id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3995 MemoryError writing compressed session anaschwarzer@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.dev202011201839 (2020-11-20 18:39:56 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session-2.cxs"" Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1.1, grid size 512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32 Opened 70S_tRNA_head.mrc as #1.3, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_body.mrc as #1.4, grid size 512,512,512, pixel 0.652, shown at level 2, step 1, values float32 Opened 70S_tRNA_LSU.mrc as #1.5, grid size 512,512,512, pixel 0.652, shown at level 2, step 1, values float32 Opened 70S_tRNA_atRNA.mrc as #1.6, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_ptRNA.mrc as #1.7, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_apra.mrc as #1.8, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_mRNA.mrc as #1.9, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2.1, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_head.mrc as #2.3, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_body.mrc as #2.4, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_LSU.mrc as #2.5, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_atrna.mrc as #2.6, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_ptrna.mrc as #2.7, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_apra.mrc as #2.8, grid size 288,288,288, pixel 1.16, shown at level 2.5, step 1, values float32 Opened 70S_hybridtRNA_1_mRNA.mrc as #2.9, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened h2_j621_3d288_95A_sharpened.mrc as #3.1, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened 70S_hybridtRNA_2_head.mrc as #3.3, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_2_body.mrc as #3.4, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_2_LSU.mrc as #3.5, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_2_atrna.mrc as #3.6, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_2_ptrna.mrc as #3.7, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_2_apra.mrc as #3.8, grid size 288,288,288, pixel 1.16, shown at level 2.5, step 1, values float32 Opened 70S_hybridtRNA_2_mRNA.mrc as #3.9, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened pre1_GDP-Pi_head.mrc as #4.1, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_body.mrc as #4.2, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_LSU.mrc as #4.3, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_atrna.mrc as #4.4, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_ptrna.mrc as #4.5, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_EFG.mrc as #4.6, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_apra.mrc as #4.7, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened pre1_GDP-Pi_mrna.mrc as #4.8, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc as #4.9, grid size 512,512,512, pixel 0.652, shown at level 4.33, step 1, values float32 Log from Mon Nov 30 18:33:50 2020UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session.cxs"" Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1.1, grid size 512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32 Opened 70S_tRNA_head.mrc as #1.3, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_body.mrc as #1.4, grid size 512,512,512, pixel 0.652, shown at level 2, step 1, values float32 Opened 70S_tRNA_LSU.mrc as #1.5, grid size 512,512,512, pixel 0.652, shown at level 2, step 1, values float32 Opened 70S_tRNA_atRNA.mrc as #1.6, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_ptRNA.mrc as #1.7, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_apra.mrc as #1.8, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_mRNA.mrc as #1.9, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2.1, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_head.mrc as #2.3, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_body.mrc as #2.4, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_LSU.mrc as #2.5, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_atrna.mrc as #2.6, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_ptrna.mrc as #2.7, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_apra.mrc as #2.8, grid size 288,288,288, pixel 1.16, shown at level 2.5, step 1, values float32 Opened 70S_hybridtRNA_1_mRNA.mrc as #2.9, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened h2_j621_3d288_95A_sharpened.mrc as #3.1, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened 70S_hybridtRNA_2_head.mrc as #3.3, grid size 288,288,288, pixel 1.16, shown at level 2, step 2, values float32 Opened 70S_hybridtRNA_2_body.mrc as #3.4, grid size 288,288,288, pixel 1.16, shown at level 2, step 2, values float32 Opened 70S_hybridtRNA_2_LSU.mrc as #3.5, grid size 288,288,288, pixel 1.16, shown at level 2, step 2, values float32 Opened 70S_hybridtRNA_2_atrna.mrc as #3.6, grid size 288,288,288, pixel 1.16, shown at level 2, step 2, values float32 Opened 70S_hybridtRNA_2_ptrna.mrc as #3.7, grid size 288,288,288, pixel 1.16, shown at level 2, step 2, values float32 Opened 70S_hybridtRNA_2_apra.mrc as #3.8, grid size 288,288,288, pixel 1.16, shown at level 2.5, step 2, values float32 Opened 70S_hybridtRNA_2_mRNA.mrc as #3.9, grid size 288,288,288, pixel 1.16, shown at level 3, step 2, values float32 Log from Mon Nov 30 17:55:28 2020UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"" Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1, grid size 512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32 Opened 70S_tRNA_head.mrc as #3, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_body.mrc as #4, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_LSU.mrc as #5, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_atRNA.mrc as #6, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_ptRNA.mrc as #7, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_mRNA.mrc as #9, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_apra.mrc as #8, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Log from Mon Nov 30 11:09:35 2020UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"" Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #1, grid size 512,512,512, pixel 0.652, shown at level 5.08, step 1, values float32 Opened 70S_tRNA_head.mrc as #3, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_body.mrc as #4, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_LSU.mrc as #5, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_atRNA.mrc as #6, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_ptRNA.mrc as #7, grid size 512,512,512, pixel 0.652, shown at level 2.5, step 1, values float32 Opened 70S_tRNA_apra.mrc as #8, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Opened 70S_tRNA_mRNA.mrc as #9, grid size 512,512,512, pixel 0.652, shown at level 3, step 1, values float32 Log from Mon Nov 30 10:37:01 2020UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-session.cxs"" Opened h1_j620_3d288_6A_sharpened_b50.mrc as #1, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened 70S_hybridtRNA_1_head.mrc as #3, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_body.mrc as #4, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_LSU.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_atrna.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_ptrna.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 2, step 1, values float32 Opened 70S_hybridtRNA_1_apra.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Opened 70S_hybridtRNA_1_mRNA.mrc as #9, grid size 288,288,288, pixel 1.16, shown at level 3, step 1, values float32 Log from Mon Nov 30 09:54:28 2020UCSF ChimeraX version: 1.2.dev202011201839 (2020-11-20) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/h1_j620_3d288_6A_sharpened_b50.mrc"" Opened h1_j620_3d288_6A_sharpened_b50.mrc as #1, grid size 288,288,288, pixel 1.16, shown at level 4.15, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_tRNA_c1_RSR-1-coot-4.pdb"" Chain information for 70S_tRNA_c1_RSR-1-coot-4.pdb #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available z | No description available > volume #1 step 1 > hide atoms > show cartoons > fitmap #2 inMap #1 resolution 6 metric correlation Opened 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 as #3, grid size 132,144,132, pixel 2, shown at level 0.107, step 1, values float32 Fit map 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 in map h1_j620_3d288_6A_sharpened_b50.mrc using 320037 points correlation = 0.9429, correlation about mean = 0.747, overlap = 3.717e+05 steps = 44, shift = 0.0161, angle = 0.0287 degrees Position of 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 (#3) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#1) coordinates: Matrix rotation and translation 0.99999996 0.00016786 0.00023238 -0.06154487 -0.00016776 0.99999990 -0.00041167 0.08234666 -0.00023245 0.00041163 0.99999989 -0.03060270 Axis 0.82062428 0.46331615 -0.33453540 Axis point 0.00000000 76.11965950 202.39508680 Rotation angle (degrees) 0.02874101 Shift along axis -0.00211499 > volume #1 level 3 > fitmap #2 inMap #1 resolution 6 metric correlation Fit map 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 in map h1_j620_3d288_6A_sharpened_b50.mrc using 320037 points correlation = 0.9429, correlation about mean = 0.747, overlap = 3.717e+05 steps = 44, shift = 0.0213, angle = 0.00769 degrees Position of 70S_tRNA_c1_RSR-1-coot-4.pdb map 6 (#3) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#1) coordinates: Matrix rotation and translation 0.99999994 0.00016524 0.00030974 -0.06304754 -0.00016515 0.99999994 -0.00030211 0.08008564 -0.00030979 0.00030206 0.99999991 -0.00692487 Axis 0.65224867 0.66884412 -0.35667804 Axis