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Opened 22 months ago
Last modified 22 months ago
#14515 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22621 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 "S:\weismanlab\Lily Hahn\All materials for Manuscript\ChimeraX\updated > 111724_siteII_.cxs" format session Opened cryosparc_P122_J2162_map_sharp (1).mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.189, step 1, values float32 Opened 011724_SDII.tif as #3, grid size 256,256,256, pixel 1.09, shown at level 0.00552, step 1, values float32 Log from Wed Jan 17 23:08:39 2024UCSF 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 2f6h 2f6h title: Myosin V cargo binding domain [more info...] Chain information for 2f6h #1 --- Chain | Description | UniProt X | Myosin-2 | MYO2_YEAST 22-440 Drag select of 390 residues, 3 pseudobonds [Repeated 1 time(s)] > show sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 2f6h_X SES surface #1.2: minimum, -19.39, mean -2.53, maximum 14.61 To also show corresponding color key, enter the above coulombic command and add key true Drag select of 2f6h_X SES surface, 49427 of 351608 triangles, 88 residues Drag select of 2f6h_X SES surface, 61051 of 351608 triangles, 109 residues Drag select of 2f6h_X SES surface, 44460 of 351608 triangles, 89 residues Drag select of 2f6h_X SES surface, 35298 of 351608 triangles, 50 residues > hide sel surfaces > show sel atoms > hide sel atoms > select /X:431 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > close session > open C:/Users/hjhahn/Downloads/AF-Q9Y2I7-F1-model_v4.pdb AF-Q9Y2I7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for 1-phosphatidylinositol 3-phosphate 5-kinase (Q9Y2I7) [more info...] Chain information for AF-Q9Y2I7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | 1-phosphatidylinositol 3-phosphate 5-kinase | FYV1_HUMAN 1-2098 > ui tool show "Show Sequence Viewer" > sequence chain /A Alignment identifier is 1/A > renumber #1/A start 297 2098 residues renumbered > renumber #1/A start 1 2098 residues renumbered > select /A:1480 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1480-1517 312 atoms, 316 bonds, 38 residues, 1 model selected > select /A:1297-1298 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:1291-1298 64 atoms, 63 bonds, 8 residues, 1 model selected > select clear > select /A:151-180 265 atoms, 273 bonds, 30 residues, 1 model selected > select /A:151-180 265 atoms, 273 bonds, 30 residues, 1 model selected > select /A:1759 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:1759-2083 2614 atoms, 2664 bonds, 325 residues, 1 model selected > select /A:2084 11 atoms, 11 bonds, 1 residue, 1 model selected > select /A:1759-2084 2625 atoms, 2676 bonds, 326 residues, 1 model selected > color sel cyan > select clear > select #1/A 1759-2084 Expected a keyword > select #1/A: 1759-2084 2625 atoms, 2676 bonds, 326 residues, 1 model selected > color #1/A: 1759-2084 red > select clear > select /A:2085 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:2085-2098 108 atoms, 111 bonds, 14 residues, 1 model selected > hide sel cartoons > select /A:1755-1785 237 atoms, 239 bonds, 31 residues, 1 model selected > select /A:721-1785 8416 atoms, 8603 bonds, 1065 residues, 1 model selected > hide sel cartoons > undo [Repeated 2 time(s)]Drag select of 1923 residues > select clear > show #1/A: 1759-2084 > hide atoms > show #1/A: 1759-2084 target s > hide surfaces > show #1/A: 1759-2084 > hide atoms Drag select of 841 residues > select clear > show ~#1/A: 1759-2084 > show ~#1/A: 1759-2084 target r [Repeated 2 time(s)] > show #1/A: 1759-2084 target r > ~show ~#1/A: 1759-2084 target r > ~show #1/A: 1759-2084 target r [Repeated 1 time(s)] > show #1/A: 1759-2084 target r > show cartoons > select #1/A: 1759-2084 2625 atoms, 2676 bonds, 326 residues, 1 model selected > show sel surfaces > hide sel surfaces > select clear > select #1/A: 1500, 1600, 1700 21 atoms, 18 bonds, 3 residues, 1 model selected > show sel atoms > style sel sphere Changed 21 atom styles > hide sel atoms > show sel atoms > color (#!1 & sel) medium blue > select #1/A: 1500 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!1 & sel) blue > color (#!1 & sel) white > select clear Drag select of 9 residues > close session > open "S:/weismanlab/Lily Hahn/PIKFyve/PVF analysis 120823.cxs" Opened emd_22634.map as #1, grid size 400,400,400, pixel 1.05, shown at level 0.00647, step 1, values float32 Opened job862_Kinase_postprocess_6.7A (1).mrc as #4, grid size 400,400,400, pixel 1.05, shown at level 0.00781, step 1, values float32 Opened job866_VF_postprocess_5.06A.mrc as #5, grid size 400,400,400, pixel 1.05, shown at level 0.0122, step 1, values float32 Log from Fri Dec 8 16:03:28 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "S:/weismanlab/Lily Hahn/All materials for > Manuscript/ChimeraX/Inp2_Mmr1_Vac17 comparisons.cxs" format session Opened postprocess.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.00761, step 1, values float32 Log from Thu Nov 30 22:13:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "S:\weismanlab\Lily Hahn\ChimeraX\Figure 3\Mmr1 Vac17 Inp2.cxs" format > session Log from Wed Nov 29 01:09:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Sun Nov 26 22:11:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Tue Nov 21 13:03:15 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "S:\weismanlab\Lily Hahn\All materials for Manuscript\ChimeraX\Fig 1C > Mmr1 with Vac17.cxs" format session Opened J1921.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.135, step 1, values float32 Opened J1921.mrc copy as #4, grid size 256,256,256, pixel 1.09, shown at level 0.173, step 1, values float32 Opened cryosparc_P122_J1962_001_volume_map.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0798, step 1, values float32 Opened cryosparc_P122_J1925_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.199, step 1, values float32 Log from Wed Nov 15 01:14:09 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "S:\weismanlab\Lily Hahn\ChimeraX\Figure 2\zoom 2A.cxs" format session Opened J1921.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.135, step 1, values float32 Opened J1921.mrc copy as #4, grid size 256,256,256, pixel 1.09, shown at level 0.173, step 1, values float32 Opened cryosparc_P122_J1962_001_volume_map.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0798, step 1, values float32 Opened cryosparc_P122_J1925_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.202, step 1, values float32 Log from Mon Nov 13 13:33:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Thu Oct 26 14:56:39 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\Users\lilyh\Desktop\Myo2 Manuscript Figures\Mmr1 Vac17_.cxs" format > session Opened J1921.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.135, step 1, values float32 Opened J1921.mrc copy as #4, grid size 256,256,256, pixel 1.09, shown at level 0.173, step 1, values float32 Opened cryosparc_P122_J1962_001_volume_map.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0798, step 1, values float32 Log from Thu Oct 26 13:12:19 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "S:\weismanlab\Lily Hahn\Official Powerpoints\Chimera photos\Mmr1 > Vac17.cxs" format session Opened J1921.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.135, step 1, values float32 Opened J1921.mrc copy as #4, grid size 256,256,256, pixel 1.09, shown at level 0.173, step 1, values float32 Opened cryosparc_P122_J1962_001_volume_map.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0798, step 1, values float32 Log from Thu Oct 26 00:23:33 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\Users\lilyh\Desktop\Myo2 Manuscript Figures\Figure 1_102523.cxs" > format session Opened J1921.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.135, step 1, values float32 Opened J1921.mrc copy as #4, grid size 256,256,256, pixel 1.09, shown at level 0.173, step 1, values float32 Opened cryosparc_P122_J1962_001_volume_map.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0798, step 1, values float32 Log from Wed Oct 25 10:37:53 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > set bgColor transparent Log from Tue Oct 24 23:04:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\Users\lilyh\Desktop\Vac17-Myo2 Reconstructions\particle reverted > .cxs" format session Opened cryosparc_P122_J1828_002_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.142, step 1, values float32 Opened cryosparc_P122_J1791_002_volume_map.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0799, step 1, values float32 Opened cryosparc_P122_J1792_001_volume_map.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0605, step 1, values float32 Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.114, step 1, values float32 Opened cryosparc_P122_J1738_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.108, step 1, values float32 Opened cryosparc_P122_J1737_001_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.107, step 1, values float32 Opened cryosparc_P122_J1704_002_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.09, shown at level 0.0889, step 1, values float32 Opened cryosparc_P122_J1702_002_volume_map_sharp.mrc as #12, grid size 256,256,256, pixel 1.09, shown at level 0.112, step 1, values float32 Opened cryosparc_P122_J1694_002_volume_map_sharp.mrc as #14, grid size 256,256,256, pixel 1.09, shown at level 0.0941, step 1, values float32 Log from Sun Oct 15 20:38:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\Users\lilyh\Desktop\Vac17-Myo2 Reconstructions\Annotated J1808.cxs" > format session Opened cryosparc_P122_J1808_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.153, step 1, values float32 Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1809_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1807_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at step 1, values float32 Log from Sun Oct 15 16:20:36 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" Opened cryosparc_P122_J1808_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.153, step 1, values float32 Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1809_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1807_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at step 1, values float32 Log from Sun Oct 15 15:05:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:\Users\lilyh\Desktop\Vac17-Myo2 Reconstructions\Annotated J1808.cxs" > format session Opened cryosparc_P122_J1808_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.153, step 1, values float32 Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1809_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.192, step 1, values float32 Opened cryosparc_P122_J1807_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at step 1, values float32 Log from Sun Oct 15 14:29:16 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/j1268 j1664 vac17 > refinement.cxs" Opened cryosparc_P122_J1747_001_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1748_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1746_001_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1737_001_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1738_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1739_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1701_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1704_002_volume_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1703_001_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1702_002_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1791_002_volume_map_sharp.mrc as #11, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #12, grid size 256,256,256, pixel 1.09, shown at level 0.06, step 1, values float32 Opened cryosparc_P122_J1335_002_volume_map_sharp.mrc as #13, grid size 256,256,256, pixel 1.09, shown at level 0.0938, step 1, values float32 Opened cryosparc_P122_J1388_002_volume_map_sharp.mrc as #14, grid size 256,256,256, pixel 1.09, shown at level 0.113, step 1, values float32 Log from Thu Oct 12 14:09:03 2023UCSF 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 C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_00_00012_volume.mrc Opened cryosparc_P122_J1783_class_00_00012_volume.mrc as #1, grid size 80,80,80, pixel 3.47, shown at level 0.107, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_02_00012_volume.mrc Opened cryosparc_P122_J1783_class_02_00012_volume.mrc as #2, grid size 80,80,80, pixel 3.47, shown at level 0.108, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_01_00012_volume.mrc Opened cryosparc_P122_J1783_class_01_00012_volume.mrc as #3, grid size 80,80,80, pixel 3.47, shown at level 0.106, step 1, values float32 > volume level 0.126 > volume level 0.2 > tile 3 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1784_001_volume_map_sharp.mrc Opened cryosparc_P122_J1784_001_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0149, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1786_001_volume_map_sharp.mrc Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > hide #!2 models > hide #!3 models > hide #!1 models > hide #!5 models > show #!5 models > volume level 0.2 > ~tile > volume level 0.1 > hide #!5 models > volume #4 level 0.08126 > show #!5 models > hide #!4 models > volume #5 level 0.07299 > volume #5 level 0.07726 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1785_001_volume_map_sharp.mrc Opened cryosparc_P122_J1785_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.0203, step 1, values float32 > hide #!5 models > volume #5 level 0.1227 > volume #5 level 0.152 > hide #!5 models > volume #6 level 0.09578 > volume #6 level 0.04696 > volume #5 level 0.08899 > tile 3 models tiled > volume #4 level 0.06434 > close #4 > ~tile > tile 2 models tiled > volume #6 level 0.05269 > volume #5 level 0.06198 > volume #6 level 0.04696 > volume #6 level 0.06273 > volume #5 level 0.07903 > volume #5 level 0.07477 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_02_00012_volume.mrc Opened cryosparc_P122_J1783_class_02_00012_volume.mrc as #4, grid size 80,80,80, pixel 3.47, shown at level 0.108, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_01_00012_volume.mrc Opened cryosparc_P122_J1783_class_01_00012_volume.mrc as #7, grid size 80,80,80, pixel 3.47, shown at level 0.106, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1783_class_00_00012_volume.mrc Opened cryosparc_P122_J1783_class_00_00012_volume.mrc as #8, grid size 80,80,80, pixel 3.47, shown at level 0.107, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1784_001_volume_map_sharp.mrc Opened cryosparc_P122_J1784_001_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.0149, step 1, values float32 > volume level 0.1 > volume level 0.2 > tile 6 models tiled > volume level 0.1 > volume level 0.12 > volume level 0.13 > volume level 0.1 > volume level 0.08 > volume level 0.2 > volume level 0.1 > volume level 0.12 > volume #9 level 0.07771 > volume #5 level 0.06868 > hide #!4 models > hide #!5 models > hide #!6 models > show #!6 models > show #!5 models > hide #!8 models > hide #!7 models > volume #9 level 0.07046 > volume #6 level 0.06378 > volume #5 level 0.07748 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_01_00011_volume.mrc Opened cryosparc_P122_J1788_class_01_00011_volume.mrc as #1, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_03_00011_volume.mrc Opened cryosparc_P122_J1788_class_03_00011_volume.mrc as #2, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > volume level 0.12 > volume level 0.2 > volume level 0.4 > tile 2 models tiled > volume #1 level 0.2783 > volume #2 level 0.2253 > ~tile > volume #2 level 0.2521 > volume #1 level 0.2329 > volume #1 level 0.2147 > volume #1 level 0.2873 > volume #2 level 0.2031 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1787_001_volume_map_sharp.mrc Opened cryosparc_P122_J1787_001_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0178, step 1, values float32 > hide #!2 models > volume #3 level 0.09925 > volume #3 level 0.07081 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1786_001_volume_map_sharp.mrc Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1785_001_volume_map_sharp.mrc Opened cryosparc_P122_J1785_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0203, step 1, values float32 > ~tile > volume level 0.4 > volume level 0.1 > tile 3 models tiled > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1790_map_sharp.mrc Opened cryosparc_P122_J1790_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.018, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1789_map_sharp.mrc Opened cryosparc_P122_J1789_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.0152, step 1, values float32 > volume level 0.1 > tile 2 models tiled > volume #1 level 0.05471 > volume #2 level 0.07182 > ~tile > hide #!2 models > hide #!1 models > open > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb Chain information for output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb #3 --- Chain | Description B | No description available C | No description available Drag select of 24 residues > ui mousemode right "rotate selected models" > view matrix models > #3,-0.087607,-0.82252,-0.56195,-1.8505,0.51751,0.44445,-0.7312,1.6931,0.85118,-0.35487,0.38672,2.3051 > select clear > show #!1 models Drag select of 1 cryosparc_P122_J1790_map_sharp.mrc > ui mousemode right "translate selected models" > view matrix models > #1,-0.20947,0.22145,0.95241,18.61,-0.46631,-0.87875,0.10176,210.33,0.85946,-0.42281,0.28733,17.656 > ui mousemode right "rotate selected models" > view matrix models > #1,-0.35281,0.45915,-0.8153,268.04,0.024216,0.87552,0.48258,-150.98,0.93538,0.15052,-0.32001,19.597 > view matrix models > #1,-0.44052,-0.56917,0.69426,195.64,-0.46812,-0.51424,-0.71862,282.78,0.76603,-0.64156,-0.039909,108.59 > view matrix models > #1,-0.11017,0.98592,0.12578,23.952,-0.17879,-0.14414,0.97327,-57.751,0.9777,0.084741,0.19215,-53.197 > ui mousemode right "translate selected models" > view matrix models > #1,-0.11017,0.98592,0.12578,-35.143,-0.17879,-0.14414,0.97327,-77.478,0.9777,0.084741,0.19215,-82.34 > ui mousemode right "rotate selected models" > view matrix models > #1,-0.46849,-0.64028,0.60874,162.68,-0.45175,-0.41853,-0.78788,258.11,0.75924,-0.64411,-0.093169,88.619 > view matrix models > #1,0.55342,0.18708,-0.81162,113.36,0.1222,-0.98214,-0.14306,155.16,-0.82389,-0.020006,-0.5664,304.5 > ui mousemode right "translate selected models" > view matrix models > #1,0.55342,0.18708,-0.81162,-8.6775,0.1222,-0.98214,-0.14306,122.84,-0.82389,-0.020006,-0.5664,246.61 > view matrix models > #1,0.55342,0.18708,-0.81162,22.497,0.1222,-0.98214,-0.14306,127.5,-0.82389,-0.020006,-0.5664,216.04 > fitmap #3 inMap #1 Fit molecule output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb (#3) to map cryosparc_P122_J1790_map_sharp.mrc (#1) using 4737 atoms average map value = 0.1224, steps = 140 shifted from previous position = 20.6 rotated from previous position = 23.3 degrees atoms outside contour = 1439, contour level = 0.05471 Position of output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb (#3) relative to cryosparc_P122_J1790_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.80473370 0.22767627 -0.54824012 140.20818836 -0.54644965 -0.64493948 0.53427143 134.99613144 -0.23194076 0.72953182 0.64341814 143.53017560 Axis 0.22737881 -0.36832749 -0.90146200 Axis point 98.31271939 16.44105582 0.00000000 Rotation angle (degrees) 154.57225869 Shift along axis -147.22941488 > show #!2 models Drag select of 2 cryosparc_P122_J1789_map_sharp.mrc > view matrix models > #2,-0.20947,0.22145,0.95241,-110.07,-0.46631,-0.87875,0.10176,169.04,0.85946,-0.42281,0.28733,-106.63 > ui mousemode right "rotate selected models" > view matrix models > #2,0.0593,-0.97269,0.22441,118.66,-0.62914,-0.21096,-0.74812,228.54,0.77503,-0.096823,-0.62446,-3.4983 > view matrix models > #2,0.21017,0.40787,-0.88852,76.317,0.080871,-0.91296,-0.39996,168.87,-0.97431,0.012206,-0.22486,174.93 > fitmap #2 inMap #1 Fit map cryosparc_P122_J1789_map_sharp.mrc in map cryosparc_P122_J1790_map_sharp.mrc using 62706 points correlation = 0.9713, correlation about mean = 0.859, overlap = 1636 steps = 192, shift = 27.9, angle = 25.3 degrees Position of cryosparc_P122_J1789_map_sharp.mrc (#2) relative to cryosparc_P122_J1790_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999590 -0.00226754 -0.00176575 0.51927107 0.00226615 0.99999717 -0.00079111 -0.17796517 0.00176753 0.00078711 0.99999818 -0.39102706 Axis 0.26477327 -0.59276847 0.76060546 Axis point 93.07002574 235.18832041 0.00000000 Rotation angle (degrees) 0.17075998 Shift along axis -0.05443607 > select clear > hide #!2 models > show #!2 models > hide #!1 models > hide #3 models > volume #2 level 0.03961 > volume #2 level 0.07048 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J1304_mask (1).mrc" Opened cryosparc_P122_J1304_mask (1).mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 5e-05, step 1, values float32 > ~tile > select #4 2 models selected > surface style #4 mesh > select clear > volume #2 level 0.05974 > volume #2 level 0.05169 > volume #2 level 0.04767 > volume #2 level 0.05035 > show #!1 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1787_001_volume_map_sharp.mrc Opened cryosparc_P122_J1787_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0178, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1786_001_volume_map_sharp.mrc Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > ~tile > volume level 0.1 > tile 4 models tiled > volume #6 level 0.07067 > volume #6 level 0.08534 > volume #5 level 0.072 > volume #6 level 0.07214 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1785_001_volume_map_sharp.mrc Opened cryosparc_P122_J1785_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.0203, step 1, values float32 > tile 5 models tiled > volume level 0.1 > tile 5 models tiled > ~tile > tile 5 models tiled > volume level 0.08 > volume level 0.06 > volume level 0.05 > volume level 0.055 > volume #6 level 0.07406 > volume #7 level 0.06536 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_05_00042_volume.mrc Opened cryosparc_P122_J1664_class_05_00042_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0272, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_04_00042_volume.mrc Opened cryosparc_P122_J1664_class_04_00042_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_03_00042_volume.mrc Opened cryosparc_P122_J1664_class_03_00042_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0268, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_02_00042_volume.mrc