id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7540 QObject::~QObject: Timers cannot be stopped from another thread koala008@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19043 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Windows fatal exception: code 0x80000003 Thread 0x0000254c (most recent call first): File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 55 in create_profile File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 391 in create_chimerax_profile File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py"", line 367 in __init__ File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\file_history.py"", line 103 in __init__ File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\file_history.py"", line 26 in __init__ File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 481 in __init__ File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py"", line 220 in build File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 688 in init File ""D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py"", line 1018 in File ""D:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 87 in _run_code File ""D:\Program Files\ChimeraX 1.3\bin\lib\runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== QObject::~QObject: Timers cannot be stopped from another thread ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open D:\\\SIMM_CHM\\\A2b\\\Figure\\\binding_pocket\\\bingding_pocket.cxs Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0254, step 1, values float32 Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.0117, step 1, values float32 Log from Thu Sep 1 15:18:30 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > D:\\\SIMM_CHM\\\A2b\\\Figure\\\overall_structure\\\overall_structures.cxs Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0254, step 1, values float32 Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.0117, step 1, values float32 Log from Wed Aug 31 21:51:59 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > D:\\\SIMM_CHM\\\A2b\\\Figure\\\overall_structure\\\overall_structures.cxs Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0254, step 1, values float32 Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.0117, step 1, values float32 Log from Wed Aug 31 20:59:20 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > D:\\\SIMM_CHM\\\Figure\\\BBBBBBBBBBBBBB0502\\\overall_structure\\\map_model_color.cxs Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0254, step 1, values float32 Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.0117, step 1, values float32 Log from Fri May 6 16:23:50 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open E:\\\copy-SIMM\\\Figure\\\BBBBBBBBBBBBBB0502\\\Two_models_color.cxs Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0254, step 1, values float32 Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.0145, step 1, values float32 Log from Mon May 2 23:27:06 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open E:/copy-SIMM/A2b_A3/structure/20220428/A2B_ADN_0214-4.pdb Chain information for A2B_ADN_0214-4.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > open E:/copy-SIMM/A2b_A3/structure/20220428/BAY- > flip3-coot-0303-xyw_20220425_5.pdb Chain information for BAY-flip3-coot-0303-xyw_20220425_5.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > open E:/copy-SIMM/Figure/ADN_map.mrc Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level 0.0168, step 1, values float32 > open E:/copy-SIMM/Figure/BAY_map.mrc Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level 0.00604, step 2, values float32 > hide atoms > show cartoons > volume #4 step 1 > volume #4 level 0.01393 > volume #3 level 0.02602 > volume #4 level 0.01316 > hide #!3 models > hide #!4 models > matchmaker #1 to #2 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 BAY-flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2) with A2B_ADN_0214-4.pdb, chain B (#1), sequence alignment score = 1718.9 RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs: 0.464) > matchmaker #1/R to #2/R 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 BAY-flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2) with A2B_ADN_0214-4.pdb, chain R (#1), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,18.404,0,1,0,6.1272,0,0,1,27.911 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.60509,-0.78919,0.10505,131.86,0.77481,0.55337,-0.3057,11.967,0.18313,0.26637,0.94631,-13.298 > view matrix models > #3,0.86712,-0.49654,0.039479,81.231,0.4684,0.78587,-0.40376,28.747,0.16946,0.36859,0.91401,-19.33 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.86712,-0.49654,0.039479,83.375,0.4684,0.78587,-0.40376,29.917,0.16946,0.36859,0.91401,-20.814 > view matrix models > #3,0.86712,-0.49654,0.039479,82.364,0.4684,0.78587,-0.40376,36.972,0.16946,0.36859,0.91401,-23.857 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.64694,-0.7582,-0.081296,146.84,0.71302,0.63927,-0.28799,15.022,0.27032,0.12834,0.95418,-12.48 > view matrix models > #3,0.96617,-0.23256,-0.11147,61.045,0.13854,0.8326,-0.53626,80.274,0.21752,0.50268,0.83666,-34.381 > ui mousemode right ""move picked models"" > view matrix models > #3,0.96617,-0.23256,-0.11147,60.964,0.13854,0.8326,-0.53626,76.336,0.21752,0.50268,0.83666,-32.798 > view matrix models > #3,0.96617,-0.23256,-0.11147,63.017,0.13854,0.8326,-0.53626,79.357,0.21752,0.50268,0.83666,-33.397 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.96617,-0.23256,-0.11147,62.139,0.13854,0.8326,-0.53626,81.078,0.21752,0.50268,0.83666,-34.608 > view matrix models > #3,0.96617,-0.23256,-0.11147,64.949,0.13854,0.8326,-0.53626,76.098,0.21752,0.50268,0.83666,-31.774 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.93244,-0.24643,-0.26424,87.409,0.041236,0.79912,-0.59976,96.818,0.35896,0.54834,0.75529,-41.604 > view matrix models > #3,0.95571,0.15286,-0.25151,40.176,-0.20648,0.95719,-0.20285,58.902,0.20973,0.2458,0.94636,-15.659 > view matrix models > #3,0.96671,0.13291,-0.21867,37.465,-0.22168,0.86184,-0.45617,99.919,0.12782,0.48946,0.86261,-24.302 > view matrix models > #3,0.96199,0.0060174,-0.27301,57.987,-0.11613,0.91387,-0.38906,75.936,0.24715,0.40597,0.87983,-29.195 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.96199,0.0060174,-0.27301,58.11,-0.11613,0.91387,-0.38906,76.515,0.24715,0.40597,0.87983,-28.892 > view matrix models > #3,0.96199,0.0060174,-0.27301,58.509,-0.11613,0.91387,-0.38906,78.784,0.24715,0.40597,0.87983,-27.548 > view matrix models > #3,0.96199,0.0060174,-0.27301,56.87,-0.11613,0.91387,-0.38906,81.862,0.24715,0.40597,0.87983,-25.422 > view matrix models > #3,0.96199,0.0060174,-0.27301,60.257,-0.11613,0.91387,-0.38906,80.148,0.24715,0.40597,0.87983,-26.709 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.96924,0.14576,-0.1983,35.742,-0.16598,0.98207,-0.089371,43.293,0.18172,0.11953,0.97606,-0.03727 > view matrix models > #3,0.98583,-0.16046,-0.048919,50.211,0.16142,0.98675,0.016519,-2.2945,0.04562,-0.024181,0.99867,26.676 > ui mousemode right ""move picked models"" > view matrix models > #1,0.93925,-0.32783,-0.10169,71.622,0.29735,0.92513,-0.23603,18.467,0.17145,0.19146,0.96641,-7.8145 > undo > view matrix models > #3,0.98583,-0.16046,-0.048919,49.415,0.16142,0.98675,0.016519,7.9814,0.04562,-0.024181,0.99867,29.489 > view matrix models > #1,0.93925,-0.32783,-0.10169,76.339,0.29735,0.92513,-0.23603,22.173,0.17145,0.19146,0.96641,-5.6807 > view matrix models > #1,0.93925,-0.32783,-0.10169,77.348,0.29735,0.92513,-0.23603,22.064,0.17145,0.19146,0.96641,-5.1299 > view matrix models > #3,0.98583,-0.16046,-0.048919,50.199,0.16142,0.98675,0.016519,1.6905,0.04562,-0.024181,0.99867,30.186 > view matrix models > #3,0.98583,-0.16046,-0.048919,49.763,0.16142,0.98675,0.016519,5.0132,0.04562,-0.024181,0.99867,29.865 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.95007,-0.29291,-0.10756,74.504,0.29645,0.95488,0.018194,-5.2841,0.097377,-0.049171,0.99403,27.913 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.95007,-0.29291,-0.10756,71.517,0.29645,0.95488,0.018194,-5.2627,0.097377,-0.049171,0.99403,26.153 > view matrix models > #3,0.95007,-0.29291,-0.10756,72.241,0.29645,0.95488,0.018194,-5.5304,0.097377,-0.049171,0.99403,25.712 > ~select #3 Nothing selected > fitmap #1 inMap #3 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 116 shifted from previous position = 7.2 rotated from previous position = 14.8 degrees atoms outside contour = 3217, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999709 -0.00228215 -0.00078051 0.30319160 0.00228311 0.99999662 0.00123941 -0.37560316 0.00077768 -0.00124119 0.99999893 0.06737381 Axis -0.45731452 -0.28726029 0.84163231 Axis point 161.45288095 137.84719352 0.00000000 Rotation angle (degrees) 0.15539468 Shift along axis 0.02594593 > fitmap #1 inMap #3 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 40 shifted from previous position = 0.0144 rotated from previous position = 0.0159 degrees atoms outside contour = 3219, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999695 -0.00237768 -0.00066673 0.29531295 0.00237835 0.99999667 0.00100573 -0.34485141 0.00066433 -0.00100731 0.99999927 0.04530441 Axis -0.37744783 -0.24957591 0.89176510 Axis point 143.59895806 126.39953189 0.00000000 Rotation angle (degrees) 0.15278733 Shift along axis 0.01500226 > hide #!3 models > show #!2 models > matchmaker #3 to #4 No 'to' model specified > show #!3 models > show #!4 models > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A2B_ADN_0214-4.pdb, chain B (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2), sequence alignment score = 1718.9 RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs: 0.464) > hide #!1 models > hide #!3 models > select #4 2 models selected > view matrix models #4,1,0,0,4.9796,0,1,0,-1.2895,0,0,1,0.21268 > view matrix models #4,1,0,0,2.5367,0,1,0,2.9519,0,0,1,0.95685 > view matrix models #4,1,0,0,2.1989,0,1,0,3.0664,0,0,1,4.7596 > view matrix models #4,1,0,0,6.2857,0,1,0,-0.1747,0,0,1,6.5534 > view matrix models #4,1,0,0,4.2705,0,1,0,-1.1232,0,0,1,4.8089 > view matrix models #4,1,0,0,3.7519,0,1,0,-1.1812,0,0,1,5.4671 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99966,-0.026166,-0.0014905,7.424,0.026177,0.99963,0.0080197,-5.563,0.0012801,-0.008056,0.99997,6.3629 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99966,-0.026166,-0.0014905,7.5705,0.026177,0.99963,0.0080197,-6.0153,0.0012801,-0.008056,0.99997,7.1986 > view matrix models > #4,0.99966,-0.026166,-0.0014905,8.2247,0.026177,0.99963,0.0080197,-4.1145,0.0012801,-0.008056,0.99997,3.9471 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99818,0.00086579,-0.06025,13.25,-0.0037961,0.99881,-0.048539,7.8131,0.060136,0.04868,0.997,-10.432 > view matrix models > #4,0.99474,0.070011,-0.0748,6.7268,-0.075812,0.99409,-0.077753,21.638,0.068914,0.083015,0.99416,-15.614 > view matrix models > #4,0.99922,0.032396,-0.022564,3.6344,-0.033658,0.99775,-0.057963,13.046,0.020635,0.058678,0.99806,-6.9269 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99922,0.032396,-0.022564,3.8442,-0.033658,0.99775,-0.057963,9.2979,0.020635,0.058678,0.99806,-6.1139 > view matrix models > #4,0.99922,0.032396,-0.022564,3.768,-0.033658,0.99775,-0.057963,8.8694,0.020635,0.058678,0.99806,-3.869 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99208,0.10035,-0.07549,3.331,-0.109,0.98665,-0.12101,28.765,0.062339,0.12828,0.98978,-17.016 > view matrix models > #4,0.99297,0.10137,-0.061151,1.0434,-0.10812,0.98691,-0.11967,28.43,0.048218,0.12544,0.99093,-15.036 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99297,0.10137,-0.061151,2.9808,-0.10812,0.98691,-0.11967,28.844,0.048218,0.12544,0.99093,-19.04 > view matrix models > #4,0.99297,0.10137,-0.061151,4.089,-0.10812,0.98691,-0.11967,28.474,0.048218,0.12544,0.99093,-17.374 > view matrix models > #4,0.99297,0.10137,-0.061151,3.6163,-0.10812,0.98691,-0.11967,28.456,0.048218,0.12544,0.99093,-18.035 > view matrix models > #4,0.99297,0.10137,-0.061151,1.0971,-0.10812,0.98691,-0.11967,37.742,0.048218,0.12544,0.99093,-18.238 > view matrix models > #4,0.99297,0.10137,-0.061151,5.2958,-0.10812,0.98691,-0.11967,40.973,0.048218,0.12544,0.99093,-19.694 > view matrix models > #4,0.99297,0.10137,-0.061151,5.4503,-0.10812,0.98691,-0.11967,40.694,0.048218,0.12544,0.99093,-19.649 > ui mousemode right ""move picked models"" > view matrix models > #4,0.99297,0.10137,-0.061151,5.808,-0.10812,0.98691,-0.11967,36.143,0.048218,0.12544,0.99093,-16.837 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.98523,0.12525,0.11675,-21.678,-0.1263,0.99199,0.0016041,20.487,-0.11562,-0.016326,0.99316,21.938 > view matrix models > #4,0.99384,0.076454,0.080204,-11.183,-0.079182,0.99637,0.031402,9.7526,-0.077512,-0.03756,0.99628,19.479 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99384,0.076454,0.080204,-9.5305,-0.079182,0.99637,0.031402,7.9219,-0.077512,-0.03756,0.99628,16.536 > view matrix models > #4,0.99384,0.076454,0.080204,-10.19,-0.079182,0.99637,0.031402,9.0183,-0.077512,-0.03756,0.99628,16.373 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.9753,0.1728,0.13757,-28.614,-0.17769,0.98379,0.023991,24.091,-0.1312,-0.047844,0.9902,25.326 > view matrix models > #4,0.98165,0.16266,0.099519,-22.666,-0.17524,0.9753,0.1345,9.1519,-0.075183,-0.14947,0.9859,32.171 > view matrix models > #4,0.99714,0.06153,0.043977,-3.4953,-0.068343,0.9821,0.17551,-11.008,-0.032391,-0.17801,0.9835,30.865 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99714,0.06153,0.043977,-3.659,-0.068343,0.9821,0.17551,-10.089,-0.032391,-0.17801,0.9835,30.602 > view matrix models > #4,0.99714,0.06153,0.043977,-4.0148,-0.068343,0.9821,0.17551,-8.9965,-0.032391,-0.17801,0.9835,30.856 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99583,0.087037,0.027364,-4.8148,-0.090719,0.97652,0.19538,-8.2874,-0.0097164,-0.19704,0.98035,30.942 > view matrix models > #4,0.98864,0.14917,0.018525,-10.765,-0.14998,0.97076,0.18742,1.0426,0.009974,-0.18807,0.9821,27.046 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.98864,0.14917,0.018525,-13.583,-0.14998,0.97076,0.18742,0.093376,0.009974,-0.18807,0.9821,26.869 > view matrix models > #4,0.98864,0.14917,0.018525,-13.081,-0.14998,0.97076,0.18742,-1.1395,0.009974,-0.18807,0.9821,26.91 > view matrix models > #4,0.98864,0.14917,0.018525,-12.618,-0.14998,0.97076,0.18742,-3.039,0.009974,-0.18807,0.9821,27.74 > view matrix models > #4,0.98864,0.14917,0.018525,-12.792,-0.14998,0.97076,0.18742,-3.0558,0.009974,-0.18807,0.9821,27.678 > view matrix models > #4,0.98864,0.14917,0.018525,-13.192,-0.14998,0.97076,0.18742,-2.9273,0.009974,-0.18807,0.9821,28.209 > view matrix models > #4,0.98864,0.14917,0.018525,-13.577,-0.14998,0.97076,0.18742,-1.8298,0.009974,-0.18807,0.9821,28.639 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99367,0.11161,-0.012524,-4.8826,-0.1071,0.97524,0.19348,-8.6643,0.033808,-0.19092,0.98102,26.17 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 68 shifted from previous position = 2.33 rotated from previous position = 5.31 degrees atoms outside contour = 2558, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999993 0.00006391 -0.00036620 0.04851337 -0.00006383 0.99999997 0.00021578 -0.04489731 0.00036622 -0.00021575 0.99999991 -0.00205420 Axis -0.50198853 -0.85201313 -0.14859726 Axis point -0.11721179 0.00000000 151.94834913 Rotation angle (degrees) 0.02462684 Shift along axis 0.01420519 > show #!1 models > hide #!4 models > hide #!2 models > show #!3 models > hide #!1 models > hide #!3 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!1 models > show #!2 models > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker A2B_ADN_0214-4.pdb, chain B (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2), sequence alignment score = 1718.9 RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs: 0.464) > hide #!1 models > show #!4 models > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99367,0.11161,-0.012524,-4.9556,-0.1071,0.97524,0.19348,-8.0408,0.033808,-0.19092,0.98102,25.55 > hide #!2 models > hide #!4 models > show #!2 models > show #!1 models > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > hide #!1 models > show #!1 models > hide #!1 models > show #!4 models > view matrix models > #4,0.99367,0.11161,-0.012524,-5.5714,-0.1071,0.97524,0.19348,-8.2228,0.033808,-0.19092,0.98102,25.402 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 84 shifted from previous position = 1.37 rotated from previous position = 5.67 degrees atoms outside contour = 2558, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999989 0.00004416 -0.00046633 0.05954713 -0.00004411 0.99999999 0.00009869 -0.02024493 0.00046634 -0.00009867 0.99999988 -0.04016215 Axis -0.20613398 -0.97417062 -0.09219749 Axis point 83.95036136 0.00000000 132.60127722 Rotation angle (degrees) 0.02742747 Shift along axis 0.01115018 > show #!1 models > hide #!4 models > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > hide #!2 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > hide #!3 models > show #!2 models > show #!4 models > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99367,0.11161,-0.012524,-5.2364,-0.1071,0.97524,0.19348,-6.776,0.033808,-0.19092,0.98102,25.03 > view matrix models > #4,0.99367,0.11161,-0.012524,-6.5132,-0.1071,0.97524,0.19348,-7.2757,0.033808,-0.19092,0.98102,24.99 > view matrix models > #4,0.99367,0.11161,-0.012524,-6.0679,-0.1071,0.97524,0.19348,-8.599,0.033808,-0.19092,0.98102,26.139 > view matrix models > #4,0.99367,0.11161,-0.012524,-5.6784,-0.1071,0.97524,0.19348,-7.8772,0.033808,-0.19092,0.98102,25.422 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.07 rotated from previous position = 5.67 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999980 0.00013116 -0.00061743 0.07544382 -0.00013098 0.99999995 0.00028568 -0.04459578 0.00061746 -0.00028560 0.99999977 -0.01945038 Axis -0.41228191 -0.89119756 -0.18918387 Axis point 27.77483149 0.00000000 130.40786548 Rotation angle (degrees) 0.03969604 Shift along axis 0.01231923 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > hide #!4 models > hide #!2 models > show #!1 models > show #!3 models > hide #!3 models > hide #!1 models > show #!2 models > show #!4 models > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99793,0.062884,0.013602,-3.572,-0.064334,0.97279,0.22259,-17.075,0.00076483,-0.223,0.97482,34.647 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.61 rotated from previous position = 2.45 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999984 0.00011944 -0.00055356 0.06578881 -0.00011927 0.99999994 0.00030093 -0.04631770 0.00055359 -0.00030086 0.99999980 -0.00963222 Axis -0.46922004 -0.86324420 -0.18612364 Axis point 13.77843114 0.00000000 128.08886628 Rotation angle (degrees) 0.03674213 Shift along axis 0.01090684 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.61 rotated from previous position = 2.45 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999983 0.00011684 -0.00056020 0.06743838 -0.00011668 0.99999995 0.00028937 -0.04511803 0.00056024 -0.00028930 0.99999980 -0.01202133 Axis -0.45121024 -0.87364474 -0.18208291 Axis point 17.87081160 0.00000000 129.37928445 Rotation angle (degrees) 0.03674062 Shift along axis 0.01117712 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.61 rotated from previous position = 2.45 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999984 0.00011944 -0.00055356 0.06578881 -0.00011927 0.99999994 0.00030093 -0.04631770 0.00055359 -0.00030086 0.99999980 -0.00963222 Axis -0.46922004 -0.86324420 -0.18612364 Axis point 13.77843118 0.00000000 128.08886618 Rotation angle (degrees) 0.03674213 Shift along axis 0.01090684 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.61 rotated from previous position = 2.45 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999983 0.00011684 -0.00056020 0.06743838 -0.00011668 0.99999995 0.00028937 -0.04511803 0.00056024 -0.00028930 0.99999980 -0.01202133 Axis -0.45121024 -0.87364474 -0.18208291 Axis point 17.87081164 0.00000000 129.37928432 Rotation angle (degrees) 0.03674062 Shift along axis 0.01117712 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > transparency #4 30 > color #4 #ffaa00 models transparency 0 > color #4 #55ff7f models transparency 0 > color #4 #ffaa7f models transparency 0 > color #4 #ffaaff models transparency 0 > transparency #4 30 > color #4 black models transparency 0 > color #4 #a3a3a3 models transparency 0 > color #4 #b3b3b3 models transparency 0 > color #4 #6c6c6c models transparency 0 > transparency #4 30 > show #!1 models > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 72 shifted from previous position = 1.61 rotated from previous position = 2.45 degrees atoms outside contour = 2557, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999983 0.00011684 -0.00056020 0.06743838 -0.00011668 0.99999995 0.00028937 -0.04511803 0.00056024 -0.00028930 0.99999980 -0.01202133 Axis -0.45121024 -0.87364474 -0.18208291 Axis point 17.87081144 0.00000000 129.37928448 Rotation angle (degrees) 0.03674062 Shift along axis 0.01117712 > transparency #4 0 > view matrix models > #4,0.99787,0.060745,0.023585,-4.7079,-0.06473,0.96569,0.2515,-20.217,-0.0074979,-0.25249,0.96757,40.568 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 56 shifted from previous position = 0.352 rotated from previous position = 1.8 degrees atoms outside contour = 2553, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999981 0.00011957 -0.00060342 0.06888708 -0.00011940 0.99999995 0.00028442 -0.04034825 0.00060345 -0.00028435 0.99999978 -0.01623753 Axis -0.41962883 -0.89040876 -0.17630623 Axis point 24.06516585 0.00000000 121.02626303 Rotation angle (degrees) 0.03882965 Shift along axis 0.00988221 > show #!3 models > hide #!2 models > hide #!1 models > ~select #4 Nothing selected > color #4 #6c6624 models transparency 0 > color #4 #6c632f models transparency 0 > color #4 #686c3a models transparency 0 > color #4 #aaffff models transparency 0 > color #4 #55ff00 models transparency 0 > color #4 #ffaa7f models transparency 0 > select #4 2 models selected > view matrix models > #4,0.99904,0.037554,0.022484,-1.6696,-0.041911,0.96887,0.244,-22.43,-0.012621,-0.2447,0.96952,39.917 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99904,0.037554,0.022484,-3.0061,-0.041911,0.96887,0.244,-22.327,-0.012621,-0.2447,0.96952,39.137 > view matrix models > #4,0.99904,0.037554,0.022484,-2.8992,-0.041911,0.96887,0.244,-22.413,-0.012621,-0.2447,0.96952,38.076 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99976,-0.0027219,0.021517,2.4066,-0.0038669,0.95383,0.30033,-33.253,-0.021341,-0.30034,0.95359,48.704 > view matrix models > #4,0.99745,0.068166,0.021151,-6.5064,-0.071339,0.96117,0.26656,-20.926,-0.0021595,-0.26739,0.96359,40.569 > view matrix models > #4,0.99835,0.052891,0.022207,-4.7759,-0.056812,0.96521,0.25523,-21.664,-0.0079348,-0.25607,0.96662,39.384 > view matrix models > #4,0.99854,0.052535,0.012754,-3.4059,-0.053942,0.95257,0.29949,-26.679,0.0035847,-0.29974,0.95401,45.435 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99854,0.052535,0.012754,-3.4063,-0.053942,0.95257,0.29949,-25.325,0.0035847,-0.29974,0.95401,45.718 > view matrix models > #4,0.99854,0.052535,0.012754,-2.0528,-0.053942,0.95257,0.29949,-26.185,0.0035847,-0.29974,0.95401,46.254 > view matrix models > #4,0.99854,0.052535,0.012754,-2.5455,-0.053942,0.95257,0.29949,-26.323,0.0035847,-0.29974,0.95401,45.775 > view matrix models > #4,0.99854,0.052535,0.012754,-2.5979,-0.053942,0.95257,0.29949,-25.992,0.0035847,-0.29974,0.95401,45.283 > ~select #4 Nothing selected > ui mousemode right ""translate selected models"" > select #4 2 models selected > ~select #4 Nothing selected > select #4 2 models selected > ~select #4 Nothing selected > select #4 2 models selected > ~select #4 Nothing selected > select #4 2 models selected > ~select #4 Nothing selected > color #3 #b27079 models transparency 0 > color #3 #928fb2 models transparency 0 > color #3 #b29ca6 models transparency 0 > color #3 #b2afb0 models transparency 0 > color #3 #b2b2b2 models transparency 0 > color #3 #4d4db2 models transparency 0 > select #3 2 models selected > view matrix models > #3,0.95007,-0.29291,-0.10756,72.188,0.29645,0.95488,0.018194,-5.9105,0.097377,-0.049171,0.99403,25.012 > ~select #3 Nothing selected > select #3 2 models selected > view matrix models > #3,0.95007,-0.29291,-0.10756,73.199,0.29645,0.95488,0.018194,-5.2449,0.097377,-0.049171,0.99403,25.678 > view matrix models > #3,0.95007,-0.29291,-0.10756,73.575,0.29645,0.95488,0.018194,-5.1691,0.097377,-0.049171,0.99403,25.699 > view matrix models > #3,0.95007,-0.29291,-0.10756,73.262,0.29645,0.95488,0.018194,-5.6719,0.097377,-0.049171,0.99403,25.164 > ~select #3 Nothing selected > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 76 shifted from previous position = 2.28 rotated from previous position = 2.94 degrees atoms outside contour = 2555, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999992 0.00005428 -0.00039989 0.04757224 -0.00005422 0.99999999 0.00014220 -0.02474018 0.00039990 -0.00014218 0.99999991 -0.02756479 Axis -0.33231711 -0.93460773 -0.12678220 Axis point 65.53109402 0.00000000 127.93016806 Rotation angle (degrees) 0.02451563 Shift along axis 0.01080802 > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > hide #!3 models > hide #!4 models > show #!1 models > show #!3 models > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 60 shifted from previous position = 1.58 rotated from previous position = 3.08 degrees atoms outside contour = 2553, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999982 0.00014338 -0.00057796 0.06595899 -0.00014322 0.99999995 0.00027420 -0.03836534 0.00057799 -0.00027411 0.99999979 -0.02323370 Axis -0.41820326 -0.88166049 -0.21858824 Axis point 35.95951023 0.00000000 122.30439953 Rotation angle (degrees) 0.03756041 Shift along axis 0.01131956 > fitmap #1 inMap #3 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 52 shifted from previous position = 1.16 rotated from previous position = 0.0173 degrees atoms outside contour = 3225, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999681 -0.00235604 -0.00090656 0.32127614 0.00235711 0.99999652 0.00118706 -0.35937366 0.00090376 -0.00118919 0.99999888 0.04156631 Axis -0.42584376 -0.32442464 0.84463350 Axis point 150.62003713 138.84957924 0.00000000 Rotation angle (degrees) 0.15985861 Shift along axis 0.01488453 > ui tool show ""Fit in Map"" Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points correlation = 0.9582, correlation about mean = 0.8117, overlap = 38.83 steps = 60, shift = 0.911, angle = 3.49 degrees Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.93903847 -0.32930428 -0.09882019 71.32499165 0.30063328 0.92591232 -0.22870506 21.72211567 0.16681239 0.18505422 0.96846712 -5.88346381 Axis 0.51777433 -0.33241002 0.78829773 Axis point -53.85717924 187.14222038 0.00000000 Rotation angle (degrees) 23.55040054 Shift along axis 25.07167981 > show #!4 models Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 64 shifted from previous position = 1.13 rotated from previous position = 3.49 degrees atoms outside contour = 3221, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999700 -0.00230959 -0.00081123 0.30653114 0.00231059 0.99999657 0.00123363 -0.36880105 0.00080838 -0.00123551 0.99999891 0.06574383 Axis -0.45030817 -0.29537407 0.84260116 Axis point 156.45642258 137.64546674 0.00000000 Rotation angle (degrees) 0.15708298 Shift along axis 0.02629661 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 44 shifted from previous position = 0.00423 rotated from previous position = 0.00846 degrees atoms outside contour = 2554, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999990 0.00010028 -0.00043705 0.05049934 -0.00010016 0.99999996 0.00026504 -0.04313308 0.00043707 -0.00026499 0.99999987 -0.00379762 Axis -0.50879702 -0.83910787 -0.19241510 Axis point 3.78327640 0.00000000 128.61928177 Rotation angle (degrees) 0.02984333 Shift along axis 0.01123011 > hide #!4 models > hide #!3 models > show #!2 models > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) > ui tool show ""Fit in Map"" Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 44 shifted from previous position = 0.00894 rotated from previous position = 0.0143 degrees atoms outside contour = 3212, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999717 -0.00230485 -0.00058894 0.28113638 0.00230551 0.99999671 0.00112094 -0.36282354 0.00058635 -0.00112230 0.99999920 0.07518789 Axis -0.42646211 -0.22343483 0.87647416 Axis point 154.92943648 126.79526989 0.00000000 Rotation angle (degrees) 0.15069141 Shift along axis 0.02707365 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 64 shifted from previous position = 0.444 rotated from previous position = 0.555 degrees atoms outside contour = 2553, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999991 0.00005757 -0.00041763 0.04525609 -0.00005749 0.99999997 0.00020017 -0.03082159 0.00041765 -0.00020015 0.99999989 -0.01517344 Axis -0.42889261 -0.89490536 -0.12327016 Axis point 33.39712799 0.00000000 118.66932590 Rotation angle (degrees) 0.02673918 Shift along axis 0.01004283 > show #!4 models > show #!3 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points correlation = 0.9582, correlation about mean = 0.8118, overlap = 38.83 steps = 44, shift = 0.0171, angle = 0.00476 degrees Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.93903876 -0.32931742 -0.09877373 71.31747725 0.30066588 0.92591737 -0.22864176 21.71270443 0.16675203 0.18500558 0.96848681 -5.85774252 Axis 0.51767144 -0.33230022 0.78841159 Axis point -53.84103831 187.09490016 0.00000000 Rotation angle (degrees) 23.54860667 Shift along axis 25.08557296 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 40 shifted from previous position = 0.0195 rotated from previous position = 0.0125 degrees atoms outside contour = 3219, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999686 -0.00235631 -0.00085286 0.31617862 0.00235727 0.99999658 0.00113243 -0.35726124 0.00085019 -0.00113443 0.99999900 0.03971978 Axis -0.41210954 -0.30961109 0.85691698 Axis point 149.87056576 136.49379601 0.00000000 Rotation angle (degrees) 0.15758144 Shift along axis 0.01434837 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 40 shifted from previous position = 0.0135 rotated from previous position = 0.00363 degrees atoms outside contour = 2555, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999990 0.00008782 -0.00042449 0.05124927 -0.00008771 0.99999996 0.00025551 -0.04418421 0.00042451 -0.00025548 0.99999988 -0.00334207 Axis -0.50777304 -0.84364852 -0.17442394 Axis point 3.04860892 0.00000000 134.88997229 Rotation angle (degrees) 0.02882943 Shift along axis 0.01183589 > hide #!3 models > hide #!4 models > show #!1 models > show #!2 models > matchmaker #2/R to #1/R 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 A2B_ADN_0214-4.pdb, chain R (#1) with BAY- flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score = 1394.8 RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs: 1.038) Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 28 shifted from previous position = 0.0182 rotated from previous position = 0.0122 degrees atoms outside contour = 3215, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999709 -0.00232241 -0.00064406 0.28952177 0.00232312 0.99999669 0.00110222 -0.36255840 0.00064150 -0.00110371 0.99999919 0.07019031 Axis -0.41614089 -0.24251744 0.87636297 Axis point 153.22672457 129.66122639 0.00000000 Rotation angle (degrees) 0.15186055 Shift along axis 0.02895708 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 52 shifted from previous position = 0.464 rotated from previous position = 0.556 degrees atoms outside contour = 2560, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999995 0.00005233 -0.00029677 0.04136720 -0.00005229 0.99999998 0.00014790 -0.03572378 0.00029678 -0.00014788 0.99999994 -0.00828863 Axis -0.44056054 -0.88409476 -0.15582958 Axis point 20.26633348 0.00000000 161.13710112 Rotation angle (degrees) 0.01923305 Shift along axis 0.01465006 > hide #!1 models > hide #!2 models > show #!3 models > show #!4 models Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points correlation = 0.9582, correlation about mean = 0.8118, overlap = 38.83 steps = 44, shift = 0.000532, angle = 0.0147 degrees Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.93902032 -0.32929446 -0.09902518 71.34739775 0.30060466 0.92594979 -0.22859093 21.70907238 0.16696607 0.18488410 0.96847313 -5.86410526 Axis 0.51745627 -0.33288307 0.78830696 Axis point -53.85428275 187.24535269 0.00000000 Rotation angle (degrees) 23.54858400 Shift along axis 25.06986085 > hide #!4 models > show #!1 models > color #3 #aaaaff models transparency 0 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 40 shifted from previous position = 0.0191 rotated from previous position = 0.0206 degrees atoms outside contour = 3220, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999679 -0.00241404 -0.00077050 0.31124352 0.00241480 0.99999660 0.00098537 -0.34369906 0.00076812 -0.00098723 0.99999922 0.03234052 Axis -0.36271689 -0.28291654 0.88791592 Axis point 140.98416812 130.70537044 0.00000000 Rotation angle (degrees) 0.15579885 Shift along axis 0.01306053 > hide #!3 models > hide #!1 models > show #!2 models > show #!4 models Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 40 shifted from previous position = 0.0149 rotated from previous position = 0.0065 degrees atoms outside contour = 2552, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999991 0.00006413 -0.00040551 0.04664867 -0.00006406 0.99999998 0.00017830 -0.02856534 0.00040552 -0.00017827 0.99999990 -0.02176817 Axis -0.39832414 -0.90599702 -0.14320361 Axis point 50.03198808 0.00000000 125.25944365 Rotation angle (degrees) 0.02564479 Shift along axis 0.01041610 > hide #!4 models > show #!3 models > hide #!3 models > show #!1 models > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > fitmap #1 inMap #3 Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms average map value = 0.03367, steps = 40 shifted from previous position = 0.00222 rotated from previous position = 0.00825 degrees atoms outside contour = 3220, contour level = 0.026017 Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999692 -0.00235038 -0.00079171 0.30792277 0.00235126 0.99999662 0.00111290 -0.35410831 0.00078909 -0.00111476 0.99999907 0.04248527 Axis -0.40968193 -0.29071987 0.86466333 Axis point 149.12240691 133.17343906 0.00000000 Rotation angle (degrees) 0.15577396 Shift along axis 0.01353138 > fitmap #2 inMap #4 Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc (#4) using 8228 atoms average map value = 0.02292, steps = 40 shifted from previous position = 0.003 rotated from previous position = 0.0123 degrees atoms outside contour = 2553, contour level = 0.013165 Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999980 0.00010306 -0.00061327 0.07117225 -0.00010298 0.99999998 0.00014402 -0.01662992 0.00061329 -0.00014395 0.99999980 -0.05095063 Axis -0.22556685 -0.96076653 -0.16139168 Axis point 80.97290895 0.00000000 119.02440807 Rotation angle (degrees) 0.03657313 Shift along axis 0.00814638 > color #4 black models transparency 0 > color #4 #969696 models transparency 0 > volume #3 color black > volume #3 color #969696 > volume #3 color #aaaaaa > volume #4 color #aaaaaa > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > volume #3 color #b4b4b4 > volume #4 color #b3b3b3 > volume #4 color #b5b5b5 > volume #4 color #b4b4b4 > hide #!4 models > hide #!3 models > color #1/R light sea green > color #2/R dark orange > color chainA medium purple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color A medium purple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword Drag select of 33 residues, 1 pseudobonds > select up 681 atoms, 691 bonds, 1 pseudobond, 83 residues, 3 models selected > select up 3937 atoms, 4015 bonds, 1 pseudobond, 471 residues, 3 models selected > color sele medium purple Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sel medium purple > select clear Drag select of 35 residues > select up 466 atoms, 468 bonds, 66 residues, 2 models selected > select up 1943 atoms, 1985 bonds, 256 residues, 2 models selected > color sel violet > select clear Drag select of 25 residues > select up 387 atoms, 387 bonds, 52 residues, 2 models selected > select up 6024 atoms, 6127 bonds, 786 residues, 2 models selected > select down 387 atoms, 387 bonds, 52 residues, 2 models selected > select clear Drag select of 34 residues > select clear Drag select of 6 residues > select up 358 atoms, 356 bonds, 43 residues, 2 models selected > select up 5156 atoms, 5247 bonds, 672 residues, 2 models selected > select down 358 atoms, 356 bonds, 43 residues, 2 models selected > select clear Drag select of 11 residues > select up 288 atoms, 297 bonds, 37 residues, 2 models selected > select up 868 atoms, 880 bonds, 114 residues, 2 models selected > color sel olive drab > select clear Drag select of 39 residues > select up 1197 atoms, 1211 bonds, 157 residues, 2 models selected > select up 5156 atoms, 5247 bonds, 672 residues, 2 models selected > color sel burly wood > select clear > set bgColor white > lighting full > lighting shadows false > hide #!2 models > select clear > hide #2.1 models > hide #1.1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel hotpink > show sel atoms > select clear > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel cornflower blue > show #!1 atoms > show #!1 cartoons > style #!1 stick Changed 8174 atom styles > hide #!1 atoms > show #!1 cartoons > show #!2 models > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > hide #!2 models > show #!2 models > show #!4 models > show #!3 models > volume #4 level 0.01552 > volume #3 level 0.02476 > hide #!4 models > volume #4 level 0.01447 > hide #!4 models > volume #3 level 0.02602 > hide #!1 models > volume #3 level 0.02539 > hide #!2 models > volume #3 level 0.02539 > save E:/copy-SIMM/Figure/BBBBBBBBBBBBBB0502/Two_models.cxs includeMaps true ——— End of log from Mon May 2 23:27:06 2022 ——— opened ChimeraX session > show #!1 models > select #1 8174 atoms, 8341 bonds, 2 pseudobonds, 1042 residues, 2 models selected > color zone #3 near sel distance 5 > hide #!1 models > hide #!3 models > show #!2 models > show #!4 models > color zone #4 near sel distance 5 > ~select #1 Nothing selected > select #2 8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected > color zone #4 near sel distance 5 > select clear > select #2 8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected > ~select #2 Nothing selected > select #2 8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected > ~select #2 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > show #!1 models > surface dust #3 size 10.4 > surface dust #4 size 8 > hide #!3 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > show #!2 models > hide #!1 models > select #2/R:184 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 53 atoms, 54 bonds, 6 residues, 1 model selected > select clear [Repeated 1 time(s)] > select add #2/L:396@C7 1 atom, 1 residue, 1 model selected > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > volume #4 level 0.01269 > show #!3 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > save E:/copy- > SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/map_model_color.cxs > includeMaps true > show #!1 models > save E:/copy-SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/ADN_model.png > width 1340 height 819 supersample 3 transparentBackground true > cartoon style width 1 > cartoon style width 1.3 > select clear > show #!2 models > hide #!2 models > cartoon style width 1.5 > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting soft > graphics silhouettes false > lighting simple > lighting soft [Repeated 1 time(s)] > lighting full > lighting soft > lighting simple > lighting soft > graphics silhouettes true > graphics silhouettes false > lighting flat [Repeated 1 time(s)] > lighting soft > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting flat [Repeated 2 time(s)] > lighting soft > graphics silhouettes false > lighting simple > lighting full > lighting simple > lighting soft > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > lighting simple > graphics silhouettes false > select clear > lighting