point -5.25527793 0.00000000 234.94764095 Rotation angle (degrees) 0.02653600 Shift along axis 0.01491208 > close #3 > hide #!1 models > select #1/A-Z Nothing selected > select #2/A-Z 88932 atoms, 96739 bonds, 422 pseudobonds, 6418 residues, 2 models selected > select #1/A-Z /0-6 Nothing selected > select #2/A-Z /0-6 92140 atoms, 99978 bonds, 433 pseudobonds, 6872 residues, 2 models selected > volume zone #2 nearAtoms sel range 4 newMap true > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #3, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > set bgColor white > set bgColor black > close #3 > select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #3, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/a-u,y-z 52213 atoms, 56371 bonds, 176 pseudobonds, 4043 residues, 2 models selected > select #2/a-u 51962 atoms, 56095 bonds, 176 pseudobonds, 4030 residues, 2 models selected > ~select #1/a:929-1068,1107-1381 /s,n,c,j,m,g,i 51962 atoms, 56095 bonds, 176 pseudobonds, 4030 residues, 2 models selected > hide #!2 models > show #!2 models > ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 36124 atoms, 39101 bonds, 170 pseudobonds, 2734 residues, 2 models selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #4, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!4 models > show #!4 models > hide #!2 models > set bgColor white > show #!2 models > hide #!3 models > hide #!4 models > select #2/A-Z /0-6 92140 atoms, 99978 bonds, 433 pseudobonds, 6872 residues, 2 models selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #5, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > show #!3 models > show #!4 models > hide #!2 models > volume #3 level 4 > volume #3 level 2 > volume #3 level 3.5 > volume #3 level 3 > volume #3 level 2.5 > show #!2 models > hide #!2 models > volume #3 level 2 > show #!2 models > hide #!2 models > select #2/x Nothing selected > show #!2 models > select #1/w /y Nothing selected > select #2/w /y 1658 atoms, 1843 bonds, 84 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #6, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!6 models > hide #!5 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > select #2/v 1643 atoms, 1834 bonds, 78 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #7, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/A:2001 20 atoms, 21 bonds, 1 residue, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #8, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/z 230 atoms, 255 bonds, 11 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #9, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > color #9 green > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!2 models > show #!2 models > ui mousemode right select > select clear > ui mousemode right translate > cartoon style nucleic width 1.5 thickness 1.5 xsection oval > cartoon style helix width 3 thickness 0.8 > cartoon style strand width 3 thickness 0.8 > cartoon style coil width 0.8 thickness 0.8 > size sel stickRadius 0.25 Changed 0 bond radii > graphics silhouettes width 1.2 > graphics silhouettes true > hide #!2 models > show #!1 models > hide #!1 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!2 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!7 models > hide #!7 models > hide #!5 models > show #!2 models > show #!8 models > select #1/A:2001 Nothing selected > show atoms > hide atoms > hide #!8 models > select #1/A:2001 Nothing selected > select #2/A:2001 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > hide #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > view name 1 > volume #4 level 2 > show #!2 models > volume #4 level 2.5 > hide #!2 models > volume #3 level 2.5 > volume #3 level 2 > volume #3 level 2.3 > volume #3 level 2.5 > volume #3 level 2 > volume #4 level 2 > volume #5 level 2 > volume #5 level 2.5 > volume #5 level 2 > show #!2 models > view 1 > hide #!2 models > volume #5 level 2.5 > volume #4 level 2.5 > volume #3 level 2.5 > volume #3 level 2 > volume #3 level 2.3 > volume #3 level 2.5 > volume #3 level 2 > volume #4 level 2 > volume #5 level 2 > volume #6 level 2.5 > volume #6 level 2 > volume #6 level 1.7 > volume #6 level 2 > volume #6 level 1.8 > volume #6 level 2 > view 1 > volume #6 level 1.8 > volume #7 level 1.8 > volume #7 level 2 > volume #6 level 2 > surface dust #6 5 Expected a keyword > surface dust #6 size 3 > surface dust #6 size 5 > surface dust #6 size 7 > surface dust #6 size 10 > surface dust #6 size 8 > volume #8 level 2 > volume #8 level 3.5 > volume #8 level 3 > view 1 > volume #6 level 2.5 > volume #6 level 2 > view 1 > cd Current working directory is: C:\Users\anasc > save 70S_hybridtRNA_1_head.mrc models #3 > save 70S_hybridtRNA_1_body.mrc models #3 > save 70S_hybridtRNA_1_body.mrc models #4 > save 70S_hybridtRNA_1_body.mrc models #4 > save 70S_hybridtRNA_1_head.mrc models #3 > save 70S_hybridtRNA_1_LSU.mrc models #5 > save 70S_hybridtRNA_1_atrna.mrc models #6 > save 70S_hybridtRNA_1_ptrna.mrc models #7 > save 70S_hybridtRNA_1_apra.mrc models #8 > save 70S_hybridtRNA_1_mRNA.mrc models #9 > surface dust #6 size 5 > surface dust #6 size 8 > view 1 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-view1.png"" > width 4000 height 2343 supersample 4 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1-session.cxs"" > includeMaps true ——— End of log from Mon Nov 30 09:54:28 2020 ——— opened ChimeraX session > close #2-9 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"" Opened h2_j621_3d288_95A_sharpened.mrc as #2, grid size 288,288,288, pixel 1.16, shown at level 4.17, step 2, values float32 > close #1 > rename #2 id #1 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb"" Summary of feedback from opening C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 1622 messages similar to the above omitted Ignored bad PDB record found on line 148850 END Chain information for 70S_tRNA_c2.pdb #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available z | No description available > hide atoms > show cartoons > volume #1 step 1 > volume #1 level 3 > volume #1 level 2.224 > fitmap #2 inMap #1 resolution 9.5 metric correlation Opened 70S_tRNA_c2.pdb map 9.5 as #3, grid size 90,98,90, pixel 3.17, shown at level 0.0946, step 1, values float32 Fit map 70S_tRNA_c2.pdb map 9.5 in map h2_j621_3d288_95A_sharpened.mrc using 101575 points correlation = 0.8582, correlation about mean = 0.6472, overlap = 7.552e+04 steps = 56, shift = 0.186, angle = 0.698 degrees Position of 70S_tRNA_c2.pdb map 9.5 (#3) relative to h2_j621_3d288_95A_sharpened.mrc (#1) coordinates: Matrix rotation and translation 0.99994789 0.00899770 0.00482375 -2.39617210 -0.00896547 0.99993762 -0.00666200 2.59597039 -0.00488340 0.00661841 0.99996617 -0.12309569 Axis 0.54523531 0.39853294 -0.73748896 Axis point 295.81443067 257.04759949 0.00000000 Rotation angle (degrees) 0.69779988 Shift along axis -0.18111622 > close #3 > select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected > volume zone #(map) nearAtoms sel range 4 newMap true Missing or invalid ""volumes"" argument: invalid density maps specifier > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #3, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > cartoon style nucleic width 1.5 thickness 1.5 xsection oval > cartoon style helix width 3 thickness 0.8 > cartoon style strand width 3 thickness 0.8 > cartoon style coil width 0.8 thickness 0.8 > size sel stickRadius 0.25 Changed 16994 bond radii > graphics silhouettes width 1.2 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes width 1.2 > select #2/a-u 51962 atoms, 56095 bonds, 159 pseudobonds, 4030 residues, 2 models selected > ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 36124 atoms, 39101 bonds, 153 pseudobonds, 2734 residues, 2 models selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #4, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/A-Z /0-6 92140 atoms, 99978 bonds, 402 pseudobonds, 6872 residues, 2 models selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #5, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!2 models > show #!2 models > select #2/w /y 1658 atoms, 1842 bonds, 84 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #6, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/v 1643 atoms, 1834 bonds, 78 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #7, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/A:2001 20 atoms, 21 bonds, 1 residue, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #8, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > select #2/z 230 atoms, 255 bonds, 11 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #9, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!2 models > graphics silhouettes false > graphics silhouettes true > graphics silhouettes width 1.2 > volume #3 level 2 > volume #4 level 2 > volume #5 level 2 > volume #6 level 2 > volume #7 level 2 > volume #8 level 3 > volume #9 level 3 > view 1 > surface dust #6 size 4 > surface dust #6 size 5 > surface dust #6 size 7 > surface dust #6 size 8 > surface dust #5 size 8 > surface dust #5 size 5 > surface dust #5 size 6 > surface dust #5 size 7 > surface dust #5 size 8 > surface dust #3 size 8 > surface dust #4 size 8 > view 1 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2-view1.png"" > width 4000 height 2343 supersample 4 > save 70S_hybridtRNA_2_head.mrc models #3 > save 70S_hybridtRNA_2_body.mrc models #4 > save 70S_hybridtRNA_2_LSU.mrc models #5 > save 70S_hybridtRNA_2_atrna.mrc models #6 > save 70S_hybridtRNA_2_ptrna.mrc models #7 > save 70S_hybridtRNA_2_apra.mrc models #8 > save 70S_hybridtRNA_2_mRNA.mrc models #9 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2-session.cxs"" > includeMaps