2.7 atoms > style sel & #2.7 stick Changed 119 atom styles > select up 5148 atoms, 5280 bonds, 392 residues, 10 models selected > show sel & #2.7 atoms > style sel & #2.7 stick Changed 383 atom styles > show #!5 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 24 atoms, 25 bonds, 1 residue, 1 model selected > select up 137 atoms, 141 bonds, 7 residues, 1 model selected > select up 1720 atoms, 1744 bonds, 115 residues, 1 model selected > view matrix models > #2.7,0.95455,-0.1456,-0.26006,115.62,0.19967,0.9602,0.19533,-89.62,0.22127,-0.23838,0.94563,20.297 > select clear > mmaker #2.7/H to #5/Ba Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6H4_J604_WA79_modelangeloFinal.cif, chain Ba (#5) with 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb H, chain H (#2.7), sequence alignment score = 43.8 RMSD between 10 pruned atom pairs is 0.474 angstroms; (across all 18 pairs: 13.657) > hide #!2 models > show #!2 models > show #2.1 models > hide #!2 models > show #!2 models > hide #2.1 models > hide #!2 models > show #!2 models > hide #2.7 models > show #2.8 models > hide #!5 models > select aromatic-ring 2464 atoms, 2524 bonds, 392 residues, 10 models selected > select up 5148 atoms, 5280 bonds, 392 residues, 10 models selected > show sel & #2.8 atoms > style sel & #2.8 stick Changed 308 atom styles > show #!5 models > select clear Drag select of 5 atoms, 3 residues, 7 bonds > select clear > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > hide #!5 models > show #2.8 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > show #4 models > hide #4 models > show #4 models > hide #4 models > show #4 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > show #2.7 models > hide #2.7 models > show #2.7 models > hide #4 models > show #!5 models > hide #2.8 models > show #2.8 models > hide #2.7 models > show #2.7 models > hide #2.7 models > show #2.7 models > hide #2.8 models > show #2.8 models > hide #2.7 models > hide #!5 models > select ::name=""HIS"" 722 atoms, 734 bonds, 68 residues, 10 models selected > select clear > show #!5 models > hide #!5 models > select ::name=""LYS"" 1960 atoms, 1786 bonds, 180 residues, 10 models selected > select up 13598 atoms, 13712 bonds, 1568 residues, 10 models selected > select down 1960 atoms, 1786 bonds, 180 residues, 10 models selected > show sel & #2.8 atoms > style sel & #2.8 stick Changed 177 atom styles > show #!5 models > select clear > select #2.8/L:86 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select add #2.8 1732 atoms, 1755 bonds, 113 residues, 1 model selected > view matrix models > #2.8,0.9912,0.12169,-0.05206,-8.0691,-0.12143,0.99257,0.0081145,25.827,0.052661,-0.0017216,0.99861,-10.923 > ui mousemode right ""translate selected models"" > view matrix models > #2.8,0.9912,0.12169,-0.05206,-10.356,-0.12143,0.99257,0.0081145,26.822,0.052661,-0.0017216,0.99861,-10.205 > ui mousemode right ""rotate selected models"" > view matrix models > #2.8,0.97637,0.17441,0.12758,-68.999,-0.16616,0.98341,-0.07275,61.469,-0.13815,0.049832,0.98916,23.877 > ui mousemode right ""translate selected models"" > view matrix models > #2.8,0.97637,0.17441,0.12758,-69.179,-0.16616,0.98341,-0.07275,61.355,-0.13815,0.049832,0.98916,23.746 > select clear > mmaker #2.8/L to #5/Bb Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6H4_J604_WA79_modelangeloFinal.cif, chain Bb (#5) with 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb L, chain L (#2.8), sequence alignment score = 30.6 RMSD between 4 pruned atom pairs is 1.201 angstroms; (across all 28 pairs: 9.863) > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > show #2.8 models > hide #2.8 models > hide #!5 models > show #!5 models > hide #!5 models > show #2.7 models > show #!3 models > hide #!3 models > select add #2.8 1732 atoms, 1755 bonds, 113 residues, 1 model selected > select subtract #2.8 Nothing selected > select add #2.7 1720 atoms, 1744 bonds, 115 residues, 1 model selected > save > /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainAromaticModelAngeloMMFit.pdb > models #2.7 relModel #3 > select clear > select #2.7/H:11 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #2.7 1720 atoms, 1744 bonds, 115 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2.7,0.96576,0.12525,0.22718,-82.907,-0.14725,0.98565,0.082539,12.423,-0.21358,-0.11317,0.97035,79.872 > ui mousemode right ""translate selected models"" > view matrix models > #2.7,0.96576,0.12525,0.22718,-84.052,-0.14725,0.98565,0.082539,13.719,-0.21358,-0.11317,0.97035,82.032 > ui mousemode right ""rotate selected models"" > view matrix models > #2.7,0.93161,0.29151,0.2171,-111.04,-0.24367,0.94409,-0.22206,129.72,-0.2697,0.15398,0.95056,39.96 > view matrix models > #2.7,0.95482,0.29232,0.053593,-70.367,-0.25536,0.89922,-0.35524,179.76,-0.15203,0.32551,0.93324,-19.429 > view matrix models > #2.7,0.95494,0.2484,0.16246,-91.116,-0.19682,0.93966,-0.27981,136.68,-0.22216,0.23523,0.94621,12.539 > view matrix models > #2.7,0.98298,0.10585,0.15015,-61.791,-0.081007,0.98332,-0.16287,68.691,-0.16488,0.14794,0.97516,11.471 > ui mousemode right ""translate selected models"" > view matrix models > #2.7,0.98298,0.10585,0.15015,-62.422,-0.081007,0.98332,-0.16287,69.016,-0.16488,0.14794,0.97516,11.602 > select add #2 15137 atoms, 15405 bonds, 1719 residues, 9 models selected > select subtract #2 Nothing selected > select add #2 15137 atoms, 15405 bonds, 1719 residues, 9 models selected > select subtract #2 Nothing selected > close #1 > volume #3 level 0.0267 > save /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainFit.pdb models #2.7 > relModel #3 > close #2 > close #5 > show #4 models > hide #4 models > show #4 models > hide #4 models > close #4 > open > /Users/aleon/Desktop/ModelBuilding/6H4new/6H4_5TG8UniProtNumbering_ReadyToBuild- > Refit-coot-3.pdb Chain information for 6H4_5TG8UniProtNumbering_ReadyToBuild-Refit-coot-3.pdb #1 --- Chain | Description A C E | No description available B D F | No description available H | No description available L | No description available > hide atoms > show cartoons > open /Users/aleon/Desktop/ModelBuilding/6H4new/HeavyChainFit.pdb Chain information for HeavyChainFit.pdb #2 --- Chain | Description H | No description available > split #1 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 3 days, 17 hours, 18 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LS24D36xG: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.13.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 biopython: 1.85 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.12 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.51 ChimeraX-AtomicLibrary: 12.1.2 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: 2.10.5 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: 1.3.2 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.dev202311280534 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-crai: 0.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 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: 1.1.8 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.14.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 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: 0.2.0 contourpy: 1.2.0 cripser: 0.0.15 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.45.1 fsspec: 2025.3.2 funcparserlib: 2.0.0a0 glfw: 2.6.3 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.0 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 mpmath: 1.3.0 mrcfile: 1.5.4 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.7 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.0.0 prompt-toolkit: 3.0.41 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 sympy: 1.13.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 torch: 2.2.0 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate all ChimeraX