Opened 5 months ago
Closed 5 months ago
#17857 closed defect (nonchimerax)
Cannot save command history: No space left on device
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Input/Output | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0606, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0778, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.08, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size 448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size 448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32 Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size 448,448,448, pixel 0.86, shown at level 0.105, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size 448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size 448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size 448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32 Log from Mon Feb 3 13:09:17 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0606, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0778, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.08, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size 448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size 448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32 Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size 448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size 448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size 448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32 Log from Fri Jan 31 04:00:50 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0606, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0778, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.08, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size 448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size 448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32 Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size 448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size 448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size 448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32 Log from Fri Jan 31 02:27:14 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0282, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.0379, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0281, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.08, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size 448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size 448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32 Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size 448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size 448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size 448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32 Log from Mon Jan 27 17:38:14 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended.cxs Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0282, step 1, values float32 Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 1, values float32 Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.0379, step 1, values float32 Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0281, step 1, values float32 Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 1, values float32 Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.08, step 1, values float32 Log from Sun Jan 26 19:47:57 2025 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/walz/Downloads/cryosparc_P91_J558_009_volume_map.mrc Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448, pixel 0.86, shown at level 0.0282, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J556_008_volume_map.mrc Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448, pixel 0.86, shown at level 0.029, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J554_008_volume_map.mrc Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448, pixel 0.86, shown at level 0.0379, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J552_008_volume_map.mrc Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448, pixel 0.86, shown at level 0.0281, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J550_008_volume_map.mrc Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448, pixel 0.86, shown at level 0.0308, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J548_008_volume_map.mrc Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448, pixel 0.86, shown at level 0.0325, step 2, values float32 > set bgColor white > surface dust #1 size 8.6 > surface dust #2 size 8.6 > surface dust #3 size 8.6 > surface dust #4 size 8.6 > surface dust #5 size 8.6 > surface dust #6 size 8.6 > tile 6 models tiled > volume all step 1 > open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I- > EGF1_2_21D10Fab/Refinement/semi-extended_aIIbb3_21D10/submission/semi- > extended_aIIbb3_21D10_final_new4.pdb Chain information for semi-extended_aIIbb3_21D10_final_new4.pdb #7 --- Chain | Description A | No description available B | No description available H | No description available L | No description available > ~tile > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > select add #7 11697 atoms, 11945 bonds, 1 pseudobond, 1569 residues, 2 models selected > ui mousemode right "translate selected models" > view matrix models > #7,0.19118,-0.77657,-0.60032,441.69,-0.69023,-0.54121,0.48029,420.28,-0.69788,0.32254,-0.63948,365.99 > view matrix models > #7,0.19118,-0.77657,-0.60032,342.52,-0.69023,-0.54121,0.48029,336.24,-0.69788,0.32254,-0.63948,462.89 > color #6 #ffb2b26f models > color #6 #ffb2b26e models > volume #6 level 0.1062 > open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I- > EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/full_21D10_semi_extended_aIIbb3_refine_new.pdb Summary of feedback from opening /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I- EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/full_21D10_semi_extended_aIIbb3_refine_new.pdb --- notes | Combining 3 symmetry atoms into CA /C:2 CA Combining 3 symmetry atoms into MG /I:1 MG Combining 3 symmetry atoms into CA /C:1 CA Chain information for full_21D10_semi_extended_aIIbb3_refine_new.pdb #8 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available L | No description available > select subtract #7 Nothing selected > select add #8 14944 atoms, 15264 bonds, 4 pseudobonds, 1970 residues, 2 models selected > hide (#!8 & sel) target a > cartoon (#!8 & sel) > hide #!7 models > view matrix models #8,1,0,0,74.674,0,1,0,14.932,0,0,1,64.535 > view matrix models #8,1,0,0,96.902,0,1,0,51.797,0,0,1,2.6908 > ui mousemode right "rotate selected models" > view matrix models > #8,-0.58626,-0.79174,-0.17161,556.77,0.10786,0.13366,-0.98514,340.08,0.80291,-0.59606,0.0070336,116.08 > view matrix models > #8,-0.95891,-0.14169,0.2458,447.89,0.13487,-0.98987,-0.044445,371.52,0.24961,-0.0094681,0.9683,-37.3 > view matrix models > #8,-0.11837,-0.75612,0.64364,329.39,0.92144,-0.3252,-0.21257,138.81,0.37004,0.56792,0.73521,-119.67 > view matrix models > #8,-0.40188,-0.5142,0.75769,322.79,0.18394,-0.85592,-0.48329,411.51,0.89703,-0.054854,0.43856,-64.14 > view matrix models > #8,-0.25181,-0.56129,0.78838,297.62,0.69428,-0.6723,-0.25689,247.57,0.67422,0.48267,0.55898,-133.34 > ui mousemode right "translate selected models" > view matrix models > #8,-0.25181,-0.56129,0.78838,205.32,0.69428,-0.6723,-0.25689,220.48,0.67422,0.48267,0.55898,-62.62 > view matrix models > #8,-0.25181,-0.56129,0.78838,214.22,0.69428,-0.6723,-0.25689,240.81,0.67422,0.48267,0.55898,-50.402 > ui tool show "Fit in Map" > fitmap #8 inMap #6 Fit molecule full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 14944 atoms average map value = 0.1808, steps = 332 shifted from previous position = 10.2 rotated from previous position = 19.9 degrees atoms outside contour = 6390, contour level = 0.10618 Position of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.95283509 0.23650967 -0.19017993 355.35625335 0.24690090 0.96849253 -0.03259015 -7.03996872 0.17647996 -0.07800863 -0.98120815 350.12189933 Axis -0.12288274 -0.99202290 0.02811416 Axis point 161.63097867 0.00000000 191.49987239 Rotation angle (degrees) 169.35028574 Shift along axis -26.83995675 > hide #!6 models > show #!6 models > volume #6 level 0.05726 > volume #6 level 0.0706 > hide #!6 models > open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I- > EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/b-tail.pdb Chain information for b-tail.pdb #9 --- Chain | Description B | No description available > view matrix models > #8,-0.47985,-0.66006,0.57799,319.59,0.60881,-0.72487,-0.32235,268.83,0.63174,0.19721,0.74968,-2.8445 > show #!6 models > fitmap #8 inMap #6 Fit molecule full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 14944 atoms average map value = 0.1808, steps = 1468 shifted from previous position = 21.5 rotated from previous position = 0.0227 degrees atoms outside contour = 5408, contour level = 0.070601 Position of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.95291596 0.23649509 -0.18979249 355.28808959 0.24685947 0.96850221 -0.03261625 -7.03180936 0.17610087 -0.07793261 -0.98128230 350.18862920 Axis -0.12286365 -0.99202565 0.02810036 Axis point 161.62837102 0.00000000 191.49498248 Rotation angle (degrees) 169.37283895 Shift along axis -26.83583113 > combine #8 > hide #9 models > hide #!8 models > hide #!6 models > select #10/A:531 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 50 atoms, 49 bonds, 7 residues, 1 model selected > select up 5067 atoms, 5188 bonds, 667 residues, 1 model selected > select up 5116 atoms, 5237 bonds, 673 residues, 1 model selected > select down 5067 atoms, 5188 bonds, 667 residues, 1 model selected > select down 50 atoms, 49 bonds, 7 residues, 1 model selected > select up 5067 atoms, 5188 bonds, 667 residues, 1 model selected > delete sel > select #10/B:369 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 59 atoms, 59 bonds, 8 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > delete sel > select clear > select #10/F:949 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 102 atoms, 103 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > select up 745 atoms, 766 bonds, 96 residues, 1 model selected > delete sel > select #10/B:43 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 51 atoms, 50 bonds, 6 residues, 1 model selected > select up 548 atoms, 557 bonds, 74 residues, 1 model selected > delete sel > select #10/D:604 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 136 atoms, 139 bonds, 19 residues, 1 model selected > select up 296 atoms, 299 bonds, 43 residues, 1 model selected > delete sel > select #10/F:780 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 89 atoms, 91 bonds, 10 residues, 1 model selected > select up 426 atoms, 440 bonds, 55 residues, 1 model selected > select up 436 atoms, 449 bonds, 57 residues, 1 model selected > select down 426 atoms, 440 bonds, 55 residues, 1 model selected > delete sel > select #10/F:752 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > delete sel > select #10/E:531 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 83 atoms, 84 bonds, 10 residues, 1 model selected > select up 296 atoms, 302 bonds, 39 residues, 1 model selected > select up 4343 atoms, 4428 bonds, 581 residues, 1 model selected > select down 296 atoms, 302 bonds, 39 residues, 1 model selected > delete sel > select #10/F:759 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 28 atoms, 27 bonds, 4 residues, 1 model selected > select up 50 atoms, 50 bonds, 8 residues, 1 model selected > select up 78 atoms, 77 bonds, 12 residues, 1 model selected > select up 4047 atoms, 4126 bonds, 542 residues, 1 model selected > select down 78 atoms, 77 bonds, 12 residues, 1 model selected > delete sel > select #10/A:703 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 75 atoms, 74 bonds, 11 residues, 1 model selected > select up 585 atoms, 589 bonds, 76 residues, 1 model selected > select up 3969 atoms, 4049 bonds, 530 residues, 1 model selected > select down 585 atoms, 589 bonds, 76 residues, 1 model selected > delete sel > rename #10 Fab > show #9 models > show #!6 models > select add #10 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,-0.4796,-0.66011,0.57813,263.4,0.60871,-0.72483,-0.32264,290.03,0.63203,0.19717,0.74944,-61.389 > view matrix models > #10,-0.4796,-0.66011,0.57813,233.83,0.60871,-0.72483,-0.32264,257.94,0.63203,0.19717,0.74944,-38.805 > view matrix models > #10,-0.4796,-0.66011,0.57813,237.38,0.60871,-0.72483,-0.32264,260.49,0.63203,0.19717,0.74944,-39.471 > view matrix models > #10,-0.4796,-0.66011,0.57813,277.45,0.60871,-0.72483,-0.32264,294.4,0.63203,0.19717,0.74944,-55.096 > ui mousemode right "rotate selected models" > view matrix models > #10,-0.0035973,0.88908,-0.45775,38.884,-0.80498,-0.27416,-0.52617,454.27,-0.5933,0.36658,0.71667,107.5 > view matrix models > #10,0.013861,0.89276,-0.45032,34.679,-0.79634,-0.2625,-0.54492,452.92,-0.6047,0.36616,0.7073,110.4 > view matrix models > #10,0.16463,0.82004,-0.54811,35.517,-0.90023,-0.10218,-0.42326,426.25,-0.4031,0.56311,0.7214,41.863 > ui mousemode right "translate selected models" > view matrix models > #10,0.16463,0.82004,-0.54811,38.796,-0.90023,-0.10218,-0.42326,427.38,-0.4031,0.56311,0.7214,53.816 > fitmap #10 inMap #6 Fit molecule Fab (#10) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 3384 atoms average map value = 0.05594, steps = 196 shifted from previous position = 18.6 rotated from previous position = 14.8 degrees atoms outside contour = 2228, contour level = 0.070601 Position of Fab (#10) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation 0.97764717 -0.19678280 -0.07404376 100.81760441 0.01420978 -0.28952043 0.95706633 156.07404631 -0.20977138 -0.93672537 -0.28025259 545.94553186 Axis -0.99133915 0.07104905 0.11044784 Axis point 0.00000000 285.75438766 219.82084075 Rotation angle (degrees) 107.22128610 Shift along axis -28.55701943 > select add #9 4058 atoms, 4143 bonds, 538 residues, 2 models selected > select subtract #9 3384 atoms, 3460 bonds, 454 residues, 1 model selected > select subtract #10 Nothing selected > show #!7 models > hide #!7 models > show #!8 models > rename #8 No name or id option specified for renaming > combine #8 > hide #!6 models > hide #!10 models > hide #9 models > select #8/L:145 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 55 atoms, 56 bonds, 6 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 14944 atoms, 15264 bonds, 1970 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 14944 atoms, 15264 bonds, 1970 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > delete sel > show #!10 models > hide #!10 models > show #9 models > hide #9 models > show #9 models > hide #9 models > hide #!8 models > hide #!11 models > show #!11 models > select #11/H:195 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 81 atoms, 81 bonds, 11 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > delete sel > select #11/L:8 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 119 atoms, 120 bonds, 17 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > delete sel > combine #11 > hide #!11 models > select #12/F:906 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 77 atoms, 77 bonds, 10 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > combine #11 > select add #12 11574 atoms, 11804 bonds, 4 pseudobonds, 1530 residues, 2 models selected > select subtract #12 Nothing selected > select add #12 11574 atoms, 11804 bonds, 4 pseudobonds, 1530 residues, 2 models selected > select subtract #12 Nothing selected > hide #!12 models > show #!12 models > hide #!13 models > hide #!12 models > show #!13 models > select #13/F:927 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 105 atoms, 109 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > delete Missing or invalid "atoms" argument: empty atom specifier > select #13/F:927 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 105 atoms, 109 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > delete sel > select #13/F:761 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 28 atoms, 27 bonds, 4 residues, 1 model selected > select up 142 atoms, 143 bonds, 20 residues, 1 model selected > select