true > close #2-9 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_APtRNA_job536_3d512_235A_sharpened_a.mrc"" Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc as #2, grid size 512,512,512, pixel 0.652, shown at level 5.08, step 2, values float32 > close #1 > rename #2 id #1 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_AP_v2.cif-coot-2.pdb"" Summary of feedback from opening C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_AP_v2.cif-coot-2.pdb --- warning | Ignored bad PDB record found on line 147610 END Chain information for 70S_AP_v2.cif-coot-2.pdb #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available z | No description available > hide atoms > show cartoons > cartoon style nucleic width 1.5 thickness 1.5 xsection oval > cartoon style helix width 3 thickness 0.8 > cartoon style strand width 3 thickness 0.8 > cartoon style coil width 0.8 thickness 0.8 > size sel stickRadius 0.25 Changed 0 bond radii > graphics silhouettes width 1.2 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes width 1.2 > select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 15838 atoms, 16994 bonds, 1296 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #3, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/a-u 51956 atoms, 56095 bonds, 4024 residues, 1 model selected > ~select #2/a:929-1068,1107-1381 /s,n,c,j,m,g,i 36118 atoms, 39101 bonds, 2728 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #4, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/A-Z /0-6 92129 atoms, 99979 bonds, 6860 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #5, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/w /y 1652 atoms, 1842 bonds, 78 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #6, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/v 1642 atoms, 1834 bonds, 77 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #7, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/A:2001 20 atoms, 21 bonds, 1 residue, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #8, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > select #2/z 230 atoms, 255 bonds, 11 residues, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #9, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > hide #2 models > view 1 > view 1 > view name 2 > volume #3 step 1 > volume #4 step 1 > volume #1 step 1 > volume #5 step 1 > volume #6 step 1 > volume #7 step 1 > volume #8 step 1 > volume #9 step 1 > volume #3 level 2 > volume #3 level 3 > volume #3 level 3.5 > volume #3 level 3.2 > volume #3 level 3.3 > volume #3 level 2 > volume #3 level 2.5 > show #2 models > hide #2 models > volume #4 level 2.5 > volume #4 level 2 > volume #4 level 3 > volume #4 level 2.5 > volume #5 level 2.5 > volume #5 level 2 > volume #5 level 3 > volume #4 level 3 > volume #3 level 3 > volume #6 level 2 > volume #6 level 3 > volume #6 level 2.5 > volume #6 level 2 > volume #6 level 2.5 > volume #7 level 2.5 > volume #7 level 3 > volume #7 level 2.5 > volume #8 level 3 > volume #9 level 3 > view 2 > view name 2 > view 2 > surface dust #6 size 8 > surface dust #6 size 5 > surface dust #5 size 5 > surface dust #7 size 5 > surface dust #8 size 5 > surface dust #3 size 5 > view 2 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-view2.png"" width > 4000 height 2343 supersample 4 > save 70S_tRNA_head.mrc models #3 > save 70S_tRNA_body.mrc models #4 > save 70S_tRNA_LSU.mrc models #5 > save 70S_tRNA_atRNA.mrc models #6 > save 70S_tRNA_ptRNA.mrc models #7 > save 70S_tRNA_apra.mrc models #8 > save 70S_tRNA_mRNA.mrc models #9 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"" > includeMaps true ——— End of log from Mon Nov 30 10:37:01 2020 ——— opened ChimeraX session > select #2/a:2001 37 atoms, 40 bonds, 1 residue, 1 model selected > volume zone #1 nearAtoms sel range 4 newMap true Opened 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc zone as #10, grid size 512,512,512, pixel 0.652, shown at step 1, values float32 > hide #!8 models > volume #10 level 2.5 > close #8 > rename #10 id #8 > cd Current working directory is: C:\Users\anasc > save 70S_tRNA_apra.mrc models #8 > view 2 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-view2.png"" width > 4000 height 2343 supersample 4 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_tRNA/70S_tRNA-session.cxs"" > includeMaps true ——— End of log from Mon Nov 30 11:09:35 2020 ——— opened ChimeraX session > rename #1-9 id #11 > rename #11 70S_APtRNA > rename #11 id #1 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/h1_j620_3d288_6A_sharpened_b50.mrc"" Opened h1_j620_3d288_6A_sharpened_b50.mrc as #2, grid size 288,288,288, pixel 1.16, shown at level 4.15, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_tRNA_c1_RSR-1-coot-4.pdb"" Chain information for 70S_tRNA_c1_RSR-1-coot-4.pdb #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available z | No description available > hide #!3 atoms > show #!3 cartoons > hide #!2 models > hide #!3 models > hide #!1 models > hide #!1.3 models > hide #!1.4 models > hide #!1.5 models > hide #!1.6 models > hide #!1.7 models > hide #!1.8 models > hide #!1.9 models > show #1.2 models > show #!3 models > mmaker #3/A to #1.2/A matrix Nucleic Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with 70S_tRNA_c1_RSR-1-coot-4.pdb, chain A (#3), sequence alignment score = 11577 RMSD between 2606 pruned atom pairs is 0.808 angstroms; (across all 2903 pairs: 3.806) > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #1.2 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_head.mrc"" Opened 70S_hybridtRNA_1_head.mrc as #4, grid size 288,288,288, pixel 1.16, shown at level 0.0507, step 2, values float32 > hide #!4 models > show #!4 models > select #3/a:929-1068,1107-1381 /s,n,c,j,m,g,i 15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected > volume zone #2 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #5, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!5 models > show #!5 models > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 step 1 > volume #2 level 3 > volume #2 level 4 > volume #2 level 2 > select #3/a:929-1068,1107-1381 /s,n,c,j,m,g,i 15838 atoms, 16994 bonds, 6 pseudobonds, 1296 residues, 2 models selected > volume zone #2 nearAtoms sel range 4 newMap true Opened h1_j620_3d288_6A_sharpened_b50.mrc zone as #6, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > hide #!5 models > close #5 > show #!4 models > hide #!4 models > show #!4 models > volume #4 step 1 > volume #4 level 2 > hide #!6 models > show #!6 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!6 models > show #!6 models > show #!4 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!4 models > close #6 > hide #!3 models > show #!3 models > ui mousemode right select > select clear > ui mousemode right translate > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_body.mrc"" Opened 70S_hybridtRNA_1_body.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 2.07, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_LSU.mrc"" Opened 70S_hybridtRNA_1_LSU.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 3.71, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_atrna.mrc"" Opened 70S_hybridtRNA_1_atrna.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 0.000495, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_ptrna.mrc"" Opened 70S_hybridtRNA_1_ptrna.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 0.000511, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_apra.mrc"" Opened 70S_hybridtRNA_1_apra.mrc as #9, grid size 288,288,288, pixel 1.16, shown at level 6.88e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_1/70S_hybridtRNA_1_mRNA.mrc"" Opened 70S_hybridtRNA_1_mRNA.mrc as #10, grid size 288,288,288, pixel 1.16, shown at level 0.000595, step 2, values float32 > select #5-10 12 models selected > volume sel step 1 > show #!4 models > volume #5 level 2 > volume #6 level 2 > volume #7 level 2 > hide #!3 models > volume #8 level 2 > volume #9 level 2.5 > volume #10 level 3 > ui mousemode right select > select clear > surface dust #6 size 5 > surface dust #7 size 5 > surface dust #7 size 7 > surface dust #8 size 7 > view 2 > rename #2-10 id #11 > rename #11 70S_hybridtRNA_1 > rename #11 #2 No name or id option specified for renaming > rename #11 id #2 > show #!2.2 models > hide #!2.2 models > show #1.2 models > hide #1.2 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"" Opened h2_j621_3d288_95A_sharpened.mrc as #3, grid size 288,288,288, pixel 1.16, shown at level 4.17, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb"" Summary of feedback from opening C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_tRNA_c2.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 1622 messages similar to the above omitted Ignored bad PDB record found on line 148850 END Chain information for 70S_tRNA_c2.pdb #4 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available y | No description available z | No description available > hide #!4 atoms > show #!4 cartoons > hide #!3 models > hide #!2.9 models > show #!3 models > hide #!2.8 models > hide #!2.7 models > hide #!2.6 models > hide #!2.5 models > hide #!2.4 models > hide #!2.3 models > hide #!4 models > show #!4 models > hide #!3 models > show #1.2 models > mmaker #4/A to #1.2/A matrix Nucleic Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with 70S_tRNA_c2.pdb, chain A (#4), sequence alignment score = 11577 RMSD between 2718 pruned atom pairs is 0.450 angstroms; (across all 2903 pairs: 3.635) > show #!2.2 models > hide #!2.2 models > show #!3 models > close #3 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/h2_j621_3d288_95A_sharpened.mrc"" Opened h2_j621_3d288_95A_sharpened.mrc as #3, grid size 288,288,288, pixel 1.16, shown at level 4.17, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"" Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.00115, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_body.mrc"" Opened 70S_hybridtRNA_2_body.