soft [Repeated 2 time(s)] > lighting simple > lighting flat > lighting soft > set bgColor white > lighting simple [Repeated 1 time(s)] > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting simple > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting soft [Repeated 1 time(s)] > select clear > lighting shadows true intensity 1 > lighting shadows true intensity 0.55 > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting simple > lighting soft > show #!3 models > hide #!3 models > show #!4 models > hide #!1 models > volume #4 level 0.01167 > show #!2 models > hide #!2 models > show #!1 models > hide #!4 models > hide #!1 models > show #!2 models > select clear > lighting flat [Repeated 1 time(s)] > lighting simple > lighting soft > lighting flat > graphics silhouettes false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft [Repeated 1 time(s)] > show #!1 models > hide #!2 models > save E:/copy- > SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/map_model_color.cxs > includeMaps true ——— End of log from Fri May 6 16:23:50 2022 ——— opened ChimeraX session > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true ——— End of log from Wed Aug 31 20:59:20 2022 ——— opened ChimeraX session > close #1 > close #2 > open D:/SIMM_CHM/A2b/Figure/A2B_ADN_0214-4-coot-21.pdb Chain information for A2B_ADN_0214-4-coot-21.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-335.pdb Chain information for BAY-flip3-coot-335.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > hide atoms > show cartoons > hide #!2 models > hide #!4 models > ui mousemode right ""translate selected models"" > select #3 2 models selected > ~select #3 Nothing selected > select #1 8282 atoms, 8460 bonds, 2 pseudobonds, 1046 residues, 2 models selected > view matrix models #1,1,0,0,24.439,0,1,0,16.022,0,0,1,26.024 > view matrix models #1,1,0,0,23.295,0,1,0,18.659,0,0,1,24.618 > view matrix models #1,1,0,0,29.011,0,1,0,21.855,0,0,1,27.724 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.96295,-0.26941,0.012165,60.467,0.26822,0.96143,0.060877,-8.4807,-0.028097,-0.055358,0.99807,36.797 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.96295,-0.26941,0.012165,57.465,0.26822,0.96143,0.060877,-8.1392,-0.028097,-0.055358,0.99807,38.939 > view matrix models > #1,0.96295,-0.26941,0.012165,58.308,0.26822,0.96143,0.060877,-8.4703,-0.028097,-0.055358,0.99807,35.958 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97609,-0.21736,-0.00060747,52.868,0.21707,0.9746,0.055054,-4.0053,-0.011375,-0.05387,0.99848,34.049 > ui mousemode right ""move picked models"" > view matrix models > #3,0.95557,-0.27781,-0.098538,70.481,0.2857,0.95517,0.07764,-10.749,0.072551,-0.10234,0.9921,33.166 > undo > show #!4 models > ui tool show ""Fit in Map"" Fit map BAY_map.mrc in map ADN_map.mrc using 97041 points correlation = 0.9635, correlation about mean = 0.8072, overlap = 89.63 steps = 48, shift = 0.0146, angle = 0.0167 degrees Position of BAY_map.mrc (#4) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.93906585 0.30039962 0.16707905 -72.54473097 -0.32913845 0.92596648 0.18507828 4.44088943 -0.09911216 -0.22879283 0.96841655 17.75539475 Axis -0.51796032 0.33313869 -0.78786783 Axis point -54.01182656 187.31870099 0.00000000 Rotation angle (degrees) 23.54818099 Shift along axis 25.06581944 Fit map BAY_map.mrc in map ADN_map.mrc using 97041 points correlation = 0.9635, correlation about mean = 0.8072, overlap = 89.62 steps = 44, shift = 0.00616, angle = 0.00177 degrees Position of BAY_map.mrc (#4) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.93906650 0.30040896 0.16705861 -72.54574878 -0.32914073 0.92596990 0.18505708 4.44933009 -0.09909844 -0.22876670 0.96842413 17.74930972 Axis -0.51791841 0.33310710 -0.78790874 Axis point -53.98555382 187.31792131 0.00000000 Rotation angle (degrees) 23.54734529 Shift along axis 25.07004625 > show #!2 models > hide #!1 models > hide #!2 models > hide #!4 models > show #!1 models Fit molecule A2B_ADN_0214-4-coot-21.pdb (#1) to map ADN_map.mrc (#3) using 8282 atoms average map value = 0.03341, steps = 92 shifted from previous position = 4.36 rotated from previous position = 6.94 degrees atoms outside contour = 3187, contour level = 0.025387 Position of A2B_ADN_0214-4-coot-21.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999899 -0.00140801 -0.00019955 0.18428754 0.00140821 0.99999849 0.00102027 -0.25071495 0.00019811 -0.00102055 0.99999946 0.09835392 Axis -0.58299173 -0.11359755 0.80449751 Axis point 178.16484102 130.82688931 0.00000000 Rotation angle (degrees) 0.10028468 Shift along axis 0.00016798 > hide #!3 models > show #!3 models > hide #!1 models > show #!2 models > show #!4 models > hide #!3 models > ui mousemode right ""translate selected models"" > view matrix models > #1,0.95516,-0.27906,-0.099012,70.887,0.28706,0.95469,0.078557,-11.624,0.072603,-0.10346,0.99198,32.094 > view matrix models > #1,0.95516,-0.27906,-0.099012,71.705,0.28706,0.95469,0.078557,-12.36,0.072603,-0.10346,0.99198,30.93 > ~select #1 Nothing selected > select #2 8278 atoms, 8460 bonds, 5 pseudobonds, 1036 residues, 2 models selected > view matrix models #2,1,0,0,1.868,0,1,0,-1.3351,0,0,1,-2.8944 > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,6.3053,0,1,0,-0.80806,0,0,1,0.80714 Fit molecule BAY-flip3-coot-335.pdb (#2) to map BAY_map.mrc (#4) using 8278 atoms average map value = 0.02305, steps = 176 shifted from previous position = 7.76 rotated from previous position = 17.7 degrees atoms outside contour = 2165, contour level = 0.011674 Position of BAY-flip3-coot-335.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999985 -0.00036405 -0.00040922 0.08893967 0.00036417 0.99999989 0.00029218 -0.08952954 0.00040911 -0.00029233 0.99999987 -0.00172172 Axis -0.47076111 -0.65908495 0.58650747 Axis point 27.40319730 0.00000000 235.88413693 Rotation angle (degrees) 0.03556970 Shift along axis 0.01612844 > hide #!4 models > hide #!2 models > ~select #2 Nothing selected > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > show #!1 models > show #!3 models > hide #!3 models > show #!3 models Fit molecule A2B_ADN_0214-4-coot-21.pdb (#1) to map ADN_map.mrc (#3) using 8282 atoms average map value = 0.0334, steps = 64 shifted from previous position = 3.43 rotated from previous position = 0.00905 degrees atoms outside contour = 3191, contour level = 0.025387 Position of A2B_ADN_0214-4-coot-21.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999901 -0.00139621 -0.00015211 0.18029397 0.00139639 0.99999834 0.00117052 -0.27922772 0.00015047 -0.00117074 0.99999930 0.13637940 Axis -0.64026055 -0.08274599 0.76368811 Axis point 199.42334543 134.41071414 -0.00000000 Rotation angle (degrees) 0.10475769 Shift along axis 0.01182118 > hide #!3 models > hide #!1 models > show #!2 models > show #!4 models > hide #!4 models > hide #!2 models > show #!3 models > show #!4 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > hide #!4 models > show #!1 models > hide #!1 models > hide #!3 models > show #!2 models > show #!1 models Drag select of 41 residues > select up 721 atoms, 742 bonds, 87 residues, 2 models selected > select up 3937 atoms, 4015 bonds, 471 residues, 2 models selected > color sel medium slate blue [Repeated 1 time(s)] > select clear Drag select of 21 residues > select up 343 atoms, 339 bonds, 48 residues, 2 models selected > select up 1943 atoms, 1983 bonds, 256 residues, 2 models selected > color sel orchid > select clear Drag select of 46 residues > select up 1119 atoms, 1126 bonds, 146 residues, 2 models selected > select up 5156 atoms, 5247 bonds, 672 residues, 2 models selected > color sel burly wood > select clear Drag select of 6 residues > select up 355 atoms, 362 bonds, 48 residues, 2 models selected > select up 868 atoms, 880 bonds, 114 residues, 2 models selected > color sel olive drab > select clear > hide #!2 models Drag select of 95 residues > select up 1663 atoms, 1698 bonds, 220 residues, 1 model selected > select up 2297 atoms, 2363 bonds, 285 residues, 1 model selected > color sel orange > hide #!1 models > show #!2 models > select clear Drag select of 108 residues > select up 1715 atoms, 1751 bonds, 227 residues, 1 model selected > select up 2332 atoms, 2403 bonds, 283 residues, 1 model selected > color sel light sea green > select clear > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > cartoon style width 1。