Opened cryosparc_P122_J1664_class_02_00042_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.028, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_01_00042_volume.mrc Opened cryosparc_P122_J1664_class_01_00042_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.0248, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_00_00042_volume.mrc Opened cryosparc_P122_J1664_class_00_00042_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0276, step 1, values float32 > volume level 0.055 > volume level 0.1 > tile 6 models tiled > ~tile > tile 6 models tiled > volume level 0.1 > volume level 0.2 > ~tile > tile 6 models tiled > volume level 0.1 > volume level 0.2 > volume level 0.07 [Repeated 1 time(s)] > ui mousemode right "translate selected models" > ~tile > volume level 0.3 > tile 5 models tiled > volume level 0.1 > volume level 0.2 > ~tile > tile 6 models tiled > volume level 0.1 > volume level 0.08 > volume level 0.06 > volume level 0.08 > set bgColor white > lighting full > lighting simple > lighting soft [Repeated 1 time(s)] > lighting full > set bgColor white > save C:\Users\lilyh\Desktop\image186.png supersample 3 > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_05_00023_volume.mrc Opened cryosparc_P122_J1768_class_05_00023_volume.mrc as #7, grid size 100,100,100, pixel 2.78, shown at level 0.033, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_04_00023_volume.mrc Opened cryosparc_P122_J1768_class_04_00023_volume.mrc as #8, grid size 100,100,100, pixel 2.78, shown at level 0.0352, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_03_00023_volume.mrc Opened cryosparc_P122_J1768_class_03_00023_volume.mrc as #9, grid size 100,100,100, pixel 2.78, shown at level 0.0365, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_02_00023_volume.mrc Opened cryosparc_P122_J1768_class_02_00023_volume.mrc as #10, grid size 100,100,100, pixel 2.78, shown at level 0.0361, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_01_00023_volume.mrc Opened cryosparc_P122_J1768_class_01_00023_volume.mrc as #11, grid size 100,100,100, pixel 2.78, shown at level 0.0355, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1768_class_00_00023_volume.mrc Opened cryosparc_P122_J1768_class_00_00023_volume.mrc as #12, grid size 100,100,100, pixel 2.78, shown at level 0.0349, step 1, values float32 > volume level 0.08 > tile 6 models tiled > lighting full > volume level 0.1 > ~tile > tile 6 models tiled > ui mousemode right "resize markers" > graphics silhouettes true > ~tile > tile 6 models tiled > ~tile > volume level 0.3 > tile 6 models tiled > volume level 0.3 > volume level 0.1 > ui mousemode right "rotate selected models" > ~tile > tile 6 models tiled > volume level 0.3 > tile 6 models tiled > volume level 0.1 > volume level 0.25 > ~tile > tile 6 models tiled > volume level 0.2 > volume level 0.1 > volume level 0.08 Drag select of 10 cryosparc_P122_J1768_class_02_00023_volume.mrc , 11 cryosparc_P122_J1768_class_01_00023_volume.mrc , 12 cryosparc_P122_J1768_class_00_00023_volume.mrc > ui mousemode right "translate selected models" > view matrix models > #10,0.99271,-0.11245,0.043449,29.198,0.12027,0.94837,-0.29349,139.91,-0.0082041,0.29657,0.95497,-54.176,#11,0.99271,-0.11245,0.043449,-35.093,0.12027,0.94837,-0.29349,121.86,-0.0082041,0.29657,0.95497,-81.748,#12,0.99271,-0.11245,0.043449,-91.93,0.12027,0.94837,-0.29349,127.05,-0.0082041,0.29657,0.95497,-119.67 > select clear > volume level 0.08 > ui mousemode right "rotate selected models" > save C:\Users\lilyh\Desktop\image187.png supersample 3 > show #!6 models > show #!5 models > show #!2 models > show #!3 models > show #!1 models > show #!4 models > hide #!12 models > hide #!11 models > hide #!9 models > hide #!10 models > hide #!8 models > hide #!7 models > volume level 0.08 > tile 6 models tiled > volume level 0.08 > volume level 0.1 > tile 6 models tiled > volume level 0.3 > tile 5 models tiled > volume level 0.2 > tile 6 models tiled > volume level 0.08 > save C:\Users\lilyh\Desktop\image188.png supersample 3 > hide #!6 models > hide #!5 models > hide #!4 models > hide #!2 models > hide #!1 models > hide #!3 models > show #!10 models > hide #!10 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_05_00022_volume.mrc Opened cryosparc_P122_J1773_class_05_00022_volume.mrc as #13, grid size 100,100,100, pixel 2.78, shown at level 0.0444, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_04_00022_volume.mrc Opened cryosparc_P122_J1773_class_04_00022_volume.mrc as #14, grid size 100,100,100, pixel 2.78, shown at level 0.0475, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_03_00022_volume.mrc Opened cryosparc_P122_J1773_class_03_00022_volume.mrc as #15, grid size 100,100,100, pixel 2.78, shown at level 0.0465, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_02_00022_volume.mrc Opened cryosparc_P122_J1773_class_02_00022_volume.mrc as #16, grid size 100,100,100, pixel 2.78, shown at level 0.0515, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_01_00022_volume.mrc Opened cryosparc_P122_J1773_class_01_00022_volume.mrc as #17, grid size 100,100,100, pixel 2.78, shown at level 0.047, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1773_class_00_00022_volume.mrc Opened cryosparc_P122_J1773_class_00_00022_volume.mrc as #18, grid size 100,100,100, pixel 2.78, shown at level 0.0485, step 1, values float32 > volume level 0.08 > tile 6 models tiled > volume level 0.1 > volume level 0.2 > tile 6 models tiled > volume level 0.15 > tile 6 models tiled > volume level 0.1 > save C:\Users\lilyh\Desktop\image189.png supersample 3 > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > show #!18 models > show #!16 models > show #!17 models > show #!15 models > show #!14 models > show #!13 models > hide #!18 models > hide #!17 models > hide #!15 models > hide #!16 models > hide #!13 models > hide #!14 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_05_00022_volume.mrc Opened cryosparc_P122_J1769_class_05_00022_volume.mrc as #19, grid size 100,100,100, pixel 2.78, shown at level 0.0421, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_04_00022_volume.mrc Opened cryosparc_P122_J1769_class_04_00022_volume.mrc as #20, grid size 100,100,100, pixel 2.78, shown at level 0.0369, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_03_00022_volume.mrc Opened cryosparc_P122_J1769_class_03_00022_volume.mrc as #21, grid size 100,100,100, pixel 2.78, shown at level 0.0337, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_02_00022_volume.mrc Opened cryosparc_P122_J1769_class_02_00022_volume.mrc as #22, grid size 100,100,100, pixel 2.78, shown at level 0.0364, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_01_00022_volume.mrc Opened cryosparc_P122_J1769_class_01_00022_volume.mrc as #23, grid size 100,100,100, pixel 2.78, shown at level 0.037, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1769_class_00_00022_volume.mrc Opened cryosparc_P122_J1769_class_00_00022_volume.mrc as #24, grid size 100,100,100, pixel 2.78, shown at level 0.0348, step 1, values float32 > volume level 0.1 > tile 6 models tiled > volume level 0.2 > tile 6 models tiled > volume level 0.15 > tile 6 models tiled > volume level 0.12 > tile 6 models tiled > volume level 0.1 > save C:\Users\lilyh\Desktop\image190.png supersample 3 > hide #!24 models > hide #!22 models > hide #!23 models > hide #!21 models > hide #!19 models > hide #!20 models > show #!18 models > hide #!18 models > show #!18 models > show #!19 models > show #!16 models > show #!15 models > hide #!19 models > show #!17 models > show #!14 models > show #!13 models > ui mousemode right "rotate selected models" > ui mousemode right "translate selected models" > hide #!18 models > hide #!17 models > hide #!15 models > hide #!16 models > hide #!13 models > show #!13 models > hide #!14 models > hide #!13 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1777_001_volume_map_sharp.mrc Opened cryosparc_P122_J1777_001_volume_map_sharp.mrc as #25, grid size 256,256,256, pixel 1.09, shown at level 0.0205, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1776_001_volume_map_sharp.mrc Opened cryosparc_P122_J1776_001_volume_map_sharp.mrc as #26, grid size 256,256,256, pixel 1.09, shown at level 0.0153, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1775_002_volume_map_sharp.mrc Opened cryosparc_P122_J1775_002_volume_map_sharp.mrc as #27, grid size 256,256,256, pixel 1.09, shown at level 0.021, step 1, values float32 > volume level 0.1 > volume level 0.1tile Invalid "level" argument: Expected a number > tile 3 models tiled > tile 3 models tiled > color #25-27 dark gray > volume #27 level 0.08141 > volume level 0.08 Drag select of 27 cryosparc_P122_J1775_002_volume_map_sharp.mrc > select clear > save C:\Users\lilyh\Desktop\image191.png supersample 3 > hide #!27 models > hide #!26 models > hide #!25 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1778_class_02_00012_volume.mrc Opened cryosparc_P122_J1778_class_02_00012_volume.mrc as #28, grid size 100,100,100, pixel 2.78, shown at level 0.0568, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1778_class_01_00012_volume.mrc Opened cryosparc_P122_J1778_class_01_00012_volume.mrc as #29, grid size 100,100,100, pixel 2.78, shown at level 0.0571, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1778_class_00_00012_volume.mrc Opened cryosparc_P122_J1778_class_00_00012_volume.mrc as #30, grid size 100,100,100, pixel 2.78, shown at level 0.05, step 1, values float32 > volume level 0.08 > volume level 0.1 > volume level 0.2 > tile 3 models tiled > volume level 0.1 [Repeated 1 time(s)] > tile 3 models tiled > volume level 0.2 > tile 3 models tiled > volume level 0.1 > volume level 0.15 > volume level 0.14 > volume level 0.13 > volume level 0.12 > ui mousemode right "translate selected models" [Repeated 1 time(s)] > ui mousemode right "rotate selected models" > tile 3 models tiled > ~tile > volume level 0.18 > tile 3 models tiled > volume level 0.11 > volume level 0.12 > ui mousemode right "translate selected models" > ui mousemode right "rotate selected models" > select #30 2 models selected > select clear > save C:\Users\lilyh\Desktop\image192.png supersample 3 > hide #!29 models > hide #!30 models > hide #!28 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1787_001_volume_map_sharp.mrc Opened cryosparc_P122_J1787_001_volume_map_sharp.mrc as #31, grid size 256,256,256, pixel 1.09, shown at level 0.0178, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1785_001_volume_map_sharp.mrc Opened cryosparc_P122_J1785_001_volume_map_sharp.mrc as #32, grid size 256,256,256, pixel 1.09, shown at level 0.0203, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1784_001_volume_map_sharp.mrc Opened cryosparc_P122_J1784_001_volume_map_sharp.mrc as #33, grid size 256,256,256, pixel 1.09, shown at level 0.0149, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1786_001_volume_map_sharp.mrc Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #34, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > volume level 0.12 > tile 4 models tiled > tile 4 models tiled > volume level 0.1 > volume level 0.08 > volume level 0.07 > volume level 0.06 > volume level 0.066 > volume level 0.067 > volume level 0.068 > volume level 0.069 > volume level 0.068 > volume level 0.07 > volume level 0.05 > volume level 0.06 > color #31-34 dark gray > hide #!31 models > show #!31 models > hide #!31 models > save C:\Users\lilyh\Desktop\image193.png supersample 3 > hide #!34 models > hide #!32 models > hide #!33 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1792_001_volume_map_sharp.mrc Opened cryosparc_P122_J1792_001_volume_map_sharp.mrc as #35, grid size 256,256,256, pixel 1.09, shown at level 0.0194, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1791_002_volume_map_sharp.mrc Opened cryosparc_P122_J1791_002_volume_map_sharp.mrc as #36, grid size 256,256,256, pixel 1.09, shown at level 0.0194, step 1, values float32 > volume level 0.06 > tile 2 models tiled > volume #35 level 0.04972 > show #!32 models > show #!34 models > volume level 0.06 > ~tile > tile 4 models tiled Drag select of 35 cryosparc_P122_J1792_001_volume_map_sharp.mrc , 36 cryosparc_P122_J1791_002_volume_map_sharp.mrc > view matrix models > #35,0.65647,-0.66759,-0.35123,92.055,0.69947,0.36435,0.61481,-217.63,-0.28248,-0.64928,0.70614,15.283,#36,0.65647,-0.66759,-0.35123,28.255,0.69947,0.36435,0.61481,-133.17,-0.28248,-0.64928,0.70614,137.93 > undo > ui mousemode right "rotate selected models" > ui mousemode right "translate selected models" > view matrix models > #35,0.051757,-0.93407,-0.35333,265.47,0.74264,-0.20055,0.63896,-153.21,-0.66769,-0.29546,0.68329,39.426,#36,0.051757,-0.93407,-0.35333,213.56,0.74264,-0.20055,0.63896,-62.07,-0.66769,-0.29546,0.68329,162.9 > select clear > volume #36 level 0.06283 > volume level 0.06 > save C:\Users\lilyh\Desktop\image194.png supersample 3 > hide #!36 models > hide #!35 models > hide #!32 models > hide #!34 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1793_class_00_00012_volume.mrc Opened cryosparc_P122_J1793_class_00_00012_volume.mrc as #37, grid size 100,100,100, pixel 2.78, shown at level 0.0656, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1793_class_04_00012_volume.mrc Opened cryosparc_P122_J1793_class_04_00012_volume.mrc as #38, grid size 100,100,100, pixel 2.78, shown at level 0.0699, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1793_class_03_00012_volume.mrc Opened cryosparc_P122_J1793_class_03_00012_volume.mrc as #39, grid size 100,100,100, pixel 2.78, shown at level 0.067, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1793_class_02_00012_volume.mrc Opened cryosparc_P122_J1793_class_02_00012_volume.mrc as #40, grid size 100,100,100, pixel 2.78, shown at level 0.0634, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1793_class_01_00012_volume.mrc Opened cryosparc_P122_J1793_class_01_00012_volume.mrc as #41, grid size 100,100,100, pixel 2.78, shown at level 0.063, step 1, values float32 > volume level 0.06 > volume level 0.1 > volume level 0.2 > tile 5 models tiled > ui mousemode right "rotate selected models" > volume level 0.1 > volume level 0.12 > volume level 0.13 > ~tile > tile 5 models tiled > volume level 0.15 > volume level 0.16 > volume level 0.17 > tile 5 models tiled > volume level 0.1 > volume level 0.15 > tile 5 models tiled > volume level 0.2 > tile 5 models tiled > volume level 0.18 > tile 5 models tiled > volume level 0.1 > volume level 0.12 > save C:\Users\lilyh\Desktop\image195.png supersample 3 > volume level 0.1 > volume level 0.12 > volume level 0.13 > volume level 0.14 > save C:\Users\lilyh\Desktop\image196.png supersample 3 > volume level 0.14 > volume level 0.15 > save C:\Users\lilyh\Desktop\image197.png supersample 3 > hide #!41 models > hide #!39 models > hide #!40 models > hide #!38 models > hide #!37 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_01_00011_volume.mrc Opened cryosparc_P122_J1788_class_01_00011_volume.mrc as #42, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_03_00011_volume.mrc Opened cryosparc_P122_J1788_class_03_00011_volume.mrc as #43, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_04_00011_volume.mrc Opened cryosparc_P122_J1788_class_04_00011_volume.mrc as #44, grid size 80,80,80, pixel 3.47, shown at level 0.133, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_02_00011_volume.mrc Opened cryosparc_P122_J1788_class_02_00011_volume.mrc as #45, grid size 80,80,80, pixel 3.47, shown at level 0.13, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_00_00011_volume.mrc Opened cryosparc_P122_J1788_class_00_00011_volume.mrc as #46, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > volume level 0.15 > volume level 0.2 > volume level 0.3 > tile 5 models tiled > ~tile > tile 5 models tiled > volume level 0.3 > volume level 0.4 > tile 5 models tiled > volume level 0.1 > volume level 0.2 > volume level 0.23 > volume level 0.24 > volume level 0.3 > volume level 0.4 > tile 5 models tiled > ~tile > tile 5 models tiled > ~tile > tile 5 models tiled > volume level 0.3\ Invalid "level" argument: Expected a number > volume level 0.2 > volume level 0.23 > volume level 0.22 > volume level 0.23 > volume level 0.24 > volume level 0.25 > volume level 0.26 > volume level 0.27 > volume level 0.26 > volume level 0.25 > color #42-46 gray > color #42-46 dark gray > save C:\Users\lilyh\Desktop\image198.png supersample 3 > save C:\Users\lilyh\Desktop\image199.png supersample 3 > volume level 0.25 > hide #!43 models > hide #!42 models > hide #!44 models > hide #!45 models > hide #!46 models > show #!36 models > show #!35 models > show #!32 models > show #!34 models > show #!25 models > show #!27 models > show #!26 models > show #!33 models > volume level 0.06 > ~TILE Unknown command: ~TILE > ~tile > volume level 0.08 > tile 8 models tiled > volume level 0.06 > hide #!27 models > show #!27 models > hide #!26 models > show #!26 models > hide #!25 models > show #!25 models Drag select of 25 cryosparc_P122_J1777_001_volume_map_sharp.mrc , 26 cryosparc_P122_J1776_001_volume_map_sharp.mrc , 27 cryosparc_P122_J1775_002_volume_map_sharp.mrc > color #25.1#26.1#27.1 gray > select clear Drag select of 32 cryosparc_P122_J1785_001_volume_map_sharp.mrc , 33 cryosparc_P122_J1784_001_volume_map_sharp.mrc , 34 cryosparc_P122_J1786_001_volume_map_sharp.mrc Drag select of 25 cryosparc_P122_J1777_001_volume_map_sharp.mrc , 26 cryosparc_P122_J1776_001_volume_map_sharp.mrc , 27 cryosparc_P122_J1775_002_volume_map_sharp.mrc , 32 cryosparc_P122_J1785_001_volume_map_sharp.mrc , 33 cryosparc_P122_J1784_001_volume_map_sharp.mrc , 34 cryosparc_P122_J1786_001_volume_map_sharp.mrc , 35 cryosparc_P122_J1792_001_volume_map_sharp.mrc , 36 cryosparc_P122_J1791_002_volume_map_sharp.mrc > color #25.1#26.1#27.1#32.1#33.1#34.1#35.1#36.1 dark gray > color #25.1#26.1#27.1#32.1#33.1#34.1#35.1#36.1 gray > lighting full > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > select clear Drag select of 32 cryosparc_P122_J1785_001_volume_map_sharp.mrc , 33 cryosparc_P122_J1784_001_volume_map_sharp.mrc , 34 cryosparc_P122_J1786_001_volume_map_sharp.mrc > ui mousemode right "translate selected models" > view matrix models > #32,0.5137,0.57763,-0.63439,150.01,-0.55115,-0.3445,-0.75997,336.25,-0.65753,0.74004,0.14139,195.16,#33,0.5137,0.57763,-0.63439,38.668,-0.55115,-0.3445,-0.75997,215.74,-0.65753,0.74004,0.14139,206.36,#34,0.5137,0.57763,-0.63439,-73.743,-0.55115,-0.3445,-0.75997,95.62,-0.65753,0.74004,0.14139,220.1 Drag select of 35 cryosparc_P122_J1792_001_volume_map_sharp.mrc , 36 cryosparc_P122_J1791_002_volume_map_sharp.mrc > view matrix models > #35,0.5137,0.57763,-0.63439,209.83,-0.55115,-0.3445,-0.75997,297.34,-0.65753,0.74004,0.14139,264.76,#36,0.5137,0.57763,-0.63439,97.267,-0.55115,-0.3445,-0.75997,176.96,-0.65753,0.74004,0.14139,278.09 > select clear > volume level 0.08 > volume level 0.07 > volume level 0.075 > volume level 0.07 > volume level 0.08 > volume level 0.07 > volume level 0.075 > volume level 0.08 > volume level 0.05 > volume level 0.06 > lighting full > lighting soft > lighting simple > lighting soft [Repeated 1 time(s)] > lighting simple > lighting soft > lighting full > lighting simple [Repeated 2 time(s)] > lighting soft > lighting full > lighting flat > lighting full > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting full > lighting flat > lighting full > lighting soft [Repeated 3 time(s)] > lighting simple [Repeated 1 time(s)] > save C:\Users\lilyh\Desktop\image200.png supersample 3 > turn x 180 [Repeated 3 time(s)] > turn y 180 [Repeated 3 time(s)] > ui mousemode right "translate selected models" > ui mousemode right "rotate selected models" > pivot x 180 Unknown command: pivot x 180 > pivot Unknown command: pivot > save C:\Users\lilyh\Desktop\image201.png supersample 3 > volume level 0.06 > volume level 0.07 > hide #!36 models > hide #!35 models > hide #!34 models > hide #!32 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > show #!32 models > show #!34 models > show #!36 models > show #!35 models > hide #!25 models > hide #!26 models > hide #!33 models > hide #!32 models > ~tile > tile 4 models tiled > volume level 0.08 > volume level 0.05 > volume level 0.06 > volume level 0.066 > volume level 0.067 > volume level 0.068 > volume level 0.07 > volume level 0.075 > volume #36 level 0.1061 > volume #36 level 0.08914 > volume #36 level 0.04388 > volume #36 level 0.05378 > volume #35 level 0.08785 > volume #27 level 0.08894 > volume #27 level 0.0688 > volume #34 level 0.07353 > volume #35 level 0.08271 [Repeated 1 time(s)] > volume #36 level 0.09763 > volume #36 level 0.05661 > hide #!27 models > show #!32 models > volume level 0.075 > volume level 0.06 > ~tile > tile 4 models tiled > volume level 0.08 > hide #!32 models > hide #!36 models > show #!36 models > hide #!35 models > volume level 0.08 > tile 2 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1789_map_sharp.mrc Opened cryosparc_P122_J1789_map_sharp.mrc as #47, grid size 256,256,256, pixel 1.09, shown at level 0.0152, step 1, values float32 > volume level 0.08 > tile 3 models tiled > ~tile > tile 3 models tiled > volume level 0.1 > volume level 0.09 > volume level 0.05 > volume level 0.06 > volume level 0.05 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1794_map_sharp.mrc Opened cryosparc_P122_J1794_map_sharp.mrc as #48, grid size 256,256,256, pixel 1.09, shown at level 0.018, step 1, values float32 > volume level 0.05 > ~tile > tile 4 models tiled > volume #48 level 0.07424 > volume #48 level 0.06212 > volume #48 level 0.05673 > volume level 0.05 > volume level 0.055 > volume #47 level 0.0467 > volume #48 level 0.1317 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1795_map_sharp.mrc Opened cryosparc_P122_J1795_map_sharp.mrc as #49, grid size 256,256,256, pixel 1.09, shown at level 0.0158, step 1, values float32 > volume level 0.055 > ~tile > tile 5 models tiled > volume #49 level 0.06633 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1796_map_sharp.mrc Opened cryosparc_P122_J1796_map_sharp.mrc as #50, grid size 256,256,256, pixel 1.09, shown at level 0.0173, step 1, values float32 > ~tile > volume level 0.055 > tile 6 models tiled > volume level 0.07 > volume level 0.06 > volume level 0.055 > volume level 0.07 > volume level 0.08 > volume level 0.09 > volume level 0.1 > volume level 0.09 > volume #50 level 0.09395 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1797_map_sharp.mrc Opened