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 2.1, step 2, values float32 > hide #!3 models > show #!3 models > hide #!4 models > show #!4 models > hide #1.2 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_LSU.mrc"" Opened 70S_hybridtRNA_2_LSU.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 3.69, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_atrna.mrc"" Opened 70S_hybridtRNA_2_atrna.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 0.00072, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_ptrna.mrc"" Opened 70S_hybridtRNA_2_ptrna.mrc as #9, grid size 288,288,288, pixel 1.16, shown at level 7.04e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_apra.mrc"" Opened 70S_hybridtRNA_2_apra.mrc as #10, grid size 288,288,288, pixel 1.16, shown at level 8.03e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_mRNA.mrc"" Opened 70S_hybridtRNA_2_mRNA.mrc as #11, grid size 288,288,288, pixel 1.16, shown at level 0.000295, step 2, values float32 > hide #!4 models > hide #!3 models > show #!4 models > hide #!4 models > show #!4 models > ui mousemode right translate > volume #3 step 1 > select #5-11 14 models selected > hide #!4 models > volume sel step 1 > show #!4 models > hide #!4 models > ui mousemode right select > select clear > ui mousemode right translate > show #!4 models > select #4/a-u 51962 atoms, 56095 bonds, 159 pseudobonds, 4030 residues, 2 models selected > ~select #4/a:929-1068,1107-1381 /s,n,c,j,m,g,i 36124 atoms, 39101 bonds, 153 pseudobonds, 2734 residues, 2 models selected > volume zone #3 nearAtoms sel range 4 newMap true Opened h2_j621_3d288_95A_sharpened.mrc zone as #12, grid size 288,288,288, pixel 1.16, shown at step 1, values float32 > show #!3 models > hide #!12 models > hide #!4 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > show #!4 models > volume #3 level 3 > show #!1.1 models > hide #!1.1 models > hide #!3 models > show #!3 models > hide #!3 models > ui mousemode right select > select clear > ui mousemode right translate > show #!5 models > hide #!4 models > show #!4 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > show #!12 models > close #12 > hide #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #5.1 models > show #!5 models > hide #!5 models > close #5 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"" Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.00115, step 2, values float32 > select #5 2 models selected > close #5 > hide #!11 models > show #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > close #6-11 > hide #!2.3 models > hide #!2.4 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_head.mrc"" Opened 70S_hybridtRNA_2_head.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.00115, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_body.mrc"" Opened 70S_hybridtRNA_2_body.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 2.1, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_LSU.mrc"" Opened 70S_hybridtRNA_2_LSU.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 3.69, step 2, values float32 > show #!4 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_atrna.mrc"" Opened 70S_hybridtRNA_2_atrna.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 0.00072, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_ptrna.mrc"" Opened 70S_hybridtRNA_2_ptrna.mrc as #9, grid size 288,288,288, pixel 1.16, shown at level 7.04e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_apra.mrc"" Opened 70S_hybridtRNA_2_apra.mrc as #10, grid size 288,288,288, pixel 1.16, shown at level 8.03e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/70S_hybridtRNA_2/70S_hybridtRNA_2_mRNA.mrc"" Opened 70S_hybridtRNA_2_mRNA.mrc as #11, grid size 288,288,288, pixel 1.16, shown at level 0.000295, step 2, values float32 > hide #!4 models > hide #!6 models > show #!6 models > volume #1.4 level 2 > volume #1.5 level 2 > hide #!7 models > show #!7 models > select #5 2 models selected > volume sel level 2 > select #6 2 models selected > volume sel level 2 > select #7 2 models selected > volume sel level 2 > select #8 2 models selected > volume sel level 2 > select #9 2 models selected > volume sel level 2 > select #10 2 models selected > volume sel level 2.5 > select #11 2 models selected > volume sel level 3 > surface dust #6 size 5 > surface dust #7 size 5 > surface dust #8 size 5 > surface dust #9 size 5 > rename #3-11 id #12 > rename #12 70S_hybridtRNA_2 > rename #12 id #3 > hide #!1 models > hide #!2 models > hide #!3 models > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session.cxs"" includeMaps > true ——— End of log from Mon Nov 30 17:55:28 2020 ——— opened ChimeraX session > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP- > Pi_job1086_3d512_31A_sharpened.mrc"" Opened pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc as #4, grid size 512,512,512, pixel 0.652, shown at level 4.33, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/Pre1_GDP- > Pi_RSR-4-coot-42.pdb"" Chain information for Pre1_GDP-Pi_RSR-4-coot-42.pdb #5 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #!4 models > hide #5 atoms > show #5 cartoons > mmaker #5/A to #1.2/A matrix Nucleic Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with Pre1_GDP- Pi_RSR-4-coot-42.pdb, chain A (#5), sequence alignment score = 11579.8 RMSD between 2721 pruned atom pairs is 0.483 angstroms; (across all 2903 pairs: 3.598) > show #1.2 models > hide #1.2 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_head.mrc"" Opened pre1_GDP-Pi_head.mrc as #6, grid size 512,512,512, pixel 0.652, shown at level 0.00136, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_body.mrc"" Opened pre1_GDP-Pi_body.mrc as #7, grid size 512,512,512, pixel 0.652, shown at level 1.55, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_LSU.mrc"" Opened pre1_GDP-Pi_LSU.mrc as #8, grid size 512,512,512, pixel 0.652, shown at level 3.48, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_atrna.mrc"" Opened pre1_GDP-Pi_atrna.mrc as #9, grid size 512,512,512, pixel 0.652, shown at level 0.00121, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_ptrna.mrc"" Opened pre1_GDP-Pi_ptrna.mrc as #10, grid size 512,512,512, pixel 0.652, shown at level 0.00111, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_EFG.mrc"" Opened pre1_GDP-Pi_EFG.mrc as #11, grid size 512,512,512, pixel 0.652, shown at level 0.0012, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_apra.mrc"" Opened pre1_GDP-Pi_apra.mrc as #12, grid size 512,512,512, pixel 0.652, shown at level 0.000806, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre1_GDP-Pi/pre1_GDP-Pi_mrna.mrc"" Opened pre1_GDP-Pi_mrna.mrc as #13, grid size 512,512,512, pixel 0.652, shown at level 0.000387, step 2, values float32 > volume #3.3 step 1 > hide #5 models > volume #3.4 step 1 > volume #3.5 step 1 > volume #3.6 step 1 > volume #3.7 step 1 > volume #3.8 step 1 > volume #3.9 step 1 > volume #4 step 1 > volume #6 step 1 > volume #7 step 1 > 2dlabels > volume #7 level 2.5 > hide #!6 models > show #!6 models > hide #!1 models > volume #6 level 2.5 > volume #8 step 1 > volume #8 level 2.5 > volume #9 step 1 > volume #9 level 2.5 > volume #10 step 1 > volume #10 level 2.5 > volume #11 step 1 > volume #11 level 2.52 > volume #11 level 2.5 > volume #12 step 1 > volume #12 level 2.5 > volume #13 step 1 > volume #13 level 3 > view 2 > rename #6-13 id #14 > rename #4 id #14.9 > rename #5 id #14.10 > rename #14 Pre1_GDP-Pi > rename #14 #4 No name or id option specified for renaming > rename #14 id #4 > hide #!4.8 models > hide #!4.7 models > hide #!4.6 models > hide #!4.5 models > hide #!4.4 models > hide #!4.3 models > hide #!4.2 models > hide #!4.1 models > hide #!4 models > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session-2.cxs"" > includeMaps true ——— End of log from Mon Nov 30 18:33:50 2020 ——— opened ChimeraX session > show #!4.1 models > show #!4.2 models > hide #!4.2 models > hide #!4.1 models > show #!4.1 models > show #!4.2 models > show #!4.3 models > show #!4.4 models > show #!4.5 models > show #!4.6 models > show #!4.7 models > show #!4.8 models > show #!4.9 models > hide #!4.9 models > hide #!4.8 models > hide #!4.7 models > hide #!4.6 models > hide #!4.5 models > hide #!4.4 models > hide #!4.3 models > hide #!4.2 models > hide #!4.1 models > hide #!4 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP- > Pi_job918_5A_sharpened_b100.mrc"" Opened pre2_GDP-Pi_job918_5A_sharpened_b100.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 3.62, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/Pre2_GDP- > Pi_RSR-0-coot-6.pdb"" Chain information for Pre2_GDP-Pi_RSR-0-coot-6.pdb #6 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #!6 atoms > show #!6 cartoons > volume #5 step 1 > volume #5 level 2.442 > hide #!6 models > show #!6 models > hide #!5 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_head.mrc"" Opened pre2_GDP-Pi_head.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 0.146, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_body.mrc"" Opened pre2_GDP-Pi_body.