up 173 atoms, 176 bonds, 24 residues, 1 model selected > select up 638 atoms, 656 bonds, 85 residues, 1 model selected > select up 10899 atoms, 11110 bonds, 1444 residues, 1 model selected > select down 638 atoms, 656 bonds, 85 residues, 1 model selected > delete sel > select #13/B:45 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 51 atoms, 50 bonds, 6 residues, 1 model selected > select up 548 atoms, 557 bonds, 74 residues, 1 model selected > select up 609 atoms, 618 bonds, 82 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 10261 atoms, 10454 bonds, 1359 residues, 1 model selected > select down 4003 atoms, 4076 bonds, 520 residues, 1 model selected > delete sel > select #13/E:559 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 116 atoms, 119 bonds, 14 residues, 1 model selected > select up 296 atoms, 302 bonds, 39 residues, 1 model selected > delete sel > select #13/D:602 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 136 atoms, 139 bonds, 19 residues, 1 model selected > select up 296 atoms, 299 bonds, 43 residues, 1 model selected > delete sel > show #!6 models > fitmap #13 inMap #6 Fit molecule copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#13) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 5666 atoms average map value = 0.2909, steps = 124 shifted from previous position = 2.86 rotated from previous position = 2.16 degrees atoms outside contour = 492, contour level = 0.070601 Position of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#13) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.94842327 0.25593793 -0.18705352 351.07511089 0.27110992 0.96066547 -0.06017652 -1.96816652 0.16429440 -0.10778487 -0.98050483 356.29542546 Axis -0.13415216 -0.99003811 0.04275207 Axis point 159.52100929 0.00000000 193.78030278 Rotation angle (degrees) 169.77922344 Shift along axis -29.91655776 > combine #13 > hide #!13 models > hide #!6 models > select #14/A:609-1000 1011 atoms, 1021 bonds, 1 pseudobond, 135 residues, 2 models selected > delete sel > rename #14 propeller_thigh > show #!13 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!14 models > show #!14 models > hide #!14 models > select #13/A:1-608 4641 atoms, 4755 bonds, 608 residues, 1 model selected > delete sel > show #!14 models > hide #!14 models > show #!14 models > rename #13 calf1 > show #!12 models > hide #!12 models > show #!12 models > fitmap #13 inMap #6 Fit molecule calf1 (#13) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 1025 atoms average map value = 0.222, steps = 108 shifted from previous position = 5.46 rotated from previous position = 9.85 degrees atoms outside contour = 51, contour level = 0.070601 Position of calf1 (#13) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.90479885 0.36361028 -0.22164510 332.88455411 0.35411327 0.93154374 0.08264379 -37.35376888 0.23652224 -0.00371146 -0.97161896 328.13909024 Axis -0.18518010 -0.98249355 -0.02036536 Axis point 150.26067531 0.00000000 184.13040294 Rotation angle (degrees) 166.51648597 Shift along axis -31.62642825 > hide #!13 models > hide #!14 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > combine #12 > hide #!12 models Drag select of 1262 residues, 1 pseudobonds > delete sel Drag select of 38 residues, 1 pseudobonds > delete sel Drag select of 39 residues, 2 pseudobonds > delete sel > select clear > select #15/A:742 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 41 atoms, 38 bonds, 6 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 41 atoms, 38 bonds, 6 residues, 1 model selected > select up 1368 atoms, 1388 bonds, 191 residues, 1 model selected > select down 41 atoms, 38 bonds, 6 residues, 1 model selected > delete sel > rename #15 calf2 > show #!6 models > show #!14 models > show #!13 models > fitmap #15 inMap #6 Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 1327 atoms average map value = 0.1854, steps = 540 shifted from previous position = 43.6 rotated from previous position = 16.1 degrees atoms outside contour = 144, contour level = 0.070601 Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.86244881 0.24947347 -0.44039186 374.61925651 0.32238960 0.94152009 -0.09800418 -45.90381986 0.39018835 -0.22650134 -0.89244056 295.70901122 Axis -0.15231671 -0.98454508 0.08643261 Axis point 157.77064194 0.00000000 188.16220864 Rotation angle (degrees) 155.05114162 Shift along axis 13.69250747 > select add #15 1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected > view matrix models > #15,-0.64948,-0.54749,0.52766,333.27,0.60821,-0.79054,-0.071614,241.5,0.45635,0.27442,0.84643,-37.123 > volume #6 level 0.1105 > view matrix models > #15,-0.64948,-0.54749,0.52766,335.65,0.60821,-0.79054,-0.071614,247.58,0.45635,0.27442,0.84643,-17.459 > fitmap #15 inMap #6 Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 1327 atoms average map value = 0.1265, steps = 212 shifted from previous position = 10.1 rotated from previous position = 10.9 degrees atoms outside contour = 547, contour level = 0.11051 Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.93563714 0.22353157 -0.27316062 371.31123811 0.27402663 0.94780873 -0.16299683 -0.88558265 0.22246909 -0.22735917 -0.94805868 374.18117390 Axis -0.12812617 -0.98665055 0.10052055 Axis point 161.45266616 0.00000000 210.98590850 Rotation angle (degrees) 165.45337216 Shift along axis -9.08802905 > view matrix models > #15,-0.52523,-0.55682,0.6435,296.33,0.60435,-0.77645,-0.17858,265.58,0.59908,0.2951,0.74433,-46.558 > view matrix models > #15,-0.52523,-0.55682,0.6435,295.45,0.60435,-0.77645,-0.17858,266.57,0.59908,0.2951,0.74433,-49.223 > fitmap #15 inMap #6 Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 1327 atoms average map value = 0.1265, steps = 60 shifted from previous position = 2.04 rotated from previous position = 0.0231 degrees atoms outside contour = 547, contour level = 0.11051 Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.93554884 0.22392329 -0.27314223 371.23060592 0.27438936 0.94772549 -0.16287060 -0.97904661 0.22239334 -0.22732072 -0.94808567 374.20391052 Axis -0.12832251 -0.98662919 0.10047976 Axis point 161.42087184 0.00000000 210.98369961 Rotation angle (degrees) 165.45587401 Shift along axis -9.07136900 > hide #!15 models > hide #!14 models > hide #!13 models > select subtract #15 Nothing selected > show #!12 models > combine #12 > hide #!12 models > hide #!6 models > select #16/A:635 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 83 atoms, 82 bonds, 11 residues, 1 model selected > select up 5067 atoms, 5188 bonds, 667 residues, 1 model selected > select up 5116 atoms, 5237 bonds, 673 residues, 1 model selected > select up 5652 atoms, 5777 bonds, 743 residues, 1 model selected > select down 5116 atoms, 5237 bonds, 673 residues, 1 model selected > select up 5652 atoms, 5777 bonds, 743 residues, 1 model selected > delete sel > select clear Drag select of 171 residues, 2 pseudobonds > delete sel > show #!6 models > fitmap #16 inMap #6 Fit molecule copy of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#16) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 4609 atoms average map value = 0.2719, steps = 104 shifted from previous position = 4.41 rotated from previous position = 3.17 degrees atoms outside contour = 884, contour level = 0.11051 Position of copy of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#16) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.96079585 0.20309126 -0.18874647 362.78748781 0.22143338 0.97175763 -0.08157396 1.47448981 0.16684886 -0.12017068 -0.97863191 360.66818396 Axis -0.10776577 -0.99285637 0.05121297 Axis point 164.86676653 0.00000000 196.75577933 Rotation angle (degrees) 169.68400198 Shift along axis -22.08913961 > volume #6 level 0.2049 > volume #6 color #ffb2b23b > combine #16 > hide #!16 models > hide #!6 models Drag select of 82 residues > delete sel > fitmap #17 inMap #6 Fit molecule copy of copy of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#17) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 4017 atoms average map value = 0.3004, steps = 92 shifted from previous position = 0.289 rotated from previous position = 0.52 degrees atoms outside contour = 1238, contour level = 0.2049 Position of copy of copy of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#17) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.96121156 0.20615041 -0.18323292 361.10306955 0.22481572 0.97046412 -0.08750557 2.47385898 0.15978167 -0.12530500 -0.97916721 362.94502097 Axis -0.10937480 -0.99253220 0.05400915 Axis point 164.44559355 0.00000000 197.26854577 Rotation angle (degrees) 170.04947598 Shift along axis -22.34860817 > show #!6 models > show #!14 models > hide #!14 models > hide #!6 models > combine #16 > hide #!17 models > select #18/B:1-1000 4003 atoms, 4076 bonds, 1 pseudobond, 520 residues, 2 models selected > delete sel > combine #18 > hide #!18 models > select #19/E:537 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 4 residues, 1 model selected > select up 296 atoms, 302 bonds, 39 residues, 1 model selected > delete sel > rename #19 I-EGF4 > rename #18 I-EGF3 > show #!18 models > hide #!19 models > select #18/D:600 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 136 atoms, 139 bonds, 19 residues, 1 model selected > select up 296 atoms, 299 bonds, 43 residues, 1 model selected > delete sel > show #!19 models > show #!17 models > show #!16 models > hide #!16 models > show #!15 models > show #!14 models > show #!13 models > show #9 models > select add #9 674 atoms, 683 bonds, 84 residues, 1 model selected > view matrix models #9,1,0,0,-59.731,0,1,0,-51.145,0,0,1,99.266 > view matrix models #9,1,0,0,-61.475,0,1,0,26.841,0,0,1,130.08 > show #!6 models > volume #6 level 0.14 > select subtract #9 Nothing selected > select add #18 310 atoms, 302 bonds, 53 residues, 1 model selected > select add #19 620 atoms, 601 bonds, 110 residues, 2 models selected > volume #6 level 0.12 > volume #6 level 0.1 > fitmap #18 inMap #6 Fit molecule I-EGF3 (#18) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 310 atoms average map value = 0.2148, steps = 240 shifted from previous position = 12.7 rotated from previous position = 10.2 degrees atoms outside contour = 62, contour level = 0.1 Position of I-EGF3 (#18) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.98025301 0.07888826 -0.18133017 391.51409030 0.07692240 0.99687709 0.01785957 -0.08929022 0.18217280 0.00355855 -0.98326007 334.22344253 Axis -0.03931124 -0.99921240 -0.00540383 Axis point 180.42475586 0.00000000 185.04858781 Rotation angle (degrees) 169.51985707 Shift along axis -17.10777214 > select subtract #19 310 atoms, 302 bonds, 53 residues, 1 model selected > view matrix models > #18,-0.35651,-0.7612,0.54174,312.45,0.72246,-0.59226,-0.35675,234.89,0.59241,0.2642,0.76108,-36.986 > fitmap #18 inMap #6 Fit molecule I-EGF3 (#18) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 310 atoms average map value = 0.2137, steps = 432 shifted from previous position = 11.8 rotated from previous position = 6.33 degrees atoms outside contour = 60, contour level = 0.1 Position of I-EGF3 (#18) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.97566674 -0.01329218 -0.21885537 411.73725830 -0.02386391 0.99866863 0.04573219 15.82705778 0.21795611 0.04984214 -0.97468500 317.92856772 Axis 0.00940579 -0.99966304 -0.02419389 Axis point 188.38591307 0.00000000 181.55464502 Rotation angle (degrees) 167.38026585 Shift along axis -19.64093810 > hide #!6 models > hide #9 models > show #9 models > show #!6 models > view matrix models > #18,-0.29884,-0.808,0.50777,309.57,0.79103,-0.50738,-0.34182,199.54,0.53382,0.29951,0.79078,-38.045 > select add #19 620 atoms, 601 bonds, 110 residues, 2 models selected > select subtract #18 310 atoms, 299 bonds, 57 residues, 1 model selected > view matrix models > #19,-0.45581,-0.64367,0.61476,301.16,0.62346,-0.72382,-0.2956,270.6,0.63524,0.24854,0.73123,-43.674 > view matrix models > #19,-0.45581,-0.64367,0.61476,301.62,0.62346,-0.72382,-0.2956,269.69,0.63524,0.24854,0.73123,-42.848 > ui mousemode right "rotate selected models" > view matrix models > #19,-0.28768,-0.9536,-0.088831,399.8,0.8518,-0.21236,-0.4789,148.38,0.43781,-0.21343,0.87337,67.435 > fitmap #19 inMap #6 Fit molecule I-EGF4 (#19) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 310 atoms average map value = 0.1095, steps = 420 shifted from previous position = 4.25 rotated from previous position = 21.3 degrees atoms outside contour = 114, contour level = 0.1 Position of I-EGF4 (#19) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation -0.96549508 0.25668139 0.04397558 333.89860864 0.22004319 0.71376560 0.66492076 -36.20855798 0.13928454 0.65165428 -0.74561818 210.20718209 Axis -0.12884238 -0.92562835 -0.35582552 Axis point 166.96183400 0.00000000 116.55795343 Rotation angle (degrees) 177.04891462 Shift along axis -84.30170199 > select subtract #19 Nothing selected > select add #9 674 atoms, 683 bonds, 84 residues, 1 model selected > view matrix models > #9,0.99966,0.0083186,-0.024648,-60.857,0.0077285,0.80974,0.58674,10.693,0.024839,-0.58674,0.8094,255.55 > view matrix models > #9,0.99873,-0.013055,-0.048604,-54.433,0.04181,0.7528,0.65692,8.8559,0.028013,-0.65812,0.75239,273.75 > ui mousemode right "translate selected models" > view matrix models > #9,0.99873,-0.013055,-0.048604,-33.494,0.04181,0.7528,0.65692,32.539,0.028013,-0.65812,0.75239,231.9 > volume #6 level 0.08 > view matrix models > #9,0.99873,-0.013055,-0.048604,-19.36,0.04181,0.7528,0.65692,40.626,0.028013,-0.65812,0.75239,249.85 > view matrix models > #9,0.99873,-0.013055,-0.048604,-19.195,0.04181,0.7528,0.65692,40.956,0.028013,-0.65812,0.75239,249.96 > ui mousemode right "rotate selected models" > view matrix models > #9,0.37609,-0.1564,-0.91329,206.98,0.50694,0.85978,0.061517,-19.077,0.77561,-0.48612,0.40264,100.19 > view matrix models > #9,-0.38756,-0.31481,-0.86643,383.85,0.35824,0.81458,-0.45621,64.366,0.84939,-0.4872,-0.20292,139 > view matrix models > #9,-0.81818,-0.17624,-0.54729,413.77,0.23062,0.77135,-0.59316,109.87,0.52669,-0.61152,-0.59046,260.59 > view matrix models > #9,-0.5182,-0.68635,-0.51028,450.27,-0.65467,0.70225,-0.27972,270,0.55034,0.18911,-0.81324,120.43 > view matrix models > #9,-0.3335,-0.40981,-0.84902,390.08,-0.54187,0.82028,-0.18309,216.46,0.77147,0.39899,-0.49562,8.394 > view matrix models > #9,-0.09313,0.38884,-0.91659,194.02,0.10176,0.91949,0.37973,21.194,0.99044,-0.057904,-0.1252,21.284 > view matrix models > #9,0.72079,0.69313,0.0055702,-106.01,-0.62134,0.64253,0.44843,211.12,0.30724,-0.32669,0.8938,118.41 > view matrix models > #9,0.65758,-0.62774,-0.41658,199.28,0.19007,0.67328,-0.71454,147.49,0.72902,0.39068,0.56205,-74.43 > view matrix models > #9,-0.58219,-0.7427,0.33083,399.99,-0.14274,-0.30721,-0.94087,422.74,0.80042,-0.59499,0.072842,145.33 > view matrix models > #9,-0.83198,-0.55101,-0.064729,446.73,0.29514,-0.34077,-0.89262,338.82,0.46978,-0.76175,0.44614,209.95 > view matrix models > #9,-0.92229,-0.29043,-0.25503,430.73,0.36161,-0.41537,-0.83469,335.11,0.13649,-0.86204,0.48811,291.29 > view matrix models > #9,-0.8213,-0.51089,-0.2539,453.45,0.48422,-0.38889,-0.78377,301.38,0.30168,-0.76665,0.56678,233.4 > show #!10 models > view matrix models > #9,-0.50825,-0.57264,0.64325,325.09,-0.41045,-0.49557,-0.76547,496.52,0.75711,-0.65307,0.016831,170.01 > view matrix models > #9,-0.61715,0.14533,0.77331,196.07,-0.78517,-0.049694,-0.61728,470.93,-0.05128,-0.98813,0.14478,382.79 > view matrix models > #9,-0.13456,0.99039,0.032029,2.4549,-0.23074,-0.062752,0.97099,224.99,0.96367,0.12326,0.23697,-40.305 > view matrix models > #9,-0.34305,0.91314,-0.2202,80.578,-0.55303,-0.0068632,0.83313,289.7,0.75926,0.40758,0.50735,-78.856 > view matrix models > #9,-0.39561,0.9008,-0.17904,89.705,-0.50118,-0.04838,0.86399,284.82,0.76962,0.43154,0.4706,-82.311 > ui mousemode right "translate selected models" > view matrix models > #9,-0.39561,0.9008,-0.17904,87.796,-0.50118,-0.04838,0.86399,294.69,0.76962,0.43154,0.4706,-78.163 > view matrix models > #9,-0.39561,0.9008,-0.17904,91.681,-0.50118,-0.04838,0.86399,297.87,0.76962,0.43154,0.4706,-72.863 > view matrix models > #9,-0.39561,0.9008,-0.17904,90.944,-0.50118,-0.04838,0.86399,291.78,0.76962,0.43154,0.4706,-74.977 > ui mousemode