cryosparc_P122_J1797_map_sharp.mrc as #51, grid size 256,256,256, pixel 1.09, shown at level 0.0163, step 1, values float32 > volume level 0.09 > ~tile > tile 7 models tiled > volume level 0.05 > volume level 0.06 > volume level 0.05 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1798_map_sharp.mrc Opened cryosparc_P122_J1798_map_sharp.mrc as #52, grid size 256,256,256, pixel 1.09, shown at level 0.0143, step 1, values float32 > volume level 0.05 > ~tile > tile 8 models tiled > volume #52 level 0.07142 > volume #52 level 0.06606 > volume #52 level 0.05402 > volume #52 level 0.06874 > volume level 0.0687 > color #34,36,47-52 gray > volume level 0.06 > volume level 0.055 > volume level 0.05 > volume level 0.055 > volume level 0.06 > hide #!52 models > hide #!51 models > hide #!49 models > hide #!50 models > hide #!48 models > hide #!47 models > show #!47 models > show #!48 models > show #!49 models > show #!50 models > show #!51 models > show #!52 models > hide #!49 models > show #!49 models Drag select of 48 cryosparc_P122_J1794_map_sharp.mrc > ui mousemode right "translate selected models" > view matrix models > #48,0.50648,0.80802,-0.30097,255.77,-0.85248,0.41684,-0.31548,266.7,-0.12945,0.41635,0.89994,2.4641 Drag select of 49 cryosparc_P122_J1795_map_sharp.mrc > view matrix models > #49,0.50648,0.80802,-0.30097,113.5,-0.85248,0.41684,-0.31548,156.54,-0.12945,0.41635,0.89994,219.44 > select clear > hide #!47 models > show #!47 models Drag select of 47 cryosparc_P122_J1789_map_sharp.mrc > view matrix models > #47,0.50648,0.80802,-0.30097,202.73,-0.85248,0.41684,-0.31548,164.87,-0.12945,0.41635,0.89994,247.76 > select clear > hide #!52 models > show #!52 models Drag select of 51 cryosparc_P122_J1797_map_sharp.mrc > view matrix models > #51,0.50648,0.80802,-0.30097,145.07,-0.85248,0.41684,-0.31548,27.437,-0.12945,0.41635,0.89994,596.29 > select #52 2 models selected > view matrix models > #52,0.50648,0.80802,-0.30097,296.19,-0.85248,0.41684,-0.31548,174.55,-0.12945,0.41635,0.89994,280.39 > select clear > select #36 2 models selected > select clear > select #48 2 models selected > view matrix models > #48,0.50648,0.80802,-0.30097,67.672,-0.85248,0.41684,-0.31548,98.295,-0.12945,0.41635,0.89994,353.48 > select clear > select #50 2 models selected > view matrix models > #50,0.50648,0.80802,-0.30097,156.13,-0.85248,0.41684,-0.31548,106.84,-0.12945,0.41635,0.89994,383.29 > select clear > select #51 2 models selected > view matrix models > #51,0.50648,0.80802,-0.30097,243.64,-0.85248,0.41684,-0.31548,115.85,-0.12945,0.41635,0.89994,411.89 > select clear > volume level 0.06 > color #34,36,47-52 gray > color #34,36,47-52 dark gray > ui mousemode right "rotate selected models" > volume level 0.04 > volume level 0.05 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1799_map_sharp.mrc Opened cryosparc_P122_J1799_map_sharp.mrc as #53, grid size 256,256,256, pixel 1.09, shown at level 0.0129, step 1, values float32 > volume level 0.05 > ui mousemode right "rotate selected models" > select #53 2 models selected > ui mousemode right "translate selected models" > view matrix models #53,1,0,0,188.65,0,1,0,16.57,0,0,1,45.348 > ui mousemode right "move picked models" > select #53 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #53,0.30928,-0.4772,0.82257,231.74,0.25533,0.87489,0.41155,-64.036,-0.91605,0.082742,0.39243,256.01 > view matrix models > #53,-0.90047,-0.1958,-0.38834,546.86,-0.41467,0.65577,0.63089,30.053,0.13113,0.72913,-0.6717,174.14 > view matrix models > #53,0.52134,-0.40662,0.75024,202.22,0.25287,0.9133,0.31928,-55.278,-0.81502,0.023256,0.57897,221.97 > view matrix models > #53,-0.86384,-0.44885,0.22871,484.86,-0.14985,0.66241,0.73401,-24.292,-0.48096,0.59979,-0.63947,275.3 > view matrix models > #53,0.52003,0.73037,-0.44287,225.15,-0.84316,0.35601,-0.40292,284.12,-0.13661,0.58294,0.80095,16.144 > view matrix models > #53,0.56597,0.81644,-0.11444,158.71,-0.78187,0.48754,-0.38856,255.5,-0.26144,0.3094,0.91429,54.249 > color #53.1 dark gray > ui mousemode right "rotate selected models" > view matrix models > #53,0.56555,0.81579,-0.12097,159.81,-0.78302,0.4851,-0.38931,256.1,-0.25891,0.31489,0.91313,53.316 > ui mousemode right "translate selected models" > view matrix models > #53,0.56555,0.81579,-0.12097,9.6106,-0.78302,0.4851,-0.38931,28.428,-0.25891,0.31489,0.91313,526.27 > ui mousemode right "rotate selected models" > view matrix models > #53,0.47597,0.85678,-0.19844,28.451,-0.8402,0.37633,-0.39043,51.457,-0.25983,0.35256,0.89899,523.42 > select clear > ui mousemode right "translate selected models" > select clear > select #53 2 models selected > view matrix models > #53,0.47597,0.85678,-0.19844,364.21,-0.8402,0.37633,-0.39043,192.67,-0.25983,0.35256,0.89899,338.97 > ui mousemode right "rotate selected models" > view matrix models > #53,0.4679,0.83925,-0.27702,379.27,-0.85154,0.34421,-0.39547,199.36,-0.23655,0.42093,0.87571,329.85 > select clear > open C:/Users/lilyh/Downloads/cryosparc_P122_J1800_map_sharp.mrc Opened cryosparc_P122_J1800_map_sharp.mrc as #54, grid size 256,256,256, pixel 1.09, shown at level 0.0151, step 1, values float32 > volume level 0.05 > select #54 2 models selected > ui mousemode right "translate selected models" > view matrix models #54,1,0,0,354.58,0,1,0,58.543,0,0,1,44.187 > view matrix models #54,1,0,0,203.42,0,1,0,-23.998,0,0,1,205.58 > ui mousemode right "rotate selected models" > view matrix models > #54,0.44428,0.88626,-0.13096,184.44,-0.88672,0.41415,-0.20545,213.14,-0.12784,0.2074,0.96987,200.75 > ui mousemode right "translate selected models" > view matrix models > #54,0.44428,0.88626,-0.13096,304.57,-0.88672,0.41415,-0.20545,149.86,-0.12784,0.2074,0.96987,475.84 > ui mousemode right "rotate selected models" > view matrix models > #54,0.42643,0.87256,-0.23831,324.75,-0.89882,0.37922,-0.21981,158.41,-0.10143,0.30793,0.94599,462.05 > ui mousemode right "rotate selected models" > view matrix models > #54,0.40226,0.88006,-0.25234,329.31,-0.90576,0.34241,-0.2497,168.73,-0.13334,0.32901,0.93487,465.48 > color #54.1 dark gray > select clear > select #54 2 models selected > view matrix models > #54,0.36084,0.89262,-0.27023,336.26,-0.91907,0.29112,-0.26563,179.87,-0.15844,0.34421,0.92543,468.47 > ui mousemode right "translate selected models" > view matrix models > #54,0.36084,0.89262,-0.27023,331.55,-0.91907,0.29112,-0.26563,134.88,-0.15844,0.34421,0.92543,446.87 > ui mousemode right "rotate selected models" > view matrix models > #54,0.45486,0.84389,-0.28452,326.55,-0.88383,0.38855,-0.26053,115.98,-0.10931,0.36997,0.92259,436.72 > ui mousemode right "translate selected models" > view matrix models > #54,0.45486,0.84389,-0.28452,328.31,-0.88383,0.38855,-0.26053,117.06,-0.10931,0.36997,0.92259,437.83 > select clear > ui mousemode right "rotate selected models" > select clear > ui mousemode right "translate selected models" > color #34,36,47-54 gray > color #34,36,47-54 dark gray > graphics silhouettes false > graphics silhouettes true > lighting soft > ui mousemode right "rotate selected models" > save C:\Users\lilyh\Desktop\image202.png supersample 3 > save C:\Users\lilyh\Desktop\image203.png supersample 3 > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/j1664 3D > Classifications.cxs" includeMaps true > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_00_00042_volume.mrc Opened cryosparc_P122_J1664_class_00_00042_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0276, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_05_00042_volume.mrc Opened cryosparc_P122_J1664_class_05_00042_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0272, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_04_00042_volume.mrc Opened cryosparc_P122_J1664_class_04_00042_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_03_00042_volume.mrc Opened cryosparc_P122_J1664_class_03_00042_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0268, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_02_00042_volume.mrc Opened cryosparc_P122_J1664_class_02_00042_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.028, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_01_00042_volume.mrc Opened cryosparc_P122_J1664_class_01_00042_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0248, step 1, values float32 > volume level 0.05 > TILE Unknown command: TILE > tile 6 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1678_001_volume_map_sharp.mrc Opened cryosparc_P122_J1678_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.0113, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1677_001_volume_map_sharp.mrc Opened cryosparc_P122_J1677_001_volume_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.09, shown at level 0.0109, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1674_001_volume_map_sharp.mrc Opened cryosparc_P122_J1674_001_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.0112, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1673_001_volume_map_sharp.mrc Opened cryosparc_P122_J1673_001_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.09, shown at level 0.0118, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1672_001_volume_map_sharp.mrc Opened cryosparc_P122_J1672_001_volume_map_sharp.mrc as #11, grid size 256,256,256, pixel 1.09, shown at level 0.0111, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1671_001_volume_map_sharp.mrc Opened cryosparc_P122_J1671_001_volume_map_sharp.mrc as #12, grid size 256,256,256, pixel 1.09, shown at level 0.0103, step 1, values float32 > volume level 0.05 > volume level 0.1 > tile 12 models tiled > volume level 0.08 > volume level 0.05 > volume level 0.06 > volume level 0.07 > volume level 0.08 > volume level 0.09 > volume level 0.1 > volume level 0.05 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_05_00022_volume.mrc Opened cryosparc_P122_J1679_class_05_00022_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0358, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_04_00022_volume.mrc Opened cryosparc_P122_J1679_class_04_00022_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0364, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_02_00022_volume.mrc Opened cryosparc_P122_J1679_class_02_00022_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0325, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_03_00022_volume.mrc Opened cryosparc_P122_J1679_class_03_00022_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0327, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_00_00022_volume.mrc Opened cryosparc_P122_J1679_class_00_00022_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.0367, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1679_class_01_00022_volume.mrc Opened cryosparc_P122_J1679_class_01_00022_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0353, step 1, values float32 > volume level 0.05 > volume level 0.1 > tile 6 models tiled > volume level 0.08 > volume level 0.04 > volume level 0.05 > volume level 0.06 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1747_001_volume_map_sharp.mrc Opened cryosparc_P122_J1747_001_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.0175, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1748_001_volume_map_sharp.mrc Opened cryosparc_P122_J1748_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.0185, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1746_001_volume_map_sharp.mrc Opened cryosparc_P122_J1746_001_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0158, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1737_001_volume_map_sharp.mrc Opened cryosparc_P122_J1737_001_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0193, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1738_001_volume_map_sharp.mrc Opened cryosparc_P122_J1738_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1739_001_volume_map_sharp.mrc Opened cryosparc_P122_J1739_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.0173, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1701_001_volume_map_sharp.mrc Opened cryosparc_P122_J1701_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.0157, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1704_002_volume_map_sharp.mrc Opened cryosparc_P122_J1704_002_volume_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.09, shown at level 0.0157, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1703_001_volume_map_sharp.mrc Opened cryosparc_P122_J1703_001_volume_map_sharp.mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.0169, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1702_002_volume_map_sharp.mrc Opened cryosparc_P122_J1702_002_volume_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.09, shown at level 0.0176, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1791_002_volume_map_sharp.mrc Opened cryosparc_P122_J1791_002_volume_map_sharp.mrc as #11, grid size 256,256,256, pixel 1.09, shown at level 0.0194, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1786_001_volume_map_sharp.mrc Opened cryosparc_P122_J1786_001_volume_map_sharp.mrc as #12, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1335_002_volume_map_sharp.mrc Opened cryosparc_P122_J1335_002_volume_map_sharp.mrc as #13, grid size 256,256,256, pixel 1.09, shown at level 0.026, step 1, values float32 > volume level 0.06 > volume level 0.1 > tile 13 models tiled > tile 13 models tiled > ui mousemode right "translate selected models" > ui mousemode right "rotate selected models" > volume level 0.08 > volume level 0.06 > volume level 0.07 > ~tile > volume level 0.1 > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > volume #1 level 0.06739 > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!12 models > volume #12 level 0.1088 > hide #!1 models > hide #1.1 models > show #1.1 models > hide #!12 models > show #!12 models > hide #1.1 models > hide #!1 models > volume #12 level 0.07361 > show #1.1 models > tile 2 models tiled > ~tile > select #12 2 models selected > transparency #12.1 50 > select clear > tile 2 models tiled > color #1,12 dark gray > set bgColor white > graphics silhouettes true > transparency #1,12 0 > select clear > tile 2 models tiled > ~tile > tile 2 models tiled > volume level 0.2 > volume level 0.1 > volume level 0.12 > volume level 0.1 > volume level 0.08 > volume level 0.07 > volume level 0.075 > volume level 0.07 > volume level 0.08 > volume level 0.075 > save C:\Users\lilyh\Desktop\image204.png supersample 3 > hide #1.1 models > hide #!1 models > hide #!12 models > show #!2 models > show #1.1 models > hide #1.1 models > show #!3 models > hide #!3 models > show #!11 models > ~TILE Unknown command: ~TILE > ~tile > hide #!11 models > show #!11 models > hide #!2 models > show #!3 models > ~tile > hide #!3 models > hide #!11 models > show #!11 models > hide #!1 models > show #!10 models > hide #!11 models > show #!13 models > hide #!13 models > show #!11 models > hide #!11 models > hide #!10 models > show #!9 models > show #!10 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!8 models > show #!7 models > tile 4 models tiled > ~tile > volume level 0.08 > volume level 0.1 > tile 4 models tiled > tile 4 models tiled > ~tile > hide #!7 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > hide #!10 models > show #!8 models > hide #!8 models > show #!6 models > volume level 0.08 > show #!10 models > hide #!10 models > hide #!6 models > show #!5 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!5 models > show #!4 models > show #!3 models > hide #!3 models > show #!2 models > show #!5 models > ~tile [Repeated 1 time(s)] > tile 3 models tiled > tile 3 models tiled > show #1.1 models > tile 4 models tiled > ~tile > tile 4 models tiled > ~tile > tile 4 models tiled Drag select of 1 cryosparc_P122_J1747_001_volume_map_sharp.mrc , 2 cryosparc_P122_J1748_001_volume_map_sharp.mrc > color #1.1#2.1 dark gray > select clear > volume level 0.075 > select clear > ui mousemode right zoom > ui mousemode right "translate selected models" > select #2 2 models selected > view matrix models > #2,-0.4805,0.72633,-0.49149,95.68,-0.42586,-0.68317,-0.59323,272.91,-0.76665,-0.075741,0.63758,306.75 > select #1 2 models selected > view matrix models > #1,-0.4805,0.72633,-0.49149,284.8,-0.42586,-0.68317,-0.59323,448.92,-0.76665,-0.075741,0.63758,65.132 > select #2 2 models selected > view matrix models > #2,-0.4805,0.72633,-0.49149,213.28,-0.42586,-0.68317,-0.59323,356.22,-0.76665,-0.075741,0.63758,170.79 > select clear > save C:\Users\lilyh\Desktop\image205.png supersample 3 > hide #!4 models > show #!4 models > show #!3 models > ~tile > tile 5 models tiled > show #!13 models > hide #!13 models > select #3 2 models selected > color #3.1 gray > color #3.1 dark gray > select clear > volume level 0.075 > save C:\Users\lilyh\Desktop\image206.png supersample 3 > show #!6 models > volume level 0.075 > ~tile > tile 6 models tiled > hide #13.1 models > hide #!6 models > select #5 2 models selected > ~tile > select clear > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #1.1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!2 models > show #!5 models > save C:\Users\lilyh\Desktop\image207.png supersample 3 > hide #!4 models > hide #!5 models > show #13.1 models > show #!2 models > ~tile > hide #!2 models > show #!12 models > hide #!12 models > show #!8 models > ~tile > hide #!8 models > show #!7 models > hide #!7 models > show #!7 models > show #!6 models > ~tile > tile 3 models tiled > show #!9 models > show #!8 models > hide #!9 models > show #!11 models > hide #!11 models > show #!11 models > ~tile > tile 5 models tiled > hide #13.1 models > show #13.1 models > hide #!8 models > show #!8 models > hide #!8 models > show #!5 models > ~tile > tile 5 models tiled > hide #!5 models > hide #!1 models > hide #!11 models > volume level 0.1 > ~tile > volume level 0.08 > tile 3 models tiled > volume level 0.05 > ~tile > tile 3 models tiled > volume level 0.05 > volume level 0.08 > tile 3 models tiled > volume #13 level 0.1138 > volume #13 level 0.09689 > volume #6 level 0.07675 > volume #7 level 0.06774 > volume #7 level 0.05242 > volume #6 level 0.05723 > volume #6 level 0.05235 > save C:\Users\lilyh\Desktop\image208.png supersample 3 > save C:\Users\lilyh\Desktop\image209.png supersample 3 > ~tile > hide #13.1 models > hide #!13 models > hide #!6 models > hide #!7 models > show #!8 models > ui mousemode right "translate selected models" > show #!9 models > hide #!9 models > show #!9 models > show #!10 models > show #!11 models > show #!13 models > show volumes Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > volume show > ~tile > tile 11 models tiled > show #13.1 models > ~tile > tile 12 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1388_002_volume_map_sharp.mrc Opened cryosparc_P122_J1388_002_volume_map_sharp.mrc as #14, grid size 256,256,256, pixel 1.09, shown at level 0.0298, step 1, values float32 > open > C:/Users/lilyh/Downloads/cryosparc_P122_J872_class_01_00044_volume_sharp.mrc Opened cryosparc_P122_J872_class_01_00044_volume_sharp.mrc as #15, grid size 128,128,128, pixel 2.17, shown at level 0.0633, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J868_002_volume_map_sharp.mrc Opened cryosparc_P122_J868_002_volume_map_sharp.mrc as #16, grid size 256,256,256, pixel 1.09, shown at level 0.074, step 1, values float32 > volume show > volume level 0.08 > ~tile > volume level 0.1 > volume level 0.4 > ~tile > tile 12 models tiled > volume level 0.08 > show #1.1 models > ~tile > volume level 0.2 > tile 16 models tiled > volume level 0.1 > select clear > ui mousemode right "rotate selected models" > select #15 2 models selected > view matrix models > #15,-0.99328,-0.099617,0.058977,475.45,-0.096035,0.99352,0.060748,-282.68,-0.064646,0.054676,-0.99641,488.43 > view matrix models > #15,0.9383,-0.34225,0.049506,246.89,0.34242,0.93953,0.0053189,-327.3,-0.048333,0.011961,0.99876,214.57 > close #15 > volume #16 level 0.3354 > close #16 > color dark gray > volume level 0.07 > volume level 0.06 > volume #14 level 0.1385 > volume #13 level 0.1022 > hide #!14 models > show #!14 models > hide #!13 models > show #!13 models Drag select of 13 cryosparc_P122_J1335_002_volume_map_sharp.mrc , 14 cryosparc_P122_J1388_002_volume_map_sharp.mrc > color #13.1#14.1 dim gray > select clear > hide #!12 models > show #!12 models > volume level 0.08 > volume level 0.07 > volume #14 level 0.1171 > volume #13 level 0.07563 > volume #13 level 0.1066 > volume #14 level 0.1328 > volume level 0.06 > volume #14 level 0.148 > volume #13 level 0.09097 > volume #13 level 0.09378 > volume #14 level 0.1134 > save C:\Users\lilyh\Desktop\image210.png supersample 3 > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/j1268 j1664 vac17 > refinement.cxs" includeMaps true [Repeated 1 time(s)] ——— End of log from Thu Oct 12 14:09:03 2023 ——— opened ChimeraX session > ui mousemode right "rotate selected models" > ui mousemode right "translate selected models" [Repeated 1 time(s)] > ui mousemode right "rotate selected models" > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_05_00042_volume.mrc Opened cryosparc_P122_J1664_class_05_00042_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0272, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_04_00042_volume.mrc Opened cryosparc_P122_J1664_class_04_00042_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0261, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_03_00042_volume.mrc Opened cryosparc_P122_J1664_class_03_00042_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0268, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_02_00042_volume.mrc Opened cryosparc_P122_J1664_class_02_00042_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.028, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_01_00042_volume.mrc Opened cryosparc_P122_J1664_class_01_00042_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.0248, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1664_class_00_00042_volume.mrc Opened cryosparc_P122_J1664_class_00_00042_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0276, step 1, values float32 > color dark gray > volume level 0.1 > tile 6 models tiled > volume level 0.08 > volume level 0.1 > volume level 0.2 > volume level 0.15 > volume level 0.14 > volume level 0.13 > volume level 0.12 > volume level 0.125 > volume level 0.14 > hide #!5 models > hide #!4 models > close #1-5 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_00_00035_volume.mrc Opened cryosparc_P122_J1720_class_00_00035_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0379, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_09_00035_volume.mrc