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 1.81, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_LSU.mrc"" Opened pre2_GDP-Pi_LSU.mrc as #9, grid size 288,288,288, pixel 1.16, shown at level 3.21, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_atrna.mrc"" Opened pre2_GDP-Pi_atrna.mrc as #10, grid size 288,288,288, pixel 1.16, shown at level 0.000352, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_ptrna.mrc"" Opened pre2_GDP-Pi_ptrna.mrc as #11, grid size 288,288,288, pixel 1.16, shown at level 5.82e-05, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_EFG.mrc"" Opened pre2_GDP-Pi_EFG.mrc as #12, grid size 288,288,288, pixel 1.16, shown at level 0.000251, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_apra.mrc"" Opened pre2_GDP-Pi_apra.mrc as #13, grid size 288,288,288, pixel 1.16, shown at level 0.00035, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP-Pi_mrna.mrc"" Opened pre2_GDP-Pi_mrna.mrc as #14, grid size 288,288,288, pixel 1.16, shown at level 0.000594, step 2, values float32 > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!6 models > show #!6 models > mmaker #6/A to #1.2/A matrix Nucleic Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with Pre2_GDP- Pi_RSR-0-coot-6.pdb, chain A (#6), sequence alignment score = 11579.8 RMSD between 2684 pruned atom pairs is 0.593 angstroms; (across all 2903 pairs: 3.693) > show #!9 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!9 models > hide #!8 models > show #!5 models > close #5 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/pre2_GDP-Pi/pre2_GDP- > Pi_job918_5A_sharpened_b100.mrc"" Opened pre2_GDP-Pi_job918_5A_sharpened_b100.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 3.62, step 2, values float32 > volume #5 step 1 > volume #5 level 2 > show #!7 models > hide #!7 models > hide #!5 models > show #!7 models Must specify one map, got 0 > show #!5 models > hide #!5 models > show #1.2 models > hide #1.2 models > show #!5 models > show #!8 models > hide #!5 models > hide #!6 models > volume #7 level 2 > volume #8 level 2 > show #!9 models > volume #9 level 2 > show #!10 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > volume #10 level 2 > volume #11 level 2 > volume #12 level 2 > volume #13 level 2 > volume #14 level 2 > volume #14 level 3 > volume #13 level 2.5 > volume #12 level 2.5 > volume #12 level 2 > view 2 > surface dust #7 size 5 > surface dust #8 size 5 > surface dust #9 size 5 > surface dust #10 size 5 > surface dust #11 size 5 > surface dust #12 size 5 > surface dust #12 size 3 > view 2 > rename #5-14 id #15 > rename #15 Pre2_GDP-Pi > rename #15 id #5 > hide #!1 models > hide #!5 models > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session-3.cxs"" > includeMaps true > volume #5.10 step 1 > volume #5.9 step 1 > volume #5.8 step 1 > volume #5.7 step 1 > volume #5.6 step 1 > volume #5.5 step 1 > volume #5.4 step 1 > volume #5.3 step 1 > show #!5 models > hide #!5 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc"" Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #6, grid size 512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb"" Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb #7 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #7 atoms > show #7 cartoons > volume #6 step 1 > hide #!6 models > mmaker #7/A to #1.2/A matrix Nucleic Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 70S_AP_v2.cif-coot-2.pdb, chain A (#1.2) with Chimeric_GDP-1-sw1-v2-RSR-0-coot-10.pdb, chain A (#7), sequence alignment score = 11574.9 RMSD between 2736 pruned atom pairs is 0.476 angstroms; (across all 2903 pairs: 3.121) > show #!6 models > close #6 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc"" Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #6, grid size 512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32 > volume #6 step 1 > volume #6 level 3 > hide #!6 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_head.mrc"" Opened chimeric_GDP1_head.mrc as #8, grid size 512,512,512, pixel 0.652, shown at level 0.000896, step 2, values float32 > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > hide #!1 models > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_body.mrc"" Opened chimeric_GDP1_body.mrc as #9, grid size 512,512,512, pixel 0.652, shown at level 1.58, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_LSU.mrc"" Opened chimeric_GDP1_LSU.mrc as #10, grid size 512,512,512, pixel 0.652, shown at level 3.46, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_atrna.mrc"" Opened chimeric_GDP1_atrna.mrc as #11, grid size 512,512,512, pixel 0.652, shown at level 0.00118, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_ptrna.mrc"" Opened chimeric_GDP1_ptrna.mrc as #12, grid size 512,512,512, pixel 0.652, shown at level 0.000534, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_EFG.mrc"" Opened chimeric_GDP1_EFG.mrc as #13, grid size 512,512,512, pixel 0.652, shown at level 0.000524, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_apra.mrc"" Opened chimeric_GDP1_apra.mrc as #14, grid size 512,512,512, pixel 0.652, shown at level 0.000586, step 2, values float32 > open ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/chimeric_GDP1/chimeric_GDP1_mrna.mrc"" Opened chimeric_GDP1_mrna.mrc as #15, grid size 512,512,512, pixel 0.652, shown at level 0.000791, step 2, values float32 > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > show #!6 models > hide #!6 models > hide #7#!8-15 target m > show #!1 models > hide #!1 models > show #!1.1 models > show #1.2 models > volume #1.1 level 3 > hide #!1 models > show #!2.1 models > show #!2.2 models > hide #!2 models > show #!4.9 models > show #4.10 models > volume #4.9 level 3 > show #!4.6 models > hide #!4.6 models > show #!4.6 models > hide #!4.6 models > hide #1.2 models > hide #!4 models > hide #!2.2 models > hide #!2.1 models > show #!2.1 models > hide #!1.1 models > show #!1.1 models > fitmap #2.1 inMap #1.1 Fit map h1_j620_3d288_6A_sharpened_b50.mrc in map 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 1019265 points correlation = 0.758, correlation about mean = 0.3486, overlap = 1.039e+07 steps = 148, shift = 0.333, angle = 2.26 degrees Position of h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) relative to 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates: Matrix rotation and translation 0.99938269 -0.01003340 -0.03366867 7.22159598 0.01062870 0.99978951 0.01754891 -4.68556235 0.03348551 -0.01789593 0.99927897 -2.24962642 Axis -0.45040638 -0.85334473 0.26255830 Axis point 73.03250787 0.00000000 215.22572937 Rotation angle (degrees) 2.25503531 Shift along axis 0.15508892 > show #!1.3 models > hide #!1.3 models > show #!2.3 models > hide #!2.3 models > hide #!1.1 models > show #!2.3 models > show #!2.4 models > show #!2.5 models > hide #!2.5 models > hide #!2.4 models > hide #!2.3 models > fitmap #2.3 inMap #2.1 Fit map 70S_hybridtRNA_1_head.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 106926 points correlation = 0.9999, correlation about mean = 0.9992, overlap = 1.181e+06 steps = 68, shift = 2.22, angle = 2.32 degrees Position of 70S_hybridtRNA_1_head.mrc (#2.3) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99999913 0.00018464 -0.00130857 0.30474276 -0.00018435 0.99999996 0.00022176 -0.01583817 0.00130861 -0.00022152 0.99999912 -0.19904439 Axis -0.16540569 -0.97656743 -0.13768446 Axis point 153.05191918 0.00000000 231.82731819 Rotation angle (degrees) 0.07677596 Shift along axis -0.00753383 > fitmap #2.4 inMap #2.1 Fit map 70S_hybridtRNA_1_body.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 248174 points correlation = 1, correlation about mean = 0.9999, overlap = 3.058e+06 steps = 60, shift = 1.36, angle = 2.26 degrees Position of 70S_hybridtRNA_1_body.mrc (#2.4) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99999999 0.00000073 -0.00015435 0.02008714 -0.00000074 1.00000000 -0.00004725 0.00026928 0.00015435 0.00004725 0.99999999 -0.00563801 Axis 0.29271365 -0.95618922 -0.00457120 Axis point 36.37090414 0.00000000 119.42835544 Rotation angle (degrees) 0.00924864 Shift along axis 0.00564807 > fitmap #2.5 inMap #2.1 Fit map 70S_hybridtRNA_1_LSU.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 645850 points correlation = 1, correlation about mean = 1, overlap = 8.787e+06 steps = 76, shift = 0.496, angle = 2.26 degrees Position of 70S_hybridtRNA_1_LSU.mrc (#2.5) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 1.00000000 0.00005443 -0.00000811 -0.01818076 -0.00005443 1.00000000 0.00005243 -0.00879512 0.00000811 -0.00005243 1.00000000 0.01425598 Axis -0.68980002 -0.10667675 -0.71609776 Axis point -155.19121641 292.56515973 0.00000000 Rotation angle (degrees) 0.00435502 Shift along axis 0.00327064 > fitmap #2.6 inMap #2.1 Fit map 70S_hybridtRNA_1_atrna.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 10321 points correlation = 0.9991, correlation about mean = 0.9847, overlap = 9.656e+04 steps = 56, shift = 1.56, angle = 2.48 degrees Position of 70S_hybridtRNA_1_atrna.mrc (#2.6) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99996704 0.00359830 -0.00727780 0.85823304 -0.00363736 0.99997901 -0.00536105 1.74125940 0.00725836 0.00538734 0.99995915 -2.07663962 Axis 0.55197485 -0.74649232 -0.37158174 Axis point 289.57156341 0.00000000 120.74485176 Rotation angle (degrees) 0.55785807 Shift along axis -0.05447235 > fitmap #2.7 inMap #2.1 Fit map 70S_hybridtRNA_1_ptrna.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 10586 points correlation = 0.9999, correlation about mean = 0.9979, overlap = 1.079e+05 steps = 56, shift = 2.08, angle = 2.37 degrees Position of 70S_hybridtRNA_1_ptrna.mrc (#2.7) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99999717 -0.00071957 -0.00226942 0.50780974 0.00071931 0.99999973 -0.00011793 -0.09132956 0.00226950 0.00011630 0.99999742 -0.37367633 Axis 0.04913293 -0.95209666 0.30182428 Axis point 164.78877149 0.00000000 223.57562255 Rotation angle (degrees) 0.13657275 Shift along axis -0.00087984 > fitmap #2.8 inMap #2.1 Fit map 70S_hybridtRNA_1_apra.