2 Invalid ""width"" argument: Expected a number > cartoon style width 1.2 > cartoon style width 1.5 > hide #1.1 models > hide #2.1 models > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel hot pink > hide #!2 models > show #!2 models > hide #!2 models Drag select of 57 residues > show #!3 models > hide #!3 models > select up 1183 atoms, 1201 bonds, 157 residues, 1 model selected > select up 2297 atoms, 2363 bonds, 285 residues, 1 model selected > color sel light sea green > select clear > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel hot pink > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > color #!1 cornflower blue > undo > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > show #!1 atoms > undo > hide #!1 models > show #!2 models Drag select of 84 residues > select up 1536 atoms, 1571 bonds, 202 residues, 1 model selected > select up 2359 atoms, 2432 bonds, 284 residues, 1 model selected > color sel orange > select clear > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > color sel cornflower blue > select clear > show #!3 models > hide #!2 models > hide #!3 models > show #!1 models > hide #!1 models > show #1.1 models > hide #1.1 models > show #!2 models > hide #!1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!2 models > show #!2 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true ——— End of log from Wed Aug 31 21:51:59 2022 ——— opened ChimeraX session > close #1 > close #2 > open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-336.pdb Chain information for BAY-flip3-coot-336.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > close #1 > open D:/SIMM_CHM/A2b/Figure/A2B_ADN_0214-4-coot-23.pdb Chain information for A2B_ADN_0214-4-coot-23.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-336.pdb Chain information for BAY-flip3-coot-336.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > hide #!2 models > show #!3 models > ui mousemode right ""translate selected models"" > select #1 8226 atoms, 8396 bonds, 2 pseudobonds, 1044 residues, 2 models selected > view matrix models #1,1,0,0,26.596,0,1,0,28.995,0,0,1,29.45 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98885,-0.094941,-0.11474,51.677,0.095143,0.99546,-0.0037279,20.323,0.11457,-0.0072301,0.99339,19.452 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.98885,-0.094941,-0.11474,52.198,0.095143,0.99546,-0.0037279,15.349,0.11457,-0.0072301,0.99339,21.816 > view matrix models > #1,0.98885,-0.094941,-0.11474,53.162,0.095143,0.99546,-0.0037279,11.901,0.11457,-0.0072301,0.99339,22.049 > style sel stick Changed 8226 atom styles > view matrix models > #1,0.98885,-0.094941,-0.11474,51.093,0.095143,0.99546,-0.0037279,10.74,0.11457,-0.0072301,0.99339,19.889 > view matrix models > #1,0.98885,-0.094941,-0.11474,50.432,0.095143,0.99546,-0.0037279,11.847,0.11457,-0.0072301,0.99339,18.399 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.96121,-0.27476,-0.024003,61.96,0.2758,0.95807,0.077674,-11.984,0.0016545,-0.081281,0.99669,37.433 > hide sel atoms > show sel cartoons > view matrix models > #1,0.9509,-0.30903,0.017236,61.791,0.30852,0.95084,0.026883,-8.4585,-0.024697,-0.020245,0.99949,33.171 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.9509,-0.30903,0.017236,62.605,0.30852,0.95084,0.026883,-7.7482,-0.024697,-0.020245,0.99949,33.779 > ui tool show ""Fit in Map"" Fit molecule A2B_ADN_0214-4-coot-23.pdb (#1) to map ADN_map.mrc (#3) using 8226 atoms average map value = 0.03351, steps = 84 shifted from previous position = 3.65 rotated from previous position = 7.48 degrees atoms outside contour = 3146, contour level = 0.025387 Position of A2B_ADN_0214-4-coot-23.pdb (#1) relative to ADN_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999890 -0.00144806 -0.00031865 0.20289001 0.00144836 0.99999849 0.00096031 -0.24567261 0.00031726 -0.00096077 0.99999949 0.08440214 Axis -0.54370590 -0.17997726 0.81975123 Axis point 169.38393278 141.14420265 0.00000000 Rotation angle (degrees) 0.10122136 Shift along axis 0.00309175 > hide #!3 models > hide #!1 models > show #!2 models > show #!4 models > select #4 2 models selected > select #2 8278 atoms, 8460 bonds, 5 pseudobonds, 1036 residues, 2 models selected > view matrix models #2,1,0,0,5.2053,0,1,0,1.8057,0,0,1,3.025 Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278 atoms average map value = 0.02305, steps = 168 shifted from previous position = 5.39 rotated from previous position = 17.7 degrees atoms outside contour = 2177, contour level = 0.011674 Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999985 -0.00038910 -0.00038050 0.09345215 0.00038926 0.99999982 0.00044010 -0.12135381 0.00038033 -0.00044025 0.99999983 0.02834974 Axis -0.62886538 -0.54348927 0.55601056 Axis point 0.00000000 35.31714124 247.41581793 Rotation angle (degrees) 0.04010415 Shift along axis 0.02294843 > show sel cartoons > hide sel atoms Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278 atoms average map value = 0.02305, steps = 48 shifted from previous position = 0.0178 rotated from previous position = 0.00748 degrees atoms outside contour = 2168, contour level = 0.011674 Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999980 -0.00039610 -0.00048192 0.10143576 0.00039627 0.99999985 0.00035813 -0.09941606 0.00048178 -0.00035832 0.99999982 -0.00571011 Axis -0.49798142 -0.66984177 0.55075086 Axis point 26.72262678 0.00000000 223.83666993 Rotation angle (degrees) 0.04121582 Shift along axis 0.01293506 Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278 atoms average map value = 0.02305, steps = 44 shifted from previous position = 0.0208 rotated from previous position = 0.00707 degrees atoms outside contour = 2180, contour level = 0.011674 Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999984 -0.00038772 -0.00041279 0.09805148 0.00038791 0.99999982 0.00045997 -0.12464496 0.00041261 -0.00046013 0.99999981 0.03089738 Axis -0.63052298 -0.56562275 0.53151828 Axis point 0.00000000 38.05416083 240.13221743 Rotation angle (degrees) 0.04180510 Shift along axis 0.02510084 Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278 atoms average map value = 0.02305, steps = 40 shifted from previous position = 0.00579 rotated from previous position = 0.0133 degrees atoms outside contour = 2173, contour level = 0.011674 Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999988 -0.00044929 -0.00019795 0.07273846 0.00044937 0.99999982 0.00039775 -0.12146203 0.00019777 -0.00039784 0.99999990 0.04264992 Axis -0.62952725 -0.31312396 0.71108989 Axis point 254.64383753 193.45071166 0.00000000 Rotation angle (degrees) 0.03620477 Shift along axis 0.02256975 > select #4 2 models selected > hide #!4 models > hide #!2 models > ~select #4 Nothing selected > select #4 2 models selected > ~select #4 Nothing selected > show #!1 models > show #!2 models > select clear Drag select of 49 residues, 1 pseudobonds > select up 734 atoms, 748 bonds, 1 pseudobond, 89 residues, 3 models selected > select up 3937 atoms, 4015 bonds, 1 pseudobond, 471 residues, 3 models selected > color sel medium slate blue > select clear Drag select of 19 residues > select up 359 atoms, 358 bonds, 50 residues, 2 models selected > select up 1943 atoms, 1983 bonds, 256 residues, 2 models selected > color sel orchid > select clear Drag select of 15 residues > select up 479 atoms, 483 bonds, 66 residues, 2 models selected > select up 5156 atoms, 5247 bonds, 672 residues, 2 models selected > color sel burly wood > select clear Drag select of 4 residues > select up 206 atoms, 207 bonds, 29 residues, 2 models selected > select up 868 atoms, 880 bonds, 114 residues, 2 models selected > color sel olive drab > select clear > hide #!2 models Drag select of 90 residues > select up 1663 atoms, 1698 bonds, 220 residues, 1 model