Opened cryosparc_P122_J1720_class_09_00035_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0387, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_08_00035_volume.mrc Opened cryosparc_P122_J1720_class_08_00035_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0372, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_07_00035_volume.mrc Opened cryosparc_P122_J1720_class_07_00035_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0377, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_06_00035_volume.mrc Opened cryosparc_P122_J1720_class_06_00035_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.036, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_05_00035_volume.mrc Opened cryosparc_P122_J1720_class_05_00035_volume.mrc as #7, grid size 100,100,100, pixel 2.78, shown at level 0.0361, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_04_00035_volume.mrc Opened cryosparc_P122_J1720_class_04_00035_volume.mrc as #8, grid size 100,100,100, pixel 2.78, shown at level 0.0368, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_03_00035_volume.mrc Opened cryosparc_P122_J1720_class_03_00035_volume.mrc as #9, grid size 100,100,100, pixel 2.78, shown at level 0.0336, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_02_00035_volume.mrc Opened cryosparc_P122_J1720_class_02_00035_volume.mrc as #10, grid size 100,100,100, pixel 2.78, shown at level 0.033, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_01_00035_volume.mrc Opened cryosparc_P122_J1720_class_01_00035_volume.mrc as #11, grid size 100,100,100, pixel 2.78, shown at level 0.041, step 1, values float32 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!6 models > color #1-5,7-11 gray > volume level 0.14 > tile 10 models tiled > volume level 0.15 > volume level 0.17 > volume level 0.19 > volume level 0.17 > hide #!11 models > show #!11 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > show #!8 models > show #!9 models > hide #!8 models > hide #!7 models > hide #!5 models > hide #!4 models > hide #!3 models > volume level 0.18 > volume level 0.19 > volume level 0.2 > volume level 0.19 > show #!6 models > hide #!6 models > show #!6 models > tile 4 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1671_001_volume_map.mrc Opened cryosparc_P122_J1671_001_volume_map.mrc as #12, grid size 256,256,256, pixel 1.09, shown at level 0.00318, step 1, values float32 > volume #12 level 0.1569 > volume #12 level 0.1595 > hide #!9 models > hide #!6 models > hide #!2 models > hide #!1 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_05_00024_volume.mrc Opened cryosparc_P122_J1818_class_05_00024_volume.mrc as #13, grid size 100,100,100, pixel 2.78, shown at level 0.0478, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_04_00024_volume.mrc Opened cryosparc_P122_J1818_class_04_00024_volume.mrc as #14, grid size 100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_03_00024_volume.mrc Opened cryosparc_P122_J1818_class_03_00024_volume.mrc as #15, grid size 100,100,100, pixel 2.78, shown at level 0.0535, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_02_00024_volume.mrc Opened cryosparc_P122_J1818_class_02_00024_volume.mrc as #16, grid size 100,100,100, pixel 2.78, shown at level 0.0523, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_01_00024_volume.mrc Opened cryosparc_P122_J1818_class_01_00024_volume.mrc as #17, grid size 100,100,100, pixel 2.78, shown at level 0.0498, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_00_00024_volume.mrc Opened cryosparc_P122_J1818_class_00_00024_volume.mrc as #18, grid size 100,100,100, pixel 2.78, shown at level 0.0479, step 1, values float32 > volume level 0.19 > tile 6 models tiled > color #13-18 gray > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_05_00016_volume.mrc Opened cryosparc_P122_J1814_class_05_00016_volume.mrc as #19, grid size 100,100,100, pixel 2.78, shown at level 0.05, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_04_00016_volume.mrc Opened cryosparc_P122_J1814_class_04_00016_volume.mrc as #20, grid size 100,100,100, pixel 2.78, shown at level 0.0664, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_03_00016_volume.mrc Opened cryosparc_P122_J1814_class_03_00016_volume.mrc as #21, grid size 100,100,100, pixel 2.78, shown at level 0.05, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_02_00016_volume.mrc Opened cryosparc_P122_J1814_class_02_00016_volume.mrc as #22, grid size 100,100,100, pixel 2.78, shown at level 0.0506, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_01_00016_volume.mrc Opened cryosparc_P122_J1814_class_01_00016_volume.mrc as #23, grid size 100,100,100, pixel 2.78, shown at level 0.0592, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1814_class_00_00016_volume.mrc Opened cryosparc_P122_J1814_class_00_00016_volume.mrc as #24, grid size 100,100,100, pixel 2.78, shown at level 0.0545, step 1, values float32 > volume level 0.19 > tile 6 models tiled > color #19-24 dark gray > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > tile 12 models tiled > close #19-24 > tile 6 models tiled > volume level 0.2 [Repeated 1 time(s)] > volume level 0.4 > volume level 0.3 > volume level 0.26 > volume level 0.25 > volume level 0.2 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_02_00021_volume.mrc Opened cryosparc_P122_J1823_class_02_00021_volume.mrc as #19, grid size 80,80,80, pixel 3.47, shown at level 0.0762, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_04_00021_volume.mrc Opened cryosparc_P122_J1823_class_04_00021_volume.mrc as #20, grid size 80,80,80, pixel 3.47, shown at level 0.0907, step 1, values float32 > volume level 0.2 > tile 8 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_05_00021_volume.mrc Opened cryosparc_P122_J1823_class_05_00021_volume.mrc as #21, grid size 80,80,80, pixel 3.47, shown at level 0.0957, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_03_00021_volume.mrc Opened cryosparc_P122_J1823_class_03_00021_volume.mrc as #22, grid size 80,80,80, pixel 3.47, shown at level 0.1, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_01_00021_volume.mrc Opened cryosparc_P122_J1823_class_01_00021_volume.mrc as #23, grid size 80,80,80, pixel 3.47, shown at level 0.0952, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_00_00021_volume.mrc Opened cryosparc_P122_J1823_class_00_00021_volume.mrc as #24, grid size 80,80,80, pixel 3.47, shown at level 0.101, step 1, values float32 > volume level 0.2 > tile 12 models tiled > ~tile > tile 12 models tiled > volume level 0.3 > ~tile > tile 12 models tiled > close #19-24 > tile 6 models tiled > volume level 0.1 > volume level 0.14 > hide #!18 models > hide #!17 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > show #!6 models > show #!5 models > hide #!5 models > hide #!6 models > show #!5 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > show #!11 models > tile 10 models tiled > show #!6 models > hide #!6 models > volume level 0.2 > tile 10 models tiled > volume level 0.1 > volume level 0.15 > tile 10 models tiled > volume level 0.1 > volume level 0.12 > hide #!1-4,7-11 target m > close #5 > show #!18 models > show #!17 models > show #!16 models > show #!15 models > show #!14 models > show #!13 models > volume level 0.12 > volume level 0.1 > volume level 0.2 > tile 6 models tiled > volume level 0.1 > volume level 0.12 > volume level 0.14 > volume level 0.16 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1808_map_sharp.mrc Opened cryosparc_P122_J1808_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.031, step 1, values float32 > volume #5 level 0.1795 > ~tile > close #1-4,7-11 > show #!12 models > hide #!12 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!17 models > hide #!18 models > show #!17 models > hide #!16 models > hide #!15 models > show #!15 models > hide #!17 models > hide #!15 models > hide #!14 models > volume #13 level 0.1236 > hide #!13 models > show #!14 models > volume #14 level 0.1476 > hide #!14 models > show #!15 models > show #!16 models > hide #!15 models > volume #16 level 0.1433 > hide #!16 models > show #!17 models > volume #17 level 0.1214 > show #!18 models > hide #!17 models > volume #18 level 0.1391 > volume #18 level 0.1061 > show #!18 models > volume #18 level 0.169 > hide #!18 models > show #!17 models > volume #17 level 0.1821 > hide #!17 models > show #!16 models > hide #!16 models > show #!15 models > hide #!15 models > show #!14 models > volume #14 level 0.2158 > volume #13 level 0.2328 > hide #!13 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_00_00016_volume.mrc Opened cryosparc_P122_J1825_class_00_00016_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0463, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_02_00016_volume.mrc Opened cryosparc_P122_J1825_class_02_00016_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0456, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_03_00016_volume.mrc Opened cryosparc_P122_J1825_class_03_00016_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0483, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_01_00016_volume.mrc Opened cryosparc_P122_J1825_class_01_00016_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0513, step 1, values float32 > hide #!5 models > volume level 0.16 > tile 4 models tiled > show #!16 models > show #!14 models > tile 6 models tiled > volume #4 level 0.234 > volume #2 level 0.1365 > volume #1 level 0.1567 > show #!6 models > tile 7 models tiled > hide #!4 models > show #!4 models > hide #!3 models > hide #!4 models > hide #!2 models > hide #!6 models > hide #!1 models > show #!5 models > hide #!14 models > hide #!16 models > hide #18.1 models > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > show #!3 models > show #!4 models > ~tile > hide #!3 models > volume #4 level 0.1378 > volume #4 level 0.2389 > volume #3 level 0.2376 > show #!2 models > hide #!2 models > hide #!3 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_00_00011_volume.mrc Opened cryosparc_P122_J1826_class_00_00011_volume.mrc as #7, grid size 100,100,100, pixel 2.78, shown at level 0.0611, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_03_00011_volume.mrc Opened cryosparc_P122_J1826_class_03_00011_volume.mrc as #8, grid size 100,100,100, pixel 2.78, shown at level 0.0631, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_02_00011_volume.mrc Opened cryosparc_P122_J1826_class_02_00011_volume.mrc as #9, grid size 100,100,100, pixel 2.78, shown at level 0.0656, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_01_00011_volume.mrc Opened cryosparc_P122_J1826_class_01_00011_volume.mrc as #10, grid size 100,100,100, pixel 2.78, shown at level 0.051, step 1, values float32 > hide #!4 models > hide #!5 models > tile 4 models tiled > volume level 0.16 > ~tile > tile 4 models tiled > volume level 0.2 > tile 4 models tiled > show #!5 models > ~tile > hide #!10 models > hide #!8 models > hide #!7 models > show #!7 models > hide #!9 models > volume #7 level 0.1676 > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > volume #9 level 0.2686 > hide #!9 models > show #!10 models > volume #10 level 0.08473 > volume #10 level 0.149 > volume #10 level 0.2111 > volume #10 level 0.1579 > show #!12 models > hide #!12 models > show #!9 models > show #!8 models > show #!7 models > tile 5 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00011_volume.mrc Opened cryosparc_P122_J1827_class_00_00011_volume.mrc as #11, grid size 80,80,80, pixel 3.47, shown at level 0.103, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_03_00011_volume.mrc Opened cryosparc_P122_J1827_class_03_00011_volume.mrc as #19, grid size 80,80,80, pixel 3.47, shown at level 0.105, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_02_00011_volume.mrc Opened cryosparc_P122_J1827_class_02_00011_volume.mrc as #20, grid size 80,80,80, pixel 3.47, shown at level 0.117, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00011_volume.mrc Opened cryosparc_P122_J1827_class_01_00011_volume.mrc as #21, grid size 80,80,80, pixel 3.47, shown at level 0.118, step 1, values float32 > volume level 0.2 > volume level 0.3 > tile 9 models tiled > hide #!10 models > hide #!11 models > show #!10 models > show #!12 models > hide #!12 models > show #!11 models > hide #!9 models > show #!9 models > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_00_00024_volume.mrc Opened cryosparc_P122_J1818_class_00_00024_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0479, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_05_00024_volume.mrc Opened cryosparc_P122_J1818_class_05_00024_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0478, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_04_00024_volume.mrc Opened cryosparc_P122_J1818_class_04_00024_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_03_00024_volume.mrc Opened cryosparc_P122_J1818_class_03_00024_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0535, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_02_00024_volume.mrc Opened cryosparc_P122_J1818_class_02_00024_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.0523, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_01_00024_volume.mrc Opened cryosparc_P122_J1818_class_01_00024_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0498, step 1, values float32 > volume level 0.3 > tile 6 models tiled > volume level 0.1 > volume level 0.2 > volume #1 level 0.185 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_00_00011_volume.mrc Opened cryosparc_P122_J1826_class_00_00011_volume.mrc as #7, grid size 100,100,100, pixel 2.78, shown at level 0.0611, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_03_00011_volume.mrc Opened cryosparc_P122_J1826_class_03_00011_volume.mrc as #8, grid size 100,100,100, pixel 2.78, shown at level 0.0631, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_02_00011_volume.mrc Opened cryosparc_P122_J1826_class_02_00011_volume.mrc as #9, grid size 100,100,100, pixel 2.78, shown at level 0.0656, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_01_00011_volume.mrc Opened cryosparc_P122_J1826_class_01_00011_volume.mrc as #10, grid size 100,100,100, pixel 2.78, shown at level 0.051, step 1, values float32 > volume level 0.2 > tile 10 models tiled > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00014_volume.mrc Opened cryosparc_P122_J1827_class_00_00014_volume.mrc as #1, grid size 80,80,80, pixel 3.47, shown at level 0.085, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00014_volume.mrc Opened cryosparc_P122_J1827_class_01_00014_volume.mrc as #2, grid size 80,80,80, pixel 3.47, shown at level 0.0781, step 1, values float32 > color dim gray > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00011_volume.mrc Opened cryosparc_P122_J1827_class_00_00011_volume.mrc as #3, grid size 80,80,80, pixel 3.47, shown at level 0.103, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_03_00011_volume.mrc Opened cryosparc_P122_J1827_class_03_00011_volume.mrc as #4, grid size 80,80,80, pixel 3.47, shown at level 0.105, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_02_00011_volume.mrc Opened cryosparc_P122_J1827_class_02_00011_volume.mrc as #5, grid size 80,80,80, pixel 3.47, shown at level 0.117, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00011_volume.mrc Opened cryosparc_P122_J1827_class_01_00011_volume.mrc as #6, grid size 80,80,80, pixel 3.47, shown at level 0.118, step 1, values float32 > volume level 0.2 > volume level 0.3 > tile 6 models tiled > volume level 0.2 > hide #!6 models > hide #!5 models > hide #!3 models > hide #!4 models > show #!4 models > hide #4.1 models > hide #!4 models > show #!4 models > hide #!4 models > ~tile > color #2 #bababaff models > hide #!2 models > show #!2 models > hide #!2 models > volume #1 level 0.09421 > show #!2 models > volume #2 level 0.1241 > hide #!2 models > show #!2 models > hide #!1 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1824_class_01_00021_volume.mrc Opened cryosparc_P122_J1824_class_01_00021_volume.mrc as #7, grid size 80,80,80, pixel 3.47, shown at level 0.0893, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1824_class_00_00021_volume.mrc Opened cryosparc_P122_J1824_class_00_00021_volume.mrc as #8, grid size 80,80,80, pixel 3.47, shown at level 0.0904, step 1, values float32 > volume level 0.2 > tile 3 models tiled > ~tile > hide #!2 models > show #!1 models > show #!2 models > ~tile > tile 4 models tiled > volume #7 level 0.22 > volume #7 level 0.3369 > volume #8 level 0.3067 > volume #7 level 0.3636 > volume #1 level 0.2 > volume #1 level 0.1964 > volume #1 level 0.2511 > volume #2 level 0.2379 > hide #!2 models > hide #!1 models > ~tile > hide #!7 models > volume #8 level 0.1877 > volume #7 level 0.1866 > tile 2 models tiled > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > hide #!8 models > hide #!7 models > tile 2 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_02_00024_volume.mrc Opened cryosparc_P122_J1818_class_02_00024_volume.mrc as #9, grid size 100,100,100, pixel 2.78, shown at level 0.0523, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_04_00024_volume.mrc Opened cryosparc_P122_J1818_class_04_00024_volume.mrc as #10, grid size 100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32 > volume level 0.2 > tile 4 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_00_00024_volume.mrc Opened cryosparc_P122_J1818_class_00_00024_volume.mrc as #11, grid size 100,100,100, pixel 2.78, shown at level 0.0479, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_05_00024_volume.mrc Opened cryosparc_P122_J1818_class_05_00024_volume.mrc as #12, grid size 100,100,100, pixel 2.78, shown at level 0.0478, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_03_00024_volume.mrc Opened cryosparc_P122_J1818_class_03_00024_volume.mrc as #13, grid size 100,100,100, pixel 2.78, shown at level 0.0535, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_01_00024_volume.mrc Opened cryosparc_P122_J1818_class_01_00024_volume.mrc as #14, grid size 100,100,100, pixel 2.78, shown at level 0.0498, step 1, values float32 > volume level 0.2 > tile 8 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_00_00035_volume.mrc Opened cryosparc_P122_J1720_class_00_00035_volume.mrc as #15, grid size 100,100,100, pixel 2.78, shown at level 0.0379, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_04_00035_volume.mrc Opened cryosparc_P122_J1720_class_04_00035_volume.mrc as #16, grid size 100,100,100, pixel 2.78, shown at level 0.0368, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_02_00035_volume.mrc Opened cryosparc_P122_J1720_class_02_00035_volume.mrc as #17, grid size 100,100,100, pixel 2.78, shown at level 0.033, step 1, values float32 > tile 11 models tiled > volume level 0.4] Invalid "level" argument: Expected a number > volume level 0.3 > volume level 0.2 > volume level 0.1 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_09_00035_volume.mrc Opened cryosparc_P122_J1720_class_09_00035_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0387, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_03_00035_volume.mrc Opened cryosparc_P122_J1720_class_03_00035_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0336, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1720_class_00_00035_volume.mrc Opened cryosparc_P122_J1720_class_00_00035_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0379, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_00_00024_volume.mrc Opened cryosparc_P122_J1818_class_00_00024_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0479, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_04_00024_volume.mrc Opened cryosparc_P122_J1818_class_04_00024_volume.mrc as #5, grid size 100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_02_00024_volume.mrc Opened cryosparc_P122_J1818_class_02_00024_volume.mrc as #6, grid size 100,100,100, pixel 2.78, shown at level 0.0523, step 1, values float32 > volume level 0.1 > volume level 0.2 > tile 6 models tiled > volume level 0.1 > volume level 0.12 > volume level 0.13 > volume level 0.14 [Repeated 1 time(s)] > volume level 0.15 > volume level 0.16 > ~tile > tile 6 models tiled > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_04_00021_volume.mrc Opened cryosparc_P122_J1823_class_04_00021_volume.mrc as #7, grid size 80,80,80, pixel 3.47, shown at level 0.0907, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_02_00016_volume.mrc Opened cryosparc_P122_J1826_class_02_00016_volume.mrc as #8, grid size 84,84,84, pixel 3.31, shown at level 0.0758, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_01_00016_volume.mrc Opened cryosparc_P122_J1826_class_01_00016_volume.mrc as #9, grid size 84,84,84, pixel 3.31, shown at level 0.0854, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_00_00016_volume.mrc Opened cryosparc_P122_J1826_class_00_00016_volume.mrc as #10, grid size 84,84,84, pixel 3.31, shown at level 0.0852, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00014_volume.mrc Opened cryosparc_P122_J1827_class_01_00014_volume.mrc as #11, grid size 80,80,80, pixel 3.47, shown at level 0.0781, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00014_volume.mrc Opened cryosparc_P122_J1827_class_00_00014_volume.mrc as #12, grid size 80,80,80, pixel 3.47, shown at level 0.085, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_05_00021_volume.mrc Opened cryosparc_P122_J1823_class_05_00021_volume.mrc as #13, grid size 80,80,80, pixel 3.47, shown at level 0.0957, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_03_00021_volume.mrc Opened cryosparc_P122_J1823_class_03_00021_volume.mrc as #14, grid size 80,80,80, pixel 3.47, shown at level 0.1, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_01_00021_volume.mrc Opened cryosparc_P122_J1823_class_01_00021_volume.mrc as #15, grid size 80,80,80, pixel 3.47, shown at level 0.0952, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_00_00021_volume.mrc Opened cryosparc_P122_J1823_class_00_00021_volume.mrc as #16, grid size 80,80,80, pixel 3.47, shown at level 0.101, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1823_class_02_00021_volume.mrc Opened cryosparc_P122_J1823_class_02_00021_volume.mrc as #17, grid size 80,80,80, pixel 3.47, shown at level 0.0762, step 1, values float32 > ~tile > volume level 0.16 > volume level 0.3 > tile 17 models tiled > volume level 0.2 > volume level 0.1 > volume level 0.12 > volume level 0.13 > volume level 0.14 > color dark gray > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!6 models > hide #!6 models > volume level 0.2 [Repeated 1 time(s)] > hide #!17 models > show #!17 models > hide #!16 models > show #!16 models > hide #!15 models > show #!15 models > hide #!14 models > show #!14 models > hide #!13 models > show #!13 models > hide #!14 models > show #!14 models > close #13-17 > tile 6 models tiled > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > show #!3 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!4 models > show #!5 models > show #!6 models > tile 9 models tiled > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > hide #!7 models > show #!7 models > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_00_00016_volume.mrc Opened cryosparc_P122_J1825_class_00_00016_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0463, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_02_00016_volume.mrc Opened cryosparc_P122_J1825_class_02_00016_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0456, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_03_00016_volume.mrc Opened cryosparc_P122_J1825_class_03_00016_volume.mrc as #3, grid size 100,100,100, pixel 2.78, shown at level 0.0483, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1825_class_01_00016_volume.mrc Opened cryosparc_P122_J1825_class_01_00016_volume.mrc as #4, grid size 100,100,100, pixel 2.78, shown at level 0.0513, step 1, values float32 > volume level 0.2 > tile 4 models tiled > ~tile > hide #!2 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!3 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!3 models > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_04_00024_volume.mrc Opened cryosparc_P122_J1818_class_04_00024_volume.mrc as #1, grid size 100,100,100, pixel 2.78, shown at level 0.0424, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1818_class_02_00024_volume.mrc Opened cryosparc_P122_J1818_class_02_00024_volume.mrc as #2, grid size 100,100,100, pixel 2.78, shown at level 0.0523, step 1, values float32 > tile 2 models tiled > volume level 0.2 [Repeated 1 time(s)] > ~tile > tile 2 models tiled > volume #1 level 0.2217 > volume #2 level 0.1435 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00014_volume.mrc Opened cryosparc_P122_J1827_class_00_00014_volume.mrc as #3, grid size 80,80,80, pixel 3.47, shown at level 0.085, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00014_volume.mrc Opened cryosparc_P122_J1827_class_01_00014_volume.mrc as #4, grid size 80,80,80, pixel 3.47, shown at level 0.0781, step 1, values float32 > volume level 0.2 > tile 4 models tiled > volume #4 level 0.3043 > volume #4 level 0.2806 > volume #3 level 0.1745 > volume #3 level 0.1599 > volume #3 level 0.127 > volume #3 level 0.08692 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1829_001_volume_map.mrc Opened cryosparc_P122_J1829_001_volume_map.