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 320 points correlation = 0.9959, correlation about mean = 0.9289, overlap = 4629 steps = 52, shift = 0.689, angle = 3 degrees Position of 70S_hybridtRNA_1_apra.mrc (#2.8) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99988320 0.01104181 -0.01056739 0.46136207 -0.01093254 0.99988675 0.01034247 0.18375324 0.01068040 -0.01022573 0.99989068 -0.36745969 Axis -0.55826931 -0.57671487 -0.59643553 Axis point 9.54818132 -34.38282742 0.00000000 Rotation angle (degrees) 1.05552809 Shift along axis -0.14437150 > fitmap #2.9 inMap #2.1 Fit map 70S_hybridtRNA_1_mRNA.mrc in map h1_j620_3d288_6A_sharpened_b50.mrc using 1152 points correlation = 0.9989, correlation about mean = 0.9566, overlap = 1.747e+04 steps = 72, shift = 0.57, angle = 2.85 degrees Position of 70S_hybridtRNA_1_mRNA.mrc (#2.9) relative to h1_j620_3d288_6A_sharpened_b50.mrc (#2.1) coordinates: Matrix rotation and translation 0.99979104 -0.01343703 0.01540542 -1.00891360 0.01309125 0.99966492 0.02233096 -6.14975350 -0.01570032 -0.02212461 0.99963193 5.22998756 Axis -0.73607439 0.51503427 0.43924275 Axis point 0.00000000 234.32729021 275.96776812 Rotation angle (degrees) 1.73046623 Shift along axis -0.12746420 > show #!2.7 models > hide #!2.7 models > show #!2.5 models > hide #!2.5 models > hide #!2.1 models > show #!2.1 models > hide #!2 models > show #!2 models > hide #!2.1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!3.1 models > hide #!3.3 models > hide #!3.4 models > hide #!3.5 models > hide #!3.6 models > hide #!3.7 models > hide #!3.8 models > hide #!3.9 models > show #!1.1 models > fitmap #3.1 inMap #1.1 Fit map h2_j621_3d288_95A_sharpened.mrc in map 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 586949 points correlation = 0.7334, correlation about mean = 0.1805, overlap = 7.27e+06 steps = 136, shift = 0.202, angle = 2.83 degrees Position of h2_j621_3d288_95A_sharpened.mrc (#3.1) relative to 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates: Matrix rotation and translation 0.99916948 -0.01437521 -0.03812740 8.91883158 0.01542745 0.99950415 0.02744894 -7.15808810 0.03771391 -0.02801435 0.99889582 -1.25644332 Axis -0.56267235 -0.76940650 0.30234660 Axis point 41.06042297 0.00000000 234.63921817 Rotation angle (degrees) 2.82500121 Shift along axis 0.10921816 > show #!3.2 models > hide #!3.1 models > hide #!3 models > hide #!1.1 models > show #1.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > hide #1.2 models > show #!3.1 models > hide #!3 models > show #!3 models > fitmap #3.3 inMap #3.1 Fit map 70S_hybridtRNA_2_head.mrc in map h2_j621_3d288_95A_sharpened.mrc using 110214 points correlation = 1, correlation about mean = 0.9997, overlap = 1.309e+06 steps = 72, shift = 2.45, angle = 2.87 degrees Position of 70S_hybridtRNA_2_head.mrc (#3.3) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.99999961 0.00020314 -0.00085583 0.19817180 -0.00020293 0.99999995 0.00024396 -0.02384413 0.00085588 -0.00024379 0.99999960 -0.12304039 Axis -0.26717286 -0.93762481 -0.22243737 Axis point 144.70241929 0.00000000 230.48398110 Rotation angle (degrees) 0.05229911 Shift along axis -0.00322050 > fitmap #3.4 inMap #3.1 Fit map 70S_hybridtRNA_2_body.mrc in map h2_j621_3d288_95A_sharpened.mrc using 251585 points correlation = 1, correlation about mean = 0.9999, overlap = 3.15e+06 steps = 64, shift = 2.07, angle = 2.81 degrees Position of 70S_hybridtRNA_2_body.mrc (#3.4) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.99999999 -0.00001982 0.00011005 -0.00098565 0.00001984 0.99999998 -0.00017740 0.03316350 -0.00011005 0.00017740 0.99999998 0.01688522 Axis 0.84596406 0.52478712 0.09456899 Axis point 0.00000000 -85.48083137 133.20998322 Rotation angle (degrees) 0.01201495 Shift along axis 0.01816677 > fitmap #3.5 inMap #3.1 Fit map 70S_hybridtRNA_2_LSU.mrc in map h2_j621_3d288_95A_sharpened.mrc using 650695 points correlation = 1, correlation about mean = 1, overlap = 8.779e+06 steps = 84, shift = 0.298, angle = 2.83 degrees Position of 70S_hybridtRNA_2_LSU.mrc (#3.5) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 1.00000000 0.00003479 0.00002320 -0.01444674 -0.00003479 1.00000000 0.00005333 -0.01032144 -0.00002319 -0.00005333 1.00000000 0.01078704 Axis -0.78699220 0.34226528 -0.51332033 Axis point 0.00000000 224.38621378 208.29890200 Rotation angle (degrees) 0.00388278 Shift along axis 0.00229959 > fitmap #3.6 inMap #3.1 Fit map 70S_hybridtRNA_2_atrna.mrc in map h2_j621_3d288_95A_sharpened.mrc using 10628 points correlation = 0.9997, correlation about mean = 0.9961, overlap = 1.157e+05 steps = 56, shift = 1.74, angle = 2.95 degrees Position of 70S_hybridtRNA_2_atrna.mrc (#3.6) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.99998258 0.00297566 -0.00509681 0.52466684 -0.00298680 0.99999316 -0.00218073 0.98182149 0.00509028 0.00219592 0.99998463 -1.23126425 Axis 0.34765674 -0.80920582 -0.47362511 Axis point 244.89166359 0.00000000 104.07713390 Rotation angle (degrees) 0.36065047 Shift along axis -0.02893404 > fitmap #3.7 inMap #3.1 Fit map 70S_hybridtRNA_2_ptrna.mrc in map h2_j621_3d288_95A_sharpened.mrc using 11809 points correlation = 0.9997, correlation about mean = 0.9961, overlap = 1.338e+05 steps = 56, shift = 2.34, angle = 2.75 degrees Position of 70S_hybridtRNA_2_ptrna.mrc (#3.7) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.99999179 -0.00346764 0.00209878 -0.02675129 0.00347092 0.99999276 -0.00156038 -0.15370001 -0.00209336 0.00156766 0.99999658 0.03950185 Axis 0.35999174 0.48245407 0.79852615 Axis point 37.01596015 -2.37894752 0.00000000 Rotation angle (degrees) 0.24892805 Shift along axis -0.05224018 > fitmap #3.8 inMap #3.1 Fit map 70S_hybridtRNA_2_apra.mrc in map h2_j621_3d288_95A_sharpened.mrc using 325 points correlation = 0.9705, correlation about mean = 0.5188, overlap = 3853 steps = 56, shift = 2.17, angle = 15.3 degrees Position of 70S_hybridtRNA_2_apra.mrc (#3.8) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.95381646 0.17724187 0.24252727 -59.19928960 -0.16152211 0.98333887 -0.08339834 43.03541118 -0.25326816 0.04037319 0.96655328 40.46604137 Axis 0.20187770 0.80866769 -0.55254136 Axis point 125.40431157 0.00000000 268.38244402 Rotation angle (degrees) 17.85148710 Shift along axis 0.49116838 > fitmap #3.9 inMap #3.1 Fit map 70S_hybridtRNA_2_mRNA.mrc in map h2_j621_3d288_95A_sharpened.mrc using 1190 points correlation = 0.9991, correlation about mean = 0.9754, overlap = 1.781e+04 steps = 72, shift = 0.734, angle = 3 degrees Position of 70S_hybridtRNA_2_mRNA.mrc (#3.9) relative to h2_j621_3d288_95A_sharpened.mrc (#3.1) coordinates: Matrix rotation and translation 0.99994023 -0.00597422 0.00915666 -0.72792573 0.00587457 0.99992364 0.01087173 -2.82053734 -0.00922091 -0.01081729 0.99989898 2.95444519 Axis -0.70422514 0.59670496 0.38472086 Axis point 0.00000000 271.90008851 259.49403869 Rotation angle (degrees) 0.88234435 Shift along axis -0.03376831 > show #!3.4 models > hide #!3.4 models > show #!3.3 models > hide #!3.3 models > show #!3.4 models > hide #!3.4 models > show #!3.5 models > hide #!3.5 models > show #!3.6 models > hide #!3.6 models > show #!1.1 models > hide #!1.1 models > show #1.2 models > hide #!3.1 models > show #!3.2 models > hide #!3.2 models > hide #!3 models > hide #4.10 models > show #4.10 models > hide #4.10 models > hide #!4.9 models > show #!4.9 models > hide #!4.9 models > show #4.10 models > hide #4.10 models > show #!4.9 models > fitmap #4.9 inMap #1.1 Fit map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc in map 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 2630225 points correlation = 0.8573, correlation about mean = 0.5417, overlap = 5.626e+07 steps = 156, shift = 0.796, angle = 2.99 degrees Position of pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc (#4.9) relative to 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates: Matrix rotation and translation 0.99919851 -0.00239100 -0.03995767 7.07517244 0.00372795 0.99943450 0.03341822 -6.28809111 0.03985517 -0.03354040 0.99864238 -0.16494756 Axis -0.64161263 -0.76478454 0.05863309 Axis point 10.68733214 0.00000000 181.02472824 Rotation angle (degrees) 2.99104905 Shift along axis 0.25984353 > show #!1.1 models > hide #!1.1 models > hide #1.2 models > fitmap #4.1 inMap #4.9 Fit map pre1_GDP-Pi_head.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 347242 points correlation = 1, correlation about mean = 0.9997, overlap = 5.734e+06 steps = 68, shift = 3.81, angle = 3.02 degrees Position of pre1_GDP-Pi_head.mrc (#4.1) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99999988 0.00009386 -0.00049056 0.11232562 -0.00009376 0.99999997 0.00020958 -0.03518945 0.00049058 -0.00020953 0.99999986 -0.05502258 Axis -0.38688943 -0.90571423 -0.17320021 Axis point 112.94959002 0.00000000 227.32288231 Rotation angle (degrees) 0.03103376 Shift along axis -0.00205609 > fitmap #4.2 inMap #4.9 Fit map pre1_GDP-Pi_body.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 813215 points correlation = 1, correlation about mean = 1, overlap = 1.676e+07 steps = 96, shift = 1.89, angle = 2.99 degrees Position of pre1_GDP-Pi_body.mrc (#4.2) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 1.00000000 0.00001201 0.00005463 -0.00655600 -0.00001201 1.00000000 0.00005452 -0.00597151 -0.00005463 -0.00005452 1.00000000 0.01524047 Axis -0.69798069 0.69942157 -0.15372840 Axis point 273.49811090 0.00000000 144.84438871 Rotation angle (degrees) 0.00447527 Shift along axis -0.00194353 > fitmap #4.3 inMap #4.9 Fit map pre1_GDP-Pi_LSU.mrc in map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc using 2109177 points correlation = 1, correlation about mean = 1, overlap = 5.063e+07 steps = 84, shift = 0.466, angle = 2.99 degrees Position of pre1_GDP-Pi_LSU.mrc (#4.3) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 1.00000000 0.00002399 0.00001315 -0.00611672 -0.00002399 1.00000000 0.00000004 0.00601174 -0.00001315 -0.00000004 1.00000000 -0.00165998 Axis -0.00140942 0.48065645 -0.87690786 Axis point 163.35017024 254.70397239 0.00000000 Rotation angle (degrees) 0.00156755 Shift along axis 0.00435385 > fitmap #4.4 inMap #4.9 Fit map pre1_GDP-Pi_atrna.