right "rotate selected models" > view matrix models > #9,-0.39655,0.75393,-0.52376,149.81,-0.76806,0.040017,0.63912,346.91,0.50282,0.65573,0.5632,-74.007 > view matrix models > #9,-0.90774,0.14834,-0.39242,356.19,-0.38999,-0.64312,0.65902,403.06,-0.15461,0.75126,0.64163,30.007 > view matrix models > #9,-0.42349,0.77359,-0.4714,146.71,-0.83024,-0.12324,0.54361,399.15,0.36244,0.62159,0.69445,-51.28 > view matrix models > #9,0.37723,0.54633,-0.74782,57.38,-0.9247,0.17748,-0.33679,436.74,-0.051277,0.81855,0.57214,2.7336 > view matrix models > #9,0.92867,0.36517,-0.064926,-75.984,-0.18027,0.29141,-0.93946,321.03,-0.32415,0.88416,0.33645,64.412 > view matrix models > #9,0.26151,0.51347,0.81729,-50.788,0.5244,0.6353,-0.56693,83.049,-0.81032,0.57684,-0.10312,258.18 > view matrix models > #9,-0.75157,-0.096853,0.65251,281.26,0.11855,0.95323,0.27803,27.229,-0.64892,0.28631,-0.70493,335.48 > view matrix models > #9,0.060311,-0.35426,0.9332,146.69,0.61328,0.75079,0.24537,-28.074,-0.78756,0.55751,0.26254,225.37 > view matrix models > #9,0.084195,-0.27473,0.95783,124.43,0.63438,0.75605,0.16109,-25.852,-0.76842,0.59407,0.23794,216.68 > ui mousemode right "translate selected models" > view matrix models > #9,0.084195,-0.27473,0.95783,108.64,0.63438,0.75605,0.16109,-27.947,-0.76842,0.59407,0.23794,224.81 > view matrix models > #9,0.084195,-0.27473,0.95783,107.27,0.63438,0.75605,0.16109,-26.987,-0.76842,0.59407,0.23794,222.16 > hide #!6 models > select subtract #9 Nothing selected > show #!11 models > hide #!11 models > delete #11 > delete #12 > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > delete #16 > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > delete #7 > delete #8 > select clear > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/b-tail.pdb models > #9 relModel #6 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/Fab.pdb models #10 > relModel #6 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/calf1.pdb models > #13 relModel #6 > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/propeller_thigh.pdb > models #14 relModel #6 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/calf2.pdb models > #15 relModel #6 > hide #!17 models > show #!17 models > rename #17 PSI_hybrid_BI_I-EGF-2 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/PSI_hybrid_BI_I- > EGF-2.pdb models #17 relModel #6 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF3.pdb models > #18 relModel #6 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF4.pdb models > #19 > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF4.pdb models > #19 relModel #6 [Repeated 1 time(s)] > save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended.cxs > includeMaps true ——— End of log from Sun Jan 26 19:47:57 2025 ——— opened ChimeraX session > show #!6 models > open /Users/walz/Downloads/cryosparc_P91_J548_008_volume_map_sharp.mrc Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size 448,448,448, pixel 0.86, shown at level 0.0706, step 2, values float32 > volume #7 step 1 > surface dust #6 size 8.6 > surface dust #7 size 8.6 > volume #7 level 0.09 > select add #7 2 models selected > ui mousemode right "translate selected models" > view matrix models #7,1,0,0,3.1183,0,1,0,2.9994,0,0,1,2.6409 > ui mousemode right "rotate selected models" > view matrix models > #7,-0.80916,0.17976,-0.55941,439.44,0.41754,0.84577,-0.33218,31.815,0.41342,-0.50236,-0.75942,432.82 > view matrix models > #7,0.18299,0.3227,-0.92864,308.72,0.90003,-0.43503,0.026182,113.2,-0.39554,-0.8406,-0.37005,563.21 > view matrix models > #7,0.35075,0.12761,-0.92773,315.72,0.73315,-0.65378,0.18725,151.12,-0.58263,-0.74585,-0.32287,568.75 > view matrix models > #7,0.16739,0.53309,-0.82933,246.61,0.95798,0.11081,0.26458,-62.1,0.23295,-0.83877,-0.49214,472.18 > view matrix models > #7,-0.85003,-0.27787,-0.44747,512.63,-0.48067,0.75663,0.44324,39.796,0.21541,0.59185,-0.77673,255.75 > view matrix models > #7,0.4788,-0.82099,-0.311,337.91,-0.54174,-0.55505,0.63121,269.77,-0.69084,-0.13374,-0.71053,556.88 > view matrix models > #7,0.10168,-0.9613,-0.25605,424.58,-0.76631,-0.23981,0.59604,257.47,-0.63438,0.13561,-0.76104,504.11 > view matrix models > #7,0.60537,-0.71386,-0.35204,302.07,-0.56214,-0.69658,0.44584,344.9,-0.56349,-0.072,-0.82298,546.53 > view matrix models > #7,-0.058499,-0.80041,-0.59659,501.75,-0.99499,-0.0018066,0.099989,368.27,-0.08111,0.59944,-0.7963,314.9 > view matrix models > #7,-0.086114,-0.83673,-0.5408,501.3,-0.82387,-0.24541,0.51089,289.23,-0.56019,0.48955,-0.66823,397.84 > ui tool show "Fit in Map" > fitmap #7 inMap #1 Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map cryosparc_P91_J558_009_volume_map.mrc using 581439 points correlation = 0.8818, correlation about mean = 0.7621, overlap = 3.252e+04 steps = 392, shift = 14.3, angle = 19.9 degrees Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99998836 0.00093539 0.00472847 -0.94260289 -0.00093004 0.99999890 -0.00113479 0.24010156 -0.00472952 0.00113038 0.99998816 0.68694229 Axis 0.22874171 0.95508751 -0.18837483 Axis point 140.15211701 0.00000000 194.09372244 Rotation angle (degrees) 0.28369412 Shift along axis -0.11569724 > fitmap #7 inMap #1 Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map cryosparc_P91_J558_009_volume_map.mrc using 581439 points correlation = 0.8819, correlation about mean = 0.7623, overlap = 3.252e+04 steps = 44, shift = 0.0102, angle = 0.0186 degrees Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99998975 0.00096269 0.00442035 -0.89219072 -0.00095810 0.99999898 -0.00103878 0.22868018 -0.00442134 0.00103454 0.99998967 0.64152730 Axis 0.22336035 0.95251825 -0.20692786 Axis point 139.29483880 0.00000000 196.38890302 Rotation angle (degrees) 0.26592301 Shift along axis -0.11420786 > fitmap #7 inMap #6 Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map cryosparc_P91_J548_008_volume_map.mrc using 581439 points correlation = 0.9517, correlation about mean = 0.8865, overlap = 3.796e+04 steps = 48, shift = 0.275, angle = 0.26 degrees Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates: Matrix rotation and translation 0.99999997 0.00009315 0.00011460 -0.03808621 -0.00009316 0.99999997 0.00006790 0.00451226 -0.00011459 -0.00006790 0.99999997 0.04777578 Axis -0.41771513 0.70502145 -0.57311328 Axis point 375.41814221 0.00000000 362.58970348 Rotation angle (degrees) 0.00931321 Shift along axis -0.00829051 > hide #!6 models > color #7 #b2b2b238 models > volume #7 level 0.12 > color #7 #b2b2b2e0 models > open /Users/walz/Downloads/cryosparc_P91_J550_008_volume_map_sharp.mrc Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size 448,448,448, pixel 0.86, shown at level 0.073, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J558_009_volume_map_sharp.mrc Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size 448,448,448, pixel 0.86, shown at level 0.0567, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J556_008_volume_map_sharp.mrc Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size 448,448,448, pixel 0.86, shown at level 0.0544, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J554_008_volume_map_sharp.mrc Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size 448,448,448, pixel 0.86, shown at level 0.0797, step 2, values float32 > open /Users/walz/Downloads/cryosparc_P91_J552_008_volume_map_sharp.mrc Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size 448,448,448, pixel 0.86, shown at level 0.0663, step 2, values float32 > surface dust #7 size 8.6 [Repeated 2 time(s)] > select subtract #7 Nothing selected > surface dust #7 size 8.6 > surface dust #8 size 8.6 > surface dust #11 size 8.6 > surface dust #12 size 8.6 > surface dust #16 size 8.6 > surface dust #20 size 8.6 > select add #8 2 models selected > select add #20 4 models selected > select add #16 6 models selected > select add #12 8 models selected > select add #11 10 models selected > view matrix models > #8,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#11,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#12,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#16,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#20,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974 > view matrix models > #8,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#11,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#12,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#16,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#20,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61 > view matrix models > #8,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#11,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#12,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#16,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#20,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253 > view matrix models > #8,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#11,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#12,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#16,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#20,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12 > view matrix models > #8,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#11,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#12,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#16,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#20,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44 > ui mousemode right "translate selected models" > view matrix models > #8,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#11,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#12,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#16,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#20,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73 > view matrix models > #8,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#11,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#12,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#16,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#20,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57 > view matrix models > #8,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#11,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#12,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#16,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#20,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88 > view matrix models > #8,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#11,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#12,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#16,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#20,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17 > view matrix models > #8,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#11,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#12,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#16,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#20,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07 > view matrix models > #8,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#11,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#12,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#16,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#20,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67 > view matrix models > #8,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#11,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#12,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#16,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#20,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28 > fitmap #8 inMap #5 Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map cryosparc_P91_J550_008_volume_map.mrc using 112244 points correlation = 0.9412, correlation about mean = 0.895, overlap = 5284 steps = 196, shift = 3.53, angle = 9.8 degrees Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to cryosparc_P91_J550_008_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999998 -0.00005942 0.00001803 0.00333361 0.00005942 0.99999998 0.00000680 -0.01378749 -0.00001802 -0.00000679 0.99999998 0.01280236 Axis -0.10875476 0.28857693 0.95126009 Axis point 270.09212416 70.43598055 0.00000000 Rotation angle (degrees) 0.00357903 Shift along axis 0.00783708 > fitmap #11 inMap #1 Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map cryosparc_P91_J558_009_volume_map.mrc using 111773 points correlation = 0.9587, correlation about mean = 0.9178, overlap = 4340 steps = 276, shift = 4.63, angle = 9.8 degrees Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99999997 -0.00012472 0.00007221 0.00739204 0.00012472 0.99999997 0.00009108 -0.04069274 -0.00007221 -0.00009106 0.99999997 0.04352525 Axis -0.53418804 0.42358484 0.73158665 Axis point 362.49134482 104.88224097 0.00000000 Rotation angle (degrees) 0.00976758 Shift along axis 0.01065692 > fitmap #12 inMap #2 Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map.mrc using 111628 points correlation = 0.966, correlation about mean = 0.9291, overlap = 4100 steps = 240, shift = 5.34, angle = 9.81 degrees Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99999997 0.00011427 -0.00006802 -0.00710718 -0.00011427 0.99999997 -0.00002242 0.02860082 0.00006802 0.00002244 0.99999998 -0.01395664 Axis 0.16632071 -0.50434360 -0.84733403 Axis point 233.59226008 56.71006184 0.00000000 Rotation angle (degrees) 0.00772706 Shift along axis -0.00378078 > fitmap #12 inMap #2 Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map.mrc using 111628 points correlation = 0.9659, correlation about mean = 0.929, overlap = 4100 steps = 44, shift = 0.0116, angle = 0.000429 degrees Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99999997 0.00011255 -0.00006076 -0.01795682 -0.00011255 0.99999997 -0.00002178 0.02850161 0.00006076 0.00002179 0.99999998 -0.01894104 Axis 0.16790249 -0.46832584 -0.86745586 Axis point 253.50692337 159.66648917 0.00000000 Rotation angle (degrees) 0.00743391 Shift along axis 0.00006748 > fitmap #12 inMap #2 Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map.mrc using 111628 points correlation = 0.9659, correlation about mean = 0.9289, overlap = 4099 steps = 64, shift = 0.0138, angle = 0.00106 degrees Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99999997 0.00011471 -0.00007550 -0.01168166 -0.00011471 0.99999997 -0.00001090 0.02858760 0.00007550 0.00001092 0.99999998 -0.00644372 Axis 0.07922118 -0.54806253 -0.83267729 Axis point 195.56697791 94.09905921 0.00000000 Rotation angle (degrees) 0.00789307 Shift along axis -0.01122769 > fitmap #12 inMap #2 Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map.mrc using 111628 points correlation = 0.9659, correlation about mean = 0.929, overlap = 4099 steps = 48, shift = 0.00571, angle = 0.00269 degrees Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates: Matrix rotation and translation 0.99999997 0.00011567 -0.00003175 -0.01630674 -0.00011567 0.99999997 -0.00002789 0.02942150 0.00003175 0.00002790 0.99999998 -0.00086915 Axis 0.22652468 -0.25778928 -0.93927166 Axis point 231.03251441 120.50255951 0.00000000 Rotation angle (degrees) 0.00705590 Shift along axis -0.01046206 > fitmap #16 inMap #3 Fit map cryosparc_P91_J554_008_volume_map_sharp.mrc in map cryosparc_P91_J554_008_volume_map.mrc using 111264 points correlation = 0.9451, correlation about mean = 0.8943, overlap = 5413 steps = 220, shift = 4.39, angle = 9.79 degrees Position of cryosparc_P91_J554_008_volume_map_sharp.mrc (#16) relative to cryosparc_P91_J554_008_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999996 -0.00006647 0.00019113 -0.01517210 0.00006647 0.99999998 0.00002949 -0.01589606 -0.00019113 -0.00002947 0.99999996 0.04861121 Axis -0.14415236 0.93465011 0.32503734 Axis point 249.00601794 0.00000000 77.04793762 Rotation angle (degrees) 0.01171651 Shift along axis 0.00313030 > fitmap #20 inMap #4 Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map cryosparc_P91_J552_008_volume_map.mrc using 111514 points correlation = 0.9457, correlation about mean = 0.8978, overlap = 4659 steps = 252, shift = 4.15, angle = 9.79 degrees Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to cryosparc_P91_J552_008_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999996 -0.00016035 0.00013379 0.00869009 0.00016034 0.99999996 0.00005400 -0.04213159 -0.00013380 -0.00005397 0.99999997 0.04478127 Axis -0.25028123 0.62028692 0.74337301 Axis point 282.03118324 61.92978627 0.00000000 Rotation angle (degrees) 0.01235881 Shift along axis 0.00498055 > fitmap #20 inMap #4 Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map cryosparc_P91_J552_008_volume_map.mrc using 111514 points correlation = 0.9457, correlation about mean = 0.8978, overlap = 4659 steps = 104, shift = 0.0171, angle = 0.00287 degrees Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to cryosparc_P91_J552_008_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999996 -0.00017266 0.00009051 0.01524728 0.00017266 0.99999996 0.00003213 -0.04231769 -0.00009051 -0.00003211 0.99999998 0.01586544 Axis -0.16256390 0.45811166 0.87390313 Axis point 223.86924828 80.74831448 0.00000000 Rotation angle (degrees) 0.01132044 Shift along axis -0.00800003 > volume all step 1 > surface dust #8 size 8.6 > surface dust #11 size 8.6 > surface dust #12 size 8.6 > surface dust #16 size 8.6 > surface dust #20 size 8.6 > surface dust #8 size 8.6 > surface dust #11 size 8.6 > surface dust #12 size 8.6 > surface dust #16 size 8.6 > surface dust #20 size 8.6 > volume #16 level 0.1589 > volume #16 level 0.2452 > volume #20 level 0.168 > volume #12 level 0.2036 > volume #11 level 0.13 > volume #8 level 0.2948 > select subtract #12 8 models selected > select subtract #11 6 models selected > select subtract #16 4 models selected > select subtract #20 2 models selected > hide #!12 models > hide #!13 models > show #!12 models > hide #!12 models > hide #!11 models > hide #!20 models > hide #!16 models > show #!7 models > hide #!7 models > show #!7 models > hide #9 models > hide #!10 models > hide #!14 models > hide #!15 models > hide #!17 models > hide #!19 models > hide #!8 models > show #!8 models > hide #!18 models > hide #!7 models > volume #8 level 0.2 > volume #8 level 0.15 > volume #8 level 0.1 > surface dust #8 size 8.6 [Repeated 3 time(s)] > volume #8 level 0.12 > lighting soft > volume #7 level 0.13 > fitmap #8 inMap #7 Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map cryosparc_P91_J548_008_volume_map_sharp.mrc using 382518 points correlation = 0.8942, correlation about mean = 0.808, overlap = 4.607e+04 steps = 160, shift = 0.604, angle = 0.82 degrees Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates: Matrix rotation and translation 0.99996146 -0.00543594 -0.00689322 2.18293687 0.00551398 0.99992035 0.01135269 -2.73838618 0.00683096 -0.01139026 0.99991179 0.97591746 Axis -0.79157027 -0.47767094 0.38111282 Axis point 0.00000000 85.39674467 243.82763462 Rotation angle (degrees) 0.82312338 Shift along axis -0.04796577 > show #!20 models > fitmap #20 inMap #7 Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map cryosparc_P91_J548_008_volume_map_sharp.mrc using 250306 points correlation = 0.9199, correlation about mean = 0.8061, overlap = 4.124e+04 steps = 120, shift = 0.45, angle = 0.541 degrees Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates: Matrix rotation and translation 0.99999605 -0.00266984 -0.00087684 0.70675136 0.00267767 0.99995547 0.00904943 -1.81387975 0.00085264 -0.00905174 0.99995867 1.60797784 Axis -0.95502489 -0.09124776 0.28213702 Axis point 0.00000000 178.45984098 201.88203609 Rotation angle (degrees) 0.54298902 Shift along axis -0.05578259 > hide #!8 models > volume #20 level 0.12 > hide #!7 models > show #!8 models > show #!7 models > show #!12 models > hide #!8 models > volume #12 level 0.12 > hide #!7 models > hide #!20 models > volume #12 level 0.1 > volume #12 level 0.11 > show #!20 models > hide #!20 models > show #!8 models > show #!7 models > hide #!8 models > show #!8 models > hide #!7 models > hide #!12 models > volume #8 level 0.11 > volume #8 level 0.08192 > volume #8 level 0.1 > volume #8 level 0.11 > volume #8 level 0.12 > volume #8 level 0.13 > volume #8 level 0.125 > volume #8 level 0.135 > volume #8 level 0.14 > volume #8 level 0.135 > show #!12 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!20 models > show #!16 models > hide #!12 models > hide #!20 models > volume #16 level 0.12 > show #!7 models > show #!8 models > show #!12 models > hide #!12 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!7 models > show #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!12 models > show #!8 models > show #!11 models > hide #!12 models > hide #!8 models > hide #!7 models > hide #!16 models > volume #11 level 0.11 > show #!7 models > show #!8 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!7 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!7 models > hide #!11 models > show #!11 models > show #!8 models > show #!7 models > show #!20 models > show #!16 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!11 models > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > hide #!20 models > volume #16 level 0.11 > volume #16 level 0.14 > surface dust #16 size 8.6 > show #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!12 models > hide #!16 models > show #!16 models > hide #!16 models > volume #11 level 0.12 > volume #11 level 0.11 > volume #11 level 0.12 > volume #11 level 0.11 > surface dust #11 size 8.6 [Repeated 1 time(s)] > show #!12 models > hide #!12 models > show #!12 models > show #!8 models > show #!7 models > hide #!7 models > show #!20 models > show #!16 models > show #!7 models > hide #!7 models > hide #!8 models > hide #!20 models > hide #!16 models > volume #12 level 0.1 > volume #12 level 0.11 > show #!12 models > hide #!12 models > show #!12 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!7 models > hide #!12 models > hide #!11 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs > includeMaps true Traceback (most recent call last): File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 899, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 630, in save fserialize(stream, data) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/serialize.py", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/safesave.py", line 136, in write self._f.write(buf) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/lz4/frame/__init__.py", line 741, in write self._fp.write(compressed) OSError: [Errno 28] No space left on device OSError: [Errno 28] No space left on device File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/lz4/frame/__init__.py", line 741, in write self._fp.write(compressed) See log for complete Python traceback. Cannot save '/Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs': [Errno 28] No space left on device > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > fitmap #8 inMap #7 Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map cryosparc_P91_J548_008_volume_map_sharp.mrc using 328138 points correlation = 0.9013, correlation about mean = 0.802, overlap = 4.571e+04 steps = 84, shift = 0.0136, angle = 0.0102 degrees Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates: Matrix rotation and translation 0.99996237 -0.00547745 -0.00672681 2.16862670 0.00555389 0.99991961 0.01139809 -2.75241339 0.00666384 -0.01143502 0.99991241 1.02460814 Axis -0.79622622 -0.46695284 0.38468021 Axis point 0.00000000 89.32530792 244.04885445 Rotation angle (degrees) 0.82155430 Shift along axis -0.04732373 > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs ——— End of log from Mon Jan 27 17:38:14 2025 ——— opened ChimeraX session > hide #!8 models > show #!8 models > show #!4 models > hide #!4 models > show #!4 models > hide #!7 models > hide #!8 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > volume #4 level 0.04 > show #!19 models > color #4 #b2b2ff38 models > color #4 #b2b2ffc0 models > color #4 #b2b2ffe3 models > color #4 #b2b2ffff models [Repeated 1 time(s)] > volume #4 color #b2b2ff8c > show #!18 models > hide #!4 models > show #!4 models > show #!17 models > show #!15 models > show #!14 models > show #!13 models > volume #4 level 0.06 > show #!10 models > show #9 models > show #!7 models > volume #4 level 0.1135 > hide #!4 models > show #!4 models > volume #4 level 0.07785 > hide #!4 models > show #!3 models > volume #3 level 0.1214 > volume #3 color #b2ffff6e > volume #3 level 0.07588 > volume #3 color #009193 > volume #3 color #00919350 > volume #3 color #00fdff > volume #3 color #00fdff2d > volume #3 level 0.1101 > show #!4 models > hide #!3 models > hide #!4 models > show #!1 models > volume #1 level 0.06056 > show #!4 models > hide #!1 models > show #!12 models > hide #!4 models > hide #!12 models > show #!12 models > color #12 #b2b2ff7d models > volume #12 level 0.1777 > volume #12 level 0.11 > show #!11 models > hide #!12 models > hide #!11 models > show #!12 models > select add #10 3384 atoms, 3460 bonds, 454 residues, 1 model selected > ui mousemode right "translate selected models" > view matrix models > #10,0.30181,0.74955,-0.58914,28.753,-0.78324,-0.15738,-0.60147,463.83,-0.54355,0.64297,0.53958,83.745 > view matrix models > #10,0.30181,0.74955,-0.58914,25.455,-0.78324,-0.15738,-0.60147,469.14,-0.54355,0.64297,0.53958,85.999 > view matrix models > #10,0.30181,0.74955,-0.58914,22.058,-0.78324,-0.15738,-0.60147,465.97,-0.54355,0.64297,0.53958,88.156 > ui tool show "Fit in Map" > fitmap #10 inMap #12 Fit molecule Fab (#10) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 3384 atoms average map value = 0.06266, steps = 116 shifted from previous position = 3.72 rotated from previous position = 5.05 degrees atoms outside contour = 2774, contour level = 0.11 Position of Fab (#10) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.98849879 -0.11361862 -0.09980451 70.83207994 0.06080833 -0.30563479 0.95020509 148.41424462 -0.13846472 -0.94534553 -0.29521067 541.19291392 Axis -0.99558763 0.02030525 0.09161312 Axis point 0.00000000 273.62288874 219.39825162 Rotation angle (degrees) 107.82876842 Shift along axis -17.92558395 > volume #12 level 0.1438 > hide #!12 models > show #!12 models > select add #18 3694 atoms, 3762 bonds, 507 residues, 2 models selected > select subtract #10 310 atoms, 302 bonds, 53 residues, 1 model selected > view matrix models > #18,-0.29884,-0.808,0.50777,310.21,0.79103,-0.50738,-0.34182,201.78,0.53382,0.29951,0.79078,-35.662 > fitmap #18 inMap #12 Fit molecule I-EGF3 (#18) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 310 atoms average map value = 0.1618, steps = 204 shifted from previous position = 2.44 rotated from previous position = 8.48 degrees atoms outside contour = 133, contour level = 0.14384 Position of I-EGF3 (#18) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.96435014 0.09915673 -0.24535025 390.98644598 0.10659231 0.99415437 -0.01718040 13.93866547 0.24221247 -0.04272037 -0.96928225 337.14979433 Axis -0.05230516 -0.99851504 0.01522787 Axis point 174.17503509 0.00000000 192.85317726 Rotation angle (degrees) 165.86875303 Shift along axis -29.23450314 > select add #19 620 atoms, 601 bonds, 110 residues, 2 models selected > select subtract #18 310 atoms, 299 bonds, 57 residues, 1 model selected > view matrix models > #19,-0.43908,-0.89642,-0.060339,419.02,0.61422,-0.25049,-0.74832,234.78,0.6557,-0.36564,0.66058,75.809 > fitmap #19 inMap #12 Fit molecule I-EGF4 (#19) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 310 atoms average map value = 0.1045, steps = 208 shifted from previous position = 4.09 rotated from previous position = 8 degrees atoms outside contour = 226, contour level = 0.14384 Position of I-EGF4 (#19) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.92089228 0.37749684 0.09722930 290.22890707 0.34559583 0.67523483 0.65162983 -52.43453428 0.18033559 0.63368293 -0.75227988 203.94421091 Axis -0.19763181 -0.91516864 -0.35129479 Axis point 148.59838551 0.00000000 115.43880334 Rotation angle (degrees) 177.39759608 Shift along axis -81.01656192 > volume #12 level 0.09872 > select add #10 3694 atoms, 3759 bonds, 511 residues, 2 models selected > select subtract #19 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,0.22495,0.78311,-0.57977,13.125,-0.78164,-0.21022,-0.58724,461.92,-0.58176,0.58527,0.56482,104.55 > view matrix models > #10,0.22495,0.78311,-0.57977,12.27,-0.78164,-0.21022,-0.58724,459.88,-0.58176,0.58527,0.56482,106.33 [Repeated 1 time(s)] > select add #15 4711 atoms, 4810 bonds, 2 pseudobonds, 639 residues, 3 models selected > select subtract #10 1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected > view matrix models > #15,-0.52545,-0.5567,0.64342,302.56,0.60405,-0.77666,-0.17867,269.51,0.59918,0.29477,0.74437,-43.358 > fitmap #15 inMap #12 Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1327 atoms average map value = 0.1701, steps = 768 shifted from previous position = 42.2 rotated from previous position = 11.2 degrees atoms outside contour = 347, contour level = 0.098719 Position of calf2 (#15) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.87648818 0.40146766 -0.26569189 327.63686451 0.45185340 0.87646330 -0.16625459 -59.25651157 0.16612335 -0.26577396 -0.94961425 358.31728090 Axis -0.22314254 -0.96821695 0.11297500 Axis point 149.91524935 0.00000000 195.12896599 Rotation angle (degrees) 167.11499011 Shift along axis 24.74433088 > volume #12 level 0.1551 > view matrix models > #15,-0.52545,-0.5567,0.64342,297.09,0.60405,-0.77666,-0.17867,270.97,0.59918,0.29477,0.74437,-45.106 > volume #12 level 0.1156 > hide #!15 models > show #!15 models > select add #13 2352 atoms, 2371 bonds, 3 pseudobonds, 334 residues, 4 models selected > select subtract #15 1025 atoms, 1021 bonds, 1 pseudobond, 149 residues, 2 models selected > view matrix models > #13,-0.58997,-0.65166,0.47673,345.78,0.54647,-0.75692,-0.3584,291.79,0.5944,0.049077,0.80267,-4.3884 > ui mousemode right "rotate selected models" > view matrix models > #13,-0.60257,-0.64676,0.46756,348.9,0.53993,-0.76181,-0.35794,293.84,0.58769,0.036763,0.80825,-1.875 > view matrix models > #13,-0.31096,-0.80971,0.49767,310.21,0.42529,-0.58683,-0.68903,337.04,0.84996,-0.0026099,0.52684,-9.6238 > view matrix models > #13,-0.18751,-0.82396,0.53473,281.81,0.90332,-0.35848,-0.2356,138.64,0.38581,0.43885,0.81151,-23.802 > view matrix models > #13,-0.37606,-0.84146,0.38796,344.15,0.2492,-0.49512,-0.83232,379.22,0.89245,-0.21633,0.39589,33.706 > view matrix models > #13,-0.56967,-0.72727,0.38282,366.79,0.5866,-0.68604,-0.4304,282.68,0.57565,-0.020624,0.81744,8.2783 > view matrix models > #13,0.18303,-0.98259,0.031768,301.96,0.39778,0.044468,-0.9164,276.16,0.89904,0.18037,0.399,-30.191 > ui mousemode right "translate selected models" > view matrix models > #13,0.18303,-0.98259,0.031768,304.33,0.39778,0.044468,-0.9164,276.47,0.89904,0.18037,0.399,-30.511 > fitmap #13 inMap #12 Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1025 atoms average map value = 0.1995, steps = 308 shifted from previous position = 11.5 rotated from previous position = 29.2 degrees atoms outside contour = 233, contour level = 0.11564 Position of calf1 (#13) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.57633215 -0.74739022 0.33052851 370.93471022 -0.27813437 0.55970271 0.78062420 54.20471398 -0.76842860 0.35796749 -0.53044958 415.07317739 Axis -0.33345799 0.86702994 0.37022271 Axis point 275.55183482 0.00000000 114.23649383 Rotation angle (degrees) 140.67280684 Shift along axis 76.97548371 > volume #12 level 0.2454 > volume #12 level 0.189 > view matrix models > #13,0.56706,-0.79248,-0.22456,235.75,0.17921,0.3848,-0.90544,296.58,0.80395,0.47319,0.36022,-52.786 > view matrix models > #13,0.56706,-0.79248,-0.22456,238.72,0.17921,0.3848,-0.90544,299.95,0.80395,0.47319,0.36022,-51.436 > ui mousemode right "rotate selected models" > view matrix models > #13,-0.68382,-0.70419,0.19108,422.89,-0.70346,0.56674,-0.4289,385.15,0.19373,-0.4277,-0.88291,391.6 > view matrix models > #13,-0.66931,-0.64212,0.37377,384.24,-0.74298,0.57711,-0.339,378.87,0.0019698,-0.5046,-0.86335,440.27 > view matrix models > #13,-0.61736,-0.58293,0.52826,342.35,-0.78069,0.53672,-0.3201,390.26,-0.096927,-0.61002,-0.78643,466.17 > ui mousemode right "translate selected models" > view matrix models > #13,-0.61736,-0.58293,0.52826,334.39,-0.78069,0.53672,-0.3201,358.05,-0.096927,-0.61002,-0.78643,474.02 > view matrix models > #13,-0.61736,-0.58293,0.52826,334.24,-0.78069,0.53672,-0.3201,353.3,-0.096927,-0.61002,-0.78643,469.83 > fitmap #13 inMap #12 Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1025 atoms average map value = 0.1951, steps = 212 shifted from previous position = 4.43 rotated from previous position = 36.1 degrees atoms outside contour = 487, contour level = 0.18897 Position of calf1 (#13) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.50319207 0.27336220 0.81979927 -87.65948442 0.68063836 0.45915770 -0.57088144 59.97575740 -0.53247456 0.84524984 0.04498371 205.93326038 Axis 0.70807040 0.67614146 0.20363945 Axis point 0.00000000 -71.16457947 148.29408539 Rotation angle (degrees) 89.78991060 Shift along axis 20.41914501 > volume #12 level 0.1213 > view matrix models > #13,-0.11267,-0.81169,0.57311,261.64,-0.97145,-0.0312,-0.23518,472.25,0.20877,-0.58325,-0.78501,397.62 > fitmap #13 inMap #12 Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1025 atoms average map value = 0.1973, steps = 152 shifted from previous position = 3.36 rotated from previous position = 14 degrees atoms outside contour = 236, contour level = 0.12128 Position of calf1 (#13) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.37728647 0.44780172 0.81063465 -87.54190524 0.60533824 0.54320089 -0.58180615 62.92894147 -0.70087126 0.71021574 -0.06612916 277.28118686 Axis 0.64773065 0.75776480 0.07897795 Axis point 98.79766814 0.00000000 194.17857056 Rotation angle (degrees) 94.17602654 Shift along axis 12.88086028 > view matrix models > #13,0.022812,-0.76253,0.64655,217.54,-0.92468,-0.26194,-0.27631,504.3,0.38005,-0.59155,-0.71108,350.88 > fitmap #13 inMap #12 Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1025 atoms average map value = 0.1973, steps = 88 shifted from previous position = 4.59 rotated from previous position = 0.0124 degrees atoms outside contour = 238, contour level = 0.12128 Position of calf1 (#13) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.37722813 0.44763916 0.81075157 -87.52700647 0.60537059 0.54332717 -0.58165455 62.86981898 -0.70087472 0.71022162 -0.06602929 277.27170471 Axis 0.64765362 0.75782050 0.07907517 Axis point 98.83074693 0.00000000 194.16452601 Rotation angle (degrees) 94.17120650 Shift along axis 12.88216273 > select subtract #13 Nothing selected > select add #15 1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected > view matrix models > #15,-0.52545,-0.5567,0.64342,296.68,0.60405,-0.77666,-0.17867,266.6,0.59918,0.29477,0.74437,-43.542 > fitmap #15 inMap #12 Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1327 atoms average map value = 0.1701, steps = 1108 shifted from previous position = 47.7 rotated from previous position = 11.2 degrees atoms outside contour = 433, contour level = 0.12128 Position of calf2 (#15) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.87681153 0.40052901 -0.26604142 327.91627250 0.45107304 0.87679974 -0.16659928 -59.10119741 0.16653721 -0.26608028 -0.94945597 358.27367084 Axis -0.22268277 -0.96830353 0.11314003 Axis point 149.99134622 0.00000000 195.15882427 Rotation angle (degrees) 167.09299228 Shift along axis 24.74168755 > volume #12 level 0.08744 > view matrix models > #15,-0.52545,-0.5567,0.64342,301.01,0.60405,-0.77666,-0.17867,268.36,0.59918,0.29477,0.74437,-42.462 > view matrix models > #15,-0.52545,-0.5567,0.64342,300.02,0.60405,-0.77666,-0.17867,271.61,0.59918,0.29477,0.74437,-41.738 > fitmap #15 inMap #12 Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 1327 atoms average map value = 0.1701, steps = 1120 shifted from previous position = 44.9 rotated from previous position = 11.2 degrees atoms outside contour = 300, contour level = 0.087438 Position of calf2 (#15) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.87644563 0.40162544 -0.26559378 327.58304345 0.45196947 0.87641891 -0.16617307 -59.28717539 0.16603208 -0.26568194 -0.94965596 358.32658500 Axis -0.22321428 -0.96820570 0.11292968 Axis point 149.90239475 0.00000000 195.12189039 Rotation angle (degrees) 167.12058576 Shift along axis 24.74667455 > hide #!12 models > select subtract #15 Nothing selected > select add #13 1025 atoms, 1021 bonds, 1 pseudobond, 149 residues, 2 models selected > view matrix models > #13,0.022777,-0.76267,0.64639,218.2,-0.92466,-0.26189,-0.27642,502.78,0.3801,-0.5914,-0.71118,354.69 > ui mousemode right "rotate selected models" > view matrix models > #13,-0.10105,-0.63942,0.76218,207.9,-0.80472,-0.39794,-0.44054,522.74,0.58499,-0.65786,-0.47434,289.35 > view matrix models > #13,-0.19184,-0.97932,0.064308,378.91,-0.08431,-0.048839,-0.99524,398.86,0.9778,-0.19635,-0.073197,79.392 > view matrix models > #13,-0.69313,-0.66949,0.26713,404.6,-0.1521,-0.2264,-0.96208,435.88,0.70459,-0.70748,0.055093,197.32 > view matrix models > #13,-0.63302,-0.71008,0.30833,392.75,-0.36466,-0.077825,-0.92788,451.44,0.68287,-0.69981,-0.20967,238.2 > select add #15 2352 atoms, 2371 bonds, 3 pseudobonds, 334 residues, 4 models selected > select subtract #13 1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected > view matrix models > #15,-0.57419,-0.54668,0.60947,313.14,0.56863,-0.80186,-0.18353,284.99,0.58904,0.24118,0.77127,-32.418 > ui mousemode right "translate selected models" > view matrix models > #15,-0.57419,-0.54668,0.60947,311.56,0.56863,-0.80186,-0.18353,280.1,0.58904,0.24118,0.77127,-33.952 > view matrix models > #15,-0.57419,-0.54668,0.60947,309.7,0.56863,-0.80186,-0.18353,275.36,0.58904,0.24118,0.77127,-35.768 > show #!12 models > view matrix models > #15,-0.57419,-0.54668,0.60947,309.8,0.56863,-0.80186,-0.18353,276.81,0.58904,0.24118,0.77127,-35.994 > view matrix models > #15,-0.57419,-0.54668,0.60947,307.07,0.56863,-0.80186,-0.18353,278.06,0.58904,0.24118,0.77127,-37.186 > ui mousemode right "rotate selected models" > view matrix models > #15,-0.35874,-0.85709,0.36974,342.8,0.93306,-0.31803,0.1681,64.378,-0.026486,0.40529,0.9138,57.11 > view matrix models > #15,-0.44855,-0.605,0.65786,283.74,0.76857,-0.6368,-0.06159,187.61,0.45619,0.47799,0.75061,-48.718 > view matrix models > #15,-0.12867,-0.66409,0.7365,212.62,0.98977,-0.1321,0.053807,29.472,0.061561,0.73589,0.67429,2.067 > view matrix models > #15,-0.12879,-0.66001,0.74013,211.48,0.98987,-0.13059,0.055793,28.945,0.05983,0.73982,0.67014,2.1975 > ui mousemode right "translate selected models" > view matrix models > #15,-0.12879,-0.66001,0.74013,213.42,0.98987,-0.13059,0.055793,34.669,0.05983,0.73982,0.67014,2.1546 > ui mousemode right "rotate selected models" > view matrix models > #15,0.18418,-0.43587,0.88096,83.882,0.9127,-0.25677,-0.31787,118.08,0.36476,0.8626,0.35053,-54.678 > view matrix models > #15,0.27455,-0.37285,0.88634,50.773,0.96148,0.093754,-0.25839,34.608,0.01324,0.92314,0.38423,10.756 > view matrix models > #15,0.10994,-0.65328,0.7491,156.44,0.4758,-0.62711,-0.61672,321.19,0.87266,0.42422,0.24188,-76.808 > view matrix models > #15,-0.65147,-0.3551,0.67044,284.01,-0.50591,-0.4552,-0.7327,527.08,0.56537,-0.81651,0.1169,239.86 > view matrix models > #15,-0.22713,-0.30991,0.92324,149.81,-0.63605,-0.67068,-0.38161,557.65,0.73746,-0.6739,-0.044787,191.96 > ui mousemode right "translate selected models" > view matrix models > #15,-0.22713,-0.30991,0.92324,149.88,-0.63605,-0.67068,-0.38161,552.63,0.73746,-0.6739,-0.044787,195.07 > view matrix models > #15,-0.22713,-0.30991,0.92324,149.7,-0.63605,-0.67068,-0.38161,555.06,0.73746,-0.6739,-0.044787,197.28 > view matrix models > #15,-0.22713,-0.30991,0.92324,149.3,-0.63605,-0.67068,-0.38161,554.75,0.73746,-0.6739,-0.044787,196.96 > ui mousemode right "rotate selected models" > view matrix models > #15,-0.20841,-0.54579,0.81159,201.73,0.23293,-0.83363,-0.5008,399.52,0.9499,0.084675,0.30087,-32.629 > view matrix models > #15,-0.13967,-0.60843,0.78122,201.12,0.55362,-0.7021,-0.44784,295.44,0.82097,0.36995,0.4349,-71.567 > view matrix models > #15,-0.19995,-0.65291,0.73057,228.97,0.44066,-0.72588,-0.52812,334.83,0.87512,0.21634,0.43285,-55.002 > view matrix models > #15,-0.30093,-0.70218,0.64528,270.94,0.19139,-0.70735,-0.68046,405.66,0.93424,-0.081271,0.34726,-3.2183 > view matrix models > #15,-0.12543,-0.58229,0.80325,190.48,0.19567,-0.80826,-0.55536,409.46,0.97261,0.087516,0.21532,-28.723 > view matrix models > #15,-0.58269,-0.6462,0.49284,342.23,0.057639,-0.63776,-0.76807,433.17,0.81065,-0.41914,0.40887,81.383 > view matrix models > #15,-0.44025,-0.64171,0.628,293.51,0.6964,-0.68553,-0.2123,233.07,0.56675,0.34388,0.74869,-43.793 > view matrix models > #15,-0.49847,-0.5342,0.68276,280.56,0.52443,-0.81294,-0.25318,300.93,0.69029,0.23186,0.68538,-44.009 > ui mousemode right "translate selected models" > view matrix models > #15,-0.49847,-0.5342,0.68276,279.29,0.52443,-0.81294,-0.25318,300.92,0.69029,0.23186,0.68538,-44.601 > view matrix models > #15,-0.49847,-0.5342,0.68276,279.51,0.52443,-0.81294,-0.25318,300.74,0.69029,0.23186,0.68538,-44.439 > view matrix models > #15,-0.49847,-0.5342,0.68276,281.14,0.52443,-0.81294,-0.25318,302.84,0.69029,0.23186,0.68538,-45.134 > volume #12 level 0.09872 > select add #10 4711 atoms, 4810 bonds, 2 pseudobonds, 639 residues, 3 models selected > select subtract #15 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,0.22495,0.78311,-0.57977,34.527,-0.78164,-0.21022,-0.58724,475.48,-0.58176,0.58527,0.56482,97.146 > select add #9 4058 atoms, 4143 bonds, 538 residues, 2 models selected > select subtract #10 674 atoms, 683 bonds, 84 residues, 1 model selected > view matrix models > #9,0.084195,-0.27473,0.95783,68.859,0.63438,0.75605,0.16109,-50.508,-0.76842,0.59407,0.23794,219.09 > hide #!12 models > view matrix models > #9,0.084195,-0.27473,0.95783,76.215,0.63438,0.75605,0.16109,-47.745,-0.76842,0.59407,0.23794,223.92 > view matrix models > #9,0.084195,-0.27473,0.95783,73.993,0.63438,0.75605,0.16109,-48.618,-0.76842,0.59407,0.23794,222.73 > view matrix models > #9,0.084195,-0.27473,0.95783,74.684,0.63438,0.75605,0.16109,-48.521,-0.76842,0.59407,0.23794,224.32 > ui mousemode right "rotate selected models" > view matrix models > #9,0.28696,0.41509,0.86334,-90.53,0.92891,0.099637,-0.35666,66.057,-0.23407,0.90431,-0.35699,111.25 > view matrix models > #9,0.80627,0.45421,0.37898,-157.83,0.59124,-0.63943,-0.4915,287.48,0.019086,0.62035,-0.7841,153.89 > view matrix models > #9,0.92669,-0.25525,-0.27584,13.318,-0.26057,-0.96529,0.017858,473.56,-0.27082,0.055325,-0.96104,335.9 > view matrix models > #9,0.93195,-0.25961,-0.25312,11.135,-0.26082,-0.96494,0.029393,472.53,-0.25188,0.038626,-0.96699,335.93 > view matrix models > #9,0.5527,-0.35332,-0.75478,147.94,0.085812,-0.87674,0.47325,348.28,-0.82895,-0.32633,-0.45426,475.21 > view matrix models > #9,0.5908,-0.60613,-0.53251,169.9,-0.25916,-0.7676,0.58619,385.14,-0.76407,-0.20831,-0.61058,453.29 > view matrix models > #9,0.88779,-0.2864,-0.36027,34.415,-0.14264,-0.91546,0.37628,409.25,-0.43758,-0.28267,-0.85359,424.75 > view matrix models > #9,0.94371,-0.26699,-0.19524,5.1708,-0.22009,-0.94751,0.2319,443.37,-0.2469,-0.17588,-0.95295,375.26 > view matrix models > #9,0.92098,-0.2522,0.29697,-36.4,-0.38961,-0.59908,0.69951,368.23,0.001495,-0.75993,-0.65,412.9 > view matrix models > #9,0.82731,-0.55688,0.073702,60.63,-0.32694,-0.37066,0.86932,296.76,-0.45679,-0.7433,-0.48872,485.73 > view matrix models > #9,0.74202,-0.66812,-0.055038,110.25,-0.18845,-0.28667,0.93931,247.1,-0.64335,-0.68661,-0.33863,498.3 > show #!12 models > view matrix models > #9,0.7454,-0.66392,-0.060001,109.21,-0.18864,-0.29641,0.93625,249.29,-0.63937,-0.68656,-0.34618,498.17 > ui mousemode right "translate selected models" > view matrix models > #9,0.7454,-0.66392,-0.060001,102.95,-0.18864,-0.29641,0.93625,246.88,-0.63937,-0.68656,-0.34618,491.38 > view matrix models > #9,0.7454,-0.66392,-0.060001,105.95,-0.18864,-0.29641,0.93625,237.94,-0.63937,-0.68656,-0.34618,488.03 > view matrix models > #9,0.7454,-0.66392,-0.060001,108.14,-0.18864,-0.29641,0.93625,237.2,-0.63937,-0.68656,-0.34618,490.24 > view matrix models > #9,0.7454,-0.66392,-0.060001,106.92,-0.18864,-0.29641,0.93625,236.03,-0.63937,-0.68656,-0.34618,489.9 > view matrix models > #9,0.7454,-0.66392,-0.060001,110.46,-0.18864,-0.29641,0.93625,238.57,-0.63937,-0.68656,-0.34618,490.71 > hide #!12 models > show #!12 models > select add #10 4058 atoms, 4143 bonds, 538 residues, 2 models selected > select subtract #9 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,0.22495,0.78311,-0.57977,35.194,-0.78164,-0.21022,-0.58724,476.94,-0.58176,0.58527,0.56482,97.169 > view matrix models > #10,0.22495,0.78311,-0.57977,36.606,-0.78164,-0.21022,-0.58724,480.32,-0.58176,0.58527,0.56482,95.513 > view matrix models > #10,0.22495,0.78311,-0.57977,36.452,-0.78164,-0.21022,-0.58724,480.22,-0.58176,0.58527,0.56482,95.67 > select add #9 4058 atoms, 4143 bonds, 538 residues, 2 models selected > select subtract #10 674 atoms, 683 bonds, 84 residues, 1 model selected > view matrix models > #9,0.7454,-0.66392,-0.060001,109.94,-0.18864,-0.29641,0.93625,239.58,-0.63937,-0.68656,-0.34618,486.89 > view matrix models > #9,0.7454,-0.66392,-0.060001,109.35,-0.18864,-0.29641,0.93625,239.22,-0.63937,-0.68656,-0.34618,486.84 > view matrix models > #9,0.7454,-0.66392,-0.060001,109.45,-0.18864,-0.29641,0.93625,239.26,-0.63937,-0.68656,-0.34618,486.9 > view matrix models > #9,0.7454,-0.66392,-0.060001,113.36,-0.18864,-0.29641,0.93625,240.55,-0.63937,-0.68656,-0.34618,489.7 > view matrix models > #9,0.7454,-0.66392,-0.060001,113.19,-0.18864,-0.29641,0.93625,240.6,-0.63937,-0.68656,-0.34618,489.34 > view matrix models > #9,0.7454,-0.66392,-0.060001,112.21,-0.18864,-0.29641,0.93625,240.26,-0.63937,-0.68656,-0.34618,488.66 > view matrix models > #9,0.7454,-0.66392,-0.060001,111.03,-0.18864,-0.29641,0.93625,238.65,-0.63937,-0.68656,-0.34618,487.05 > view matrix models > #9,0.7454,-0.66392,-0.060001,112.88,-0.18864,-0.29641,0.93625,238.51,-0.63937,-0.68656,-0.34618,487.67 > volume #12 level 0.12 > volume #12 level 0.1 > select subtract #9 Nothing selected > select add #10 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,0.22495,0.78311,-0.57977,34.772,-0.78164,-0.21022,-0.58724,479.07,-0.58176,0.58527,0.56482,96.507 > fitmap #10 inMap #12 Fit molecule Fab (#10) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 3384 atoms average map value = 0.0571, steps = 100 shifted from previous position = 7.49 rotated from previous position = 3.07 degrees atoms outside contour = 2686, contour level = 0.1 Position of Fab (#10) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.97928041 -0.14481400 -0.14155840 83.61835583 0.08949133 -0.31760009 0.94399231 139.44098174 -0.18166226 -0.93710143 -0.29805995 549.68289905 Axis -0.99210977 0.02115122 0.12357523 Axis point 0.00000000 270.38783251 229.41553400 Rotation angle (degrees) 108.55348773 Shift along axis -12.08204694 > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs ——— End of log from Fri Jan 31 02:27:14 2025 ——— opened ChimeraX session > combine #9,10,13,14,15,17,18,19 conformation1 true Expected a keyword > combine #9,10,13,14,15,17,18,19 conformation1 keepModels true Expected a keyword > combine #9,10,13,14,15,17,18,19 name conformation1 keepModels true Expected a keyword > combine #9, 10, 13, 14, 15, 17, 18, 19 name conformation1 keepModels true Expected a keyword > combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1 Expected a keyword > combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1 Expected a keyword > combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1 Expected a keyword > combine #9, 10, 13, 14, 15, 17, 18, 19 Remapping chain ID 'C' in calf1 #13 to 'D' Remapping chain ID 'I' in calf1 #13 to 'K' Remapping chain ID 'J' in calf1 #13 to 'M' Remapping chain ID 'A' in propeller_thigh #14 to 'E' Remapping chain ID 'C' in propeller_thigh #14 to 'F' Remapping chain ID 'I' in propeller_thigh #14 to 'N' Remapping chain ID 'J' in propeller_thigh #14 to 'O' Remapping chain ID 'C' in calf2 #15 to 'G' Remapping chain ID 'F' in calf2 #15 to 'P' Remapping chain ID 'I' in calf2 #15 to 'Q' Remapping chain ID 'J' in calf2 #15 to 'R' Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S' Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T' Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U' Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V' Remapping chain ID 'C' in I-EGF3 #18 to 'W' Remapping chain ID 'E' in I-EGF3 #18 to 'X' Remapping chain ID 'I' in I-EGF3 #18 to 'Y' Remapping chain ID 'J' in I-EGF3 #18 to 'Z' Remapping chain ID 'C' in I-EGF4 #19 to 'a' Remapping chain ID 'D' in I-EGF4 #19 to 'b' Remapping chain ID 'I' in I-EGF4 #19 to 'c' Remapping chain ID 'J' in I-EGF4 #19 to 'd' > hide #!21 models > show #!21 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!10 models > hide #9 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!21 models > show #!21 models > select #21/E:459 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select #21/E:547 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 70 atoms, 71 bonds, 9 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select clear > select #21/A:632 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #21/A:631 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 83 atoms, 82 bonds, 11 residues, 1 model selected > select up 426 atoms, 432 bonds, 59 residues, 1 model selected > select up 475 atoms, 481 bonds, 65 residues, 1 model selected > select up 1011 atoms, 1021 bonds, 135 residues, 1 model selected > color sel blue > select #21/P:927 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 105 atoms, 109 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > select up 745 atoms, 766 bonds, 96 residues, 1 model selected > color sel blue > select #21/B:615 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 46 atoms, 45 bonds, 6 residues, 1 model selected > select up 674 atoms, 683 bonds, 84 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 674 atoms, 683 bonds, 84 residues, 1 model selected > color sel blue > select #21/P:828 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 42 atoms, 43 bonds, 5 residues, 1 model selected > select up 496 atoms, 513 bonds, 65 residues, 1 model selected > select up 514 atoms, 529 bonds, 68 residues, 1 model selected > color sel blue > select #21/S:350 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 110 atoms, 110 bonds, 14 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > select up 3522 atoms, 3586 bonds, 455 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4003 atoms, 4076 bonds, 520 residues, 1 model selected > color sel red > select #21/X:536 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 4 residues, 1 model selected > select up 296 atoms, 302 bonds, 39 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 296 atoms, 302 bonds, 39 residues, 1 model selected > color sel red > select #21/b:569 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 107 atoms, 106 bonds, 16 residues, 1 model selected > select up 296 atoms, 299 bonds, 43 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 296 atoms, 299 bonds, 43 residues, 1 model selected > color sel red > select #21/H:4 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 35 atoms, 34 bonds, 4 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1734 atoms, 1783 bonds, 227 residues, 1 model selected > color sel forest green > select #21/L:87 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 46 atoms, 47 bonds, 5 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > ui tool show "Color Actions" > color sel chartreuse > show #!12 models > ui tool show "Color Zone" > color zone #12 near #21 distance 15 > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 25 [Repeated 2 time(s)] > hide #!12 models > show #!12 models > volume #12 level 0.1592 > volume #12 level 0.1296 > volume #12 level 0.12 > hide #!21 models > volume #12 level 0.1 > color zone #12 near #21 distance 3 > color zone #12 near #21 distance 30 [Repeated 2 time(s)] > hide #!12 models > show #!12 models > show #!21 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > volume #12 level 0.2629 > hide #!21 models > show #!14 models > ui tool show "Fit in Map" > fitmap #14 inMap #12 Fit molecule propeller_thigh (#14) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms average map value = 0.3683, steps = 64 shifted from previous position = 0.362 rotated from previous position = 0.848 degrees atoms outside contour = 1979, contour level = 0.26287 Position of propeller_thigh (#14) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.94940963 0.24528192 -0.19610742 354.76956495 0.26078501 0.96370214 -0.05717829 -1.66005707 0.17496434 -0.10542750 -0.97891395 353.82671079 Axis -0.12883067 -0.99080226 0.04139494 Axis point 160.56747216 0.00000000 193.61017366 Rotation angle (degrees) 169.20717929 Shift along axis -29.41377446 > fitmap #14 inMap #12 Fit molecule propeller_thigh (#14) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms average map value = 0.3683, steps = 40 shifted from previous position = 0.00842 rotated from previous position = 0.0144 degrees atoms outside contour = 1980, contour level = 0.26287 Position of propeller_thigh (#14) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.94947078 0.24508837 -0.19605335 354.79344879 0.26056554 0.96376718 -0.05708260 -1.65492422 0.17495950 -0.10528301 -0.97893036 353.80249907 Axis -0.12872296 -0.99081885 0.04133298 Axis point 160.58355030 0.00000000 193.59629166 Rotation angle (degrees) 169.20909591 Shift along axis -29.40662240 > show #!21 models > hide #!21 models > show #!21 models > close #21 > combine #9, 10, 13, 14, 15, 17, 18, 19 Remapping chain ID 'C' in calf1 #13 to 'D' Remapping chain ID 'I' in calf1 #13 to 'K' Remapping chain ID 'J' in calf1 #13 to 'M' Remapping chain ID 'A' in propeller_thigh #14 to 'E' Remapping chain ID 'C' in propeller_thigh #14 to 'F' Remapping chain ID 'I' in propeller_thigh #14 to 'N' Remapping chain ID 'J' in propeller_thigh #14 to 'O' Remapping chain ID 'C' in calf2 #15 to 'G' Remapping chain ID 'F' in calf2 #15 to 'P' Remapping chain ID 'I' in calf2 #15 to 'Q' Remapping chain ID 'J' in calf2 #15 to 'R' Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S' Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T' Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U' Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V' Remapping chain ID 'C' in I-EGF3 #18 to 'W' Remapping chain ID 'E' in I-EGF3 #18 to 'X' Remapping chain ID 'I' in I-EGF3 #18 to 'Y' Remapping chain ID 'J' in I-EGF3 #18 to 'Z' Remapping chain ID 'C' in I-EGF4 #19 to 'a' Remapping chain ID 'D' in I-EGF4 #19 to 'b' Remapping chain ID 'I' in I-EGF4 #19 to 'c' Remapping chain ID 'J' in I-EGF4 #19 to 'd' > volume #12 level 0.12 > hide #!14 models > hide #!12 models > select #21/E:456 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > select #21/E:456 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > color sel medium blue > select #21/S:346 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 110 atoms, 110 bonds, 14 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > color sel orange red > select #21/S:369 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 59 atoms, 59 bonds, 8 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > select up 3522 atoms, 3586 bonds, 455 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4003 atoms, 4076 bonds, 520 residues, 1 model selected > color sel red > select #21/X:548 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 28 atoms, 27 bonds, 4 residues, 1 model selected > select up 296 atoms, 302 bonds, 39 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 296 atoms, 302 bonds, 39 residues, 1 model selected > color sel red > select #21/b:569 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 107 atoms, 106 bonds, 16 residues, 1 model selected > select up 296 atoms, 299 bonds, 43 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 296 atoms, 299 bonds, 43 residues, 1 model selected > color sel red > select clear > select #21/B:625 8 atoms, 7 bonds, 1 residue, 1 model selected > select #21/B:666 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 45 atoms, 45 bonds, 5 residues, 1 model selected > select up 674 atoms, 683 bonds, 84 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 674 atoms, 683 bonds, 84 residues, 1 model selected > color sel red > select #21/H:22 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 62 atoms, 61 bonds, 9 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > color sel forest green > select #21/L:19 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 23 atoms, 22 bonds, 3 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > ui tool show "Color Actions" > color sel chartreuse > show #!12 models > color zone #12 near #21 distance 30 > volume #12 level 0.1 > volume #12 level 0.11 > volume #12 level 0.12 > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 25 [Repeated 1 time(s)] > select add #21 15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected > hide #!12 models > show #!12 models > hide #!21 models > show #!21 models > hide #!21 models > volume #12 level 0.11 > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 20 [Repeated 1 time(s)] > color zone #12 near #21 distance 25 [Repeated 1 time(s)] > color zone #12 near #21 distance 3 > color zone #12 near #21 distance 30 [Repeated 1 time(s)] > select subtract #21 Nothing selected > select add #21 15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected > hide #!12 models > show #!12 models > show #!17 models > hide #!12 models > show #!12 models > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 48 shifted from previous position = 0.0681 rotated from previous position = 0.418 degrees atoms outside contour = 618, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95974100 0.21021955 -0.18629263 360.69372189 0.22838448 0.97012286 -0.08186667 0.88971904 0.16351676 -0.12111714 -0.97907758 361.54098690 Axis -0.11135741 -0.99244325 0.05153567 Axis point 164.06818466 0.00000000 196.82105777 Rotation angle (degrees) 169.84937905 Shift along axis -22.41665958 > color zone #12 near #21 distance 3 > color zone #12 near #21 distance 30 [Repeated 1 time(s)] > hide #!17 models > volume #12 level 0.139 > volume #12 level 0.1439 > volume #12 level 0.12 > color zone #12 near #21 distance 1 > color zone #12 near #21 distance 15 [Repeated 1 time(s)] > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 20 [Repeated 1 time(s)] > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 22 [Repeated 1 time(s)] > volume #12 level 0.11 > hide #!12 models > show #!12 models > show #!21 models > hide #!12 models > color single #12 > show #!12 models > show #!17 models > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 44 shifted from previous position = 0.0153 rotated from previous position = 0.0418 degrees atoms outside contour = 614, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95961963 0.21089946 -0.18614936 360.50801404 0.22900220 0.97000330 -0.08155727 0.73751865 0.16336511 -0.12089257 -0.97913064 361.53119730 Axis -0.11168883 -0.99241299 0.05140100 Axis point 163.99722730 0.00000000 196.79079982 Rotation angle (degrees) 169.85771465 Shift along axis -22.41357586 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 44 shifted from previous position = 0.008 rotated from previous position = 0.00824 degrees atoms outside contour = 615, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95960728 0.21084503 -0.18627461 360.54629056 0.22897118 0.97000641 -0.08160739 0.75347645 0.16348106 -0.12096256 -0.97910265 361.52223861 Axis -0.11166828 -0.99241370 0.05143202 Axis point 164.00449613 0.00000000 196.79966706 Rotation angle (degrees) 169.85064877 Shift along axis -22.41552400 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 80 shifted from previous position = 0.0134 rotated from previous position = 0.0214 degrees atoms outside contour = 610, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95958246 0.21110236 -0.18611097 360.45194872 0.22916859 0.96998108 -0.08135395 0.67083132 0.16335011 -0.12071661 -0.97915486 361.50604045 Axis -0.11178297 -0.99240737 0.05130487 Axis point 163.97647346 0.00000000 196.77157215 Rotation angle (degrees) 169.85922264 Shift along axis -22.41110365 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 80 shifted from previous position = 0.0103 rotated from previous position = 0.0196 degrees atoms outside contour = 614, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95964783 0.21079345 -0.18612404 360.52750241 0.22888918 0.97003133 -0.08154107 0.75113892 0.16335782 -0.12085249 -0.97913681 361.53376039 Axis -0.11163224 -0.99242012 0.05138626 Axis point 164.00789795 0.00000000 196.79160454 Rotation angle (degrees) 169.85874481 Shift along axis -22.41407191 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 48 shifted from previous position = 0.0153 rotated from previous position = 0.0314 degrees atoms outside contour = 610, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95957850 0.21129275 -0.18591521 360.37382819 0.22936243 0.96992226 -0.08150871 0.67690037 0.16310110 -0.12085597 -0.97917918 361.57720508 Axis -0.11187996 -0.99239259 0.05137929 Axis point 163.95425559 0.00000000 196.78353624 Rotation angle (degrees) 169.87211260 Shift along axis -22.41277795 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 48 shifted from previous position = 0.0162 rotated from previous position = 0.0343 degrees atoms outside contour = 612, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95958311 0.21089382 -0.18634390 360.54478483 0.22900288 0.97001214 -0.08145010 0.71355509 0.16357852 -0.12083143 -0.97910256 361.47471908 Axis -0.11168940 -0.99241509 0.05135911 Axis point 164.00037708 0.00000000 196.78248769 Rotation angle (degrees) 169.84577334 Shift along axis -22.41215583 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 96 shifted from previous position = 0.00738 rotated from previous position = 0.0176 degrees atoms outside contour = 612, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95957811 0.21110882 -0.18612605 360.45928970 0.22918514 0.96997307 -0.08140276 0.67971066 0.16335242 -0.12076963 -0.97914793 361.51745168 Axis -0.11178913 -0.99240533 0.05133088 Axis point 163.97821398 0.00000000 196.77870461 Rotation angle (degrees) 169.85869128 Shift along axis -22.41297101 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 64 shifted from previous position = 0.00773 rotated from previous position = 0.00523 degrees atoms outside contour = 612, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95956408 0.21119416 -0.18610155 360.43749216 0.22926829 0.96995345 -0.08140241 0.67098548 0.16331813 -0.12077801 -0.97915262 361.53320433 Axis -0.11183218 -0.99240036 0.05133304 Axis point 163.96968676 0.00000000 196.78275078 Rotation angle (degrees) 169.86036429 Shift along axis -22.41579832 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 44 shifted from previous position = 0.0121 rotated from previous position = 0.0387 degrees atoms outside contour = 614, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95964202 0.21059688 -0.18637636 360.62043575 0.22873840 0.97005863 -0.08163941 0.79096944 0.16360299 -0.12097604 -0.97908062 361.49727976 Axis -0.11154580 -0.99242688 0.05144341 Axis point 164.03051104 0.00000000 196.80159120 Rotation angle (degrees) 169.84422573 Shift along axis -22.41402439 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 84 shifted from previous position = 0.00761 rotated from previous position = 0.0264 degrees atoms outside contour = 613, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95958207 0.21101868 -0.18620782 360.49695973 0.22912300 0.96997830 -0.08151524 0.71425710 0.16341631 -0.12088506 -0.97912303 361.52773419 Axis -0.11175106 -0.99240661 0.05138902 Axis point 163.98776890 0.00000000 196.79320085 Rotation angle (degrees) 169.85443304 Shift along axis -22.41619638 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 72 shifted from previous position = 0.0128 rotated from previous position = 0.016 degrees atoms outside contour = 609, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95954580 0.21126698 -0.18611321 360.41658157 0.22934204 0.96993667 -0.08139458 0.65677831 0.16332204 -0.12078542 -0.97915106 361.52499098 Axis -0.11186996 -0.99239610 0.05133319 Axis point 163.95951785 0.00000000 196.77817913 Rotation angle (degrees) 169.85986379 Shift along axis -22.41334077 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 40 shifted from previous position = 0.0101 rotated from previous position = 0.0714 degrees atoms outside contour = 615, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95979460 0.21005947 -0.18619704 360.70208368 0.22819673 0.97017411 -0.08178290 0.89463278 0.16346428 -0.12098434 -0.97910276 361.53175294 Axis -0.11126687 -0.99245631 0.05147965 Axis point 164.08002323 0.00000000 196.80972123 Rotation angle (degrees) 169.85385591 Shift along axis -22.41054795 > hide #!21 models > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 44 shifted from previous position = 0.00678 rotated from previous position = 0.0504 degrees atoms outside contour = 615, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95962794 0.21091572 -0.18608807 360.49719426 0.22901518 0.96999812 -0.08158240 0.74174563 0.16329807 -0.12090575 -0.97914020 361.54953831 Axis -0.11169575 -0.99241172 0.05141049 Axis point 163.99675182 0.00000000 196.79365817 Rotation angle (degrees) 169.86146501 Shift along axis -22.41468177 > fitmap #17 inMap #12 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms average map value = 0.3293, steps = 124 shifted from previous position = 0.0125 rotated from previous position = 0.00852 degrees atoms outside contour = 615, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.95962444 0.21102274 -0.18598477 360.44560145 0.22910763 0.96997772 -0.08156540 0.72522072 0.16318893 -0.12088268 -0.97916124 361.57201046 Axis -0.11174590 -0.99240661 0.05140010 Axis point 163.98072134 0.00000000 196.79239867 Rotation angle (degrees) 169.86764198 Shift along axis -22.41319629 > combine #9, 10, 13, 14, 15, 17, 18, 19 Remapping chain ID 'C' in calf1 #13 to 'D' Remapping chain ID 'I' in calf1 #13 to 'K' Remapping chain ID 'J' in calf1 #13 to 'M' Remapping chain ID 'A' in propeller_thigh #14 to 'E' Remapping chain ID 'C' in propeller_thigh #14 to 'F' Remapping chain ID 'I' in propeller_thigh #14 to 'N' Remapping chain ID 'J' in propeller_thigh #14 to 'O' Remapping chain ID 'C' in calf2 #15 to 'G' Remapping chain ID 'F' in calf2 #15 to 'P' Remapping chain ID 'I' in calf2 #15 to 'Q' Remapping chain ID 'J' in calf2 #15 to 'R' Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S' Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T' Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U' Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V' Remapping chain ID 'C' in I-EGF3 #18 to 'W' Remapping chain ID 'E' in I-EGF3 #18 to 'X' Remapping chain ID 'I' in I-EGF3 #18 to 'Y' Remapping chain ID 'J' in I-EGF3 #18 to 'Z' Remapping chain ID 'C' in I-EGF4 #19 to 'a' Remapping chain ID 'D' in I-EGF4 #19 to 'b' Remapping chain ID 'I' in I-EGF4 #19 to 'c' Remapping chain ID 'J' in I-EGF4 #19 to 'd' > close #21 > hide #!12 models Drag select of 55 residues > select #17/B:63 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 49 atoms, 48 bonds, 6 residues, 1 model selected > select up 548 atoms, 557 bonds, 74 residues, 1 model selected > select up 609 atoms, 618 bonds, 82 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 4017 atoms, 4076 bonds, 534 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > color (#!17,22 & sel) red > select #22/E:459 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > color sel blue > hide #!17 models > select #22/S:99 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 75 atoms, 75 bonds, 9 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > select up 3522 atoms, 3586 bonds, 455 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > color (#!22 & sel) red > select #22/E:489 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 79 atoms, 79 bonds, 11 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > select #22/A:631 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 83 atoms, 82 bonds, 11 residues, 1 model selected > select up 426 atoms, 432 bonds, 59 residues, 1 model selected > select up 475 atoms, 481 bonds, 65 residues, 1 model selected > select up 1011 atoms, 1021 bonds, 135 residues, 1 model selected > color sel blue > select #22/P:949 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 102 atoms, 103 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > color sel blue > select #22/P:827 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 42 atoms, 43 bonds, 5 residues, 1 model selected > select up 496 atoms, 513 bonds, 65 residues, 1 model selected > select up 514 atoms, 529 bonds, 68 residues, 1 model selected > select down 496 atoms, 513 bonds, 65 residues, 1 model selected > color sel cornflower blue > color sel blue > select #22/P:752 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > select up 142 atoms, 143 bonds, 20 residues, 1 model selected > color sel blue > select #22/H:210 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 43 atoms, 43 bonds, 6 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1734 atoms, 1783 bonds, 227 residues, 1 model selected > color sel forest green > select #22/L:19 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 23 atoms, 22 bonds, 3 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > ui tool show "Color Actions" > color sel chartreuse > show #!12 models > color zone #12 near #22 distance 22 > hide #!12 models > show #!12 models > hide #!22 models > volume #12 level 0.1439 > volume #12 level 0.12 > volume #12 level 0.11 > color zone #12 near #22 distance 22 > color zone #12 near #22 distance 2 > color zone #12 near #22 distance 25 [Repeated 1 time(s)] > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > show #!14 models > fitmap #14 inMap #12 Fit molecule propeller_thigh (#14) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms average map value = 0.3683, steps = 48 shifted from previous position = 0.00438 rotated from previous position = 0.0101 degrees atoms outside contour = 706, contour level = 0.11 Position of propeller_thigh (#14) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation -0.94946112 0.24514462 -0.19602982 354.78067515 0.26064686 0.96373629 -0.05723256 -1.63223903 0.17489080 -0.10543465 -0.97892632 353.83996994 Axis -0.12875844 -0.99081102 0.04140990 Axis point 160.57782997 0.00000000 193.61078246 Rotation angle (degrees) 169.21172439 Shift along axis -29.41128727 > close #22 > combine #9, 10, 13, 14, 15, 17, 18, 19 Remapping chain ID 'C' in calf1 #13 to 'D' Remapping chain ID 'I' in calf1 #13 to 'K' Remapping chain ID 'J' in calf1 #13 to 'M' Remapping chain ID 'A' in propeller_thigh #14 to 'E' Remapping chain ID 'C' in propeller_thigh #14 to 'F' Remapping chain ID 'I' in propeller_thigh #14 to 'N' Remapping chain ID 'J' in propeller_thigh #14 to 'O' Remapping chain ID 'C' in calf2 #15 to 'G' Remapping chain ID 'F' in calf2 #15 to 'P' Remapping chain ID 'I' in calf2 #15 to 'Q' Remapping chain ID 'J' in calf2 #15 to 'R' Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S' Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T' Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U' Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V' Remapping chain ID 'C' in I-EGF3 #18 to 'W' Remapping chain ID 'E' in I-EGF3 #18 to 'X' Remapping chain ID 'I' in I-EGF3 #18 to 'Y' Remapping chain ID 'J' in I-EGF3 #18 to 'Z' Remapping chain ID 'C' in I-EGF4 #19 to 'a' Remapping chain ID 'D' in I-EGF4 #19 to 'b' Remapping chain ID 'I' in I-EGF4 #19 to 'c' Remapping chain ID 'J' in I-EGF4 #19 to 'd' > hide #!12 models > select #21/S:380 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 22 atoms, 22 bonds, 3 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > select up 3522 atoms, 3586 bonds, 455 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > select up 31404 atoms, 31892 bonds, 4276 residues, 33 models selected > color (#!14,21 & sel) red > select #14/A:460 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 4655 atoms, 4755 bonds, 622 residues, 1 model selected > color sel blue > hide #!14 models > select #21/E:458 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > select #21/A:631 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 83 atoms, 82 bonds, 11 residues, 1 model selected > select up 426 atoms, 432 bonds, 59 residues, 1 model selected > select up 475 atoms, 481 bonds, 65 residues, 1 model selected > select up 1011 atoms, 1021 bonds, 135 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1011 atoms, 1021 bonds, 135 residues, 1 model selected > color sel blue > select #21/P:930 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 105 atoms, 109 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > select up 745 atoms, 766 bonds, 96 residues, 1 model selected > select up 1171 atoms, 1207 bonds, 151 residues, 1 model selected > select up 1181 atoms, 1216 bonds, 153 residues, 1 model selected > select down 1171 atoms, 1207 bonds, 151 residues, 1 model selected > color sel blue > select clear > select #21/P:752 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > select up 142 atoms, 143 bonds, 20 residues, 1 model selected > select up 173 atoms, 176 bonds, 24 residues, 1 model selected > select down 142 atoms, 143 bonds, 20 residues, 1 model selected > color sel blue > select #21/H:207 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 43 atoms, 43 bonds, 6 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1734 atoms, 1783 bonds, 227 residues, 1 model selected > color sel forest green > select clear > select #21/L:122 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 45 atoms, 44 bonds, 6 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1636 atoms, 1677 bonds, 213 residues, 1 model selected > ui tool show "Color Actions" > color sel chartreuse > select #21/B:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 28 atoms, 28 bonds, 3 residues, 1 model selected > select up 674 atoms, 683 bonds, 84 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 674 atoms, 683 bonds, 84 residues, 1 model selected > color sel blue > show #!12 models > color zone #12 near #21 distance 25 > hide #!21 models > show #!21 models > hide #!12 models > show #!12 models > hide #!21 models > show #!21 models > hide #!21 models > volume #12 level 0.1 > show #!21 models > color zone #12 near #21 distance 1 > color zone #12 near #21 distance 15 > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 20 [Repeated 2 time(s)] > color zone #12 near #21 distance 2 > color zone #12 near #21 distance 25 [Repeated 1 time(s)] > hide #!21 models > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs > includeMaps true > show #!11 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!12 models > hide #!11 models > show #!11 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!11 models > hide #!6 models > show #!11 models > show #!12 models > hide #!11 models > show #!21 models > hide #!21 models > show #!21 models > hide #!12 models > select #21/E:309 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 40 atoms, 39 bonds, 6 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > ui tool show "Color Actions" > color sel dark blue > show #!12 models > color zone #12 near #21 distance 25 [Repeated 1 time(s)] > hide #!12 models > select #21/E:458 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > show #!12 models > fitmap #21 inMap #12 Fit molecule combination (#21) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms average map value = 0.2298, steps = 2000 shifted from previous position = 0.219 rotated from previous position = 0.0977 degrees atoms outside contour = 5836, contour level = 0.1 Position of combination (#21) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.71825256 0.55816695 -0.41540693 -18.37414359 -0.68346231 0.45413509 -0.57152479 330.03831857 -0.13035538 0.69441412 0.70766977 129.05569312 Axis 0.70487855 -0.15871755 -0.69134287 Axis point 0.00000000 137.69258986 403.03762522 Rotation angle (degrees) 63.89428697 Shift along axis -154.55614618 > fitmap #21 inMap #12 Fit molecule combination (#21) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms average map value = 0.2304, steps = 184 shifted from previous position = 0.356 rotated from previous position = 0.222 degrees atoms outside contour = 5784, contour level = 0.1 Position of combination (#21) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.71931590 0.55516676 -0.41758172 -18.45715539 -0.68280504 0.45433929 -0.57214778 329.95179623 -0.12791365 0.69668190 0.70588414 128.40160768 Axis 0.70638833 -0.16126526 -0.68920900 Axis point 0.00000000 138.18749460 401.28374388 Rotation angle (degrees) 63.91081405 Shift along axis -154.74322329 > fitmap #21 inMap #12 Fit molecule combination (#21) to map cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms average map value = 0.2304, steps = 252 shifted from previous position = 0.0272 rotated from previous position = 0.0277 degrees atoms outside contour = 5780, contour level = 0.1 Position of combination (#21) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.71928919 0.55489943 -0.41798288 -18.42114133 -0.68289991 0.45429114 -0.57207278 329.97883918 -0.12755693 0.69692624 0.70570748 128.30043184 Axis 0.70643417 -0.16167610 -0.68906574 Axis point 0.00000000 138.31627114 401.13032877 Rotation angle (degrees) 63.91883695 Shift along axis -154.77044903 > color zone #12 near #21 distance 25 [Repeated 1 time(s)] > hide #!21 models > hide #!12 models > show #!11 models > volume #11 color #b2ffff7f > volume #11 color #b2ffff91 > show #9 models > show #!10 models > show #!13 models > show #!14 models > show #!15 models > show #!17 models > show #!18 models > show #!19 models > fitmap #14 inMap #11 Fit molecule propeller_thigh (#14) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 4655 atoms average map value = 0.3795, steps = 104 shifted from previous position = 0.368 rotated from previous position = 1.22 degrees atoms outside contour = 788, contour level = 0.11 Position of propeller_thigh (#14) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.95535955 0.23579762 -0.17801013 353.39435096 0.25000471 0.96627070 -0.06179453 0.37538213 0.15743497 -0.10353937 -0.98208646 357.18725485 Axis -0.12338459 -0.99147009 0.04199168 Axis point 161.27504695 0.00000000 193.63149625 Rotation angle (degrees) 170.26069577 Shift along axis -28.97670604 > fitmap #13 inMap #11 Fit molecule calf1 (#13) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 1025 atoms average map value = 0.2012, steps = 172 shifted from previous position = 1.1 rotated from previous position = 19.9 degrees atoms outside contour = 171, contour level = 0.11 Position of calf1 (#13) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.48543806 0.42982238 0.76131636 99.53778763 0.75489325 0.64532616 0.11700561 -84.52017329 -0.44100574 0.63151156 -0.63773590 316.56695185 Axis 0.38180056 0.89220980 0.24122605 Axis point 134.55284379 0.00000000 151.32517876 Rotation angle (degrees) 137.63982897 Shift along axis 38.95805253 > fitmap #15 inMap #11 Fit molecule calf2 (#15) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 1327 atoms average map value = 0.1289, steps = 216 shifted from previous position = 19.2 rotated from previous position = 5.82 degrees atoms outside contour = 597, contour level = 0.11 Position of calf2 (#15) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.92993056 0.27975594 -0.23867502 360.83130959 0.31017179 0.94536206 -0.10041925 -26.91312653 0.19754143 -0.16741319 -0.96589347 359.49105011 Axis -0.15144056 -0.98607224 0.06875536 Axis point 162.05664276 0.00000000 199.26663712 Rotation angle (degrees) 167.22112794 Shift along axis -3.38927214 > show #!21 models > select add #21 15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected > hide #!21 models > select subtract #21 Nothing selected > select add #15 1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #15,-0.64782,-0.46146,0.60612,327.89,0.46645,-0.86934,-0.16333,310.66,0.6023,0.17692,0.77842,-30.526 > ui mousemode right "translate selected models" > view matrix models > #15,-0.64782,-0.46146,0.60612,315.32,0.46645,-0.86934,-0.16333,309.85,0.6023,0.17692,0.77842,-30.758 > view matrix models > #15,-0.64782,-0.46146,0.60612,314.46,0.46645,-0.86934,-0.16333,312.88,0.6023,0.17692,0.77842,-32.019 > view matrix models > #15,-0.64782,-0.46146,0.60612,312.54,0.46645,-0.86934,-0.16333,311.18,0.6023,0.17692,0.77842,-32.804 > fitmap #15 inMap #11 Fit molecule calf2 (#15) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 1327 atoms average map value = 0.1065, steps = 448 shifted from previous position = 4.66 rotated from