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.00923, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1829_001_volume_map_sharp.mrc Opened cryosparc_P122_J1829_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.0136, step 1, values float32 > hide #!2 models > volume #1 level 0.04246 > volume #1 level 0.09072 > hide #!1 models > volume #2 level 0.07756 > volume #2 level 0.1248 > volume #2 level 0.1002 > volume #2 level 0.1238 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1738_001_volume_map_sharp.mrc Opened cryosparc_P122_J1738_001_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.017, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1737_001_volume_map_sharp.mrc Opened cryosparc_P122_J1737_001_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0193, step 1, values float32 > volume level 0.2 [Repeated 1 time(s)] > volume level 0.1 > tile 3 models tiled > volume #2 level 0.06754 > volume #2 level 0.06552 > volume #3 level 0.07699 > volume #3 level 0.09655 > volume #2 level 0.09493 > volume #4 level 0.1103 > volume #3 level 0.1173 > volume #3 level 0.1575 > volume #3 level 0.1023 > close session > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_84/vac17_rank1colab_rebuilt.pdb Chain information for vac17_rank1colab_rebuilt.pdb #1 --- Chain | Description B1 | No description available > close session > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_81/myo2_rank1_colab_processed.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_81/myo2_rank1_colab_processed.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_processed.pdb #1 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_79/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3_processed.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_79/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3_processed.pdb --- warning | Ignored bad PDB record found on line 98 Chain information for output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3_processed.pdb #2 --- Chain | Description B1 | No description available > close #2 > close session > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_processed.pdb #1 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > close session > open C:/Users/lilyh/Desktop/P122/MapToModel_69/map_to_model.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/MapToModel_69/map_to_model.pdb --- warnings | Ignored bad PDB record found on line 1 Ignored bad PDB record found on line 2 REMARK MODEL FROM PHENIX.MAP_TO_MODEL Ignored bad PDB record found on line 3 REMARK MAP FILE: C:\Users\lilyh\Downloads\cryosparc_P122_J1808_map_sharp.mrc Ignored bad PDB record found on line 4 Ignored bad PDB record found on line 731 Chain information for map_to_model.pdb #1 --- Chain | Description A | No description available U | No description available > style stick Changed 725 atom styles > show atoms > open C:/Users/lilyh/Downloads/cryosparc_P122_J1808_map_sharp.mrc Opened cryosparc_P122_J1808_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.031, step 1, values float32 > volume #2 level 0.2305 [Repeated 1 time(s)] > select clear > select #2 2 models selected > transparency #2.1 40 > select clear > volume #2 level 0.1927 > hide #!2 models > show #!2 models > hide #1 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1828_002_volume_map_sharp.mrc Opened cryosparc_P122_J1828_002_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0191, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1828_002_volume_map.mrc Opened cryosparc_P122_J1828_002_volume_map.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.01, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1828_001_volume_map_sharp.mrc Opened cryosparc_P122_J1828_001_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.0123, step 1, values float32 > hide #!2 models > hide #2.1 models > volume level 0.1 > tile 3 models tiled > color #3-5 light gray > volume #3 level 0.1253 > volume #5 level 0.09708 > volume #3 level 0.1225 > volume #3 level 0.09017 > volume #3 level 0.07052 > volume #3 level 0.06209 > volume #3 level 0.1 > volume #4 level 0.08709 > volume #4 level 0.07511 > volume #5 level 0.08929 > volume #3 level 0.02699 > volume #3 level 0.1126 > hide #!4 models > show #!4 models > hide #!4 models > hide #!3 models > show #!4 models > hide #!4 models > hide #!5 models > show #!3 models > show #2.1 models > surface style #2-3 solid > transparency #2-3 0 > tile 2 models tiled > ~tile > volume #3 level 0.1197 > volume #2 level 0.2329 > select #3 2 models selected > transparency #3.1 40 > color #3.1 cornflower blue > set bgColor white > lighting soft > lighting full > transparency #3.1 60 > select clear > graphics silhouettes true > volume #3 level 0.08596 > volume #3 level 0.09719 > volume #3 level 0.07613 > volume #2 level 0.1834 > volume #3 level 0.1 > volume #3 level 0.1084 > volume #3 level 0.1449 > volume #3 level 0.1 > volume #3 level 0.1253 > hide #2.1 models > hide #!2 models > hide #!3 models > show #!3 models > volume #3 level 0.08175 > volume #3 level 0.1154 > show #!4 models > hide #!3 models > volume #4 level 0.03086 > volume #4 level 0.04192 > tile 1 model tiled > volume #5 level 0.07468 > volume #5 level 0.09805 > volume #5 level 0.06007 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1830_001_volume_map_sharp.mrc Opened cryosparc_P122_J1830_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.0139, step 1, values float32 > volume #6 level 0.08233 [Repeated 1 time(s)] > open C:/Users/lilyh/Downloads/cryosparc_P122_J1832_map_sharp.mrc Opened cryosparc_P122_J1832_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.0172, step 1, values float32 > volume #7 level 0.08181 > volume #7 level 0.1425 > volume #7 level 0.1174 > volume #7 level 0.07786 > volume #7 level 0.1016 > volume #7 level 0.1504 > volume #7 level 0.06995 > tile 3 models tiled > transparency #3-5,7 0 > color #3-5,7 dark gray > ~tile > tile 4 models tiled > volume #7 level 0.09632 > volume #7 level 0.1266 > volume #5 level 0.09805 > volume #5 level 0.101 > volume #5 level 0.09513 > volume #4 level 0.06866 > volume #4 level 0.08525 > volume #4 level 0.09262 > volume #4 level 0.09078 > volume #4 level 0.09447 > volume #4 level 0.09816 > volume #5 level 0.1049 > volume #4 level 0.08986 > volume #4 level 0.1101 > volume #4 level 0.09539 > volume #3 level 0.0663 > volume #3 level 0.09579 > volume #3 level 0.1407 > volume #7 level 0.09895 > volume #7 level 0.1201 > volume #7 level 0.1332 > volume #7 level 0.1359 > volume #7 level 0.1438 > volume #7 level 0.1095 > volume #7 level 0.1201 > volume #7 level 0.08841 > volume #7 level 0.08313 > volume #7 level 0.09236 > volume #3 level 0.1393 > volume #3 level 0.1239 > volume #3 level 0.094 > volume #7 level 0.09368 > volume #7 level 0.1253 > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1831_001_volume_map_sharp.mrc Opened cryosparc_P122_J1831_001_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.0143, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1830_001_volume_map_sharp.mrc Opened cryosparc_P122_J1830_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.0139, step 1, values float32 > volume level 0.1 > tile 2 models tiled > color gray > set bgColor white > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > volume #1 level 0.1194 > volume #1 level 0.1042 > volume #2 level 0.05511 [Repeated 1 time(s)] > open C:/Users/lilyh/Downloads/cryosparc_P122_J1832_map_sharp.mrc Opened cryosparc_P122_J1832_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0172, step 1, values float32 > volume #3 level 0.1003 > ~tile > tile 3 models tiled > hide #!1 models > ~tile > select #2 2 models selected > select clear > show #!1 models > tile 3 models tiled > volume #2 level 0.08317 > hide #!1 models > tile 2 models tiled > ~tile > volume #3 level 0.06599 > volume #3 level 0.06863 > volume #3 level 0.09764 > volume #2 level 0.07868 > select #3 2 models selected > transparency #3.1 40 > select clear > tile 2 models tiled > show #!1 models > tile 3 models tiled > ~tile > tile 3 models tiled > hide #!1 models > volume #2 level 0.0798 > volume #2 level 0.1426 > volume #2 level 0.109 > volume #2 level 0.118 > ~tile > volume #2 level 0.1056 > show #!1 models > ~tile > tile 3 models tiled > volume #2 level 0.07868 > volume #2 level 0.06072 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_00_00014_volume.mrc Opened cryosparc_P122_J1827_class_00_00014_volume.mrc as #4, grid size 80,80,80, pixel 3.47, shown at level 0.085, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_02_00016_volume.mrc Opened cryosparc_P122_J1826_class_02_00016_volume.mrc as #5, grid size 84,84,84, pixel 3.31, shown at level 0.0758, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_01_00016_volume.mrc Opened cryosparc_P122_J1826_class_01_00016_volume.mrc as #6, grid size 84,84,84, pixel 3.31, shown at level 0.0854, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1826_class_00_00016_volume.mrc Opened cryosparc_P122_J1826_class_00_00016_volume.mrc as #7, grid size 84,84,84, pixel 3.31, shown at level 0.0852, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1827_class_01_00014_volume.mrc Opened cryosparc_P122_J1827_class_01_00014_volume.mrc as #8, grid size 80,80,80, pixel 3.47, shown at level 0.0781, step 1, values float32 > hide #!1 models > hide #!2 models > hide #!3 models > volume level 0.1 > volume level 0.2 > tile 5 models tiled > hide #!4 models > hide #!8 models > volume #7 level 0.2035 > volume #7 level 0.1474 > volume #7 level 0.186 > volume #6 level 0.1962 > volume #5 level 0.2612 > show #!4 models > show #!8 models > tile 5 models tiled > ~tile > tile 5 models tiled > hide #!8 models > hide #!7 models > volume #4 level 0.2547 > volume #4 level 0.3167 > volume #5 level 0.1519 > volume #6 level 0.154 > tile 3 models tiled > ~tile > hide #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #!4 models > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_processed.pdb #9 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > close session > open C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_hs.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_hs.pdb --- warning | Ignored bad PDB record found on line 1673 Chain information for myo2_rank1_colab_hs.pdb #1 --- Chain | Description U | No description available > close session > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_processed.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_processed.pdb #1 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_03_00011_volume.mrc Opened cryosparc_P122_J1788_class_03_00011_volume.mrc as #1, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1788_class_01_00011_volume.mrc Opened cryosparc_P122_J1788_class_01_00011_volume.mrc as #2, grid size 80,80,80, pixel 3.47, shown at level 0.132, step 1, values float32 > volume #1 level 0.3994 > volume #1 level 0.2969 > volume #2 level 0.2823 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1791_002_volume_map.mrc Opened cryosparc_P122_J1791_002_volume_map.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0125, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1792_001_volume_map.mrc Opened cryosparc_P122_J1792_001_volume_map.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0116, step 1, values float32 > volume level 0.1 > volume #3 level 0.08874 > volume #4 level 0.07495 > volume #4 level 0.07295 > volume #4 level 0.06794 > volume #4 level 0.04289 > volume #4 level 0.02986 > volume #4 level 0.05391 > volume #4 level 0.06794 > close session > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_full_docked.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_full_docked.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_full_docked.pdb #1 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_docked.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_docked.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_docked.pdb #2 --- Chain | Description A | No description available > hide #!1 models > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Chain information for myo2_rank1_colab_rebuilt.pdb #3 --- Chain | Description A | No description available > hide #!2 models > close #1-2 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1808_map_sharp.mrc Opened cryosparc_P122_J1808_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.031, step 1, values float32 > volume #1 level 0.1876 Must specify one map, got 0 > volume #1 level 0.223 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1573_001_volume_map_sharp.mrc Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.018, step 1, values float32 > volume #2 level 0.1983 > volume #2 level 0.1918 > hide #!1 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1807_map_sharp.mrc Opened cryosparc_P122_J1807_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0182, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1808_map_sharp.mrc Opened cryosparc_P122_J1808_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.09, shown at level 0.031, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1809_map_sharp.mrc Opened cryosparc_P122_J1809_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.0252, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1813_map_sharp.mrc Opened cryosparc_P122_J1813_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.0187, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1812_map_sharp.mrc Opened cryosparc_P122_J1812_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.09, shown at level 0.0228, step 1, values float32 > open "C:/Users/lilyh/Downloads/cryosparc_P122_J1811_map_sharp (1).mrc" Opened cryosparc_P122_J1811_map_sharp (1).mrc as #9, grid size 256,256,256, pixel 1.09, shown at level 0.02, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1810_map_sharp.mrc Opened cryosparc_P122_J1810_map_sharp.mrc as #10, grid size 256,256,256, pixel 1.09, shown at level 0.028, step 1, values float32 > close #1 > volume level 0.1 [Repeated 1 time(s)] > volume level 0.17 > volume level 0.18 > volume level 0.19 > tile 7 models tiled > color #4-10 dark gray [Repeated 1 time(s)] > color #4-10 gray > volume level 0.2 > tile 7 models tiled > show #!2 models > tile 8 models tiled > select #2 2 models selected > color #2.1 gray > color #2.1 dark gray > select clear > volume level 0.17 > volume #2 level 0.1872 > volume level 0.187 > volume #5 level 0.1948 > volume level 0.195 > volume #5 level 0.1794 > volume #5 level 0.1585 > volume level 0.159 > hide #!6 models > show #!6 models > hide #!9 models > show #!9 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!9 models > show #!9 models > hide #!4 models > show #!4 models > hide #!7 models > show #!7 models > close session > open C:/Users/lilyh/Downloads/cryosparc_P122_J1808_map_sharp.mrc Opened cryosparc_P122_J1808_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.09, shown at level 0.031, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1573_001_volume_map_sharp.mrc Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.09, shown at level 0.018, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1809_map_sharp.mrc Opened cryosparc_P122_J1809_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.09, shown at level 0.0252, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1807_map_sharp.mrc Opened cryosparc_P122_J1807_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.09, shown at level 0.0182, step 1, values float32 > volume level 0.159 > hide #!2 models > hide #!3 models > hide #!4 models > volume #1 level 0.1798 > hide #!1 models > show #!2 models > volume #2 level 0.1633 > volume #3 level 0.1939 > volume #3 level 0.187 > volume #3 level 0.1963 > hide #!3 models > volume #4 level 0.1788 > volume #4 level 0.1294 > volume #4 level 0.1768 > color #4 gray > volume #4 level 0.1689 > volume #4 level 0.161 > volume #4 level 0.1728 > volume #4 level 0.1748 > volume #4 level 0.1373 > volume #4 level 0.1748 > volume #4 level 0.159 > volume #4 level 0.1807 > volume #4 level 0.1669 > volume #4 level 0.1748 > volume #4 level 0.18 > volume #4 level 0.17 > volume #4 level 0.173 > volume #4 level 0.174 > volume #4 level 0.173 > show #!3 models > hide #!4 models > volume #3 level 0.1823 > volume #3 level 0.187 > hide #!3 models > show #!2 models > show #!3 models > hide #!3 models > volume #2 level 0.09462 > volume #2 level 0.1654 > volume #2 level 0.1933 > color #2 gray > volume #2 level 0.1848 > show #!1 models > hide #!1 models > hide #!2 models > show #!3 models > color #3 gray > hide #!3 models > show #!4 models > volume #4 level 0.1651 > show #!2 models > hide #!4 models > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Chain information for myo2_rank1_colab_rebuilt.pdb #5 --- Chain | Description A | No description available > select #2 2 models selected > transparency #2.1 30 > set bgColor white > lighting full > graphics silhouettes true > select clear > volume #2 level 0.1933 > volume #2 level 0.2255 > volume #2 level 0.2019 > volume #2 level 0.2234 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > show #!4 models > hide #!3 models > hide #!4 models > hide #!2 models > show #!3 models > volume #3 level 0.1939 > hide #!3 models > show #!4 models > volume #4 level 0.1849 > volume #2 level 0.1805 > volume #2 level 0.1869 > volume #2 level 0.2298 > volume #2 level 0.2684 > volume #2 level 0.2062 > volume #1 level 0.2085 > volume #1 level 0.245 > color #1,5 gray > color #5 #ffaaffff > color #5 #00aa7fff > select #1 2 models selected > select #1 2 models selected > transparency #1.1 30 > select clear > volume #1 level 0.1929 > volume #1 level 0.2424 > volume #1 level 0.159 > volume #1 level 0.2267 > volume #1 level 0.2424 > volume #2 level 0.1633 > transparency 0 > hide #!5 models > tile 4 models tiled > volume #4 level 0.1592 > volume #4 level 0.175 > volume level 0.175 > show #!5 models > ~tile > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > select #1 2 models selected > transparency #1.1 20 > select clear > volume #1 level 0.2219 > volume #1 level 0.1958 [Repeated 1 time(s)] > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.19 > show #!1 models > show #!3 models > show #!4 models > hide #!5 models > tile 4 models tiled > volume #2 level 0.195 > volume level 0.192 > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!5 models > ~tile > volume #2 level 0.2306 > volume #2 level 0.2006 > volume #2 level 0.192 > hide #!2 models > show #!2 models > hide #!2 models > hide #!5 models > open C:/Users/lilyh/Downloads/cryosparc_P122_J1833_001_volume_map_sharp.mrc Opened cryosparc_P122_J1833_001_volume_map_sharp.mrc as #6, grid size 256,256,256, pixel 1.09, shown at level 0.0138, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1834_001_volume_map_sharp.mrc Opened cryosparc_P122_J1834_001_volume_map_sharp.mrc as #7, grid size 256,256,256, pixel 1.09, shown at level 0.015, step 1, values float32 > open C:/Users/lilyh/Downloads/cryosparc_P122_J1835_001_volume_map_sharp.mrc Opened cryosparc_P122_J1835_001_volume_map_sharp.mrc as #8, grid size 256,256,256, pixel 1.09, shown at level 0.0153, step 1, values float32 > volume level 0.192 > tile 3 models tiled > volume #6 level 0.08491 > volume #7 level 0.09321 > volume #8 level 0.1082 > volume #8 level 0.1224 > volume #6 level 0.08601 > volume #7 level 0.07439 > close #6 > close #7 > close #8 > show #!5 models > hide #!2 models > color #5 gray > open C:/Users/lilyh/Downloads/2f6h.pdb 2f6h.pdb title: Myosin V cargo binding domain [more info...] Chain information for 2f6h.pdb #6 --- Chain | Description | UniProt X | class V unconventional myosin MYO2; TYPE V myosin heavy chain MYO2; myosin V MYO2; cell divison control protein 66 | MYO2_YEAST 22-440 > matchmaker #6 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker myo2_rank1_colab_rebuilt.pdb, chain A (#5) with 2f6h.pdb, chain X (#6), sequence alignment score = 1787.6 RMSD between 361 pruned atom pairs is 0.873 angstroms; (across all 364 pairs: 1.088) > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > color #5.1 #ffff7fff models > color #5.1 yellow models > color #5.1 #ffff7fff models > select add #5.1 6 pseudobonds, 1 model selected > select subtract #5.1 Nothing selected > hide #5.1 models > show #5.1 models > select clear > select add #5.1 6 pseudobonds, 1 model selected > select subtract #5.1 Nothing selected > color #5.1 #ffe372ff models > color #5.1 #ffff7fff models > hide #!5 models > hide #5.1 models > show #!5 models > show #5.1 models > hide #5.1 models > show #5.1 models > select add #5.1 6 pseudobonds, 1 model selected > select subtract #5.1 Nothing selected > select add #5.1 6 pseudobonds, 1 model selected > select clear Drag select of 4 residues, 1 pseudobonds > select clear Drag select of 1 pseudobonds No visible atoms or bonds selected > select clear > hide #!5 models > show #!5 models > color #5 #ffff00ff > color #5 #ffff7fff > select add #5 2974 atoms, 3028 bonds, 6 pseudobonds, 364 residues, 2 models selected > select subtract #5 Nothing selected > color #5 black > color #5 #7e7e7eff > color #5 #a3a3a3ff > split #5 Did not split myo2_rank1_colab_rebuilt.pdb, has only one piece > select add #5 2974 atoms, 3028 bonds, 6 pseudobonds, 364 residues, 2 models selected > select subtract #5 Nothing selected > color #5.1 #ffff7fff models > color #5.1 yellow models > color #5.1 #ffff7fff models > select clear > hide #4.1 models > show #4.1 models > hide #!5 models > show #!5 models > hide #5.1 models > show #5.1 models > hide #5.1 models > show #5.1 models > hide #!4 models > graphics silhouettes false > color #5 gray > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_docked.