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 31295 points correlation = 0.9987, correlation about mean = 0.9861, overlap = 4.67e+05 steps = 72, shift = 2.49, angle = 2.92 degrees Position of pre1_GDP-Pi_atrna.mrc (#4.4) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99999613 0.00242962 -0.00135281 -0.06193794 -0.00243446 0.99999062 -0.00358249 1.14611174 0.00134409 0.00358577 0.99999267 -0.75288229 Axis 0.79007845 -0.29725038 -0.53611403 Axis point 0.00000000 208.52431006 320.53712370 Rotation angle (degrees) 0.25991875 Shift along axis 0.01401278 > fitmap #4.5 inMap #4.9 Fit map pre1_GDP-Pi_ptrna.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 37262 points correlation = 0.9998, correlation about mean = 0.9983, overlap = 6.319e+05 steps = 80, shift = 2.58, angle = 3.03 degrees Position of pre1_GDP-Pi_ptrna.mrc (#4.5) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99999976 -0.00047111 -0.00050364 0.13930594 0.00047128 0.99999983 0.00035362 -0.16354536 0.00050347 -0.00035386 0.99999981 -0.01943440 Axis -0.45639766 -0.64969767 0.60794252 Axis point 75.97965458 -0.00000000 304.52766118 Rotation angle (degrees) 0.04440799 Shift along axis 0.03086114 > fitmap #4.6 inMap #4.9 Fit map pre1_GDP-Pi_EFG.mrc in map pre1_GDP-Pi_job1086_3d512_31A_sharpened.mrc using 72149 points correlation = 0.9999, correlation about mean = 0.9991, overlap = 9.429e+05 steps = 92, shift = 4.77, angle = 3 degrees Position of pre1_GDP-Pi_EFG.mrc (#4.6) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99999991 0.00004762 -0.00042343 0.04112513 -0.00004771 0.99999997 -0.00022630 0.06814932 0.00042342 0.00022632 0.99999988 -0.11199685 Axis 0.46906646 -0.87762003 -0.09879141 Axis point 271.41553503 0.00000000 129.69563440 Rotation angle (degrees) 0.02764323 Shift along axis -0.02945447 > fitmap #4.7 inMap #4.9 Fit map pre1_GDP-Pi_apra.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 1530 points correlation = 0.996, correlation about mean = 0.972, overlap = 3.929e+04 steps = 56, shift = 1.56, angle = 1.61 degrees Position of pre1_GDP-Pi_apra.mrc (#4.7) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99964109 0.00848759 0.02540955 -5.64171230 -0.00823457 0.99991563 -0.01004566 3.20970290 -0.02549267 0.00983281 0.99962665 2.66465996 Axis 0.34784583 0.89071874 -0.29261479 Axis point 102.57055802 0.00000000 225.07857793 Rotation angle (degrees) 1.63737420 Shift along axis 0.11677752 > fitmap #4.8 inMap #4.9 Fit map pre1_GDP-Pi_mrna.mrc in map pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc using 5665 points correlation = 0.9982, correlation about mean = 0.9826, overlap = 1.481e+05 steps = 76, shift = 1.65, angle = 3.47 degrees Position of pre1_GDP-Pi_mrna.mrc (#4.8) relative to pre1_GDP- Pi_job1086_3d512_31A_sharpened.mrc (#4.9) coordinates: Matrix rotation and translation 0.99997555 -0.00275719 -0.00642686 1.70478645 0.00278904 0.99998385 0.00495222 -1.37214422 0.00641310 -0.00497002 0.99996708 -0.27159665 Axis -0.57860172 -0.74874473 0.32342138 Axis point 41.32673193 0.00000000 260.88493337 Rotation angle (degrees) 0.49127847 Shift along axis -0.04684678 > show #!4.8 models > hide #!4.8 models > show #!4.1 models > hide #!4.1 models > show #!4.2 models > hide #!4.2 models > hide #!4 models > show #!1.1 models > hide #!5.3 models > hide #!5.4 models > hide #!5.5 models > hide #!5.6 models > hide #!5.7 models > hide #!5.8 models > hide #!5.10 models > hide #!5.9 models > show #!5.1 models > fitmap #5.1 inMap #1.1 Fit map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc in map 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 889296 points correlation = 0.7608, correlation about mean = 0.356, overlap = 8.617e+06 steps = 200, shift = 0.719, angle = 2.62 degrees Position of pre2_GDP-Pi_job918_5A_sharpened_b100.mrc (#5.1) relative to 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates: Matrix rotation and translation 0.99927516 0.00172680 -0.03802852 6.04543288 -0.00075966 0.99967627 0.02543193 -4.22182369 0.03806012 -0.02538461 0.99895298 -1.35811292 Axis -0.55518187 -0.83128524 -0.02716510 Axis point 39.97630304 0.00000000 160.98461928 Rotation angle (degrees) 2.62309569 Shift along axis 0.19011823 > fitmap #5.3 inMap #5.1 Fit map pre2_GDP-Pi_head.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 93826 points correlation = 1, correlation about mean = 0.9994, overlap = 9.106e+05 steps = 72, shift = 3.55, angle = 2.7 degrees Position of pre2_GDP-Pi_head.mrc (#5.3) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99999892 0.00051730 -0.00137436 0.28373044 -0.00051681 0.99999980 0.00035954 -0.02658987 0.00137455 -0.00035883 0.99999899 -0.17584155 Axis -0.23759161 -0.90916149 -0.34201698 Axis point 123.87461941 0.00000000 209.27025801 Rotation angle (degrees) 0.08661878 Shift along axis 0.01690331 > fitmap #5.4 inMap #5.1 Fit map pre2_GDP-Pi_body.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 212965 points correlation = 1, correlation about mean = 0.9999, overlap = 2.233e+06 steps = 64, shift = 1.32, angle = 2.63 degrees Position of pre2_GDP-Pi_body.mrc (#5.4) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 1.00000000 0.00008537 0.00001950 -0.02014495 -0.00008537 0.99999998 0.00015206 -0.01976849 -0.00001949 -0.00015206 0.99999999 0.03978210 Axis -0.86657156 0.11110461 -0.48652800 Axis point -0.00000000 248.50989590 127.03866056 Rotation angle (degrees) 0.01005385 Shift along axis -0.00409443 > fitmap #5.5 inMap #5.1 Fit map pre2_GDP-Pi_LSU.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 555366 points correlation = 1, correlation about mean = 1, overlap = 6.164e+06 steps = 80, shift = 0.586, angle = 2.62 degrees Position of pre2_GDP-Pi_LSU.mrc (#5.5) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 1.00000000 0.00004679 0.00000773 -0.01437486 -0.00004679 1.00000000 -0.00004642 0.01041546 -0.00000773 0.00004642 1.00000000 -0.00730890 Axis 0.69947950 0.11647881 -0.70509653 Axis point 231.76331831 252.08005120 0.00000000 Rotation angle (degrees) 0.00380226 Shift along axis -0.00368827 > fitmap #5.6 inMap #5.1 Fit map pre2_GDP-Pi_atrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 7392 points correlation = 0.9985, correlation about mean = 0.9643, overlap = 5.814e+04 steps = 48, shift = 2.2, angle = 2.71 degrees Position of pre2_GDP-Pi_atrna.mrc (#5.6) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99997110 0.00435468 -0.00623160 0.60271668 -0.00441370 0.99994524 -0.00948900 2.69778464 0.00618994 0.00951623 0.99993556 -2.39843357 Axis 0.78086075 -0.51035936 -0.36026352 Axis point 0.00000000 255.53107136 280.56572185 Rotation angle (degrees) 0.69727299 Shift along axis -0.04213372 > fitmap #5.7 inMap #5.1 Fit map pre2_GDP-Pi_ptrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 9819 points correlation = 0.9998, correlation about mean = 0.9967, overlap = 8.684e+04 steps = 56, shift = 2.43, angle = 2.7 degrees Position of pre2_GDP-Pi_ptrna.mrc (#5.7) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99999663 -0.00189626 -0.00177369 0.58902917 0.00189572 0.99999816 -0.00030632 -0.24437857 0.00177427 0.00030296 0.99999838 -0.32193593 Axis 0.11652836 -0.67856763 0.72523590 Axis point 128.85957840 310.33743994 0.00000000 Rotation angle (degrees) 0.14978881 Shift along axis 0.00098650 > fitmap #5.8 inMap #5.1 Fit map pre2_GDP-Pi_EFG.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 13847 points correlation = 0.9999, correlation about mean = 0.9966, overlap = 9.133e+04 steps = 60, shift = 4.14, angle = 2.72 degrees Position of pre2_GDP-Pi_EFG.mrc (#5.8) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99999603 0.00166220 -0.00227738 0.12036839 -0.00166318 0.99999852 -0.00043071 0.46680606 0.00227667 0.00043450 0.99999731 -0.53839913 Axis 0.15165996 -0.79826752 -0.58289641 Axis point 246.93295335 0.00000000 55.12319995 Rotation angle (degrees) 0.16343406 Shift along axis -0.04055012 > fitmap #5.9 inMap #5.1 Fit map pre2_GDP-Pi_apra.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 233 points correlation = 0.9958, correlation about mean = 0.8491, overlap = 2534 steps = 44, shift = 1.14, angle = 3.24 degrees Position of pre2_GDP-Pi_apra.mrc (#5.9) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99635246 -0.01906506 0.08317637 -12.11764764 0.01877923 0.99981476 0.00421751 -3.33803710 -0.08324137 -0.00264013 0.99652592 13.33580403 Axis -0.04014914 0.97431866 0.22156535 Axis point 153.34643675 0.00000000 152.31969587 Rotation angle (degrees) 4.89914817 Shift along axis 0.18895328 > fitmap #5.10 inMap #5.1 Fit map pre2_GDP-Pi_mrna.mrc in map pre2_GDP-Pi_job918_5A_sharpened_b100.mrc using 860 points correlation = 0.9988, correlation about mean = 0.9342, overlap = 1.143e+04 steps = 52, shift = 1.57, angle = 3.42 degrees Position of pre2_GDP-Pi_mrna.mrc (#5.10) relative to pre2_GDP- Pi_job918_5A_sharpened_b100.mrc (#5.1) coordinates: Matrix rotation and translation 0.99978500 -0.02018208 0.00475772 1.88844381 0.02007967 0.99958468 0.02067083 -6.68983380 -0.00517292 -0.02057085 0.99977502 3.54784779 Axis -0.70516611 0.16979791 0.68841080 Axis point 0.00000000 169.73864150 326.83981200 Rotation angle (degrees) 1.67571236 Shift along axis -0.02520962 > show #!5.3 models > show #!5.4 models > show #!5.5 models > hide #!5.5 models > hide #!5.4 models > hide #!5.3 models > hide #!5.1 models > hide #!5 models > fitmap #6 inMap #1.1 Fit map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc in map 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc using 2582330 points correlation = 0.8915, correlation about mean = 0.5999, overlap = 5.811e+07 steps = 180, shift = 0.747, angle = 4.9 degrees Position of chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) relative to 70S_APtRNA_job536_3d512_235A_sharpened_a.mrc (#1.1) coordinates: Matrix rotation and translation 0.99673555 0.04201445 -0.06894226 4.97827100 -0.04008241 0.99877042 0.02917258 1.73392276 0.07008316 -0.02631397 0.99719403 -6.37784818 Axis -0.32500711 -0.81432804 -0.48087443 Axis point 93.47108066 0.00000000 67.95774460 Rotation angle (degrees) 4.89684458 Shift along axis 0.03698874 > show #!6 models > hide #!1.1 models > show #7 models > hide #!6 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > fitmap #8 inMap #6 Fit map chimeric_GDP1_head.