previous position = 11.9 degrees atoms outside contour = 742, contour level = 0.11 Position of calf2 (#15) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.78904840 0.56096248 -0.25044702 278.09886634 0.58511067 0.81046619 -0.02810780 -64.43248189 0.18721142 -0.16871764 -0.96772219 376.04023242 Axis -0.30545770 -0.95075951 0.05245899 Axis point 126.31916183 0.00000000 203.22808361 Rotation angle (degrees) 166.69335882 Shift along axis -3.96095490 > fitmap #17 inMap #11 Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 4017 atoms average map value = 0.3528, steps = 104 shifted from previous position = 0.731 rotated from previous position = 1.23 degrees atoms outside contour = 666, contour level = 0.11 Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.96384812 0.19986036 -0.17621758 361.25432493 0.21467272 0.97422824 -0.06924558 -0.55078014 0.15783670 -0.10457133 -0.98191263 360.04241355 Axis -0.10506008 -0.99348969 0.04405250 Axis point 165.27476559 0.00000000 195.30526299 Rotation angle (degrees) 170.32137342 Shift along axis -21.54544606 > fitmap #18 inMap #11 Fit molecule I-EGF3 (#18) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 310 atoms average map value = 0.2097, steps = 240 shifted from previous position = 16.4 rotated from previous position = 10.3 degrees atoms outside contour = 60, contour level = 0.11 Position of I-EGF3 (#18) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation -0.95150098 -0.02774992 -0.30639162 421.86579542 -0.04658311 0.99743605 0.05432623 19.58686766 0.30409850 0.06596413 -0.95035405 295.37727295 Axis 0.01905069 -0.99934311 -0.03082903 Axis point 188.04663111 0.00000000 180.44188194 Rotation angle (degrees) 162.21501936 Shift along axis -20.64335842 > select add #19 1637 atoms, 1649 bonds, 2 pseudobonds, 242 residues, 3 models selected > select subtract #15 310 atoms, 299 bonds, 57 residues, 1 model selected > view matrix models > #19,-0.55276,-0.83257,-0.035838,425.27,0.53511,-0.32165,-0.78115,268.5,0.63884,-0.45097,0.62331,96.671 > hide #!11 models > show #!11 models > hide #!10 models > show #!10 models > select add #11 310 atoms, 299 bonds, 57 residues, 3 models selected > select subtract #19 2 models selected > view matrix models > #11,0.19113,-0.77654,-0.60038,451.77,-0.69033,-0.54117,0.48019,338.33,-0.69779,0.32268,-0.6395,449.52 > fitmap #11 inMap #12 Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map_sharp.mrc using 389830 points correlation = 0.6822, correlation about mean = 0.3325, overlap = 2.291e+04 steps = 116, shift = 4.96, angle = 2.16 degrees Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99930359 -0.03560552 -0.01116185 9.27365006 0.03567823 0.99934294 0.00638341 -8.92862256 0.01092723 -0.00677720 0.99991733 -5.51109902 Axis -0.17367024 -0.29149227 0.94067577 Axis point 288.81962012 234.35889751 0.00000000 Rotation angle (degrees) 2.17143674 Shift along axis -4.19208985 > fitmap #11 inMap #12 Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map cryosparc_P91_J556_008_volume_map_sharp.mrc using 389830 points correlation = 0.6823, correlation about mean = 0.3329, overlap = 2.291e+04 steps = 40, shift = 0.0161, angle = 0.00976 degrees Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates: Matrix rotation and translation 0.99929895 -0.03575863 -0.01108736 9.29073645 0.03583081 0.99933750 0.00638144 -8.96341199 0.01085183 -0.00677424 0.99991817 -5.51184549 Axis -0.17304946 -0.28858747 0.94168527 Axis point 288.40170845 233.78310259 0.00000000 Rotation angle (degrees) 2.17841411 Shift along axis -4.21145226 > select subtract #11 Nothing selected > hide #!11 models > show #!11 models > select add #10 3384 atoms, 3460 bonds, 454 residues, 1 model selected > view matrix models > #10,0.22685,0.78149,-0.58122,42.25,-0.81155,-0.17826,-0.55643,452.34,-0.53845,0.59791,0.59378,84.971 > view matrix models > #10,0.22685,0.78149,-0.58122,40.013,-0.81155,-0.17826,-0.55643,450.17,-0.53845,0.59791,0.59378,86.566 > view matrix models > #10,0.22685,0.78149,-0.58122,42.621,-0.81155,-0.17826,-0.55643,451.64,-0.53845,0.59791,0.59378,82.587 > fitmap #10 inMap #11 Fit molecule Fab (#10) to map cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 3384 atoms average map value = 0.05102, steps = 164 shifted from previous position = 7.29 rotated from previous position = 10.5 degrees atoms outside contour = 2912, contour level = 0.11 Position of Fab (#10) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates: Matrix rotation and translation 0.93247940 -0.33984058 -0.12243588 147.60775306 0.00582998 -0.32474496 0.94578365 155.97567602 -0.36117610 -0.88263757 -0.30083673 549.39252651 Axis -0.97460589 0.12725603 0.18425326 Axis point 0.00000000 285.46900361 231.86978513 Rotation angle (degrees) 110.27651223 Shift along axis -22.78317865 > view matrix models > #10,0.36101,0.73569,-0.57308,37.183,-0.83434,-0.019722,-0.5509,426.19,-0.4166,0.67703,0.6067,43.741 > select add #9 4058 atoms, 4143 bonds, 538 residues, 2 models selected > select subtract #10 674 atoms, 683 bonds, 84 residues, 1 model selected > view matrix models > #9,0.7454,-0.66392,-0.060001,113.26,-0.18864,-0.29641,0.93625,222.91,-0.63937,-0.68656,-0.34618,478.49 > view matrix models > #9,0.7454,-0.66392,-0.060001,115.85,-0.18864,-0.29641,0.93625,224.9,-0.63937,-0.68656,-0.34618,482.77 > view matrix models > #9,0.7454,-0.66392,-0.060001,119.49,-0.18864,-0.29641,0.93625,220.74,-0.63937,-0.68656,-0.34618,485.08 > view matrix models > #9,0.7454,-0.66392,-0.060001,120.83,-0.18864,-0.29641,0.93625,221.87,-0.63937,-0.68656,-0.34618,485.58 > combine #9, 10, 13, 14, 15, 17, 18, 19 Remapping chain ID 'C' in calf1 #13 to 'D' Remapping chain ID 'I' in calf1 #13 to 'K' Remapping chain ID 'J' in calf1 #13 to 'M' Remapping chain ID 'A' in propeller_thigh #14 to 'E' Remapping chain ID 'C' in propeller_thigh #14 to 'F' Remapping chain ID 'I' in propeller_thigh #14 to 'N' Remapping chain ID 'J' in propeller_thigh #14 to 'O' Remapping chain ID 'C' in calf2 #15 to 'G' Remapping chain ID 'F' in calf2 #15 to 'P' Remapping chain ID 'I' in calf2 #15 to 'Q' Remapping chain ID 'J' in calf2 #15 to 'R' Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S' Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T' Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U' Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V' Remapping chain ID 'C' in I-EGF3 #18 to 'W' Remapping chain ID 'E' in I-EGF3 #18 to 'X' Remapping chain ID 'I' in I-EGF3 #18 to 'Y' Remapping chain ID 'J' in I-EGF3 #18 to 'Z' Remapping chain ID 'C' in I-EGF4 #19 to 'a' Remapping chain ID 'D' in I-EGF4 #19 to 'b' Remapping chain ID 'I' in I-EGF4 #19 to 'c' Remapping chain ID 'J' in I-EGF4 #19 to 'd' > volume #11 color #b2fffffb > color zone #11 near #22 distance 15 > volume #11 color #b2fffffc > hide #!11 models > select #22/S:100 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 75 atoms, 75 bonds, 9 residues, 1 model selected > select up 3455 atoms, 3519 bonds, 446 residues, 1 model selected > select up 3522 atoms, 3586 bonds, 455 residues, 1 model selected > select up 4003 atoms, 4076 bonds, 520 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 47106 atoms, 47838 bonds, 6414 residues, 34 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select up 47106 atoms, 47838 bonds, 6414 residues, 34 models selected > select down 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > color sel red > select clear > hide #!19 models > hide #!18 models > hide #!17 models > hide #!15 models > hide #!14 models > hide #!13 models > hide #!10 models > hide #9 models > select #22/E:460 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 10 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 4641 atoms, 4755 bonds, 608 residues, 1 model selected > color sel blue > select #22/A:704 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 75 atoms, 74 bonds, 11 residues, 1 model selected > select up 585 atoms, 589 bonds, 76 residues, 1 model selected > select up 602 atoms, 605 bonds, 79 residues, 1 model selected > select up 1011 atoms, 1021 bonds, 135 residues, 1 model selected > select down 602 atoms, 605 bonds, 79 residues, 1 model selected > select up 1011 atoms, 1021 bonds, 135 residues, 1 model selected > color sel blue > select #22/P:928 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 105 atoms, 109 bonds, 12 residues, 1 model selected > select up 675 atoms, 694 bonds, 86 residues, 1 model selected > select up 745 atoms, 766 bonds, 96 residues, 1 model selected > color sel blue > select #22/P:814 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 77 atoms, 78 bonds, 9 residues, 1 model selected > select up 496 atoms, 513 bonds, 65 residues, 1 model selected > select up 514 atoms, 529 bonds, 68 residues, 1 model selected > color sel blue > select up 1313 atoms, 1350 bonds, 171 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 1313 atoms, 1350 bonds, 171 residues, 1 model selected > select down 514 atoms, 529 bonds, 68 residues, 1 model selected > select down 496 atoms, 513 bonds, 65 residues, 1 model selected > select down 77 atoms, 78 bonds, 9 residues, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > select #22/P:752 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 64 atoms, 64 bonds, 8 residues, 1 model selected > select up 142 atoms, 143 bonds, 20 residues, 1 model selected > color sel blue > select #22/B:656 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 42 atoms, 42 bonds, 5 residues, 1 model selected > select up 674 atoms, 683 bonds, 84 residues, 1 model selected > select up 15702 atoms, 15946 bonds, 2138 residues, 1 model selected > select down 674 atoms, 683 bonds, 84 residues, 1 model selected > color sel blue > select #22/H:21 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 62 atoms, 61 bonds, 9 residues, 1 model selected > select up 1734 atoms, 1783 bonds, 227 residues, 1 model selected > color sel forest green > select #22/L:36 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 54 atoms, 57 bonds, 5 residues, 1 model selected > select up 1636 atoms, 1677 bonds, 213 residues, 1 model selected > ui tool show "Color Actions" > color sel chartreuse > show #!11 models > color zone #11 near #22 distance 15 > color zone #11 near #22 distance 2 > color zone #11 near #22 distance 25 > hide #!22 models > volume #11 level 0.1 > color zone #11 near #22 distance 20 [Repeated 1 time(s)] > color zone #11 near #22 distance 22 [Repeated 1 time(s)] > color zone #11 near #22 distance 23 [Repeated 1 time(s)] > volume #11 level 0.105 > volume #11 level 0.11 > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs > includeMaps true ——— End of log from Fri Jan 31 04:00:50 2025 ——— opened ChimeraX session > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/conformation2_structure.pdb > models #22 > hide #!11 models > show #!11 models > show #!22 models > hide #!11 models > style sel stick Changed 1636 atom styles > show sel target ab > cartoon hide sel > show sel target ab > select add #22 15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected > show (#!22 & sel) target ab Drag select of 24 atoms > delete sel Drag select of 14 atoms > delete sel Drag select of 4 atoms > delete sel > select #22/T:9@CA 1 atom, 1 residue, 1 model selected > select add #22/T:8@CA 2 atoms, 2 residues, 1 model selected > select add #22/W:8@CA 3 atoms, 3 residues, 1 model selected > select add #22/W:7@CA 4 atoms, 4 residues, 1 model selected > select add #22/T:7@CA 5 atoms, 5 residues, 1 model selected > select add #22/T:10@CA 6 atoms, 6 residues, 1 model selected > delete sel > select #22/W:9@CA 1 atom, 1 residue, 1 model selected > select #22/W:9@CA 1 atom, 1 residue, 1 model selected > select up 4 atoms, 4 residues, 1 model selected > select up 15654 atoms, 15946 bonds, 2090 residues, 1 model selected > select down 4 atoms, 4 residues, 1 model selected > color sel blue > select #22/G:2@CA 1 atom, 1 residue, 1 model selected > color sel blue > select #22/F:8@CA 1 atom, 1 residue, 1 model selected > color sel blue > select #22/E:369@CA 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 67 atoms, 67 bonds, 8 residues, 1 model selected > select up 4641 atoms, 4755 bonds, 608 residues, 1 model selected > select up 15654 atoms, 15946 bonds, 2090 residues, 1 model selected > select up 47058 atoms, 47838 bonds, 6366 residues, 34 models selected > select down 15654 atoms, 15946 bonds, 2090 residues, 1 model selected Drag select of 2 atoms > delete sel > select #22/a:9@CA 1 atom, 1 residue, 1 model selected > select add #22/a:8@CA 2 atoms, 2 residues, 1 model selected > delete sel > select #22/O:1@O 1 atom, 1 residue, 1 model selected > delete sel > select add #22 15649 atoms, 15946 bonds, 4 pseudobonds, 2085 residues, 2 models selected > hide (#!22 & sel) target a > cartoon (#!22 & sel) > show #!21 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!21 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > show #!11 models > ui tool show "Color Zone" > color zone #11 near #22 distance 25 > volume #11 level 0.1 > hide #!22 models > volume #11 level 0.105 > lighting soft > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save > /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs ——— End of log from Mon Feb 3 13:09:17 2025 ——— opened ChimeraX session > open > /Users/walz/Desktop/aIIbb3_21D/21D_extend_local_resolution_evaluation/cryosparc_P67_J376_011_volume_map_sharp.mrc Opened cryosparc_P67_J376_011_volume_map_sharp.mrc as #23, grid size 400,400,400, pixel 0.86, shown at level 0.137, step 2, values float32 > volume #23 step 1 > volume #23 level 0.3047 > surface dust #11 size 8.6 > surface dust #23 size 8.6 > surface dust #11 size 8.6 > surface dust #23 size 8.6 > select add #23 Traceback (most recent call last): File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 138, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb self.history_dialog.add(self._just_typed_command or cmd_text, File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/cmd_line/tool.py", line 456, in add self._history.enqueue((item, typed)) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/history.py", line 171, in enqueue self.save() File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/history.py", line 201, in save self._history.save(self._queue) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/history.py", line 108, in save with SaveTextFile(self._filename) as f: File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/safesave.py", line 180, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/safesave.py", line 74, in __init__ self._f = open(self._tmp_filename) File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/safesave.py", line 179, in open_text return open(filename, 'w', newline=newline, encoding=encoding) OSError: [Errno 28] No space left on device: '/Users/walz/Library/Application Support/ChimeraX/commands.33359.tmp' Error processing trigger "command started": OSError: [Errno 28] No space left on device: '/Users/walz/Library/Application Support/ChimeraX/commands.33359.tmp' File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/safesave.py", line 179, in open_text return open(filename, 'w', newline=newline, encoding=encoding) See log for complete Python traceback. 15649 atoms, 15946 bonds, 4 pseudobonds, 2085 residues, 4 models selected OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac20,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0) OS Loader Version: 582~2132 Software: System Software Overview: System Version: macOS 15.1 (24B83) Kernel Version: Darwin 24.1.0 Time since boot: 41 days, 23 hours, 15 minutes Graphics/Displays: AMD Radeon Pro 5300: Chipset Model: AMD Radeon Pro 5300 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0047 ROM Revision: 113-D3220I-231 VBIOS Version: 113-D322A1XL-012 Option ROM Version: 113-D322A1XL-012 EFI Driver Version: 01.01.231 Metal Support: Metal 3 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0
Change History (2)
comment:1 by , 5 months ago
Component: | Unassigned → Input/Output |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Cannot save command history: No space left on device |
comment:2 by , 5 months ago
Resolution: | → nonchimerax |
---|---|
Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.