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_docked.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_docked.pdb #7 --- Chain | Description A | No description available > close #7 > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_full_docked.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_full_docked.pdb --- warning | Ignored bad PDB record found on line 2983 Chain information for myo2_rank1_colab_full_docked.pdb #7 --- Chain | Description C1 | No description available C2 | No description available C3 | No description available > close #7 > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #5.1 models > hide #!5 models > hide #4.1 models > color #6 gray > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > matchmaker #6 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker myo2_rank1_colab_rebuilt.pdb, chain A (#5) with 2f6h.pdb, chain X (#6), sequence alignment score = 1787.6 RMSD between 361 pruned atom pairs is 0.873 angstroms; (across all 364 pairs: 1.088) > hide #!5 models > show #!5 models > hide #!6 models > show #5.1 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #5.1 models > close #5 > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Chain information for myo2_rank1_colab_rebuilt.pdb #5 --- Chain | Description A | No description available > open "C:/Users/lilyh/Desktop/P122/DockAndRebuild_23/Myo2 only afold > 1150-1574_rebuilt.pdb" Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_23/Myo2 only afold 1150-1574_rebuilt.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Chain information for Myo2 only afold 1150-1574_rebuilt.pdb #7 --- Chain | Description A | No description available > hide #!6 models > hide #!5 models > hide #!7 models > show #!7 models > hide #!7 models > show #!6 models > show #!5 models > hide #!6 models > show #!7 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!6 models > show #!5 models > hide #!6 models > hide #!7 models > show #!7 models > hide #!7 models > show #!6 models > show #!7 models > close #7 > close #6 > show #4.1 models > hide #4.1 models > open C:/Users/lilyh/Downloads/2f6h.pdb 2f6h.pdb title: Myosin V cargo binding domain [more info...] Chain information for 2f6h.pdb #6 --- Chain | Description | UniProt X | class V unconventional myosin MYO2; TYPE V myosin heavy chain MYO2; myosin V MYO2; cell divison control protein 66 | MYO2_YEAST 22-440 > matchmaker #6 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker myo2_rank1_colab_rebuilt.pdb, chain A (#5) with 2f6h.pdb, chain X (#6), sequence alignment score = 1787.6 RMSD between 361 pruned atom pairs is 0.873 angstroms; (across all 364 pairs: 1.088) > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select #5/A:159 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:160 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show #!6 models > hide #!6 models > select clear > show #!1 models > select #1 2 models selected > hide #!1 models > show #!2 models > select #2 2 models selected > ui mousemode right "translate selected models" > view matrix models > #2,-0.87187,0.47698,0.11105,145.56,0.4779,0.87819,-0.019876,-47.373,-0.107,0.035742,-0.99362,295.34 > ui mousemode right "rotate selected models" > view matrix models > #2,0.98311,0.1829,0.007014,-51.317,-0.18277,0.98303,-0.015975,27.363,-0.0098167,0.014423,0.99985,6.6113 > view matrix models > #2,0.78736,0.3814,-0.48435,15.643,-0.28783,0.92219,0.25829,12.123,0.54517,-0.063955,0.83588,-35.109 > view matrix models > #2,0.95372,0.28887,-0.083441,-49.847,-0.28139,0.95527,0.090948,29.88,0.10598,-0.06326,0.99235,2.9607 > ui mousemode right "translate selected models" > view matrix models > #2,0.95372,0.28887,-0.083441,-30.096,-0.28139,0.95527,0.090948,28.508,0.10598,-0.06326,0.99235,-4.0328 > fitmap #5 inMap #2 Fit molecule myo2_rank1_colab_rebuilt.pdb (#5) to map cryosparc_P122_J1573_001_volume_map_sharp.mrc (#2) using 2974 atoms average map value = 0.2142, steps = 96 shifted from previous position = 9.4 rotated from previous position = 17.8 degrees atoms outside contour = 1302, contour level = 0.192 Position of myo2_rank1_colab_rebuilt.pdb (#5) relative to cryosparc_P122_J1573_001_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99998872 -0.00474036 0.00015796 0.67026719 0.00474077 0.99998565 -0.00249689 -0.24379159 -0.00014613 0.00249759 0.99999684 -0.41681097 Axis 0.46588054 0.02836597 0.88439284 Axis point 51.49261248 147.49184487 0.00000000 Rotation angle (degrees) 0.30712114 Shift along axis -0.06327559 > select clear > select #2 2 models selected > transparency #2.1 20 > select clear > hide #!4 models > hide #!2 models > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Distances > select add #5/A:162 18 atoms, 16 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! > show sel atoms > select #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:164 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:165 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! [Repeated 1 time(s)] > hide sel atoms Drag select of 6 atoms, 58 residues, 5 bonds > hide sel atoms > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:166 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > select #5/A:166@CE 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! [Repeated 2 time(s)] > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! > select clear Drag select of 2 residues > select add #5/A:163 28 atoms, 8 bonds, 3 residues, 1 model selected Exactly two atoms must be selected! > ui mousemode right distance > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > ui mousemode right distance > select subtract #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:166 18 atoms, 16 bonds, 2 residues, 1 model selected > select subtract #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > select subtract #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > select clear > ui mousemode right distance > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > ui mousemode right distance > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > ui mousemode right distance > select clear [Repeated 1 time(s)] > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected Drag select of 1 atoms, 5 residues Drag select of 1 atoms, 3 residues > select clear > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! [Repeated 1 time(s)] > select clear > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > select clear Drag select of 2 atoms, 2 bonds > select clear [Repeated 1 time(s)]Exactly two atoms must be selected! > select clear > ui mousemode right distance > select clear > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > select clear > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > distance #5/A 166 163 Expected a keyword > distance #5/A: 166 163 Expected a keyword > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear Drag select of 1 atoms Exactly two atoms must be selected! > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:166 18 atoms, 16 bonds, 2 residues, 1 model selected > select subtract #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:166@CD 10 atoms, 8 bonds, 2 residues, 1 model selected > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select add #5/A:163@NZ 1 atom, 1 bond, 1 residue, 1 model selected Drag select of 3 atoms, 2 bonds > select clear [Repeated 1 time(s)] > select add #5/A:163@NZ 1 atom, 1 bond, 1 residue, 1 model selected > select add #5/A:166 10 atoms, 8 bonds, 2 residues, 1 model selected > select add #5/A:162 19 atoms, 16 bonds, 3 residues, 1 model selected > select subtract #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:166 18 atoms, 16 bonds, 2 residues, 1 model selected > ui mousemode right distance > select subtract #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/A:166 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:163 18 atoms, 16 bonds, 2 residues, 1 model selected > ui mousemode right distance [Repeated 1 time(s)] > style sel stick Changed 18 atom styles > hide sel atoms [Repeated 1 time(s)] > select clear > distsance Unknown command: distsance > distance Missing or invalid "objects" argument: empty atom specifier > distance Missing or invalid "objects" argument: empty atom specifier > distance help Missing or invalid "objects" argument: invalid objects specifier > distances Unknown command: distances > Incomplete command: measure > select #5/A:162 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/A:159 17 atoms, 15 bonds, 2 residues, 1 model selected > select subtract #5/A:162 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/A:162 17 atoms, 15 bonds, 2 residues, 1 model selected > select subtract #5/A:162 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #5/A:163 17 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > select clear > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > show #!6 models > hide #!6 models > hide #!5 models > hide #!2 models > show #!5 models > select #5: Proline Nothing selected > select #5: Pro 77 atoms, 77 bonds, 11 residues, 1 model selected > select #5: gly 40 atoms, 30 bonds, 10 residues, 1 model selected > select #5: ser 120 atoms, 100 bonds, 20 residues, 1 model selected > select #5: asp 128 atoms, 114 bonds, 16 residues, 1 model selected > select clear Drag select of 48 residues Drag select of 19 residues > show sel atoms > select clear Drag select of 105 atoms, 81 residues, 1 pseudobonds, 93 bonds > show sel atoms > select clear > select #5/A:160 14 atoms, 15 bonds, 1 residue, 1 model selected > select #5/A:99 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #5/A:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide #!5 atoms > show #!6 models > matchmaker #6 in #5 Expected a keyword > matchmaker #6 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker myo2_rank1_colab_rebuilt.pdb, chain A (#5) with 2f6h.pdb, chain X (#6), sequence alignment score = 1787.6 RMSD between 361 pruned atom pairs is 0.873 angstroms; (across all 364 pairs: 1.088) > hide #!6 models > show #!6 models > hide #!5 models > color #6 dark gray > lighting full > lighting soft > graphics silhouettes true > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > ui tool show "Show Sequence Viewer" > sequence chain #5/A Alignment identifier is 5/A > sequence chain #6/X Alignment identifier is 6/X > select #6/X:174 8 atoms, 7 bonds, 1 residue, 1 model selected > select > #6/X:22-47,64-85,87-108,110-142,150-196,224-242,245-270,276-297,301-316,322-333,337-348,358-378,402-407,425-438 2433 atoms, 2464 bonds, 298 residues, 1 model selected > select #6/X:150-151 15 atoms, 14 bonds, 2 residues, 1 model selected > select #6/X:150-196 397 atoms, 403 bonds, 47 residues, 1 model selected > hide #!5 models > select > #6/X:22-47,64-85,87-108,110-142,150-196,224-242,245-270,276-297,301-316,322-333,337-348,358-378,402-407,425-438 2433 atoms, 2464 bonds, 298 residues, 1 model selected > select #6/X:197 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/X:197-198 14 atoms, 13 bonds, 2 residues, 1 model selected > select #6/X:150-159 88 atoms, 89 bonds, 10 residues, 1 model selected > select #6/X:150-196 397 atoms, 403 bonds, 47 residues, 1 model selected > select #6/X:198 6 atoms, 5 bonds, 1 residue, 1 model selected > select #6/X:150-198 411 atoms, 417 bonds, 49 residues, 1 model selected > select #6/X:151 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/X:151-152 17 atoms, 16 bonds, 2 residues, 1 model selected > select #6/X:150 7 atoms, 6 bonds, 1 residue, 1 model selected > select #6/X:150-196 397 atoms, 403 bonds, 47 residues, 1 model selected > show #!5 models > hide #!6 models > select #5/A:130 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:132 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:131 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/A:131-178 405 atoms, 411 bonds, 48 residues, 1 model selected > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select clear > open C:/Users/lilyh/Desktop/P122/myo2_rank1_colab_rebuilt-coot-1152-1574.pdb Chain information for myo2_rank1_colab_rebuilt-coot-1152-1574.pdb #7 --- Chain | Description A | No description available > hide #!5 models > close #7 > open > C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb Summary of feedback from opening C:/Users/lilyh/Desktop/P122/DockAndRebuild_89/myo2_rank1_colab_rebuilt.pdb --- warnings | Ignored bad PDB record found on line 1203 BREAK Ignored bad PDB record found on line 2133 BREAK Chain information for myo2_rank1_colab_rebuilt.pdb #7 --- Chain | Description A | No description available > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/1152-1574 Job > 89.pdb" models #7 > open "C:/Users/lilyh/Desktop/P122/1152-1574 Job 89-coot-annotated.pdb" Chain information for 1152-1574 Job 89-coot-annotated.pdb #8 --- Chain | Description A | No description available > ui tool show "Show Sequence Viewer" > sequence chain #5/A #7/A #8/A Alignment identifier is 1 > ui tool show "Show Sequence Viewer" > sequence chain #5/A #7/A #8/A Alignment identifier is 1 > sequence chain #6/X Alignment identifier is 6/X > select #6/X:121-153 240 atoms, 243 bonds, 1 pseudobond, 29 residues, 2 models selected > select #6/X:121-251 936 atoms, 957 bonds, 2 pseudobonds, 112 residues, 2 models selected > ui tool show "Show Sequence Viewer" > sequence chain #5/A #7/A #8/A Alignment identifier is 1 > ui tool show "Show Sequence Viewer" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:421 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:282-421 954 atoms, 969 bonds, 3 pseudobonds, 120 residues, 2 models selected > select #8/A:3 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:3-4 13 atoms, 12 bonds, 2 residues, 1 model selected > select clear > renumber sequence Expected a keyword > renumber 1709 residues renumbered > renumber residues Expected a keyword > renumber residue Expected a keyword > renumber #8/A 0 residues renumbered > renumber #8/A start from: 1152 Invalid "start" argument: Expected an integer > renumber #8/A start from 1152 Invalid "start" argument: Expected an integer > renumber #8/A start 1152 364 residues renumbered > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!7 models > close #7 > ui tool show "Show Sequence Viewer" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:1570 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:1570 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:1152 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:1152 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > close #5 > color #8 gray > color #8 dark gray > graphics silhouettes false > cartoon style width 1.5 thickness 0.3 > cartoon style width 2 thickness 0.3 > cartoon style width 2 thickness 1 > cartoon style width 2 thickness 0.5 > show #!6 models > hide #!6 models > color #8.1 #ffff7fff models > select clear > show #!8 surfaces > hide #8.1 models > hide #!8 surfaces > show #8.1 models > select #8/A: 1222 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color (#!8 & sel) cyan > select #8/A: 1297. 1293 Expected an objects specifier or a keyword > select #8/A: 1297. 1293 Expected an objects specifier or a keyword > select #8/A: 1297 1293 Expected a keyword > select #8/A: 1293 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A: 1293, 1297 17 atoms, 15 bonds, 2 residues, 1 model selected > show sel atoms > color (#!8 & sel) medium blue > select clear > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" > includeMaps true > select #8/A: 1229, 1233. 1304, 1301, 1307 Expected an objects specifier or a keyword > select #8/A:1229, 1233. 1304, 1301, 1307 Expected an objects specifier or a keyword > select #8/A:1229, 1233. 1304, 1301, 1307 Expected an objects specifier or a keyword > select #8/A: 1229, 1233. 1304, 1301, 1307 Expected an objects specifier or a keyword > select #8/A: 1229, 1233, 1304, 1301, 1307 41 atoms, 36 bonds, 5 residues, 1 model selected > show sel atoms > color (#!8 & sel) red > color (#!8 & sel) medium blue > color (#!8 & sel) #ff5500ff > color (#!8 & sel) #ff557fff > color (#!8 & sel) #aa00ffff > color (#!8 & sel) #ff007fff > color (#!8 & sel) #ff0000ff > color (#!8 & sel) #aa00ffff > color (#!8 & sel) #aa55ffff > color (#!8 & sel) #aa00ffff > color (#!8 & sel) #0055ffff > color (#!8 & sel) #aa55ffff > select clear > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > select #8/A:1222 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel surfaces > select clear > show #!8 surfaces > select #8/A:1323@ND2 1 atom, 1 residue, 1 model selected > select clear > hide #!8 surfaces > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 58 atoms, 51 bonds, 7 residues, 1 model selected > color (#!8 & sel) cornflower blue > color (#!8 & sel) medium blue > select #8/A:1222 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!8 & sel) dark gray > hide sel atoms > select clear > show #!8 surfaces > select surface #8 Expected an objects specifier or a keyword > select surface #8 target r Expected an objects specifier or a keyword > select add #8 2974 atoms, 3028 bonds, 6 pseudobonds, 364 residues, 2 models selected > select subtract #8 1 model selected > select add #8.2 2974 atoms, 364 residues, 1 model selected > select subtract #8.2 1 model selected > select add #8.2 2974 atoms, 364 residues, 1 model selected > select subtract #8.2 1 model selected > hide #8.2 models > show #8.2 models > hide #8.2 models > show #8.2 models > select add #8.2 2974 atoms, 364 residues, 1 model selected > transparency (#!8 & sel) 40 > select clear > select #8/A:1552@CA 1 atom, 1 residue, 1 model selected > select #8/A:1552@CE3 1 atom, 1 residue, 1 model selected > select clear > select add #8.2 2974 atoms, 364 residues, 1 model selected > transparency (#!8 & sel) 70 > transparency (#!8 & sel) 50 > select clear > hide #8.1 models > show #!2 models > select #2 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #2,0.97628,0.21652,0.00020535,-34.498,-0.21542,0.97139,-0.10002,43.862,-0.021856,0.097602,0.99499,-9.9748 > fitmap #8 inMap #2 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1573_001_volume_map_sharp.mrc (#2) using 2974 atoms average map value = 0.2142, steps = 104 shifted from previous position = 8.91 rotated from previous position = 13.6 degrees atoms outside contour = 1302, contour level = 0.192 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1573_001_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99998974 -0.00452247 0.00003990 0.65928234 0.00452258 0.99998741 -0.00217174 -0.25606220 -0.00003009 0.00217188 0.99999761 -0.38711415 Axis 0.43288284 0.00697534 0.90142320 Axis point 56.94076302 151.90494315 0.00000000 Rotation angle (degrees) 0.28745944 Shift along axis -0.06534779 > hide #!2 models > show #!2 models > hide #8.2 models > hide #!8 models > show #!8 models > hide #!2 models > show #!2 models > hide #!8 models > transparency #2.1 0 > select clear > lighting simple > lighting soft > lighting full > lighting simple > show #!8 models > hide #!8 models > show #!8 models > view name p1 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > ui tool show "Color Zone" > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select: 8/A: 1293 Unknown command: select: 8/A: 1293 > select: 8/A:1293 Unknown command: select: 8/A:1293 > select: 8/A: 1293 Unknown command: select: 8/A: 1293 > select #8/A 1293 Expected a keyword > select #8/A: 1293 9 atoms, 8 bonds, 1 residue, 1 model selected > show #!6 models > hide #!6 models > show #!2 models > color zone #2 near sel distance 6.51 > color zone #2 near sel distance 6.56 > color zone #2 near sel distance 1.09 > color single #2 > select #8/A: 1297 8 atoms, 7 bonds, 1 residue, 1 model selected > color zone #2 near sel distance 1.09 [Repeated 3 time(s)] > color single #2 > hide #!2 models > select #8/A: 1222 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!8 & sel) medium blue > color zone #2 near sel distance 1.09 > show #!2 models > color zone #2 near sel distance 1.09 > color single #2 > hide #!2 models > hide sel atoms > color (#!8 & sel) dark gray > show #!2 models > show #!1 models > hide #!2 models > select #1 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #1,0.94134,0.26231,-0.21232,4.0697,-0.29255,0.94793,-0.12591,63.613,0.16824,0.18064,0.96905,-44.31 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 120 shifted from previous position = 10.5 rotated from previous position = 12.9 degrees atoms outside contour = 1242, contour level = 0.192 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999980 -0.00056514 0.00029340 0.07544177 0.00056597 0.99999614 -0.00274613 0.36831658 -0.00029185 0.00274629 0.99999619 -0.44471026 Axis 0.97415501 0.10380075 0.20061760 Axis point 0.00000000 163.76011578 133.03714558 Rotation angle (degrees) 0.16152084 Shift along axis 0.02250680 > volume #1 level 0.1894 > volume #1 level 