selected > select up 2241 atoms, 2299 bonds, 283 residues, 1 model selected > color sel light sea green > hide #!1 models > show #!2 models > select clear Drag select of 59 residues > select up 1257 atoms, 1277 bonds, 167 residues, 1 model selected > select up 2332 atoms, 2403 bonds, 283 residues, 1 model selected > color sel orange > select clear > cartoon style width 1.5 > select ::name=""CLR"" 252 atoms, 279 bonds, 9 residues, 2 models selected > show sel & #!2 atoms > color sel dark gray > select clear > show #!1 models > hide #!1 models > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel hot pink > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel cornflowerblue > select clear > show #!2 atoms > undo > select clear > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > show #!2 atoms > undo > select clear > show #!1 models > select ::name=""ADN"" 19 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""BAY"" 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > select clear > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select ::name=""CLR"" 252 atoms, 279 bonds, 9 residues, 2 models selected > show sel & #!1 atoms > select clear > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > ui tool show ""Color Zone"" > color zone #3 near #1 distance 1.04 > color zone #3 near #1 distance 1.16 [Repeated 1 time(s)] > color zone #3 near #1 distance 15.37 > hide #!3 models > hide #!1 models > show #!2 models > show #!4 models > color zone #4 near #2 distance 5 > color zone #4 near #2 distance 5.51 > select ::name=""CLR"" 252 atoms, 279 bonds, 9 residues, 2 models selected > ui tool show ""Color Actions"" > color sel blue > color sel dark slate gray > color zone #4 near #2 distance 5.51 > color sel medium purple > color zone #4 near #2 distance 5.51 > color sel pale violet red > color zone #4 near #2 distance 5.51 > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > hide #!2 models > hide #!4 models > show #!3 models > show #!1 models > color zone #3 near #2 distance 15.48 > color zone #3 near #1 distance 15.48 > select ::name=""CLR"" 252 atoms, 279 bonds, 9 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dodger blue > color zone #3 near #1 distance 15.48 > hide #!1 models > hide #!3 models > show #!2 models > show #!4 models > color zone #4 near #2 distance 5.51 > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > ui mousemode right ""map eraser"" > volume erase #4 center 115.3,130.78,116.84 radius 7.3853 > volume erase #4 center 127.69,99.408,103.58 radius 7.3853 > volume erase #4 center 131.99,95.46,105.55 radius 7.3853 > volume erase #4 center 120.89,121.83,93.851 radius 7.3853 > volume erase #4 center 130.43,135.59,89.244 radius 7.3853 > volume erase #4 center 127.02,134.71,94.101 radius 7.3853 > volume erase #4 center 122.79,127.73,94.539 radius 7.3853 > volume erase #4 center 122.79,125.5,96.644 radius 7.3853 > volume erase #4 center 121.8,141.98,113.61 radius 7.3853 > select clear > volume erase #4 center 120.23,142.41,116.66 radius 7.3853 > volume erase #4 center 118.51,136.95,116.21 radius 7.3853 > volume erase #4 center 113.97,130.1,121.42 radius 7.3853 > volume erase #4 center 114.9,116.89,124.37 radius 7.3853 > volume erase #4 center 117.51,114.96,121.9 radius 7.3853 > volume erase #4 center 132.17,109.78,146.56 radius 4.3003 > volume erase #4 center 145.09,113.41,132.56 radius 3.9264 > volume erase #4 center 142.6,110.01,129.63 radius 3.9264 > volume erase #4 center 137.36,112.96,138.18 radius 3.9264 > volume erase #4 center 133.68,109.88,133.04 radius 3.9264 > volume erase #4 center 131.88,110.03,136.94 radius 3.9264 > volume erase #4 center 157.25,126.21,130.87 radius 3.9264 > volume erase #4 center 159.18,131.28,133.04 radius 3.9264 > volume erase #4 center 158.36,122.01,137.45 radius 3.9264 > volume erase #4 center 157.07,140.51,126.71 radius 3.9264 > volume erase #4 center 157.22,138.66,128.19 radius 3.9264 > volume erase #4 center 156.11,140.63,131.98 radius 3.9264 > volume erase #4 center 156.12,139.28,129.55 radius 3.9264 > volume erase #4 center 155.2,140.25,131.33 radius 3.9264 > volume erase #4 center 130.25,151.86,131.27 radius 3.9264 > volume erase #4 center 134.19,148.41,125.19 radius 2.5241 > volume erase #4 center 129.15,149.64,127.52 radius 2.5241 > volume erase #4 center 132.31,149.48,130.45 radius 2.5241 > volume erase #4 center 134.24,98.808,102.04 radius 7.5723 > volume erase #4 center 159.19,117.25,116.43 radius 5.6091 > volume erase #4 center 157.38,113.82,118.32 radius 5.6091 > volume erase #4 center 154.12,120.73,139.44 radius 0.93485 > volume erase #4 center 147.04,117.73,139.32 radius 0.93485 > volume erase #4 center 146.14,117.45,139.42 radius 0.93485 > volume erase #4 center 146.48,118.3,139.42 radius 0.93485 > volume erase #4 center 145.64,117.96,138.86 radius 0.93485 > volume erase #4 center 145.18,118.09,139.05 radius 0.93485 > volume erase #4 center 137.89,101.42,110.17 radius 0.93485 > hide #!4 models > hide #5 models > hide #!2 models > show #!1 models > show #!3 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > hide #!1 models > hide #!3 models > show #!4 models > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > hide #!4 models > show #!4 models > hide #!4 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > show #5 models > hide #5 models > show #5 models > close #5 > show #!1 models > select add #1/R:401@N3 1 atom, 1 residue, 1 model selected > select up 19 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > show #!2 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select ::name=""CLR"" 252 atoms, 279 bonds, 9 residues, 2 models selected > color sel byhetero > select clear > hide #!2 models > select clear > show #!2 models > hide #!1 models > select clear > cartoon style width 2 > cartoon style width 2.2 > cartoon style width 2.5 > cartoon style width 2 > select clear > show #!1 models > hide #!2 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_model.png width 1342 > height 834 supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_model.png width 1342 > height 834 supersample 3 transparentBackground true > hide #!2 models > show #!3 models > close #5 > hide #!3 models > show #!4 models > close #5 > save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_map.png width 1342 height > 834 supersample 3 transparentBackground true > hide #!4 models > show #!3 models > close #5 > save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_map.png width 1342 height > 834 supersample 3 transparentBackground true > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs > includeMaps true > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models Drag select of 3 atoms, 2 residues, 4 bonds > select clear Drag select of 2 atoms, 3 bonds > select up 5 atoms, 3 bonds, 2 residues, 2 models selected > select up 46 atoms, 50 bonds, 2 residues, 2 models selected > size sel stickRadius 0.3 Changed 50 bond radii > select clear > hide #!2 models > show #!2 models > hide #!2 models > hide #1.1 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_model2.png width 1342 > height 834 supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_model2.png width 1342 > height 834 supersample 3 transparentBackground true > save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures2.cxs > includeMaps true ——— End of log from Thu Sep 1 15:18:30 2022 ——— opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 512.15 OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: IPASON Model: OS: Microsoft Windows 10 企业版 (Build 19043) Memory: 17,130,639,360 MaxProcessMemory: 137,438,953,344 CPU: 6 AMD Ryzen 5 3500X 6-Core Processor OSLanguage: zh-CN Locale: ('zh_CN', 'cp936') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.1 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 comtypes: 1.1.10 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 MolecularDynamicsViewer: 1.2 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pywin32: 228 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect feedback normal Window Toolkit Tom Goddard all ChimeraX