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 153790 points correlation = 0.9999, correlation about mean = 0.9998, overlap = 8.809e+05 steps = 100, shift = 8.22, angle = 4.93 degrees Position of chimeric_GDP1_head.mrc (#8) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 0.99999982 0.00002670 -0.00059450 0.14477295 -0.00002658 0.99999998 0.00021029 -0.04663208 0.00059450 -0.00021027 0.99999980 -0.07365861 Axis -0.33316354 -0.94192378 -0.04220958 Axis point 124.06592046 0.00000000 242.81214249 Rotation angle (degrees) 0.03616253 Shift along axis -0.00120011 > fitmap #9 inMap #6 Fit map chimeric_GDP1_body.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 167699 points correlation = 1, correlation about mean = 1, overlap = 2.052e+06 steps = 100, shift = 0.9, angle = 4.89 degrees Position of chimeric_GDP1_body.mrc (#9) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 1.00000000 -0.00002372 0.00005887 -0.00551886 0.00002372 1.00000000 0.00005608 -0.01289350 -0.00005887 -0.00005608 1.00000000 0.02325899 Axis -0.66214550 0.69508141 0.28004495 Axis point 389.33106877 0.00000000 80.19525840 Rotation angle (degrees) 0.00485286 Shift along axis 0.00120582 > fitmap #10 inMap #6 Fit map chimeric_GDP1_LSU.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 167597 points correlation = 1, correlation about mean = 1, overlap = 5.139e+06 steps = 120, shift = 2.22, angle = 4.9 degrees Position of chimeric_GDP1_LSU.mrc (#10) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 1.00000000 0.00005749 0.00002314 -0.01671964 -0.00005749 1.00000000 -0.00005001 0.01924092 -0.00002314 0.00005001 1.00000000 -0.00364929 Axis 0.62799409 0.29061433 -0.72191878 Axis point 346.16272008 265.99659198 0.00000000 Rotation angle (degrees) 0.00456280 Shift along axis -0.00227366 > fitmap #11 inMap #6 Fit map chimeric_GDP1_atrna.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 16417 points correlation = 0.9981, correlation about mean = 0.9951, overlap = 6.038e+04 steps = 80, shift = 3.41, angle = 4.95 degrees Position of chimeric_GDP1_atrna.mrc (#11) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 0.99999756 0.00004752 -0.00220774 0.46424097 -0.00005368 0.99999610 -0.00279156 0.59428195 0.00220760 0.00279168 0.99999367 -0.81073365 Axis 0.78429009 -0.62023136 -0.01421658 Axis point 0.00000000 290.86084881 214.04141267 Rotation angle (degrees) 0.20394035 Shift along axis 0.00703315 > fitmap #12 inMap #6 Fit map chimeric_GDP1_ptrna.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 17350 points correlation = 0.9991, correlation about mean = 0.9978, overlap = 9.266e+04 steps = 96, shift = 4.32, angle = 4.88 degrees Position of chimeric_GDP1_ptrna.mrc (#12) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 0.99999912 -0.00131485 -0.00018403 0.19658134 0.00131495 0.99999901 0.00050208 -0.32974506 0.00018337 -0.00050232 0.99999986 0.08526727 Axis -0.35379255 -0.12941147 0.92632797 Axis point 245.76146418 163.36447906 0.00000000 Rotation angle (degrees) 0.08133006 Shift along axis 0.05210924 > fitmap #13 inMap #6 Fit map chimeric_GDP1_EFG.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 50191 points correlation = 1, correlation about mean = 0.9999, overlap = 1.808e+05 steps = 96, shift = 5.46, angle = 4.89 degrees Position of chimeric_GDP1_EFG.mrc (#13) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 1.00000000 -0.00007450 -0.00000784 0.00431330 0.00007449 0.99999996 -0.00028369 0.04169017 0.00000786 0.00028369 0.99999996 -0.03220365 Axis 0.96686348 -0.02675683 0.25388794 Axis point 0.00000000 108.95423277 146.45648771 Rotation angle (degrees) 0.01681138 Shift along axis -0.00512124 > fitmap #14 inMap #6 Fit map chimeric_GDP1_apra.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 555 points correlation = 0.9897, correlation about mean = 0.978, overlap = 4553 steps = 64, shift = 3.09, angle = 5.26 degrees Position of chimeric_GDP1_apra.mrc (#14) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 0.99972466 0.02147684 0.00945209 -4.39025179 -0.02149551 0.99976718 0.00187810 3.23895043 -0.00940956 -0.00208076 0.99995356 1.67873632 Axis -0.08405903 0.40049152 -0.91243664 Axis point 145.94628769 205.76268949 -0.00000000 Rotation angle (degrees) 1.34933314 Shift along axis 0.13447195 > fitmap #15 inMap #6 Fit map chimeric_GDP1_mrna.mrc in map chimeric_GDP1_job1099_3d512_31A_sharpened.mrc using 2808 points correlation = 0.9945, correlation about mean = 0.9862, overlap = 1.156e+04 steps = 100, shift = 4.32, angle = 5.06 degrees Position of chimeric_GDP1_mrna.mrc (#15) relative to chimeric_GDP1_job1099_3d512_31A_sharpened.mrc (#6) coordinates: Matrix rotation and translation 0.99998260 0.00573335 0.00138856 -0.94639803 -0.00573756 0.99997890 0.00304728 0.24427763 -0.00137106 -0.00305519 0.99999439 0.73376284 Axis -0.45942034 0.20775636 -0.86357990 Axis point 47.28720648 177.08135346 0.00000000 Rotation angle (degrees) 0.38053196 Shift along axis -0.14811811 > show #!6 models > hide #7 models > show #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > volume #8 step 1 > volume #9 step 1 > volume #10 step 1 > volume #11 step 1 > volume #12 step 1 > volume #13 step 1 > volume #14 step 1 > volume #15 step 1 > hide #!9 models > hide #!6 models > show #!9 models > show #!15 models > show #!14 models > show #!13 models > show #!12 models > show #!11 models > show #!10 models > show #!8 models > hide #!8 models > show #!8 models > volume #8 level 2 > volume #8 level 2.5 > volume #9 level 2.5 > volume #10 level 2.5 > volume #11 level 2 > volume #12 level 2 > volume #13 level 2.5 > volume #14 level 2.5 > volume #15 level 3 > surface dust #8 size 5 > surface dust #9 size 5 > surface dust #10 size 5 > surface dust #11 size 5 > surface dust #12 size 5 > surface dust #13 size 5 > surface dust #13 size 5view 2 Invalid ""size"" argument: Expected a number > view 2 > rename #6-15 id #16 > rename #16 Chimeric_GDP1 > rename #16 id #6 > save ""C:/Users/anasc/Documents/IMPRS - Göttingen/Rotation 2 > -Stark/temporary/Figures_paper_20201130/all_states-session-4.cxs"" > includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 280, in write self.fileobj.write(self.compress.compress(data)) MemoryError During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 325, in close fileobj.write(self.compress.flush()) ValueError: I/O operation on closed file. The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> ValueError: error processing: 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 280, in write self.fileobj.write(self.compress.compress(data)) MemoryError During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\gzip.py"", line 325, in close fileobj.write(self.compress.flush()) ValueError: I/O operation on closed file. The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\ui\gui.py"", line 1601, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 102, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 78, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> ValueError: error processing: 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> : Error while saving session data for 'named views' -> -> -> 'surface' -> '70S_APtRNA_job536_3d512_235A_sharpened_a.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011201839\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 442.94 OpenGL renderer: GeForce MX250/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK COMPUTER INC. Model: ZenBook UX463FL_UX463FL OS: Microsoft Windows 10 Home (Build 19041) Memory: 8,356,536,320 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz OSLanguage: en-GB Locale: ('en_DE', 'cp1252') PyQt version: 5.15.1 Compiled Qt version: 5.15.1 Runtime Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.11.8 cftime: 1.3.0 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.9.4 ChimeraX-AtomicLibrary: 1.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202011201839 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 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: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.1 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.2.2 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.3.1 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 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: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.0 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.5.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.2.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.1 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.4 pywin32: 228 pyzmq: 20.0.0 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.0 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.35.1 WMI: 1.5.1 }}} " defect closed normal Sessions nonchimerax Greg Couch all ChimeraX