0.1998 > volume #1 level 0.205 > volume #1 level 0.179 > volume #1 level 0.2024 > volume #1 level 0.2311 > volume #1 level 0.2207 > volume #1 level 0.2311 > volume #1 level 0.2181 > volume #1 level 0.1633 > volume #1 level 0.1555 > ui tool show "Hide Dust" > volume #1 level 0.1373 > surface dust #1 size 6.51 > surface dust #1 size 77.63 > volume #1 level 0.1503 > volume #1 level 0.1894 > volume #1 level 0.179 > volume #1 level 0.192 > surface dust #1 size 77.1 > surface undust #1 [Repeated 4 time(s)] > volume #1 level 0.1816 > volume #1 level 0.1451 > volume #1 level 0.1529 > surface dust #1 size 1.09 [Repeated 1 time(s)] > surface dust #1 size 16.15 > select clear No atoms selected for color zoning > select #8/A: 1297 8 atoms, 7 bonds, 1 residue, 1 model selected > color zone #2 near sel distance 1.09 > color zone #2 near sel distance 47.77 [Repeated 3 time(s)] > select #1 2 models selected > select clear > hide #!1 models > show #!1 models > open > C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb Chain information for output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb #5 --- Chain | Description B | No description available C | No description available > matchmaker #9 to #8 No molecules/chains to match specified > matchmaker #5 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1152-1574 Job 89-coot-annotated.pdb, chain A (#8) with output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb, chain C (#5), sequence alignment score = 1791.8 RMSD between 363 pruned atom pairs is 0.808 angstroms; (across all 364 pairs: 0.992) > select #5: 127, 130, 134, 138, 142 37 atoms, 33 bonds, 5 residues, 1 model selected > color #5 #00aaffff > color #5 #0055ffff [Repeated 1 time(s)] > color #5 #00557fff > color #5 #0055ffff > color #5 #00aaffff > color #5 #0055ffff > color #5 #55aaffff > color #5 #0055ffff > color #5 #00aaffff > color #5 #0055ffff > color #5 #00557fff > color #5 #0055ffff > color zone #2 near sel distance 47.77 > color zone #2 near sel distance 1.09 > color zone #1 near sel distance 6.51 > color zone #1 near sel distance 10.37 > select #5: 127, 130, 134, 138, 142, 145 45 atoms, 40 bonds, 6 residues, 1 model selected > select #5: 127, 130, 132, 138, 142, 145 49 atoms, 44 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 10.37 > color single #1 > color zone #1 near sel distance 10.37 > color zone #1 near sel distance 8.46 > color zone #1 near sel distance 8.4 > color zone #1 near sel distance 8.34 > color zone #1 near sel distance 8.28 > color zone #1 near sel distance 8.34 > color zone #1 near sel distance 1.16 > select #5: 127, 130, 132, 136, 142, 145 47 atoms, 43 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 1.16 > color zone #1 near sel distance 7.51 > color zone #1 near sel distance 1.09 [Repeated 2 time(s)] > color zone #1 near sel distance 1.31 > select #5: 128, 130, 132, 136, \145 28 atoms, 26 bonds, 4 residues, 1 model selected > color zone #1 near sel distance 2.76 [Repeated 2 time(s)] > color single #1 > color zone #1 near sel distance 2.76 > color zone #1 near sel distance 2.74 > color zone #1 near sel distance 1.09 [Repeated 1 time(s)] > color zone #1 near sel distance 3.21 > select #5: 128, 130, 133, 135, 145 38 atoms, 33 bonds, 5 residues, 1 model selected > color zone #1 near sel distance 3.21 [Repeated 2 time(s)] > color zone #1 near sel distance 3.16 > select #5: 128, 130, 133, 145 27 atoms, 23 bonds, 4 residues, 1 model selected > color zone #1 near sel distance 3.16 > color zone #1 near sel distance 4.83 > select #5: 128, 130, 133, 145, 143. 142 Expected an objects specifier or a keyword > color zone #1 near sel distance 4.83 > color zone #1 near sel distance 4.67 > select #5: 128, 130, 133, 145, 143. 142, 140 Expected an objects specifier or a keyword > select #5: 128, 130, 133, 145, 143, 142, 141 56 atoms, 51 bonds, 7 residues, 1 model selected > color zone #1 near sel distance 4.67 > color zone #1 near sel distance 1.09 > select #5: 128, 130, 133, 145, 143, 142, 140 55 atoms, 49 bonds, 7 residues, 1 model selected > select #5: 128, 130, 133, 145, 143, 140 44 atoms, 38 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 1.09 > select #5: 128, 130, 133, 145, 141 36 atoms, 31 bonds, 5 residues, 1 model selected > color zone #1 near sel distance 4.51 > select #5: 128, 130, 133, 145, 141, 135 47 atoms, 41 bonds, 6 residues, 1 model selected > select #5: 128, 130, 133, 145, 141, 136 43 atoms, 38 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 4.51 > color zone #1 near sel distance 3.94 > select #5: 128, 130, 133, 145, 141, 135 47 atoms, 41 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 3.94 > select #5: 128, 130, 133, 145, 141, 137 44 atoms, 38 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 3.94 [Repeated 1 time(s)] > select #5: 128, 130, 133, 145, 141, 134 43 atoms, 39 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 3.94 > color zone #1 near sel distance 7.64 > select #5: 128, 130, 133, 145, 141, 136 43 atoms, 38 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 7.64 > color zone #1 near sel distance 4.29 > select #5: 128, 130, 133, 145, 141, 136, 145 43 atoms, 38 bonds, 6 residues, 1 model selected > color zone #1 near sel distance 4.36 > select #5: 128, 130, 133, 145, 141, 136, 145, 143 52 atoms, 46 bonds, 7 residues, 1 model selected > select #5: 128, 130, 133, 145, 141, 136, 145, 144 54 atoms, 49 bonds, 7 residues, 1 model selected > color zone #1 near sel distance 4.36 > color zone #1 near sel distance 5.44 > color zone #1 near sel distance 4.67 > select #5: 128, 130, 133, 145, 141, 136, 145, 144, 146 60 atoms, 55 bonds, 8 residues, 1 model selected > color zone #1 near sel distance 4.67 [Repeated 1 time(s)] > color zone #1 near sel distance 5.54 > select #5: 128, 130, 133, 145, 141, 145, 144, 146 53 atoms, 48 bonds, 7 residues, 1 model selected > color zone #1 near sel distance 5.54 > color zone #1 near sel distance 5.44 > color zone #1 near sel distance 5.17 > select #5: 128, 130, 133, 145, 141, 145, 135, 144, 146 64 atoms, 58 bonds, 8 residues, 1 model selected > color zone #1 near sel distance 5.17 > color zone #1 near sel distance 4.44 > select #5: 128, 130, 134, 145, 141, 145, 135, 144, 146 62 atoms, 58 bonds, 8 residues, 1 model selected > color zone #1 near sel distance 4.44 [Repeated 1 time(s)] > color zone #1 near sel distance 6.56 > color zone #1 near sel distance 6.61 > color zone #1 near sel distance 5.73 > color zone #1 near sel distance 5.17 > color zone #1 near sel distance 6.23 > select #5: 128, 130, 133, 145, 141, 145, 135, 144, 146 64 atoms, 58 bonds, 8 residues, 1 model selected > color zone #1 near sel distance 6.23 [Repeated 1 time(s)] > color zone #1 near sel distance 4.36 > select #5: 128, 130, 133, 145, 141, 145, 144, 146 53 atoms, 48 bonds, 7 residues, 1 model selected > color zone #1 near sel distance 4.36 [Repeated 2 time(s)] > color zone #1 near sel distance 4.83 > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 135 64 atoms, 58 bonds, 8 residues, 1 model selected > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 136 60 atoms, 55 bonds, 8 residues, 1 model selected > color zone #1 near sel distance 4.83 > color zone #1 near sel distance 4.8 > color zone #1 near sel distance 4.77 > color zone #1 near sel distance 4.74 > color zone #1 near sel distance 4.71 > color zone #1 near sel distance 4.68 > color zone #1 near sel distance 4.65 > color zone #1 near sel distance 4.67 > color zone #1 near sel distance 4.51 > color zone #1 near sel distance 4.29 > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 136, 147 68 atoms, 63 bonds, 9 residues, 1 model selected > color zone #1 near sel distance 4.29 > color zone #1 near sel distance 4.15 > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 136, 147, 143 77 atoms, 72 bonds, 10 residues, 1 model selected > color zone #1 near sel distance 4.15 > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 136, 147, 142 79 atoms, 74 bonds, 10 residues, 1 model selected > color zone #1 near sel distance 4.15 > color zone #1 near sel distance 4.01 > select #5: 128, 130, 133, 145, 141, 145, 144, 146, 136, 147, 141 68 atoms, 63 bonds, 9 residues, 1 model selected > color zone #1 near sel distance 4.01 [Repeated 1 time(s)] > color zone #1 near sel distance 5.17 > color zone #1 near sel distance 5.08 > hide #5 models > color #5 #00aaffff > color #5 #0055ffff > color zone #1 near sel distance 5.08 [Repeated 1 time(s)] > color zone #1 near sel distance 5.17 > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" > includeMaps true > hide #!8 models > view name p2 > save C:\Users\lilyh\Desktop\image224.png supersample 3 > show #!8 models > select #1 2 models selected > transparency #1.1 70 > transparency #1.1 80 > select clear > lighting flat > show #8.1 models > graphics silhouettes false > lighting full > lighting soft > lighting simple > transparency #1#8.1#!8 90 > select clear > select #1 2 models selected > transparency #1.1 70 > transparency #1.1 80 > select clear > save C:\Users\lilyh\Desktop\image225.png supersample 3 > select surface #8 target r Expected an objects specifier or a keyword > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 58 atoms, 51 bonds, 7 residues, 1 model selected > color (#!8 & sel) red > select clear > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 58 atoms, 51 bonds, 7 residues, 1 model selected > color (#!8 & sel) dim gray > color (#!8 & sel) dark gray > select clear > hide #!8 atoms > save C:\Users\lilyh\Desktop\image226.png supersample 3 > surface zone #1 nearAtoms #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 > ui tool show "Surface Zone" > surface zone #1 nearAtoms #8 distance 1.09 > surface unzone #1 > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 58 atoms, 51 bonds, 7 residues, 1 model selected > surface zone #1 nearAtoms sel distance 1.61 > surface zone #1 nearAtoms sel distance 20.32 > surface zone #1 nearAtoms sel distance 20.47 > surface zone #1 nearAtoms sel distance 20.61 > surface zone #1 nearAtoms sel distance 20.47 > surface zone #1 nearAtoms sel distance 6.55 > surface unzone #1 > hide #!1 models > surface zone #1 nearAtoms #8/A: 1279-1327 > surface zone #1 nearAtoms #8/A: 1282-1327 > select #8/A: 1282-1327 390 atoms, 396 bonds, 46 residues, 1 model selected > surface zone #1 nearAtoms sel distance 6.55 > show #!1 models > surface zone #1 nearAtoms sel distance 6.51 > surface zone #1 nearAtoms sel distance 6.47 > surface zone #1 nearAtoms sel distance 6.43 > surface zone #1 nearAtoms sel distance 6.39 > surface zone #1 nearAtoms sel distance 6.35 > surface zone #1 nearAtoms sel distance 6.31 > surface zone #1 nearAtoms sel distance 6.27 > surface zone #1 nearAtoms sel distance 6.22 > surface zone #1 nearAtoms sel distance 6.18 > surface zone #1 nearAtoms sel distance 6.14 > surface zone #1 nearAtoms sel distance 6.1 > surface zone #1 nearAtoms sel distance 6.06 > surface zone #1 nearAtoms sel distance 6.02 > surface zone #1 nearAtoms sel distance 5.93 > surface unzone #1 > select #8/A: 1282-1327, 1222 399 atoms, 404 bonds, 47 residues, 1 model selected > surface zone #1 nearAtoms #8/A: 1282-1327, 1222 > surface zone #1 nearAtoms #5/A:110-150 No atoms specified > surface zone #1 nearAtoms #5110-150 No atoms specified > surface zone #1 nearAtoms #5:110-150 > surface zone #1 nearAtoms sel distance 4.73 > show #5 models > hide #5 models > surface zone #1 nearAtoms sel distance 8.33 > surface zone #1 nearAtoms #5:110-150 > surface zone #1 nearAtoms #5:110-150 and #8/A: 1222, 1293, 1297, 1304 Expected a keyword > surface zone #1 nearAtoms #5:110-150 and near #8/A: 1222, 1293, 1297, 1304 Expected a keyword > surface zone #1 nearAtoms #5:110-150 and surface zone #1 near #8/A: 1222, > 1293, 1297, 1304 Expected a keyword > surface zone #1 nearAtoms #5:110-150, surface zone #1 near #8/A: 1222, 1293, > 1297, 1304 Expected a keyword > surface zone #1 nearAtoms #5:110-150 > show #5 models > hide #5 models > surface unzone #1 > surface zone #1 nearAtoms #5:110-150 > surface zone #1 nearAtoms sel distance 8.1 > surface zone #1 nearAtoms sel distance 16.67 > show #5 models > surface zone #1 nearAtoms #5/B:110-150 > hide #5 models > surface zone #1 nearAtoms sel distance 5.15 > surface zone #1 nearAtoms sel distance 8.45 > show #5 models > hide #!1 models > show #!1 models > surface zone #1 nearAtoms #5/B:110-150 > surface zone #1 nearAtoms sel distance 16.2 > surface zone #1 nearAtoms #5/B:120-150 > surface zone #1 nearAtoms sel distance 12.39 > hide #!8 models > show #!8 models > hide #5 models > show #5 models > hide #5 models > surface unzone #1 > surface dust #1 size 16.15 > hide #!1 models > surface zone #1 nearAtoms #8/A: 1282-1327 > show #!1 models > surface zone #1 nearAtoms sel distance 12.39 [Repeated 1 time(s)] > surface zone #1 nearAtoms sel distance 4.47 > surface zone #1 nearAtoms sel distance 8.21 > surface zone #1 nearAtoms #8/A: 1282-1300 > surface zone #1 nearAtoms #8/A: 1282-1312 > surface zone #1 nearAtoms sel distance 8.21 [Repeated 1 time(s)] > surface zone #1 nearAtoms sel distance 231.86 > surface dust #1 size 16.15 > hide #!1 models > surface zone #1 nearAtoms #8/A: 1290-1312 [Repeated 1 time(s)] > select clear > show #!1 models No atoms selected for zoning > surface unzone #1 No atoms selected for zoning [Repeated 2 time(s)] > surface zone #1 nearAtoms #8/A: 1290-1312 No atoms selected for zoning [Repeated 2 time(s)] > surface unzone #1 No atoms selected for zoning > surface zone #1 nearAtoms #8/A: 1290-1312 No atoms selected for zoning > surface zone #1 nearAtoms #8/A: 1290-1312 No atoms selected for zoning > surface unzone #1 > surface dust #1 size 16.15 > surface zone #1 nearAtoms #8/A: 1290-1312 > surface zone #1 nearAtoms #8/A: 1282-1312 > surface zone #1 nearAtoms #8/A: 1282-1327 No atoms selected for zoning [Repeated 2 time(s)] > surface unzone #1 > surface zone #1 nearAtoms #8/A: 1282-1327 No atoms selected for zoning [Repeated 2 time(s)] > surface unzone #1 [Repeated 2 time(s)] > hide #!1 models Drag select of 12 residues Drag select of 22 residues > select #8/A:1307 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A: 1282-1327 390 atoms, 396 bonds, 46 residues, 1 model selected > surface zone #1 nearAtoms sel distance 1.61 [Repeated 1 time(s)] > show #!1 models > surface unzone #1 > surface zone #1 nearAtoms sel distance 1.61 > surface zone #1 nearAtoms sel distance 1.6 > surface zone #1 nearAtoms sel distance 5.53 > surface zone #1 nearAtoms sel distance 4.94 > show #8.2 models > hide #8.2 models > show #!4 models > hide #!4 models > show #5 models > hide #!8 models > show #!8 models > hide #8.1 models > hide #!8 models > surface unzone #1 > hide #!1 models Drag select of 13 residues Drag select of 17 residues Drag select of 19 residues Drag select of 36 residues Drag select of 29 residues > show #!2 models > show #!1 models > hide #!2 models > surface zone #1 nearAtoms sel distance 4.94 > surface zone #1 nearAtoms sel distance 6.19 > hide #!1 models Drag select of 34 residues [Repeated 1 time(s)]Drag select of 43 residues Drag select of 40 residues > show #!1 models > surface zone #1 nearAtoms sel distance 6.19 > surface zone #1 nearAtoms sel distance 8.33 Drag select of 1 cryosparc_P122_J1808_map_sharp.mrc , 321 residues > hide #!1 models Drag select of 335 residues > hide sel cartoons Drag select of 19 residues > select clear Drag select of 96 residues > hide sel cartoons Drag select of 3 residues > hide sel cartoons Drag select of 72 residues Drag select of 30 residues Drag select of 14 residues > hide sel cartoons Drag select of 13 residues > show sel cartoons > hide sel cartoons > select clear > show #5 cartoons [Repeated 1 time(s)] > ui tool show "Show Sequence Viewer" > sequence chain #5/C Alignment identifier is 5/C > sequence chain #5/B Alignment identifier is 5/B > select #5/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/B:1-109 915 atoms, 921 bonds, 109 residues, 1 model selected > hide sel cartoons > select #5/B:110 7 atoms, 6 bonds, 1 residue, 1 model selected > select #5/B:110-131 157 atoms, 159 bonds, 22 residues, 1 model selected > select #5/B:109 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5/B:109-123 108 atoms, 110 bonds, 15 residues, 1 model selected > hide sel cartoons > select #5/C:1150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/C:1150-1299 1209 atoms, 1228 bonds, 150 residues, 1 model selected > select #5/C:1150 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/C:1150-1225 611 atoms, 619 bonds, 76 residues, 1 model selected > select #5/C:1574 10 atoms, 10 bonds, 1 residue, 1 model selected > select #5/C:1420-1574 1230 atoms, 1256 bonds, 155 residues, 1 model selected > hide sel cartoons > select #5/C:1330 6 atoms, 5 bonds, 1 residue, 1 model selected > select #5/C:1330-1419 742 atoms, 761 bonds, 90 residues, 1 model selected > select #5/C:1360-1361 18 atoms, 18 bonds, 2 residues, 1 model selected > select #5/C:1360-1449 754 atoms, 772 bonds, 90 residues, 1 model selected > hide sel cartoons Drag select of 73 residues Drag select of 88 residues > hide sel cartoons Drag select of 31 residues > hide sel cartoons Drag select of 1 residues > hide sel cartoons Drag select of 1 residues > hide sel cartoons > select clear > show #!1 models > surface unzone #1 > hide #!1 models Drag select of 126 residues > surface zone #1 nearAtoms sel distance 8.33 > show #!1 models > surface zone #1 nearAtoms sel distance 5.93 > surface zone #1 nearAtoms sel distance 5.22 > hide #!1 models Drag select of 27 residues > hide sel cartoons Drag select of 7 residues > hide sel cartoons > select #5/C:1223 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel cartoons Drag select of 91 residues > show #!1 models > surface zone #1 nearAtoms sel distance 5.22 > surface zone #1 nearAtoms sel distance 4.73 > surface zone #1 nearAtoms sel distance 4.94 > surface zone #1 nearAtoms sel distance 5.08 > surface zone #1 nearAtoms sel distance 4.53 > hide #!1 models Drag select of 2 residues Drag select of 4 residues > hide sel cartoons Drag select of 8 residues Drag select of 9 residues > hide sel cartoons > show #!1 models > surface zone #1 nearAtoms sel distance 4.53 > surface unzone #1 > surface zone #1 nearAtoms sel distance 4.53 > surface unzone #1 > hide #!1 models Drag select of 78 residues > surface zone #1 nearAtoms sel distance 4.53 > show #!1 models > surface zone #1 nearAtoms sel distance 6.28 > hide #!1 models > hide #1.1 models Drag select of 2 residues > hide sel cartoons Drag select of 76 residues > show #!1 models > show #1.1 models > surface zone #1 nearAtoms sel distance 6.28 > surface zone #1 nearAtoms sel distance 5.37 > surface zone #1 nearAtoms sel distance 5.3 > surface zone #1 nearAtoms selected atoms Invalid "nearAtoms" argument: invalid atoms specifier > surface zone #1 nearAtoms Missing "nearAtoms" keyword's argument > surface zone #1 Missing required "near_atoms" argument > surface zone #1 nearAtoms sel distance 5.3 > surface zone #1 nearAtoms sel distance 4.41 > surface zone #1 nearAtoms sel distance 4.22 > surface zone #1 nearAtoms sel distance 12.56 > surface dust #1 size 16.15 [Repeated 1 time(s)] > surface zone #1 nearAtoms sel distance 12.56 > surface dust #1 size 16.15 > surface zone #1 nearAtoms sel distance 12.56 > surface zone #1 nearAtoms sel distance 5.69 > surface zone #1 nearAtoms #5/B: 128-145 > surface zone #1 nearAtoms sel distance 5.69 > surface zone #1 nearAtoms #5/B: 128-145 > surface zone #1 nearAtoms #5/B: 120-150 > surface zone #1 nearAtoms sel distance 5.69 > surface zone #1 nearAtoms sel distance 5.73 > surface zone #1 nearAtoms sel distance 5.77 > surface zone #1 nearAtoms sel distance 5.15 [Repeated 2 time(s)] > surface zone #1 nearAtoms sel distance 5 [Repeated 1 time(s)] > hide #!1 models > hide #1.1 models > surface zone #1 nearAtoms #5/C:1328-1222 No atoms specified > surface zone #1 nearAtoms #5/C:1328-1222 No atoms specified > select clear > surface zone #1 nearAtoms #5/C:1328-1222 No atoms specified > surface zone #1 nearAtoms #5/C:1328 > show #1.1 models > hide #!1 models > show #!1 models No atoms selected for zoning [Repeated 1 time(s)] > surface unzone #1 No atoms selected for zoning [Repeated 1 time(s)] > surface unzone #1 > hide #!1 models Drag select of 48 residues > surface zone #1 nearAtoms sel distance 12.21 > show #!1 models > surface zone #1 nearAtoms sel distance 35.79 > surface unzone #1 [Repeated 2 time(s)] > hide #1.1 models Drag select of 76 residues > select clear Drag select of 23 residues Drag select of 9 residues > select clear Drag select of 39 residues > show #1.1 models > surface zone #1 nearAtoms sel distance 35.79 [Repeated 1 time(s)] > surface unzone #1 > surface zone #1 nearAtoms sel distance 35.79 [Repeated 3 time(s)] > surface zone #1 nearAtoms sel distance 35.54 > surface zone #1 nearAtoms sel distance 35.3 > surface unzone #1 > surface zone #1 nearAtoms sel distance 35.3 > surface zone #1 nearAtoms sel distance 5.85 > surface zone #1 nearAtoms sel distance 5.81 > surface unzone #1 > hide #1.1 models > show #1.1 models > hide #!1 models > hide #1.1 models Drag select of 26 residues [Repeated 1 time(s)]Drag select of 35 residues Drag select of 44 residues Drag select of 39 residues > show #1.1 models > surface zone #1 nearAtoms sel distance 5.81 > surface zone #1 nearAtoms sel distance 8.21 > hide #1.1 models > surface zone #1 nearAtoms sel distance 8.16 > surface unzone #1 [Repeated 1 time(s)] > surface zone #1 nearAtoms sel distance 8.16 > surface unzone #1 [Repeated 1 time(s)] > show #1.1 models > hide #1.1 models Drag select of 26 residues Drag select of 43 residues > show #1.1 models > surface zone #1 nearAtoms sel distance 8.16 > surface zone #1 nearAtoms sel distance 5.22 > surface zone #1 nearAtoms sel distance 4.86 > hide #1.1 models Drag select of 18 residues > select clear Drag select of 44 residues Drag select of 39 residues Drag select of 27 residues Drag select of 47 residues > show #1.1 models > surface zone #1 nearAtoms sel distance 4.86 [Repeated 1 time(s)] > surface zone #1 nearAtoms sel distance 5.53 > surface dust #1 size 16.15 > surface undust #1 > surface dust #1 size 16.15 > surface unzone #1 > surface zone #1 nearAtoms sel distance 5.53 > surface dust #1 size 16.15 > surface zone #1 nearAtoms sel distance 5.53 > surface zone #1 nearAtoms sel distance 5.37 > hide #!1 models > hide #1.1 models > show #1.1 models > hide #5 models > show #!6 models > hide #!6 models > show #!8 models > show #5 models > hide #5 models > show #8.2 models > hide #8.2 models > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" > includeMaps true > hide #8 [Repeated 1 time(s)] > hide #!8 models > show #!8 models > hide #!8 models > surface zone #1 nearAtoms sel distance 5.08 > surface zone #1 nearAtoms sel distance 4.94 > surface zone #1 nearAtoms sel distance 5.15 > show #8: 1227-1327 > show #!8 models > hide #!8 models > show #8: 1227-1327 target r [Repeated 1 time(s)] > show #!8 models > show #8: 1282-1327 target r > hide #!8 models > show #8: 1282-1327 target r > show #8/A: 1282-1327 target r > show #8/A: 1282-1327 > show #8.2 models > hide #8.2 models > show #8.2/A: 1282-1327 > hide #!8 models > show #8.2/A: 1282-1327 > show #!8 models > hide #!8 models > show #8: 1282-1327 > show #!8 models > hide #!8 atoms > hide #!8 cartoons > show #8: 1282-1327 > show #8: 1282-1327 target r > hide #!8 atoms > show #8: 1282-1327, 1222 target r > show #!6 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!6 models > show #5 models > hide #5 models > show #5 models > hide #!8 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > hide #5 models > show #!6 models > hide #!1 models > hide #1.1 models > show #!8 models > hide #!6 models > hide #!8 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #8.2 models > hide #8.2 models > hide #!8 models > show #!8 models > show #8.1 models > hide #8.1 models > hide #!8 models > show #1.1 models > show #!8 models > show #8: 1282-1327 target r > hide #!8 models > show #8.2 models > hide #8.2 models > show #8.1 models > hide #8.1 models > hide #!8 models > show #!6 models > hide #!6 models > show #!6 models > hide #1.1 models > hide #!6 models > show #8.2 models > hide #!8 models > hide #8.2 models > show #8.2 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!8 cartoons > hide #8.2 models Drag select of 2 residues > select #8/A:1238 9 atoms, 8 bonds, 1 residue, 1 model selected > hide ~#8: 1279-1329, 1216-1238 target r > show #1.1 models > select clear No atoms selected for zoning [Repeated 4 time(s)] > view p1 [Repeated 2 time(s)] > select clear > select #1 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #1,0.84726,0.031359,0.53025,-35.661,0.094579,0.9734,-0.20869,14.599,-0.52269,0.22696,0.82175,81.478 > ui mousemode right "translate selected models" > view matrix models > #1,0.84726,0.031359,0.53025,-37.762,0.094579,0.9734,-0.20869,8.9107,-0.52269,0.22696,0.82175,60.494 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 224 shifted from previous position = 28.8 rotated from previous position = 35.3 degrees atoms outside contour = 963, contour level = 0.15292 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999982 -0.00053892 0.00025400 0.07924356 0.00053964 0.99999612 -0.00276169 0.37768045 -0.00025252 0.00276183 0.99999616 -0.45153591 Axis 0.97751259 0.08963948 0.19087668 Axis point 0.00000000 165.41736832 135.70415282 Rotation angle (degrees) 0.16187760 Shift along axis 0.02512898 > view p1 > ui mousemode right "rotate selected models" > view matrix models > #1,-0.12724,-0.38598,0.91369,103.75,0.21757,0.88788,0.40538,-67.243,-0.96771,0.25038,-0.028993,244.63 > view matrix models > #1,0.91909,-0.37715,-0.11414,96.171,0.37387,0.92615,-0.049746,-35.359,0.12447,0.0030491,0.99222,7.4837 > ui mousemode right "translate selected models" > view matrix models > #1,0.91909,-0.37715,-0.11414,93.611,0.37387,0.92615,-0.049746,-43.405,0.12447,0.0030491,0.99222,-14.287 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 180 shifted from previous position = 23.3 rotated from previous position = 35.5 degrees atoms outside contour = 963, contour level = 0.15292 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999985 -0.00049102 0.00028537 0.06611629 0.00049182 0.99999628 -0.00271370 0.37381464 -0.00028404 0.00271384 0.99999630 -0.44189894 Axis 0.97879520 0.10268696 0.17724376 Axis point 0.00000000 164.63710399 136.58260351 Rotation angle (degrees) 0.15885632 Shift along axis 0.02477637 > select clear > view p1 > select #1 2 models selected > ui mousemode right "rotate selected models" > view matrix models > #1,0.92908,-0.36981,0.0071565,78.365,0.36948,0.92701,-0.064357,-33.05,0.017166,0.062437,0.9979,12.204 > ui mousemode right "translate selected models" > view matrix models > #1,0.92908,-0.36981,0.0071565,75.642,0.36948,0.92701,-0.064357,-41.282,0.017166,0.062437,0.9979,-12.064 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 184 shifted from previous position = 24.6 rotated from previous position = 34 degrees atoms outside contour = 964, contour level = 0.15292 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999985 -0.00046464 0.00031218 0.05884500 0.00046553 0.99999598 -0.00282897 0.39377295 -0.00031087 0.00282911 0.99999596 -0.45393330 Axis 0.98098087 0.10802193 0.16126936 Axis point 0.00000000 162.19055985 137.92441707 Rotation angle (degrees) 0.16523489 Shift along axis 0.02705640 > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #1.1 models > show #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!6 models > hide #!6 models > show #!6 models > show #5 models > hide #5 models > show #5 models > hide #5 models > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 58 atoms, 51 bonds, 7 residues, 1 model selected > show sel atoms > style sel sphere Changed 58 atom styles > color (#!8 & sel) #ffff7fff > color (#!8 & sel) #ffff00ff > color (#!8 & sel) #ffff7fff > color (#!8 & sel) #55aa7fff > color (#!8 & sel) #55aa00ff > color (#!8 & sel) #aa557fff > color (#!8 & sel) #ff557fff > color (#!8 & sel) #ff0000ff > color (#!8 & sel) #aa00ffff > color (#!8 & sel) #55ff7fff > color (#!8 & sel) #ffff7fff > color (#!8 & sel) #ffff00ff > color (#!8 & sel) #ffff7fff > color (#!8 & sel) #000000ff > color (#!8 & sel) #949494ff > color (#!8 & sel) #7a7a7aff > color (#!8 & sel) #666666ff > color (#!8 & sel) #6f6f6fff > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 target r Missing or invalid "percent" argument: Expected a number > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 70 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 10 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > select #1 2 models selected > transparency #1.1 90 > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 0 target r > surface style #1 mesh > select clear > transparency #1,6#!8 0 > surface style #1 mesh > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 55 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 75 target r > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > graphics silhouettes false > lighting soft > lighting simple > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 80 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 90 target r > graphics silhouettes true > lighting simple > graphics silhouettes false > select add #6 3389 atoms, 3223 bonds, 3 pseudobonds, 617 residues, 2 models selected > select subtract #6 Nothing selected > select add #8 2974 atoms, 3028 bonds, 6 pseudobonds, 364 residues, 2 models selected > color (#!8 & sel) dark gray > color (#!8 & sel) gray > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 70 target r > save C:\Users\lilyh\Desktop\image227.png supersample 3 > save C:\Users\lilyh\Desktop\image228.png supersample 3 > show #5 models > select add #5 4737 atoms, 4823 bonds, 585 residues, 1 model selected > show sel cartoons > view position Missing or invalid "models" argument: empty atom specifier > view p2 > view p1 > view p2 > select clear > matchmaker #6 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb, chain C (#5) with 2f6h.pdb, chain X (#6), sequence alignment score = 2115.9 RMSD between 380 pruned atom pairs is 0.609 angstroms; (across all 390 pairs: 0.925) > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > matchmaker #8 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb, chain C (#5) with 1152-1574 Job 89-coot-annotated.pdb, chain A (#8), sequence alignment score = 1791.8 RMSD between 363 pruned atom pairs is 0.808 angstroms; (across all 364 pairs: 0.992) > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!6 models > show #!6 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > hide #!6 models > show #5 models > hide #5 models Must specify one map, got 0 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 40 shifted from previous position = 0.0181 rotated from previous position = 0.0214 degrees atoms outside contour = 965, contour level = 0.15292 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999987 -0.00044283 0.00024114 0.06041474 0.00044359 0.99999518 -0.00309573 0.42007987 -0.00023977 0.00309583 0.99999519 -0.50938298 Axis 0.98699342 0.07666131 0.14130477 Axis point 0.00000000 165.65457721 134.94331173 Rotation angle (degrees) 0.17971291 Shift along axis 0.01985458 > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #5 models > hide #5 models > show #1.1 models Must specify one map, got 0 > fitmap #8 inMap #1 Fit molecule 1152-1574 Job 89-coot-annotated.pdb (#8) to map cryosparc_P122_J1808_map_sharp.mrc (#1) using 2974 atoms average map value = 0.2257, steps = 40 shifted from previous position = 0.00175 rotated from previous position = 0.00193 degrees atoms outside contour = 965, contour level = 0.15292 Position of 1152-1574 Job 89-coot-annotated.pdb (#8) relative to cryosparc_P122_J1808_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99999986 -0.00047052 0.00022762 0.06673500 0.00047124 0.99999513 -0.00310940 0.41948050 -0.00022616 0.00310950 0.99999515 -0.51218461 Axis 0.98616410 0.07195916 0.14933938 Axis point 0.00000000 165.86248326 134.19208724 Rotation angle (degrees) 0.18065827 Shift along axis 0.01950779 > select #1 2 models selected > surface style #1 mesh > select clear > save C:\Users\lilyh\Desktop\image229.png supersample 3 > view name p3 > show #5 models > hide #5 models > turn x 90 > turn x -90 > save C:\Users\lilyh\Desktop\image230.png supersample 3 > show #5 models > hide #5 models > show #5 models > hide #5 models > view p2 > rainbow #8 > rainbow #8 target r > save C:\Users\lilyh\Desktop\image231.png supersample 3 > show #8 target r > show #8.1 models > save C:\Users\lilyh\Desktop\image232.png supersample 3 > show #8.2 models > hide #8.2 models > show #8.2 models > hide #8.2 models > show #8.2 models > hide #8.2 models > undo [Repeated 8 time(s)] > show #5 models > hide #5 models > show #5 models > hide #5 target r > show #5/B:110-157 > show #5/B:110-157 target t r Invalid "target" argument: Target option can only include letters a = atoms, b = bonds, p = pseudobonds, c = cartoons, r = cartoons, s = surfaces, m = models, got t > hide #5B Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #5/B > show #5/B:127-149 > show #5/B:127-148 > hide #!8 models > show #!8 models > hide #1.1 models Drag select of 6 atoms, 7 bonds Drag select of 11 atoms, 12 bonds Drag select of 10 atoms, 10 bonds > hide sel atoms > show sel atoms > show #!6 models > show #8.1 models > hide #8.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #5/B:127-148 > hide #5/B:127-149 > show #5/B:127-148 > show #5/B:127-148 target t r Invalid "target" argument: Target option can only include letters a = atoms, b = bonds, p = pseudobonds, c = cartoons, r = cartoons, s = surfaces, m = models, got t > show #5/B:127-148 target r > show #8.1 models > hide #8.1 models > show #8.2 models > hide #8.2 models > show #!2 models > hide #!2 models > show #1.1 models > hide sel atoms Drag select of 1 cryosparc_P122_J1808_map_sharp.mrc , 146 atoms, 96 residues, 91 bonds > hide sel atoms > select clear > select add #5 4737 atoms, 4823 bonds, 585 residues, 1 model selected > select clear > undo [Repeated 5 time(s)] > select clear > select #5/B:127-148 177 atoms, 179 bonds, 22 residues, 1 model selected > hide sel atoms > transparency #5/B:127-148 0 target r > select clear > transparency #5/B:127-148 0 target r > select #5/B:127-148 0 target r Expected a keyword > select #5/B:127-148 target r Expected a keyword > show #5/B:127-148 > select clear > hide #5/B:147-148 > hide #5/B:147-148 target r > save C:\Users\lilyh\Desktop\image233.png supersample 3 > turn x 90 > turn x -90 [Repeated 1 time(s)] > show #5/B:127-150 [Repeated 1 time(s)]Drag select of 21 atoms, 21 bonds > hide sel atoms Drag select of 1 atoms, 1 bonds Drag select of 1 residues, 1 bonds > select clear [Repeated 1 time(s)]Drag select of 3 atoms, 2 bonds > hide sel atoms > select clear [Repeated 1 time(s)]Drag select of 1 atoms > hide sel atoms > show #5/B:127-148 target r > show #5/B:127-147 target r > hide sel atoms > hide sel cartoons Drag select of 1 residues > hide sel cartoons > show #5/B:127-147 > show #5/B:127-147 target r > save C:\Users\lilyh\Desktop\image234.png supersample 3 > turn x -90 > view p3 > save C:\Users\lilyh\Desktop\image235.png supersample 3 > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 90 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 Missing or invalid "percent" argument: Expected a number > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 Missing or invalid "percent" argument: Expected a number > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 90 > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 0 > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 > transparency #8/A 0 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 50 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 0 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 30 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 0 target r > select #1 2 models selected > surface style #1 mesh > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 75 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 65 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 75 target r > hide #5 models > select #1 2 models selected > transparency #1.1 50 > select clear > view p2 > select #1 2 models selected > transparency #1.1 40 > select clear > select #8/A:1220 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 75 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > select clear > save C:\Users\lilyh\Desktop\image236.png supersample 3 > turn x -90 > turn x 90 > select #1 2 models selected > transparency #1.1 30 > select clear > select #1 2 models selected > surface style #1 solid > transparency #1.1 30 > transparency #1.1 70 > transparency #8/A 0 target r > select clear No atoms selected for zoning > save C:\Users\lilyh\Desktop\image237.png supersample 3 > turn x -90 > save C:\Users\lilyh\Desktop\image238.png supersample 3 > show #5 models > select add #5 4737 atoms, 4823 bonds, 585 residues, 1 model selected > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > hide sel atoms [Repeated 1 time(s)] > show sel atoms > hide sel atoms [Repeated 1 time(s)] > show #5/B: 127-148 > show #5/B: 127-148 target r > hide sel atoms > set transparency #5/B: 127-148 0 target r Expected a keyword > transparency #5/B: 127-148 0 target r > select clear > select #1 2 models selected > select clear > select #1 2 models selected > select #1 2 models selected > select #1 2 models selected > surface style #1 mesh > select clear > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 75 target r > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 70 target r > select #5/B: 132, 137, 142 target r Expected a keyword > select #5: 132, 137, 142 target r Expected a keyword > select #5/B: 132, 137, 142 target r Expected a keyword > select #5/B: 132, 137, 142 30 atoms, 28 bonds, 3 residues, 1 model selected > show sel atoms > style sel sphere Changed 30 atom styles > style sel stick Changed 30 atom styles > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency #5/B: 127-148 85 target r > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" > includeMaps true ——— End of log from Sun Oct 15 14:29:16 2023 ——— opened ChimeraX session > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297 85 target r > transparency #5/B: 127-148 85 target r > select #8: 1222 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color (#!8 & sel) red > select #1 2 models selected > surface style #1 mesh > select clear > ui tool show Contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 5 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 5 radius 0.125 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 5 radius 0.155 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 5 radius 0.155 70289 contacts > save "C:/Users/lilyh/Desktop/Vac17-Myo2 Reconstructions/Annotated J1808.cxs" > includeMaps true > select add #7 70289 pseudobonds, 1 model selected > select subtract #7 Nothing selected > select add #6 3389 atoms, 3223 bonds, 3 pseudobonds, 617 residues, 2 models selected > select subtract #6 Nothing selected > hide #!1 models > hide #!8 models > show #!8 models > hide #7 models > show #7 models > hide #!6 models > show #!6 models > hide #!6 models > show #!1 models > select #1 2 models selected > surface style #1 mesh > select clear > select #5/B: 132, 137, 142 30 atoms, 28 bonds, 3 residues, 1 model selected > contacts sel restsrict both reveal true showDist true Expected a keyword > contacts sel restsrict both reveal true showDist true Expected a keyword > contacts sel restsrict both reveal true showDist t Expected a keyword > contacts sel restsrict both reveal true showDist Expected a keyword > contacts sel restsrict both reveal showDist Expected a keyword > contacts sel restsrict both reveal showDist Expected a keyword > contacts sel restrict both reveal showDist Invalid "reveal" argument: Expected true or false (or 1 or 0) > contacts sel restrict both reveal true showDist Missing "showDist" keyword's argument > contacts sel restrict both reveal true showDist true No contacts > contacts sel restrict reveal true showDist true Invalid "restrict" argument: Expected one of 'any', 'both', or 'cross' or an atoms specifier > contacts sel restrict any reveal true showDist true 164 contacts > contacts sel restrict any reveal true showDist false 164 contacts > hide #!1 models > show #!1 models > hide #!1 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > contacts sel restrict cross reveal true showDist false 164 contacts > contacts sel restrict both reveal true showDist false No contacts > contacts sel restrict cross reveal true showDist false 164 contacts > contacts sel restrict cross reveal true showDist false intraModel false 120 contacts > hide ~#5/B: 137, 132, 142 > select add #8 3004 atoms, 3056 bonds, 6 pseudobonds, 367 residues, 3 models selected > select subtract #8 30 atoms, 28 bonds, 3 residues, 2 models selected > select add #8 3004 atoms, 3056 bonds, 6 pseudobonds, 367 residues, 3 models selected > select subtract #8 30 atoms, 28 bonds, 3 residues, 2 models selected > hide #!8 models > show #!8 models > transparency ~#8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297, 1222 Missing or invalid "percent" argument: Expected a number > select #8/A: 1229, 1233, 1304, 1301, 1307, 1293, 1297, 1222 67 atoms, 59 bonds, 8 residues, 1 model selected > show sel atoms [Repeated 1 time(s)] > hide sel atoms > show sel cartoons > style sel stick Changed 67 atom styles > style sel stick Changed 67 atom styles > show sel atoms > show #!1 models > select #1 2 models selected > surface style #1 mesh > select clear > select #5/B:138 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #5/B:140 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #5/B:135 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select clear > contacts sel restrict cross reveal true showDist false intraModel false No atoms match given atom specifier > contacts sel restrict cross reveal true showDist false intraModel false No atoms match given atom specifier > select #5/B: 132, 137, 142, 135, 140, 138 58 atoms, 54 bonds, 6 residues, 1 model selected > contacts sel restrict cross reveal true showDist false intraModel false 166 contacts > select #8/A:1303 12 atoms, 12 bonds, 1 residue, 1 model selected > transparency #8/B: 1303 target 0 Missing or invalid "percent" argument: Expected a number > transparency #8/B: 1303 target 0 target r Missing or invalid "percent" argument: Expected a number > transparency #8/B: 1303 0 target r > color (#!8 & sel) dark gray > color (#!8 & sel) gray > transparency #8/B: 1303 0 > transparency #8/A: 1303 0 > transparency #8/A: 1303 0 target r > select clear > select #8/A:1300 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:1300 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #8/A:1311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:1311 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/A:1305 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/A:1306 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/A:1308@CD1 1 atom, 1 residue, 1 model selected > hide sel atoms > select #8/A:1308 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #1 2 models selected > select #8/A:1230@CB 1 atom, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > show sel atoms > hide sel atoms > select #8/A:1230 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #5/B:141 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/B:140 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #8/A:1222 9 atoms, 8 bonds, 1 residue, 1 model selected > transparency #8: 1222 0 > transparency #8: 1222 0 target r > color #7 yellow models > select #5/B: 132, 137, 142, 135, 140, 138 58 atoms, 54 bonds, 6 residues, 1 model selected > select #5/B: 132, 137, 142, 135, 138 50 atoms, 47 bonds, 5 residues, 1 model selected > transparency #5: 132, 137, 142, 135, 138 0 target r > select clear > transparency #5: 135, 138 0 target r > transparency #5: 135, 138 85 target r > transparency #5: 135, 138 85 > transparency #5: 135, 138 Missing or invalid "percent" argument: Expected a number > transparency #5: 135, 138 90 > transparency #5: 135, 138 95 > select #5/B:138 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > transparency #5: 135, 138 Missing or invalid "percent" argument: Expected a number > transparency #5: 135, 138 85 target r > transparency #5: 135, 138 85 > select #5/B:138 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > transparency #5: 135, 138 0 target r > select clear > ui tool show Contacts > select add #7 166 pseudobonds, 1 model selected > ui tool show Contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 5 radius 0.155 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 4 radius 0.155 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 4 radius 0.125 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 > dashes 4 radius 0.105 70289 contacts > contacts resSeparation 5 intraModel false intraMol false color #ffff00 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